title: isp-1(qm150);ctb-1(qm189) grown whole life on control L4440 plates biological rep 1


title: N2 wild type worms grown whole life on control L4440 plates biological rep 1

status: Public on Jun 13 2019

type: RNA

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

description: Gene expression data from N2 wild type worms grown whole life on control L4440 plates

hyb_protocol: Reversely transcribed RNAs were hybridized to Affymetrix EleGene 1.0 ST microarrays, according to the manufacturer's instructions.

scan_protocol: The scan protocol for the samples was the  library files EleGene-1_0-st.

data_processing:
CEL files were processed by the Affymetrix Power Tools, version 1.15.2 , and RMA normalization.
Analysis of differentially regulated genes was carried out using the R language for statistical computing, version 3.0.2.

label: Biotin

molecule: total RNA

organism: Caenorhabditis elegans

label_protocol: Fragmenting and Labeling was done with the Encore Biotin Module ( Nugen).

growth_protocol: Worms were grown on RNAi plates from egg stage until fifth day of adulthood. Wild type N2 and isp-1(qm150);ctb-1(qm189) were grown on control L4440 plates as control. isp-1(qm150);ctb-1(qm189) was also grown on klf-1 RNAi plates until larval L4 stage and then switched to L4440 plates, or switched at L4 larval stage to klf-1 RNAi plates from control L4440 plates.

extract_protocol: RNA was isolated using Rneasy Mini Kit (QIAGEN) according to manufacturors protocol. The samples were amplified with the NuGen Applause WT-Amp Plus ST Kit.

treatment_protocol: Worms were washed in M9 buffer.

tag: strain

tag: Stage

value: fifth day of adulthood


title: Arabidopsis_thaliana_COL_Rep2_30

type: SRA

city: East Lansing

first: Kevin

last: Childs

state: MI

address: 612 Wilson Rd, Room S108, Plant Biology Laboratories

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Sequencing adapters and low quality bases were trimmed from sequencing reads using Trimmomatic version 0.32.
Cleaned reads were examined using FASTQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality evaluation.
Reads were aligned to the reference genome, A. thaliana TAIR10, using the STAR (2.3.0e) alignment program.
The featureCounts function in the Rsubread (version 3) package for R was used to calculate read counts for each gene, and data were normalized as reads per kilobase of transcript per million mapped reads (RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, Genes as rows, Samples as columns (sample names match "Sample name" entry in "SAMPLE" section of this file).

organism: Arabidopsis thaliana

source_name: fully expanded leaf

growth_protocol: Wild-type Arabidopsis thaliana ecotype Columbia-0 (WT Col) and Wassilewskija (WT WS) were used. Plants were grown in a fluorescently lit growth chamber under a 12 h photoperiod with a photosynthetically active radiation (PAR) of 120 µmol m-2 s-1 until high light treatment when light was changed to 500 µmol m-2 s-1. The daytime temperature was 23°C and the nighttime temperature was 20°C. Humidity was held at a minimum of 60% relative humidity.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Plant Mini Kit according to the manufacturer’s directions.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA) following the manufacturer's recommendations.

treatment_protocol: High light treatment consisted of changing light levels from 120 µmol m-2 s-1 to 500 µmol m-2 s-1.

tag: tissue

value: fully expanded leaf

tag: hours high intensity light

tag: ecotype

tag: replicate


title: ChIPseq_H2Bub_WT2

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
mapping of the reads to reference genome
filter for mapping quality < 37
merge BAM files of replicate samples
extend each read with 150 bp
normalize for sequencing depth
convert to bigwig
Genome_build: R64-2-1
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Yeast strains were grown in YEPD.

extract_protocol:
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.

tag: antibody


title: isp-1(qm150);ctb-1(qm189) grown whole life on control L4440 plates biological rep 3

description: Gene expression data from isp-1(qm150);ctb-1(qm189) mutant grown whole life on control L4440 plates


title: Clarke_Bulk-Stim_Donor-33_T_CD103pos

city: La Jolla

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_Bulk_raw-counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_Bulk_TPM.txt contains Transcript per Million normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor tissue

growth_protocol: Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were sonstructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).

