title: RNA-Seq TotalRNA_Control_rep3

city: Glasgow

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

data_processing:
cutadapt v1.16 to remove adapter sequence
deduplication of UMIs with cd-hit-dup v4.6.6
alignment to rRNA fasta file with bowtie (v1.1.2)
alignment to transcriptome with bowtie (v1.1.2)
get counts of RPF start positions with python script
Supplementary_files_format_and_content: csv file with DESeq2 results for log2FC ribosome protected fragments, log2FC total RNA and log2FC translational efficiency (siCNOT1/siControl)
Supplementary_files_format_and_content: RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)
Total RNA samples
cutadapt v1.16 to remove adapter sequence
deduplication of UMIs with cd-hit-dup v4.6.6
alignment to genome with tophat2 (v2.1.1)
HTseq (v0.9.1) used for counts
hg38, gencode v28
Supplementary_files_format_and_content: RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)

source_name: HEK293 cells

growth_protocol: HEK293 cells grown in DMEM with 10% FBS and 2mM L-glutamine

extract_protocol:
Cells were lysed with 400ul lysis buffer (20mM Tris-Cl pH 7.4, 150mM NaCl, 5mM MgCl2, 1mM DTT and 100ug/ml CHX, 25U/ml Turbo DNase, 1% Triton X100), 50ul lysate taken for total RNA and the rest digested with RNase I and ran on a sucrose cushion to produce the RPF sample
All samples were rRNA depleted using Illumina RiboZero Gold; libraries for Ribo-Seq were prepared with Nextflex small RNA-seq; libraries for RNA-Seq were prepared with Nextflex rapid directional qRNA-seq

treatment_protocol: Cells treated with 20nM CNOT1-targeting siRNA for 48 hrs

tag: sirna

value: Control siRNA


title: RICU200721-1_001A

status: Public on Aug 23 2021

type: SRA

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

library_source: transcriptomic

data_processing:
Sequence reads were mapped to the human reference genome GRCh38 by HISAT2 (version 2.2.0).
Read counts were calculated by featureCounts (Version 2.0.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PAXgene Blood miRNA Kit.
Universal Plus mRNA-Seq library preparation kit with NuQuant.

tag: cell type

value: PBMC

tag: time

value: Immunocompromised

tag: patient

tag: diagnosis

value: Sepsis


title: RICU200214-1_001A


title: RICU200130-1_001A


title: BL_15min_3

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

country: USA

institute: Iowa State University

description:
BR102
QuantSeq_all_TMM.csv

data_processing:
Raw reads were trimmed and aligned to the genome using the QuantSeq pipeline provided by Lexogen on BlueBee
Adapters trimmed using bbtools
Reads aligned using STAR Aligner. BL_15min_1, WT_15min_3, and BL_8hr_4 had low number of reads aligned and were discarded at this step.
Counts obtained using HTSeq
TMM normalization performed using edgeR
Differential expression performed using PoissonSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: .csv file of  TMM expression in all samples except those discarded after the alignment step

organism: Arabidopsis thaliana

source_name: 7-day old seedling tissue

growth_protocol: Arabidopsis seeds were grown on media plates containing 1uM BRZ on top of nylon mesh for 7 days

extract_protocol:
RNA was extracted using Qiagen RNEasy Mini prep kid
Library was constructed using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina
Sequencing was performed on a HiSeq4000 with 50bp single end reads. All libraries were run twice, and reads were merged prior to data processing.

treatment_protocol: At 7 days, seedlings were transferred to liquid media containing 1uL brassinolide (BL) or 0uL brassinolide (Mock) for 15 min, 30 min, 1 hr, 2 hr, 4hr, or 8 hr. Three or four biological replicates were collected for each time+treatment combination

tag: treatment

value: BL

value: 15 min

tag: tissue

value: 7-day old seedling tissue

tag: replicate


title: GEX_IFNgDay12_1 [GEX_01]

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Genome_build: refdata-cellranger-mm10-3.1.0
Supplementary_files_format_and_content: sparse matrix (mtx)

organism: Mus musculus

source_name: BM

extract_protocol:
BM cells were sorted for viability (Annexin V) and split in B cell and non-B cells: one gate to collect CD19+ OFP+/- cells and one gate to collect CD45+CD19- cells. After sorting cells were washed and counted
Chromium(TM) Single Cell 5' Library & Gel Bead Kit and ChromiumTM Single Cell V(D)J Enrichment Kit, Mouse T Cell (10xGENOMICS) according to manufacturer’s instructions.

treatment_protocol: lineage negative transduced cells transplant

tag: timepoint

tag: celltype

value: BM


title: RNA-Seq TotalRNA_Control_rep2

first: Sarah

country: United Kingdom

tag: cell line


title: HaCat cells, siRNA control rep 2

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

data_processing:
Raw reads from fastq files were aligned to the hg38 genome using STAR 2.6.1d (using options --sjdbGTFfile gencode.v29.annotation.gtf --sjdbOverhang 75 --outSAMtype BAM   Unsorted --outSAMstrandField intronMotif  --twopassMode Basic).
Bam files were sorted with samtools sort and indexed with samtools index.
The number of reads mapping to each gene was quantified with htseq-count (using options --format=bam --order=pos --stranded=reverse  --idattr=gene_name --nonunique=all) on features from the gtf file gencode.v29.annotation.gtf.
The raw counts of reads were then imported into EdgeR in R to perform the differential expression analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per million (CPM) from EgdeR in excel format

molecule: polyA RNA

source_name: Cell line (HaCat)

growth_protocol: HaCat cells were cultured in RPMI (Roswell Park Memorial Institute) media supplemented with 10% (v/v) FBS. All cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
RNA was isolated from the cells after compound treatment using Quick-RNA Miniprep kit (Zymo Research)
Total RNA, 2.5μg, was used for RNASequencing library preparation with the TruSeq Stranded mRNA Library Prep kit (Illumina) largely according to manufacturer’s instructions.

treatment_protocol: HaCat were treated with siRNA knockdown against Agrin.

value: human keratinocytes cell line HaCat

tag: genotype

value: control


title: RNA-Seq TotalRNA_Control_rep1


title: RICU200130-3_001A


title: GEX_IFNgDay17_2 [GEX_04]


title: GEX_IFNgDay12_2 [GEX_02]


title: RICU191209-2_001A


title: WT_BMDCs

type: RNA

city: Kumamoto

first: Hisashi

last: Kanemaru

state: Kumamoto

address: 1-1-1 Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

hyb_protocol: 2 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (Agilent) for 17 hours at 65°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°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: bone marrow-derived dendritic cells (BMDCs)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Mouse bone marrow cells were obtained from femurs and differentiated into DCs in MEM with 10% FBS containing 10 ng/ml granulocyte macrophage colony-stimulating factor (GM-CSF; Prospec, East Brunswick, NJ, USA).

extract_protocol: RNA was extracted from cells using a High Pure RNA Isolation kit (Roche).

treatment_protocol: Medium was replaced with fresh medium containing GM-CSF every two days. On day 6, cells were collected.

tag: gender

value: male

tag: strain

value: WT


title: Gclc CON-3

city: New Haven

first: Brian

last: Thompson

address: 60 College Street

institute: Yale

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic and mapped to mm9 using HISAT2 v2.1.0+galaxy5.
Mapped reads were counted using FeatureCounts v1.6.4+galaxy1.
Differential gene expression was conducted using DESeq2 (v2.11.0.6)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include log2FC and Benjamini-Hochberg corrected p value (adj. pvalue) values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: P1 Mouse Lens_Gclc CON

extract_protocol:
Lenses were removed, placed into RNAlater solution and stored at -80C. RNa was harvested using the RNeasy Micro Kit and 1 ug of total RNA was prepared for sequencing using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: Gclc CON

value: Lens


title: GEX_IFNgDay17_1 [GEX_03]


title: RICU191225-1_001A


title: Ribo-Seq RPF_Control_rep3

data_processing:
Library strategy: Ribo-Seq
cutadapt v1.16 to remove adapter sequence
deduplication of UMIs with cd-hit-dup v4.6.6
alignment to rRNA fasta file with bowtie (v1.1.2)
alignment to transcriptome with bowtie (v1.1.2)
get counts of RPF start positions with python script
Supplementary_files_format_and_content: csv file with DESeq2 results for log2FC ribosome protected fragments, log2FC total RNA and log2FC translational efficiency (siCNOT1/siControl)
Supplementary_files_format_and_content: RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)
Total RNA samples
cutadapt v1.16 to remove adapter sequence
deduplication of UMIs with cd-hit-dup v4.6.6
alignment to genome with tophat2 (v2.1.1)
HTseq (v0.9.1) used for counts
hg38, gencode v28
Supplementary_files_format_and_content: RPF counts at each nt normalised for mRNA abundance (TPM of Total RNA)


title: WT_BMDCs_LA

description: Gene expression after 4hr in LA-stimulated WT BMDCs

growth_protocol: Mouse bone marrow cells were obtained from femurs and differentiated into DCs in MEM with 10% FBS containing 10 ng/ml granulocyte macrophage colony-stimulating factor (GM-CSF; Prospec, East Brunswick, NJ, USA). Medium was replaced with fresh medium containing GM-CSF every two days. On day 6, cells were collected.

treatment_protocol: BMDCs were stimulated with LPS (100 ng/ml; LPS-SM ultrapure, InvivoGen, San Diego, CA, USA) and/or L-(+)-LA (20 mM) (Sigma-Aldrich, St. Louis, MO, USA) for 4 hours.