treatment_protocol: Were noted samples were stimulated with 4 hours of PMA/ionomycine treatment, otherwise sampled were directly ex-vivo

tag: cell type surface markers

tag: cell type

value: Lymphocyte

tag: donor #


title: isp-1(qm150);ctb-1(qm189) switched from klf-1 RNAi at L4 stage biological rep 3

description: Gene expression data from isp-1(qm150);ctb-1(qm189) mutant switched from klf-1 RNAi at L4 stage


title: N2 wild type worms grown whole life on control L4440 plates biological rep 2


title: Arabidopsis_thaliana_COL_Rep2_15


title: Clarke_Bulk-Stim_Donor-33_SN_CD103pos

source_name: non-involved lung tissue - 4 hours ex-vivo stimulation


title: ChIPseq_H2Bub_WT1


title: isp-1(qm150);ctb-1(qm189) switched from klf-1 RNAi at L4 stage biological rep 2


title: ChIPseq_H2B_WT1


title: Clarke_Bulk-Stim_Donor-33_ST_CD103pos

source_name: Tumor tissue - 4 hours ex-vivo stimulation


title: Arabidopsis_thaliana_COL_Rep2_0


title: Clarke_Bulk-Stim_Donor-32_N_CD103pos

source_name: non-involved lung tissue


title: Arabidopsis_thaliana_COL_Rep1_240


title: isp-1(qm150);ctb-1(qm189) switched from klf-1 RNAi at L4 stage biological rep 1


title: isp-1(qm150);ctb-1(qm189) switched to klf-1 RNAi at L4 stage biological rep 3

description: Gene expression data from isp-1(qm150);ctb-1(qm189) mutant switched to klf-1 RNAi at L4 stage


title: ChIPseq_H3_KO1


title: Clarke_Bulk-Stim_Donor-32_SN_CD103pos


title: Arabidopsis_thaliana_COL_Rep1_120


title: Clarke_Bulk-Stim_Donor-32_T_CD103pos


title: isp-1(qm150);ctb-1(qm189) switched to klf-1 RNAi at L4 stage biological rep 2


title: ChIPseq_H3_WT2


title: Arabidopsis_thaliana_COL_Rep1_60


title: ChIPseq_H3_WT1

extract_protocol:
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the TruSeq DNA LT Sample Preparation kit (Illumina), using ten times less adapter in the adapter ligation step. After fifteen PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.


title: Clarke_Bulk-Stim_Donor-32_ST_CD103pos


title: Arabidopsis_thaliana_COL_Rep1_30


title: ChIPseq_H3K79me3_KO2


title: ChIPseq_H3K79me3_KO1


title: Clarke_Bulk-Stim_Donor-31_N_CD103pos


title: ChIPseq_H3_KO2


title: Clarke_Bulk-Stim_Donor-31_SN_CD103pos


title: Clarke_Bulk-Stim_Donor-31_T_CD103pos


title: ISH1&2_induction_rep1

city: Kisarazu

first: Shigeru

last: Hanano

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Frontier Research and Development

country: Japan

institute: Kazusa DNA Research Institute

description: Gene expression after 1-week chemical induction in the roots of ISH1&2 plants

hyb_protocol: Hybridization to the Agilent Arabidopsis Oligo DNA Microarray Ver. 4 (Agilent Technologies) were carried out with Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture’s manual.

scan_protocol: The hybridized images were scanned with Agilent Technology Scanner G2505C and were processed by Feature Extraction version 10.7.3.1 software (Agilent).

data_processing: Normalization and analysis of microarray data were performed by using GeneSpring GX ver. 12 software (Tomy Digital Biology, Tokyo, Japan, www.digital-biology.co.jp).