value: bone marrow-derived dendritic cells (BMDCs)

value: LA-stimulated


title: Gclc CON-2


title: RICU190905-1_001A


title: RICU191223-1_001A


title: Ribo-Seq RPF_Control_rep2


title: Gclc KO-3

source_name: P1 Mouse Lens_Gclc KO

value: Gclc KO


title: WT_BMDCs_LPS+LA

description: Gene expression after 4hr in LPS and LA-stimulated WT BMDCs

value: LPS and LA-stimulated


title: Gclc CON-1


title: WT BMDCs-input DNA

library_source: genomic

data_processing:
Base-calling, alignment, filtering, and peak-calling were performed using CLC Genomics Workbench 10 software (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: WT BMDCs

extract_protocol:
ChIP analysis was performed using ChIP-IT Express Enzymatic (Active Motif) and protein-DNA complexes were isolated with antibody.
ChIP-seq was performed by Filgen (Aichi, Japan). Libraries were prepared according to Illumina's instructions and sequenced on the Illumina HiSeq 6000 following the manufacturer's protocols.

treatment_protocol: BMDCs were stimulated with LPS (100 ng/ml; LPS-SM ultrapure, InvivoGen, San Diego, CA, USA) and L-(+)-lactic acid (20 mM) (Sigma-Aldrich, St. Louis, MO, USA) for 24 h.

value: bone marrow-derived dendritic cells

tag: chip antibody

value: Stimulated with LPS (100 ng/ml) and LA (20 mM) for 24 h.


title: RICU191107-1_001A

value: PBMC

value: Immunocompromised

value: Sepsis


title: RNA-Seq siCNOT1 Replicate 3

value: CNOT1 siRNA


title: EGR1_KO_BMDCs


title: RICU190502-1_001A


title: RICU190902-1_001A


title: RICU191118-1_001A


title: EGR1 KO BMDCs-input DNA

source_name: EGR1-deficient BMDCs


title: RNA-Seq siCNOT1 Replicate 2


title: WT_BMDCs_LPS

description: Gene expression after 4hr in LPS-stimulated WT BMDCs

value: LPS-stimulated


title: RICU190108-1_001A


title: RNA-Seq siCNOT1 Replicate 1


title: WT_BMDCs_MediumCtrl

description: Gene expression of WT BMDCs without stimulations

value: without stimulation


title: Ribo-Seq siCNOT1 Replicate 3

description:
ribosome protected fragments (RPF)
RibosomeProfiling_DESeq2results.csv


title: RICU181211-1_001A


title: Gclc KO-2


title: WT BMDCs-H3K27Ac

value: anti-histone H3 (acetyl K27) (ab4729; abcam)


title: B16-F10 cells, Control_set_2

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (Agilent) Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C.

scan_protocol: Slides were scanned on the SureScan Microarray Scanner G2600D (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction 12.0.3.1 (Agilent).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the Low Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: B16-F10  cella were maintained in the Dulbecco's modified Eagle medium containing 10% fetal bovine serum.

extract_protocol: Totral RNA was extracted using NucleoSpin RNA (Macherey-Nagel, Düren, Germany).

treatment_protocol: B16-F10 cells were cultured  in the presence or absence of recombinant Cdh1 (100 ng/mL) for 24 hours.

value: B16-F10 mouse melanoma cell line

value: control


title: Ribo-Seq RPF_Control_rep1

value: Control siRNA


title: B16-F10 cells, Sample_set_2

source_name: B16-F10, treated with recombinant Cdh1 for 24h

value: recombinant Cdh1


title: Ribo-Seq siCNOT1 Replicate 2


title: EGR1 KO BMDCs-H3K27Ac


title: Ribo-Seq siCNOT1 Replicate 1


title: HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 3

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The raw paired-end reads were trimmed to remove 3p- and 5p-adapters using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC) (Martin 2011). The resulting trimmed reads were joined using fastq-join. The low quality reads and duplicated reads were discarded using  fastq_quality_filter (-q 30 -p 90) and fastx_collapser (FASTX-Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13), respectively. Next, the 4-nt randomized barcodes in both ends of reads were trimmed. The reads were mapped to the sequence of transfected pri-mir-342 or its variants using BWA (Li and Durbin, 2009). Pri-mir-342 variants were designed to introduce the bulge or delete the mismatches on the upper stem of pri-mir-342 wild type. Since the 3p-end annotation of miRNAs are not accurate due to the modifications, we used the 5p miRNAs for cleavage site analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count, transfected_primiRNAs.fasta.gz contains the sequence of transfected pri-mir-342 and its variants

source_name: HCT116 cells

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
1.5 μg of pcDNA3.0 plasmids encoding pri-mir-342 or its variants plus 0.5 μg of pcDNA3.0 encoding pri-mir-1266 were co-transfected into HCT116 cells pre-seeded in one well of 6-well plate using lipofectamine 3000 (Thermo Fisher Scientific). One and a half days after transfection, total RNAs were extracted from the transfected cells using TRIzol reagent (Invitrogen). Fifteen μg of each total RNA was loaded into 15% urea-PAGE. The small RNAs within the 19-24 nt region were gel-purified. The purified small RNAs were ligated to the 3’-adapter (4N-RA3) using T4 RNA ligase 2, truncated KQ (NEB). The 3’-adapter ligated RNAs were separated from free 3’-adapter and unligated small RNAs by gel-purification. After which, the purified 3’-adapter RNAs were ligated with 5’-adapter (RA5-4N) using and T4 RNA ligase 1 (NEB). Next, the 3’- and 5’-adapter-ligated RNAs were reverse transcribed using SuperScript™ IV Reverse Transcriptase with the R-RA3 primer, which generated cDNAs. The resulting cDNAs were amplified using PCR with RP1 and RPI primer (Illumina), which produced DNA libraries. We used a RPI primer with a unique index sequence for each small RNA sample.

tag: disease state

value: colon carcinoma

tag: plasmid transfection

value: pCDNA3.0 pri-mir-342midB_3p plasmid

tag: index

value: TTTCAC


title: IP-NEM_CovR_TAG_ATc200_Rep2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
FLAG-CovR with 200 ng/ml aTc induction (Replicate 2)
NEM200.2

data_processing:
Trimming was performed with fastq-mcf (ea-utils version 1.1.2-806) with custom parameters : -t 0 -C 500000 -q 30 -l 25 -S --qual-mean 30 --max-ns 1
Bowtie2 version 2.1.0 in very sensitive mode was used to align reads against reference genome.
MarkDuplicate from picard-tools version 2.8.1 was used to mark duplicates on all samples
Quality peak control was done by PhantomPeakQualtTools version  1.14
Peaks were called by MACS2 version 2.1.0 with custom parameters : macs2 callpeak --nomodel --keep-dup 40 -p 0.01 --extsize $size (where $size is the fagment size estimated by PhantomPeakQualTools)
Reproducible peaks between replicates were selected using the IDR method with a threshold of 0.05, according to ENCODE specifications.
Genome_build: Streptococcus agalactiae NEM316 (from NCBI id=165229)
Genome_build: Streptococcus agalactiae BM110 (from NCBI id=318722)
Supplementary_files_format_and_content:
Coverage file (bedgraph format)
Peak calling output file (MACS2 output)
Reproducible peaks with information merged for both replicates (chr start_idr end_idr name IDRscore strand signalValue_idr log10pvalue_idr log10qvalue_idr summit_idr log10localIDR log10globalIDR start_rep1 end_rep1 summit_rep1 signalValue_rep1 fold_change_rep1 log10pvalue_rep1 start_rep2 end_rep2 summit_rep2 signalValue_rep2 fold_change_rep2 log10pvalue_rep2)

organism: Streptococcus agalactiae

growth_protocol: From an overnight culture, 100 ml of fresh medium (THY supplemented with 50 mM HEPES, 500 ug/ml Kanamycine and 0, 50, 200 ng/ml aTc) were inoculated (1/50) and incubated at 37°C in static condition up to mid-exponential growth phase (OD600 = 0.5-0.6).

extract_protocol:
CovR was immunoprecipitated with a Anti-FLAG monoclonal antibody coupled to magnetic beads for 2h at 4°C and samples treated with RNAse and Proteinase K overnight at 65°C prior to DNA purification for library construction.
Libraries were prepared with Illumina TruSeq ChIP library preparation Kit (Illumina). Briefly, DNA was end-repaired and phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters. DNA was amplified by PCR with Illumina primers for 16 cycles and library fragments of ~350 bp were isolated from an agarose gel. Libraries were sequenced on an Illumina NextSeq 500/550 apparatus by single-end sequencing (75 bp).

treatment_protocol: DNA-CovR complexes were crosslinked with 1% formaldehyde for 20 min and the reaction was quenched with 0,5 M glycine for 15 min. Chromatin was shared in fragments of 300-500 bp lenght by sonication.

tag: genotype background

value: {delta}covR

tag: genotype/variation

value: FLAG-CovR

tag: growth condition/phase

value: THY medium + 50mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)

value: 200 ng/ml aTc induction

tag: chip-antibody

value: Anti-FLAG M2 (mouse monoclonal) antibody coupled to magnetic beads (Millipore)


title: C_24_104

city: Southampton

first: Jodie

last: Ackland

state: Hampshire

address: Mail Point 810, Level F, South Block Southampton General Hospital, Tremona Road

department: Clinical and Experimental Sciences, Faculty of Medicine

institute: University of Southampton

description: Uninfected (C, control) sample at 24h (24) for sample ID 104 (104)

data_processing:
The Spliced Transcripts Alignment to a Reference (STAR) software (version 2.5) was used to map reads to the human genome (hg38) and Bowtie (version 2.2.3) was used to map reads to the NTHi ST14 genome
Aligned reads were quantified using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for MDM or NTHi data

extract_protocol:
miRNeasy kit
ribosomal RNA (rRNA) was removed from all samples using Ribo-Zero™ Magnetic Kit and libraries were generated using the NEBNext®Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Samples from five biological replicates (indicated as numbers at end of sample names; 005, 016, 082, 104, 124) were either infected with NTHi (T, treated) or left uninfected (C, control) for 6h, with RNA extracted after a 90 min gentamicin wash (6h) or after a prolonged incubation until 24h (24)

tag: cell type

value: Monocyte-derived macrophage

tag: treatment/time point


title: C_6h_124

description: Uninfected (C, control) sample at 6h (6h) for sample ID 124 (124)


title: proximal subiculum neurons

city: Stanford

first: Justus

last: Kebschull

state: CA

address: 327 Campus Drive

institute: Stanford University

data_processing:
Basecalling through Illumina pipeline
STAR alignment to (I) mouse genome mm10
Count reads in exons using Htseq
Produce count matrix
Analyse in Seurat
Genome_build: mm10
Supplementary_files_format_and_content: seurat v3 object containing count matrix, dimensionality reduction, cluster assignment, metadata

source_name: vGlut1Cre+ neurons

extract_protocol:
vGlut1Cre+ neurons were labeled by crossing to a tdTomato reporter (Ai14), dissected at P8, and dissociated with papain. Hoechst and tdTomato+ cells were FAC-sorted into 384-well plates for SmartSeq2 single cell RNA sequencing.
smartseq2

tag: Sex

value: pooled male and female

tag: region

value: proximal subiculum

value: vGlut1Cre+ neurons


title: B16-F10 cells, Control_set_1

tag: cell line

tag: treatment


title: B16-F10 cells, Sample_set_1


title: WT BMDCs-EGR1

value: bone marrow-derived dendritic cells

value: anti-EGR1 (15F7) (Cell Signaling Technology)

value: Stimulated with LPS (100 ng/ml) and LA (20 mM) for 24 h.


title: Gclc KO-1

tag: genotype

value: Gclc KO

tag: tissue

value: Lens


title: distal subiculum neurons

tag: age

value: distal subiculum


title: C_24_124

description: Uninfected (C, control) sample at 24h (24) for sample ID 124 (124)


title: C_6h_104

description: Uninfected (C, control) sample at 6h (6h) for sample ID 104 (104)


title: lateral entorhinal cortex neurons

value: lateral entorhinal cortex


title: HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 2

value: colon carcinoma

value: pCDNA3.0 pri-mir-342midB_3p plasmid

value: GCGGAC


title: HCT116 cells pCDNA3.0 pri-mir-342midB_3p plasmid replicate 1

value: CTCTAC


title: medial entorhinal cortex neurons

value: medial entorhinal cortex


title: C_6h_082

description: Uninfected (C, control) sample at 6h (6h) for sample ID 082 (082)


title: HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 3

value: pCDNA3.0 pri-mir-342midB_5p plasmid

value: GGACGG


title: INPUT-NEM_CovR_noTAG-noATc_Rep2

description:
non-flagged CovR form with 0 ng/ml aTc induction (Replicate 2)
NEM.2

tag: strain

value: {delta}covR

value: non-flagged CovR form

value: THY medium + 50mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)

value: 0 ng/ml aTc induction

value: Anti-FLAG M2 (mouse monoclonal) antibody coupled to magnetic beads (Millipore)


title: IP-NEM_CovR_TAG_ATc050_Rep2

description:
FLAG-CovR with 50 ng/ml aTc induction (Replicate 2)
NEM50.2

value: FLAG-CovR

value: 50 ng/ml aTc induction


title: IP-NEM_CovR_TAG_ATc200_Rep1

description:
FLAG-CovR with 200 ng/ml aTc induction (Replicate 1)
NEM200.1

value: 200 ng/ml aTc induction


title: C_24_082

description: Uninfected (C, control) sample at 24h (24) for sample ID 082 (082)

value: Monocyte-derived macrophage


title: HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 2

tag: disease state

value: TGACAT


title: INPUT-NEM_CovR_noTAG-noATc_Rep1

description:
non-flagged CovR form with 0 ng/ml aTc induction (Replicate 1)
NEM.1


title: IP-NEM_CovR_TAG_ATc000_Rep2

description:
FLAG-CovR with 0 ng/ml aTc induction (Replicate 2)
NEM0.2


title: proximal CA1 neurons

value: pooled male and female

value: proximal CA1

value: vGlut1Cre+ neurons


title: C_6h_016

description: Uninfected (C, control) sample at 6h (6h) for sample ID 016 (016)


title: IP-NEM_CovR_TAG_ATc050_Rep1

description:
FLAG-CovR with 50 ng/ml aTc induction (Replicate 1)
NEM50.1


title: HCT116 cells pCDNA3.0 pri-mir-342midB_5p plasmid replicate 1

value: colon carcinoma

tag: plasmid transfection

value: GGAACT


title: IP-NEM_CovR_TAG_ATc000_Rep1

description:
FLAG-CovR with 0 ng/ml aTc induction (Replicate 1)
NEM0.1


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 2

value: pCDNA3.0 pri-mir-342midB_none plasmid

tag: index

value: TACAAG


title: C_24_016

description: Uninfected (C, control) sample at 24h (24) for sample ID 016 (016)


title: C_24_005

description: Uninfected (C, control) sample at 24h (24) for sample ID 005 (005)


title: distal CA1 neurons

value: distal CA1


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 3

value: TTGACT


title: IP-BMA_CovR_TAG_ATc200_Rep2

description:
FLAG-CovR with 200 ng/ml aTc induction (Replicate 2)
BMA200.2

tag: genotype background

value: {delta}covR

value: THY medium + 50mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)


title: C_6h_005

description: Uninfected (C, control) sample at 6h (6h) for sample ID 005 (005)


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342midB_none plasmid replicate 1

value: GTAGCC


title: IP-BMA_CovR_TAG_ATc200_Rep1

description:
FLAG-CovR with 200 ng/ml aTc induction (Replicate 1)
BMA200.1

tag: genotype/variation

value: FLAG-CovR

value: Anti-FLAG M2 (mouse monoclonal) antibody coupled to magnetic beads (Millipore)


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 3

value: pCDNA3.0 pri-mir-342 WT plasmid

value: AAGCTA


title: L3_batch3

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Single-nuclei seq
SCN_COUNTS_META.RData

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M21). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.
ChIP-seq
ChIP-seq reads were aligned with BWA v0.7.16a to the reference sequence (mm10 from UCSC). Reads were filtered for MAPQ >10 and duplicated reads were removed using samtools. MACS2 v2.1.1 was used to identify peaks. Bedtools v2.25.0 was used to integrate dark/light ChIP-seq data. HOMER v4.9.1 was used for motif analysis.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: bed-files including coordinates of the detected peaks from ChIP-Seq.
Single-nuclei RNA-seq
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR v2.5.2b to the reference sequence (mm10 from UCSC). Human reference was used for gene annotation and counting (gencode M17). Gene level expression was calculated using featureCounts v1.6.2. Downstream analysis was performed using Seurat v3.0
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Rdata containing count and meta data tab separated tables

source_name: Superchiasmatic Nuclei

extract_protocol:
Nuclei wer extracted following  a modified protocal based on CG00055_SamplePrepDemonstratedProtocol_-_MouseNeuralTissue_RevA (10x Genomics)
10X libraries were constructed using CG000075_Chromium_Single_Cell_3__V2_Ref_Cards_Rev_C (10x Genomics)

tag: experiment

value: snSCN

value: WT

tag: condition

value: Light

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

tag: batch

tag: protocol

value: Protocol 3


title: L4_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: Sex


title: D4_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: Dark


title: PDAC_CAF_10plex

city: Toronto

first: Curtis

middle: William

last: McCloskey

state: ON

address: 101 College Street, PMCRT, Room 13-303

department: Medical Biophysics

country: Canada

institute: University Health Network

data_processing:
Raw sequencing reads were aligned using CellRanger 3.1.0
MULTI-seq sample barcode libraries were trimmed to 28bp using Trimmomatic v0.36 prior to demultiplexing.
MULTIseq sample barcode alignment and classification were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Further doublet removal and QC was performed as described in the paper
Genome_build: GRCh38-3.0.0 Human genome
Supplementary_files_format_and_content: Expression libraries: gene-cell matrix provided as raw UMI counts post-demultiplexing, doublet removal and QC as described in the paper, along with metadata for each cell (ex/ PDAC subTME classification)

source_name: human PDAC CAFs

growth_protocol: Cells were cultured in FCS-reduced growth medium (DMEM/F12, 8% FCS, GlutaMAX, HEPES, Anti/Anti). Cells were passaged subconfluently in fixed intervals 2 times per week using 0.05% Trypsin

extract_protocol:
Cells were lysed in droplets in the 10x Chromium system
10x Genomics Single Cell 3' Reagent Kit (v3 chemistry)

tag: source

value: human PDAC CAF primary cultures


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 2

tag: cell line

value: colon carcinoma

value: CTGATC


title: L2_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData


title: IP-BMA_CovR_TAG_ATc050_Rep2

description:
FLAG-CovR with 50 ng/ml aTc induction (Replicate 2)
BM50.2

value: {delta}covR

tag: growth condition/phase

value: THY medium + 50mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)

tag: treatment

value: 50 ng/ml aTc induction

tag: chip-antibody


title: IP-BMA_CovR_TAG_ATc050_Rep1

description:
FLAG-CovR with 50 ng/ml aTc induction (Replicate 1)
BM50.1

value: FLAG-CovR

value: Anti-FLAG M2 (mouse monoclonal) antibody coupled to magnetic beads (Millipore)


title: L1_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: genotype

tag: tissue

tag: age


title: 8A_C4_iPREX1_withDox_2

city: Ottawa

first: David

last: Cook

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

data_processing:
Sequencing data was pseudoaligned to the human GRCh38 reference transcriptome and transcript counts were quantified using Kallisto.
Differential expression between conditions was performed using Sleuth.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential expression results: Statistics from differential expresison testing along with gene-level TPM quantifications for each sample

source_name: Glioblastoma

growth_protocol: Cells were grown as monolayers on tissue culture plates coated with laminin (Sigma-Aldrich, Oakville ON, Canada) using neurobasal A medium with B27 and N2 supplements and EGF and FGF2 (all from Thermo Fisher Scientific Inc., Waltham MA, USA). Cells were incubated in 5% O2 and 5% CO2 at 37˚C

extract_protocol:
Total RNA was isolated using the GE Illustra RNA Spin Kit (Thermo Fisher Scientific, Ottawa, ON, Canada) according to kit protocol including DNase treatment
RNA-seq libraries were generated from 250ng of total RNA. The NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs) and cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra directional RNA Second Strand Synthesis Modules (New England BioLabs). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Glioblastoma PREX1 knockout cells were generated by electroporation of preformed crRNA/tracrRNA/Cas9 complexes. For the crRNA:tracrRNA duplex, a crRNA sequence targeting exon 2 of PREX1.

tag: cell type

value: glioblastoma

value: PREX1 KO with doxycycline-inducible PREX1 (With doxycycline)


title: IP-BMA_CovR_TAG_ATc000_Rep1

description:
FLAG-CovR with 0 ng/ml aTc induction (Replicate 1)
BMA0.1

tag: strain

value: 0 ng/ml aTc induction


title: IP-BMA_CovR_TAG_ATc000_Rep2

description:
FLAG-CovR with 0 ng/ml aTc induction (Replicate 2)
BMA0.2

tag: genotype background


title: 8A_C4_iPREX1_noDox_2

value: PREX1 KO with doxycycline-inducible PREX1 (No doxycycline)


title: HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 3

tag: disease state

tag: plasmid transfection

value: pCDNA3.0 empty plasmid

tag: index

value: GATCTG


title: 8A_C4_iPREX1_withDox_1


title: D3_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

tag: experiment

value: snSCN

value: WT

tag: condition

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

tag: batch


title: HCT116 cells transfected with pCDNA3.0 pri-mir-342 WT plasmid replicate 1

value: colon carcinoma

value: pCDNA3.0 pri-mir-342 WT plasmid

value: TCAAGT


title: 8A_C4_iPREX1_noDox_1


title: D1_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: Dark

tag: Sex

tag: protocol

value: Protocol 3


title: HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 1

tag: cell line

value: CGTGAT


title: JS6_3 Bent stage Seed coat RNA-seq replicate 3

status: Public on Aug 22 2021

city: Saskatoon

first: Daoquan

last: Xiang

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council of Canada

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Salmon was used for fast and accurate alignment of cleaned reads to released brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/), respectively.
Salmon was used to obtain transcripts per million reads (TPM) of each sample.
To summarize expression levels from the transcript level to the gene level, we used R tximport package to process the TPM values obtained from Salmon.
Genome_build: Brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/)
Supplementary_files_format_and_content: Matrix table files include TPM for each Sample

organism: Brassica juncea

source_name: Bent stage Seed coat

growth_protocol: Plants were grown under 16h of light, 22°C and 8h of dark, 20°C photoperiod 120-150 μE m−2 s−1 light intensity.

extract_protocol:
Embryo isolations were performed using a dissecting microscope, fine forceps and needles in a 4.8% Sucrose solution that contained 0.1% RNALater solution.For seed coat isolation, the embryos were manually removed, and the remaining seed coat was kept. Total RNA was extracted from each stage embryo sample following the protocol of RNAqueous-micro kit.
RNA-seq libraries were prepared using the NEBNext Single Cell/Low Input RNA library Prep Kit for Illumina.

treatment_protocol: Brassica flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

value: Seed coat

tag: satge

value: Bent stage

tag: ecotype

value: AC Vulcan


title: JS7_3 Mature_stage Seed coat RNA-seq replicate 3

source_name: Mature_stage Seed coat


title: JS3_3 Globular stage Seed coat RNA-seq replicate 3

source_name: Globular stage Seed coat

value: Globular stage


title: JUO_3 Unfertilized stage ovule RNA-seq replicate 3

source_name: Unfertilized stage ovule

value: ovule

value: Unfertilized stage


title: JS5_3 Torpedo stage Seed coat RNA-seq replicate 3

source_name: Torpedo stage Seed coat

value: Torpedo stage


title: INPUT-BMA_CovR_noTAG-noATc_Rep2

description:
non-flagged CovR form with 0 ng/ml aTc induction (Replicate 2)
BMA.2

value: {delta}covR

tag: genotype/variation

value: non-flagged CovR form

tag: growth condition/phase

value: THY medium + 50mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)

tag: treatment

value: 0 ng/ml aTc induction

tag: chip-antibody

value: Anti-FLAG M2 (mouse monoclonal) antibody coupled to magnetic beads (Millipore)


title: JE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3

source_name: Heart stage Embryo

tag: tissue

value: Embryo

value: Heart stage


title: JS2_3 Octant stage Seed coat RNA-seq replicate 3

source_name: Octant stage Seed coat

value: Octant stage


title: JS1_3 Zygote stage Seed coat RNA-seq replicate 3

source_name: Zygote stage Seed coat

value: Zygote stage


title: JS4_3 Heart stage Seed coat RNA-seq replicate 3

source_name: Heart stage Seed coat


title: JE5_3 Torpedo stage Embryo RNA-seq replicate 3

source_name: Torpedo stage Embryo


title: JE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

source_name: Bent stage Embryo


title: JE3_3 Globular stage Embryo RNA-seq replicate 3

source_name: Globular stage Embryo


title: JE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3

source_name: Zygote stage Embryo


title: D2_batch3

description:
Single-nuclei seq
SCN_COUNTS_META.RData

value: snSCN

tag: genotype

value: WT

value: Dark

value: Superchiasmatic Nuclei

tag: age

value: 11-12 weeks

value: male

value: Protocol 3


title: INPUT-BMA_CovR_noTAG-noATc_Rep1

description:
non-flagged CovR form with 0 ng/ml aTc induction (Replicate 1)
BMA.1

tag: strain

tag: genotype background


title: JE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3

source_name: Mature_stage Embryo

value: AC Vulcan


title: JS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Seed coat

tag: Stage

value: Zygote


title: HCT116 cells transfected with pCDNA3.0 empty plasmid replicate 2

source_name: HCT116 cells

tag: disease state

value: colon carcinoma

tag: plasmid transfection

value: pCDNA3.0 empty plasmid

tag: index

value: ACATCG


title: JE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3

source_name: Octant stage Embryo

value: Embryo


title: JE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: JE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Octant


title: JE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Globular


title: JE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Heart


title: JE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: JE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: ovule

value: Unfertilized


title: Replicate 3 siCNOT1 8hr

data_processing:
fastp v0.19.5 was used to remove adapter sequences
cd-hit-dup v4.6.6 was used to deduplicate reads based opn the 12nt UMI
alignment using STAR v2.6 was used for alignments
featureCounts v1.6.4 was used to obtain read counts
Genome_build: hg38, gencode v28
Supplementary_files_format_and_content: csv file with the log2FC mRNA half-life (siCNOT1/siControl)

source_name: HEK293_CNOT1 siRNA_8hr

extract_protocol:
Cells were washed with ice-cold PBS and Trizol added directly to the well. The RNA was extracted with Trizol and acid-phenol purification
Total RNA was poly(A) selected using the lexogen poly(A) selection kit. 4ng poly(A) selected RNA was then used as input into the lexogen CORALL Total RNA-seq kit and 10 PCR cycles used to produce the libraries.

treatment_protocol: Cells treated with 20nM of control or CNOT1-targeting siRNA for 48 hrs

tag: sirna

value: CNOT1 siRNA

tag: timepoint


title: Replicate 3 siCNOT1 1hr

source_name: HEK293_CNOT1 siRNA_1hr

tag: cell line


title: JS7_2 Mature stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Mature stage Seed coat

value: Mature

tag: ecotype


title: Replicate 3 siCNOT1 2hr

source_name: HEK293_CNOT1 siRNA_2hr


title: Replicate 3 siCNOT1 0.5hr

source_name: HEK293_CNOT1 siRNA_0.5hr


title: Replicate 3 siCNOT1 4hr

source_name: HEK293_CNOT1 siRNA_4hr


title: JS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Torpedo stage Seed coat

value: Torpedo


title: Replicate 3 siCNOT1 16hr

source_name: HEK293_CNOT1 siRNA_16hr


title: Replicate 3 siControl 8hr

source_name: HEK293_Control siRNA_8hr

value: Control siRNA


title: JS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Heart stage Seed coat


title: JS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: JS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Zygote stage Seed coat


title: JS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Bent stage Seed coat

value: Bent


title: JS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: AC Vulcan


title: JS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Octant stage Seed coat

value: Seed coat


title: Replicate 3 siControl 0.5hr

source_name: HEK293_Control siRNA_0.5hr


title: JS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: Replicate 3 siControl 0hr

source_name: HEK293_Control siRNA_0hr


title: Replicate 3 siControl 2hr

source_name: HEK293_Control siRNA_2hr


title: Replicate 2 siCNOT1 16hr


title: Replicate 3 siControl 1hr

source_name: HEK293_Control siRNA_1hr


title: JS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Globular stage Seed coat


title: JUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Unfertilized stage ovule


title: JS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: JE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Mature stage Embryo


title: Replicate 3 siControl 4hr

source_name: HEK293_Control siRNA_4hr


title: Replicate 3 siControl 16hr

source_name: HEK293_Control siRNA_16hr


title: Replicate 2 siCNOT1 4hr

source_name: HEK293_CNOT1 siRNA_4hr


title: Replicate 3 siCNOT1 0hr

source_name: HEK293_CNOT1 siRNA_0hr


title: Replicate 2 siCNOT1 8hr

source_name: HEK293_CNOT1 siRNA_8hr


title: JE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Bent stage Embryo


title: Replicate 2 siCNOT1 0hr


title: JE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Torpedo stage Embryo


title: JE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: JS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: Replicate 2 siControl 16hr


title: Replicate 2 siCNOT1 1hr

source_name: HEK293_CNOT1 siRNA_1hr


title: Replicate 2 siControl 2hr


title: Replicate 2 siCNOT1 0.5hr

source_name: HEK293_CNOT1 siRNA_0.5hr


title: naive RGC rep3

city: Palo Alto

first: Xue

last: Feng

address: 1651 Page Mill road

institute: Stanford

data_processing:
Illumina's bcl2fastq 2.17 software used for basecalling.
The adaptor sequences of RNA-seq raw data were trimmed by trim-galore with the parameter -q 25 --phred33 --length 36 -e 0.1 --stringency 3 --paired -o. Then the RNA-seq was aligned with Hisat2 to the mouse reference genome (version mm10). The parameter used for alignment is hisat -t -x mm10/genome -1 R1.fq -2 R2.fq -S align.sam. MultiQC was used to assess the quality of the sequence data.
The count matrix of all the genes in the individual samples were determined by featureCounts, with the parameter featureCounts -T 10 -p -t exon -g gene_id -a reference/gencode.vM23.annotation.gtf -o sample.txt sample.bam.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: retina

extract_protocol:
The fresh isolated retinas at one week post SO injection were homogenized with pestle in homogenization buffer. 10 µl anti-HA antibody was added into each sample and incubated for 4 hours at room temperature with rotation before incubated with Protein G magnetic beads overnight at 4 °C with rotation. The beads were washed for 10 minutes x 3 in a high-salt buffer before resuspended in Trizol for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sillicon oil was injected into the anterior chamber 1 week before sample harvest.

tag: cell type

value: retinal ganglion cells (RGCs)

value: retina

value: 10 weeks

value: wild type

tag: condition

value: naive


title: SOHU RGC rep2

value: Silicone oil-induced ocular hypertension under-detected (SOHU) mouse model


title: Replicate 2 siControl 1hr

city: Glasgow

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research


title: naive RGC rep1


title: Replicate 2 siControl 8hr

source_name: HEK293_Control siRNA_8hr


title: IMQ+VEH-2

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: Mouse back skin treated with IMQ and vehicle lotion.

data_processing:
Reads were mapped to the mouse (GRCm38/mm10) genome using the tophat2 algorithm with default settings (Kim et al. 2013, Genome biology 14:R36).
FPKM and FPKM confidence intervals were calculated using Cufflinks (Trapnell et al. 2012, Nature protocols 7: 562-578.
Raw gene counts for differential expression analysis were computed using the HTseq library (Anders et al. 2015, Bioinformatics (Oxford, England) 31:166-169).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all mouse genes (GRCm38/mm10) and each sample (.txt files).

source_name: Skin

growth_protocol: Male BALB/c mice 8-9 weeks of age were maintained under standard conditions in a temperature-controlled environment and provided ad libitum access to mouse chow with water.

extract_protocol:
Total RNA was extracted from frozen skin samples using the RNeasy Fibrous Tissue Mini Kit (Qiagen, cat. no. 74704) with on-column DNase digestion (Qiagen, cat. no. 79254).
Samples were submitted for H4K Single End 50 Cycle sequencing (University of Michigan Sequencing Core, Ann Arbor, MI) and RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: From Day 1 to Day 5, all mice received 5% IMQ cream (47 mg/day) applied topically once daily on the back skin (~area: 4cmx2cm). Placebo or IDMF lotions were applied ~1h after IMQ application without any anesthesia. On Day 6, at the end of final in-life assessments, all animals underwent necropsy for back skin tissue collection.

tag: treatment

value: IMQ + VEH

value: BALB/c

tag: Sex

value: Male


title: IMQ+IDMF

description: Mouse back skin treated with IMQ and IDMF.

value: IMQ + IDMF


title: Replicate 2 siControl 0hr

source_name: HEK293_Control siRNA_0hr


title: JE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

tag: tissue

value: Embryo


title: naive RGC rep2

tag: genotype


title: SOHU RGC rep1

tag: age


title: IMQ

description: Mouse back skin treated with IMQ only.

value: IMQ

tag: strain


title: Replicate 1 siCNOT1 4hr

value: CNOT1 siRNA


title: Replicate 1 siCNOT1 16hr

source_name: HEK293_CNOT1 siRNA_16hr


title: Replicate 2 siCNOT1 2hr

source_name: HEK293_CNOT1 siRNA_2hr


title: SOHU RGC rep3


title: IMQ+VEH-1


title: Replicate 1 siCNOT1 8hr


title: Replicate 2 siControl 4hr

value: Control siRNA


title: Replicate 1 siCNOT1 0.5hr


title: input DNA for ChIP with anti-GFP antibody in HP1 KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

data_processing:
Reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases.
Reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded.
Reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: All mapping and unique mapping bigwig files for sense and antisense.

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were grown at 27º C, 2.5% CO2.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006).
NEBNext Ultra DNA Library Prep Kit Illumina (NEB).

value: OSC

tag: genotype/variation

value: HP1 depletion

tag: chip antibody


title: input DNA for ChIP with anti-GFP antibody in HP1 KD Panx-GFP-tagged OSCs


title: input DNA for ChIP with anti-GFP antibody in Piwi KD Panx-GFP-tagged OSCs

value: Piwi depletion


title: Replicate 1 siCNOT1 0hr


title: Replicate 2 siControl 0.5hr

source_name: HEK293_Control siRNA_0.5hr


title: input DNA for ChIP with anti-GFP antibody in control KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction

value: control depletion


title: Replicate 1 siCNOT1 2hr


title: input DNA for ChIP with anti-GFP antibody in control KD Panx-GFP-tagged OSCs


title: chromatin immunoprecipitation with anti-GFP antibody in HP1 KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction

value: anti-GFP antibody (Thermo Scientific, A-111222)


title: input DNA for ChIP with anti-GFP antibody in Piwi KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction


title: Replicate 1 siCNOT1 1hr


title: chromatin immunoprecipitation with anti-GFP antibody in Piwi KD Panx-GFP-tagged OSCs


title: Replicate 1 siControl 16hr


title: chromatin immunoprecipitation with anti-GFP antibody in Sov-GFP-tagged OSCs


title: input DNA for ChIP with anti-GFP antibody in WT OSCs


title: ChIP_CDC6_stock_Oregon_ovary_1-13_chambers

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq and FAIRE-Seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Total DNA reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
RNA-Seq data were analyzed with TopHat2 (using UseGalaxy.eu online tools)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.

source_name: Oregon-R-modENCODE (Bloomington stock 25211)

growth_protocol: The flies of Oregon-R-modENCODE (oregon) (corresponds to Bloomington stock 25211), su(Hw)v/E8 and su(Hw)v/f stocks (a kind gift of A. Golovnin laboratory) were used. All flies were raised at 25°C on standard agar medium.

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total DNA analysis, RNA-Seq and ChIP-Seqs by anti-Su(Hw) antibodies were performed using ovaries with egg chambers corresponding to 1-13 stages, which were dissected from Oregon-R-modENCODE and su(hw)v/f Drosophila stocks.  FAIRE-Seq and ChIP-Seqs by anti-Su(Hw), anti-ORC2, anti-CDC6, anti-Brm, anti-ISWI, anti-CHD1, anti-Mi2, anti-Gcn5 antibodies were performed using ovaries with egg chambers corresponding to 1-8 stages dissected from Oregon-R-modENCODE and su(hw)v/e8 Drosophila stocks.

tag: analysed tissue

value: Ovaries were dissected from females 32-34 hours after eclosion (containing egg chambers corresponding to 1-13 stages).

tag: chip antibodies

value: raised in a current study using antigen corresponding to epitope corresponding to 9-179 amino acid residues of CDC6 Drosophila protein

value: no treatment


title: ChIP_Input_stock_Oregon_ovary_1-8_chambers

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq and FAIRE-Seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Total DNA reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
RNA-Seq data were analyzed with TopHat2 (using UseGalaxy.eu online tools)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.

source_name: Ovaries were dissected from females 15 hours after eclosion (containing egg chambers corresponding to 1-8 stages).

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: female

value: ovary

value: none (input)


title: ChIP_Input_stock_SuHw_ve8__ovary_1-8_chambers

value: su(Hw)v/e8 stock (a gift of A. Golovnin)


title: chromatin immunoprecipitation with anti-GFP antibody in control KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction


title: Replicate 1 siControl 1hr

first: Sarah

source_name: HEK293_Control siRNA_1hr


title: Replicate 1 siControl 8hr


title: Replicate 1 siControl 2hr

source_name: HEK293_Control siRNA_2hr


title: input DNA for ChIP with anti-GFP antibody in Sov-GFP-tagged OSCs


title: Replicate 1 siControl 0.5hr


title: Replicate 1 siControl 4hr

source_name: HEK293_Control siRNA_4hr


title: input DNA for ChIP with anti-GFP antibody in Panx-GFP-tagged OSCs


title: ChIP_CDC6_stock_SuHw_vf__ovary_1-13_chambers

source_name: su(Hw)v/f  stock (a gift of A. Golovnin)


title: input DNA for ChIP with anti-GFP antibody in Panx-GFP-tagged OSCs after CSK buffer pre-extraction


title: chromatin immunoprecipitation with anti-GFP antibody in control KD Panx-GFP-tagged OSCs


title: Replicate 1 siControl 0hr


title: ChIP_ORC2_stock_SuHw_vf__ovary_1-13_chambers

value: raised in a current study using antigen corresponding to epitope corresponding to 28-194 amino acid residues of ORC2 Drosophila protein


title: ChIP_Input_stock_Oregon_ovary_1-13_chambers

source_name: Ovaries were dissected from females 32-34 hours after eclosion (containing egg chambers corresponding to 1-13 stages).


title: ChIP_ORC2_stock_Oregon_ovary_1-13_chambers


title: chromatin immunoprecipitation with anti-GFP antibody in WT OSCs after CSK buffer pre-extraction


title: ChIP_Input_(for_ChIP_ORC2_Cdc6)_stock_Oregon_ovary_1-13_chambers


title: input DNA for ChIP with anti-GFP antibody in WT OSCs after CSK buffer pre-extraction


title: FAIRE-Seq_stock_Oregon_ovary_1-8_chambers


title: chromatin immunoprecipitation with anti-GFP antibody in Panx-GFP-tagged OSCs


title: chromatin immunoprecipitation with anti-GFP antibody in HP1 KD Panx-GFP-tagged OSCs


title: ChIP_Input_(for_ChIP_ORC2_Cdc6)_stock_SuHw_vf__ovary_1-13_chambers


title: chromatin immunoprecipitation with anti-GFP antibody in Piwi KD Panx-GFP-tagged OSCs after CSK buffer pre-extraction


title: total RNAs from HP1 KD in OSCs with polyA selection replicate1

data_processing:
Reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases.
Reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded.
Reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b).
Reads mapping to rRNA, tRNA, mitoRNA were excluded.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: All mapping and unique mapping bigwig files for sense and antisense.

extract_protocol:
RNA was extracted using Trizol. PolyA selection.
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).


title: total RNAs from Sov2 KD in OSCs with polyA selection replicate3

value: Sov depletion with siRNA-2


title: Total_DNA_stock_Oregon_embryo_2-4h

data_processing:
Library strategy: total DNA-seq
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq and FAIRE-Seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Total DNA reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
RNA-Seq data were analyzed with TopHat2 (using UseGalaxy.eu online tools)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.

source_name: Embryos were collected for 2 hours using agar plates and incubated for 2h at RT


title: total RNAs from Sov1 KD in OSCs with polyA selection replicate2

value: Sov depletion with siRNA-1


title: ChIP_Brm_stock_SuHw_ve8__ovary_1-8_chambers

value: anti-Brm antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178-189)


title: total RNAs from Sov1 KD in OSCs with polyA selection replicate1

value: OSC


title: ChIP_Brm_stock_Oregon_ovary_1-8_chambers


title: chromatin immunoprecipitation with anti-H3K9me3 antibody in WT OSCs

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: ChIP_Gcn5_stock_Oregon_ovary_1-8_chambers

value: anti-Gcn5 antibodies (Vorobyeva et al (2013) NAR, 41:11, 5717–5730)


title: total RNAs from HP1 KD in OSCs with polyA selection replicate2

value: HP1 depletion


title: total RNAs from Piwi KD in OSCs with polyA selection replicate3

value: Piwi depletion


title: total RNAs from Panx KD in OSCs with polyA selection replicate1

value: Panx depletion


title: ChIP_CDC6_stock_Oregon_ovary_1-8_chambers

value: raised in a current study using antigen corresponding to epitope corresponding to 9-179 amino acid residues of ORC2 Drosophila protein


title: ChIP_Mi2_stock_Oregon_ovary_1-8_chambers

value: anti-Mi2 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178-189)


title: chromatin immunoprecipitation with anti-GFP antibody in Panx-GFP-tagged OSCs after CSK buffer pre-extraction

value: anti-GFP antibody (Thermo Scientific, A-111222)


title: ChIP_Mi2_stock_SuHw_ve8__ovary_1-8_chambers

value: female


title: ChIP_ORC2_stock_SuHw_ve8__ovary_1-8_chambers

value: ovary


title: ChIP_Input_stock_SuHw_vf__ovary_1-13_chambers

value: su(Hw)v/f stock (a gift of A. Golovnin)

value: none (input)


title: ChIP_CHD1_stock_Oregon_ovary_1-8_chambers

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: anti-CHD1 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178-189)


title: chromatin immunoprecipitation with anti-GFP antibody in WT OSCs


title: total RNAs from HP1 KD in OSCs with polyA selection replicate3


title: total RNAs from Sov2 KD in OSCs with polyA selection replicate1

value: Sov depletion with siRNA-2


title: total RNAs from control KD in OSCs with polyA selection replicate3

value: control depletion


title: ChIP_CHD1_stock_SuHw_ve8__ovary_1-8_chambers

value: su(Hw)v/e8 stock (a gift of A. Golovnin)


title: ChIP_SuHw_stock_SuHw_ve8__ovary_1-8_chambers

value: raised in a current study using antigen corresponding to N-part of Su(Hw) (antibodies raised with the same epitope was described in Golovnin et al (2008)EMBO Rep 9:440-445.


title: total RNAs from control KD in OSCs with polyA selection replicate2

value: OSC


title: ChIP_SuHw_stock_Oregon_ovary_1-8_chambers


title: total RNAs from control KD in OSCs with polyA selection replicate1


title: total RNAs from Sov2 KD in OSCs with polyA selection replicate2


title: total RNAs from Sov1 KD in OSCs with polyA selection replicate3

value: Sov depletion with siRNA-1


title: ChIP_SuHw_stock_Oregon_ovary_1-13_chambers


title: DTXR

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
The FASTQ-formatted sequence data was analyzed using a standard HISAT-StringTie-Ballgown pipeline workflow. In brief, raw sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were comprehensively quantified with StringTie software, which performed transcript assembly and quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values. Cuffnorm was utilized for normalization of FPKM values (Cuffnorm output), which were were utilized for downstream analysis steps.
Processed data are StringTie-Cuffnorm output files and contain Gene Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: GRCh38, Dec. 2013
Supplementary_files_format_and_content: Tab-delimited text files include Gene_Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the StringTie-Cuffnorm gene-level output files.

source_name: Cells

growth_protocol: Cells were maintained in complete RPMI 1640 medium {supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 0.1 mg/ml streptomycin). TaxR and DTXR were maintained under 5nM docetaxel selection. CabR and CTXR were maintained under 5nM cabazitaxel selection.

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen)
Indexed, stranded mRNA-Seq libraries were prepared from 100 ng total RNA using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) according to the manufacturer’s standard protocol.

treatment_protocol: Cells were untreated prior to harvest and RNA extraction.

value: human castration-resistant prostate carcinoma

tag: phenotype

value: docetaxel-resistant DU145 cells

value: Untreated


title: total RNAs from Panx KD in OSCs with polyA selection replicate3

value: Panx depletion


title: FAIRE-Seq_stock_SuHw_ve8__ovary_1-8_chambers


title: total RNAs from Panx KD in OSCs with polyA selection replicate2


title: Total_DNA_stock_Oregon_ovary_1-13_chambers_rep1


title: ChIP_ISWI_stock_SuHw_ve8__ovary_1-8_chambers

value: anti-ISWI antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178-189)


title: CabR

value: cabazitaxel-resistant TaxR cells


title: OUO_3 Unfertilized stage ovule RNA-seq replicate 3

organism: Brassica oleracea

source_name: Unfertilized stage ovule

value: ovule

tag: satge

value: Unfertilized stage

value: Chinese Kale


title: ChIP_ISWI_stock_Oregon_ovary_1-8_chambers

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: female

value: ovary


title: TaxR_old

value: docetaxel-resistant C4-2B cells


title: Total_DNA_stock_SuHw_vf_ovary_1-13_chambers_rep2

value: su(Hw)v/f stock (a gift of A. Golovnin)


title: OS6_3 Bent stage Seed coat RNA-seq replicate 3

source_name: Bent stage Seed coat

value: Seed coat

value: Bent stage


title: C4-2B MDVR ARVib-31

data_processing:
The FASTQ-formatted sequence data was analyzed using a standard HISAT-Cufflinks workflow. In brief, raw sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values (Cuffnorm output) were utilized for downstream analysis steps.
Processed data are Cufflinks-Cuffnorm output files and contain Gene Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: GRCh38, Dec. 2013
Supplementary_files_format_and_content: Tab-delimited text files include Gene_Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

source_name: LNCaP-C42B-MDVR cells cultured in medium with with ARVib-31 (analog #31)

growth_protocol: C4-2B MDVR cells were maintained in complete RPMI 1640 medium {supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 0.1 mg/ml streptomycin) containing enzalutamide (20 μM).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2b-MDVR with DMSO, ARVib-7, or ARVib-31 for 24 hours.
Indexed RNA-Seq libraries were prepared from 200 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Poly-adenylated mRNA was purified by binding to oligo(dT) beads and to remove rRNA, which was followed by fragmentation by incubation at 94ºC in the presence of magnesium. Double-stranded cDNA was then generated by random-primed first-strand synthesis and second strand synthesis in the presence of dUTP for strand marking. Subsequently, the cDNA was 3’-A tailed and indexed, Illumina-compatible adapters were ligated. The libraries were then enriched by high-fidelity PCR amplification (13 cycles) with KAPA HiFi HotStart DNA Polymerase and adapter-specific primers.

treatment_protocol: C4-2B MDVR cells were treated with vehicle or the AR/AR-V7 inhibitors ARVib-7 (1.5 uM) or ARVib-31 (1.5 uM) for 24 hours before RNA extraction.

value: human castration-resistant prostate carcinoma (CRPC) cell line

value: Parental cell line

value: ARVib-31 (analog #31)


title: total RNAs from Piwi KD in OSCs with polyA selection replicate2

value: OSC

value: Piwi depletion


title: C4_2B

value: human castration-resistant prostate carcinoma

value: C4-2B parental cell line

value: Untreated


title: C4-2B MDVR ARVib-7

source_name: LNCaP-C42B-MDVR cells cultured in medium with ARVib-7 (analog #7)

value: ARVib-7 (analog #7)


title: ChIP_CDC6_stock_SuHw_ve8__ovary_1-8_chambers

value: su(Hw)v/e8 stock (a gift of A. Golovnin)

value: raised in a current study using antigen corresponding to epitope corresponding to 9-179 amino acid residues of ORC2 Drosophila protein


title: OS5_3 Torpedo stage Seed coat RNA-seq replicate 3

source_name: Torpedo stage Seed coat

value: Torpedo stage

value: Chinese Kale


title: ChIP_ORC2_stock_Oregon_ovary_1-8_chambers

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: female

value: ovary

value: raised in a current study using antigen corresponding to epitope corresponding to 28-194 amino acid residues of ORC2 Drosophila protein


title: OS4_3 Heart stage Seed coat RNA-seq replicate 3

source_name: Heart stage Seed coat

value: Seed coat

value: Heart stage


title: total RNAs from Piwi KD in OSCs with polyA selection replicate1

source_name: OSCs


title: ChIP_Gcn5_stock_SuHw_ve8__ovary_1-8_chambers

value: anti-Gcn5 antibodies (Vorobyeva et al (2013) NAR, 41:11, 5717–5730)


title: OS3_3 Globular stage Seed coat RNA-seq replicate 3

source_name: Globular stage Seed coat

value: Globular stage


title: PUO_3 Unfertilized stage ovule RNA-seq replicate 3

organism: Brassica napus

value: ovule

value: Unfertilized stage


title: OS7_3 Mature_stage Seed coat RNA-seq replicate 3

source_name: Mature_stage Seed coat


title: Total_DNA_stock_SuHw_vf__ovary_1-13_chambers_rep1

value: su(Hw)v/f stock (a gift of A. Golovnin)


title: RNA-Seq_stock_SuHw_vf__ovary_1-13_chambers_rep1


title: RNA-Seq_stock_Oregon_ovary_1-13_chambers_rep2


title: RNA-Seq_stock_Oregon_ovary_1-13_chambers_rep1


title: RNA-Seq_stock_SuHw_vf_ovary_1-13_chambers_rep2


title: ChIP_SuHw_stock_SuHw_vf__ovary_1-13_chambers

value: raised in a current study using antigen corresponding to N-part of Su(Hw) (antibodies raised with the same epitope was described in Golovnin et al (2008)EMBO Rep 9:440-445.


title: OS1_3 Zygote stage Seed coat RNA-seq replicate 3

source_name: Zygote stage Seed coat

value: Zygote stage


title: PS5_3 Torpedo stage Seed coat RNA-seq replicate 3


title: OE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3

source_name: Mature_stage Embryo

value: Embryo


title: OE5_3 Torpedo stage Embryo RNA-seq replicate 3

source_name: Torpedo stage Embryo


title: OE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

source_name: Bent stage Embryo

value: Bent stage


title: CTXR

value: human castration-resistant prostate carcinoma

value: cabazitaxel-resistant DTXR cells

value: Untreated


title: PS4_3 Heart stage Seed coat RNA-seq replicate 3


title: PS2_3 Octant stage Seed coat RNA-seq replicate 3

source_name: Octant stage Seed coat

value: Octant stage


title: PS1_3 Zygote stage Seed coat RNA-seq replicate 3


title: OE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3

source_name: Octant stage Embryo

value: Chinese Kale


title: OE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3

source_name: Heart stage Embryo


title: PE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3


title: OS2_3 Octant stage Seed coat RNA-seq replicate 3


title: OE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3

source_name: Zygote stage Embryo


title: PS6_3 Bent stage Seed coat RNA-seq replicate 3


title: Total_DNA_stock_Oregon_ovary_1-13_chambers_rep2

source_name: Ovaries were dissected from females 32-34 hours after eclosion (containing egg chambers corresponding to 1-13 stages).

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: female

value: ovary


title: C4-2B MDVR DMSO vehicle control

source_name: LNCaP-C42B-MDVR cells cultured in medium with DMSO vehicle control.

value: human castration-resistant prostate carcinoma (CRPC) cell line

value: Parental cell line

value: DMSO vehicle control.


title: PE5_3 Torpedo stage Embryo RNA-seq replicate 3

value: Torpedo stage


title: OE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Mature stage Embryo

tag: Stage

value: Mature


title: PE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3

value: Heart stage


title: PE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3

value: Zygote stage


title: OE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Globular stage Embryo

value: Embryo

value: Globular


title: PE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: DU145

source_name: Cells

tag: cell line

value: human castration-resistant prostate carcinoma

value: DU145 parental cell line


title: PE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

value: Bent stage

tag: ecotype


title: PS3_3 Globular stage Seed coat RNA-seq replicate 3

value: Seed coat

value: Globular stage


title: PE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS7_3 Mature_stage Seed coat RNA-seq replicate 3


title: OE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Octant

value: Chinese Kale


title: PE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OS7_2 Mature stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Mature stage Seed coat


title: OE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Bent


title: OS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Bent stage Seed coat


title: PE3_3 Globular stage Embryo RNA-seq replicate 3


title: OS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Heart


title: OE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Zygote


title: PE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OE3_3 Globular stage Embryo RNA-seq replicate 3


title: OE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Unfertilized stage ovule

value: ovule

value: Unfertilized


title: PS7_2 Mature stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Mature


title: OUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Heart stage Seed coat


title: PS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: PE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: PE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Zygote stage Seed coat


title: OE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Torpedo stage Seed coat

value: Torpedo


title: PS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: PE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3

value: Octant stage


title: OS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Torpedo stage Embryo

value: Embryo


title: OE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: OE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Globular


title: PS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: RS6_3 Bent stage Seed coat RNA-seq replicate 3

organism: Brassica rapa

value: Parkland


title: PE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: PE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: total nascent RNA from HP1-KD ovarian somatic cells

data_processing:
Library strategy: GRO-seq
Reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases.
Reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded.
Reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: All mapping and unique mapping bigwig files for sense and antisense.

source_name: OSCs

extract_protocol: Global nuclear run-on procedure was according to Core et al. (2008).

value: OSC

value: HP1 depletion


title: PS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Globular stage Seed coat

value: Seed coat


title: PS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: OS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: PE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Bent stage Embryo


title: RS2_3 Octant stage Seed coat RNA-seq replicate 3

source_name: Octant stage Seed coat


title: OS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: IDMF, replicate 1

description: Gene expression data from IDMF-treated KCs

hyb_protocol: Hybridizations were performed by the University of Michigan microarray core facility (Ann Arbor, MI) using the GeneChip® 3' IVT Express Kit (Thermo Fisher Scientific, Waltham, MA). Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on the array platform. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Raw CEL files were normalized using the Robust Multichip Average (RMA) algorithm.

source_name: Keratinocytes (cytokine-stimulated)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Keratinocyte cultures were established by incubating epidermal keratinocyte progenitors from stratum basale (Zen-Bio, Research Triangle Park, NC) with media supplemented with cytokines IL-17A/IL-22/TNF-alpha (100ng/ml;100ng/ml;10ng/ml).

extract_protocol: Total RNA was extracted with NucleoSpin II kit (Machery Nagel, Bethlehem, PA)

treatment_protocol: IDMF or water control was added to cultures that had been treated with cytokines for 24 hours. Cultures were then maintained for another 24 hours prior to RNA extraction.

value: IDMF


title: WYY35_HCP-3_ChiP_rep2

first: Zhongyang

last: LIN

address: 4S17 Kadoorie Biological Sciences Building, Pokfulam Road

country: China

institute: the University of Hong Kong

description: log2_ChIP03-InPut03ab.bw (Mapping to the C. elegans genome)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WS245 whole genome using BWA-MEM (0.7.15)
Mapped reads from ChIP and input were used to call peaks and obtain read coverage per base using MACS version 1.4.2 under broad domain setting with P-value = 1e-3 cutoff.
Genome_build: WS245
Supplementary_files_format_and_content: bigwig

organism: Caenorhabditis elegans

source_name: Early embryos

growth_protocol: Synchronized  Caenorhabditis elegans cultures were grown at 22 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice.

extract_protocol:
ChIP was performed as previously described (Gassmann et al., 2012)  with slightly modification. Fixed embryos were suspended in 5 pellet volumes of ChIP buffer (+ protease inhibitors). 1 mL suspension was transferred to a milliTUBE (Covaris). Chromatin shearing was performed at 6-10 °C with Covaris M220 following settings: Processing Time: 8-20 min，Duty Cycle: 10%，Intensity: 75 Watts, Cycles per Burst: 200. The chromatin fragmentation was assessed by the smear pattern on 1% agarose gel, which was found to be between 200 and 500 bp. About 3 mg protein was diluted to 900 ml with ChIP buffer with 1 % Sarcosyl, 0.1 % Na-deoxycholate and 1 mM PMSF. 25 ml of the embryo lysate was used for the preparation of input DNA. 5 ml of antibodies was added (rabbit anti-HCP3, Novus Biologicals Q0804,1 mg/ml) to the extract and rotated gently at 4 °C overnight. 50 ml of dynabeads were added afterward and rotated at 4 °C for 2 hrs. Beads washing was performed using 2 X 1 ml FA buffer for 5 min, 1 ml FA-1000 for 10 min and 1 ml FA-500 buffer, successively. Beads were resuspended in 1 ml FA-500 buffer and transferred into new 1.5-ml Eppendorf tube, followed by 10 min FA-500 buffer washing, 10 min TEL buffer washing and brief washing by TE buffer. All washing steps were performed at 4 °C. Then, 50 ml of Elution buffer was added and incubated at 67 °C for 15 min. Dynabeads were separated from the eluted protein-DNA complex by a magnetic rack. The elutes were bought up to 150 ml by Elution buffer, followed by proteinase K digestion and reverse cross-linking at 65°C overnight. Both input DNA and ChIP-ed DNA were purified by ChIP DNA Clean & Concentrator Kit (Zymo research).
Library preparation and Illumina sequencing (Pair-End sequencing of 101 bp) were performed at the University of Hong Kong, Centre for Genomic Sciences (HKU, CGS). The 4 libraries (two replicates of Input and ChIP-ed DNA) were prepared based on the protocol of KAPA Hyper Prep Kit (KR0961 – v5.16). For each library, 0.8 ng of DNA was performed with reactions of end-repair, 3’ end A-tailing, and indexed adaptor ligation, followed by 16 cycles of PCR amplification reaction for library enrichment. After AMPure beads purification, each library was validated by Agilent Bioanalyzer, Qubit and qPCR for quality control analysis. The library was denatured and diluted to optimal concentration and applied in the cluster generation steps. HiSeq PE Cluster Kit v4 with cBot was used for cluster generation on the flow-cell. Illumina HiSeq SBS Kit v4 was used for Pair-End 101bp sequencing that runs on HiSeq 1500.

tag: developmental stage

value: Early embryos

value: SDQ0804 (Rabbit anti-HCP-3)


title: OS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Chinese Kale


title: RE5_3 Torpedo stage Embryo RNA-seq replicate 3

value: Torpedo stage


title: RS3_3 Globular stage Seed coat RNA-seq replicate 3

value: Globular stage


title: PS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RS5_3 Torpedo stage Seed coat RNA-seq replicate 3


title: WYY35_HCP-3_ChIP_rep1

description:
log2_ChIP2.bw (Mapping to the C. elegans genome)
log2_Hcp3ChIP02_AC.bw (Mapping to the artificial chromosome)
log2_ChIP02-InPut02_NGR.bw (Mapping to the NeoR::gfph2b::mCherry markers on the artificial chromosome)


title: PUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: ovule


title: Control, replicate 1

description: Gene expression data from CTL-treated KCs

value: CTL


title: NUO_3 Unfertilized stage ovule RNA-seq replicate 3

organism: Brassica nigra

value: Unfertilized stage


title: WYY35_HCP-3_Input_rep1

description: Input for WYY35_HCP-3_ChIP_rep1


title: NS7_3 Mature_stage Seed coat RNA-seq replicate 3

source_name: Mature_stage Seed coat


title: RUO_3 Unfertilized stage ovule RNA-seq replicate 3


title: RS4_3 Heart stage Seed coat RNA-seq replicate 3

value: Heart stage


title: Huh7-shCtrl-2

city: Changsha

first: Xin

middle: xin

last: Ren

address: Xiangya road 87

institute: Xiangya hospital

data_processing:
using Illumina Novaseq platform
Index of the reference genome was built using Hisat2 v2.0.5
Genome_build: hg18
Supplementary_files_format_and_content: FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent. Sequencing was completed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver cancer

tag: cell type


title: Huh7-shNME7-1


title: PE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Embryo

value: Bent


title: OE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Torpedo


title: PS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NS5_3 Torpedo stage Seed coat RNA-seq replicate 3


title: RS7_3 Mature_stage Seed coat RNA-seq replicate 3

value: Parkland


title: Huh7-shCtrl-1


title: RE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3

source_name: Heart stage Embryo


title: RE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

value: Bent stage


title: WYY35_HCP-3_Input_rep2

description: Input for WYY35_HCP-3_ChiP_rep2


title: DMSO_IFN_3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: GRCh38
Supplementary_files_format_and_content: tad-delimited, raw counts

growth_protocol: A549 were kept in Dulbecco’s modified Eagle’s medium (DMEM,Gibco Life Technologies) supplemented with 10% v/v fetal calf serum(Gibco Life Technologies), 2mM L-glutamine (Gibco Life Technologies) and 100 units/mL penicillin and 100 µg/mL streptomycin(Gibco Life Technologies). Cells were split regularly every 3 days using 2.5% Trypsin-EDTA (Life Technologies) and seeded one day prior the experiment in 12well plates at a density of 100.000 cells/ well.

extract_protocol:
RNA was harvested by using ReliaPrep™ RNA Miniprep system from Qiagen. Cells were washed once with ice-cold PBS, followed by cell lysis using 150ul BL-TG buffer and processing according to the manufacturers instructions. RNA was eluted in 20ul ddH2O.
TruSeq RNA stranded; PolyA, TruSeq RNA Kit

treatment_protocol: Depending on the treatment group, cells were either pretreated with 125nM of dBRD9-A or DMSO for 6h in fully supplemented DMEM, afterwards media was refreshed with DMEM containing again either 125nM dBRD9-A or DMSO but supplemented with 100IU/mL IFN-alpha2 (Novus Biological) and incubated for 6h before RNA was harvested.

value: lung epithelial cells

tag: treatment

value: DMSO pretreated plus IFN-alpha2


title: DMSO_no_2

value: DMSO pretreated no IFN


title: RE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3

source_name: Mature_stage Embryo


title: RE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3

source_name: Zygote stage Embryo

value: Zygote stage


title: NS6_3 Bent stage Seed coat RNA-seq replicate 3

source_name: Bent stage Seed coat

value: Seed coat


title: RS1_3 Zygote stage Seed coat RNA-seq replicate 3


title: PCLS

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
CelRanger v4.0/v5.0
Genome_build: hg38
Supplementary_files_format_and_content: sparse matrix

source_name: lung

extract_protocol:
single-cell suspension from fresh tissue removed at the time of organ transplant surgery
10X Genomics 5' v1

value: lung

value: peripheral tissue

tag: tissue type

value: percision-cut-lung-slice


title: RE3_3 Globular stage Embryo RNA-seq replicate 3

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Salmon was used for fast and accurate alignment of cleaned reads to released brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/), respectively.
Salmon was used to obtain transcripts per million reads (TPM) of each sample.
To summarize expression levels from the transcript level to the gene level, we used R tximport package to process the TPM values obtained from Salmon.
Genome_build: Brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/)
Supplementary_files_format_and_content: Matrix table files include TPM for each Sample

source_name: Globular stage Embryo

tag: tissue

value: Globular stage


title: IDMF, replicate 2

value: IDMF


title: DMSO_IFN_2


title: NS1_3 Zygote stage Seed coat RNA-seq replicate 3

source_name: Zygote stage Seed coat


title: Control, replicate 2

value: CTL


title: dBRD9-A_no_2

value: dBRD9-A pretreated no IFN


title: RE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Embryo

value: Zygote


title: Fresh_VU_HD_105

description: IPF_VUHD105_1_LU_Whole_C1_X5SCR_F02609_HLKH5DSXY

value: fresh


title: NE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3


title: NS4_3 Heart stage Seed coat RNA-seq replicate 3

source_name: Heart stage Seed coat

value: Heart stage


title: RE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Parkland


title: dBRD9-A_IFN_2

value: lung epithelial cells

value: dBRD9-A pretreated plus IFN-alpha2


title: NS2_3 Octant stage Seed coat RNA-seq replicate 3

value: Octant stage


title: Huh7-shNME7-2

value: Liver cancer


title: RE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3

source_name: Octant stage Embryo


title: RE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Heart


title: NE5_3 Torpedo stage Embryo RNA-seq replicate 3

source_name: Torpedo stage Embryo

value: Torpedo stage


title: DMSO_no_3

value: DMSO pretreated no IFN


title: NS3_3 Globular stage Seed coat RNA-seq replicate 3

source_name: Globular stage Seed coat

value: Seed coat


title: RE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Globular


title: NE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3


title: Cut and Run H3K9me3 profiling of OSCs with Sov knockdown replicate 3

data_processing:
Library strategy: CUT&RUN
Reads were trimmed by removal of the adaptor sequences.
Reads were mapped to Drosophila melanogaster genome.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: All mapping and unique mapping bigwig files for sense and antisense.

source_name: OSCs

extract_protocol:
Cut and Run protocol V3.
NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: siRNA transfection.

value: OSC

value: Sov depletion

tag: antibody

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: DMSO_no_1


title: DMSO_IFN_1

value: DMSO pretreated plus IFN-alpha2


title: RE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Embryo

value: Octant


title: Cut and Run H3K9me3 profiling of OSCs with Sov knockdown replicate 1


title: NE3_3 Globular stage Embryo RNA-seq replicate 3

value: Globular stage


title: Cut and Run H3K9me3 profiling of OSCs with control knockdown replicate 2

value: control depletion


title: NE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3


title: RS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Zygote

value: Parkland


title: Cut and Run H3K9me3 profiling of OSCs with control knockdown replicate 1


title: dBRD9-A_IFN-3

value: lung epithelial cells

value: dBRD9-A pretreated plus IFN-alpha2


title: Cut and Run profiling using control IgG of OSCs with Sov knockdown

value: Rabbit IgG control antibody (CST Cat #2729S)


title: dBRD9-A_no_1

value: dBRD9-A pretreated no IFN


title: dBRD9-A_no_3


title: RE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Heart


title: NE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

source_name: Bent stage Embryo

value: Bent stage


title: Cut and Run H3K9me3 profiling of OSCs with Sov knockdown replicate 2


title: CS5_3 Torpedo stage Seed coat RNA-seq replicate 3

organism: Brassica carinata

source_name: Torpedo stage Seed coat

value: Seed coat

value: Torpedo stage


title: RE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: Cut and Run profiling using control IgG of OSCs with control knockdown

value: OSC


title: CS7_3 Mature_stage Seed coat RNA-seq replicate 3


title: Cut and Run H3K9me3 profiling of OSCs with control knockdown replicate 3

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: dBRD9-A_IFN_1