source_name: ISH1&2 with chemical induction

label_protocol: Total RNA extracted from the root was labeled with the Low Input Quick Amp Labeling Kit (one color, Cyanine3-CTP, Agilent Technologies, Santa Clare, CA, USA, www.agilent.com) . The labeling reaction was checked with RNA Spike In Kit (Agilent Technologies). The cDNA concentration and quality were confirmed with NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Seeds were surface sterilized with a 70% ethanol rinse, immediately followed by a rinse with 33% bleach for 5 min, and then a twice washed with sterile water. The seeds were then aseptically sown on 25 µg/L hygromycin-containing 1/2 MS plates, following by imbibition at 4°C for 3 days in the dark. Seedlings were grown for 8 days at 22°C under the constant light condition for 40 µmol m-2 sec-1 cool white fluorescent light, and then the antibiotic-resistant seedlings were transferred to 1/2 MS-1.2% phytagel plates without antibiotics with or without 5 µM estradiol for the chemical induction. The roots of 2-weeks-old plants were harvested for the subjects of RNA isolation.

extract_protocol: Total RNA was isolated from the roots with an RNeasy Plant Mini Kit and then was treated with an RNase-Free DNase Set according to the manufacturer’s manual (QIAGEN).

tag: ecotype background

tag: genotype/variation

value: ISH1&2 with chemical induction

value: root

tag: age


title: Arabidopsis_thaliana_COL_Rep1_0


title: ChIPseq_H3K79me3_WT2


title: C6orf203_rescued_C [1163_9]

city: Warsaw

first: Sylwia

last: Czarnomska

state: Mazowieckie

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
RNAseq raw data were preprocessed with FastQC v 0.11.3 and trimmed of adapters using cutadapt v 1.9.2.dev0. Low-quality bases and not properly paired reads were removed prior to mapping using Trimmomatic v 0.32 with the settings SLIDINGWINDOW:4:20 MINLEN:10. Trimmed reads were mapped to the human genome (GRCh38) using STAR aligner v 2.5.2b with soft-clipping allowed (default type of alignment) and the basic GENECODE v26 annotation with introduced features that allowed for quantification of all reads mapped in the D-loop region. Mapped reads were counted using htseq-count v 0.9.1 with settings -f bam -r pos -s reverse -t exon -i gene_id -m union and additionally re-counted with the option --nonunique all to collect data for 7SRNA and whole D-loop region separately.
Differential gene expression was performed in DESeq2 package v 1.16.1 and for the purpose of figure preparation counted reads were normalized in the edgeR package v 3.18.1.  Wiggle files of uniquely mapped reads were converted to BigWig format with the use of wigToBigWig package.
Genome_build: GRCh38
Supplementary_files_format_and_content: edger_cpm_normalized_counts

source_name: transgenic 293 cells expressing in the tet-inducible manner  miRNAs silencing endogenous copy of C6orf203 gene and miRNA-insensitive form of C6orf203-FLAG

extract_protocol:
Total RNA was isolated with the use of TRI Reagent (T9424, Sigma) according to the manufacturer’s instructions. RNA was subjected to TURBO DNase (AM2238, Ambion) treatment and depletion of nuclear-encoded rRNAs (RiboZero Kit, Epicenter).
Libraries were constructed as previously described in Sultan et al., 2012 (PMID: 22609201) with minor modifications. Fragmentation and first strand cDNA synthesis were performed as in TruSeq RNA Library Prep kit v2 protocol (Illumina, RS-122-2001, instruction number 15026495 Rev. D), using SuperScript III reverse transcriptase (18080-085, Thermo Fisher Scientific). CutSmart buffer (NEB) was used for digestion with the USER Enzyme (NEB).  Enriched library quality was verified using 2100 Bioanalyzer and High Sensitivity DNA kit (5067-4626, Agilent). The libraries’ concentration was estimated by qPCR means with KAPA Universal Library Quantification Kit (KK4824, Kapa Biosystems), according to the supplied protocol. Sequencing was carried out on an Illumina NextSeq 500 sequencing platform, using NextSeq 500 High Output Kit (150 cycles) (FC-404-1002, Illumina) and pair-end sequencing procedures of 2x75 cycles (Instructions: 15048776 Rev. D, 15046563 Rev. F).

tag: experimental set

value: transcriptome (C6orf203)

value: embrionic kidney (PubMed ID:886304)

tag: parental cells

value: 293 - ATCC  number CRL-1573

tag: sequenced rna species

value: > ~100 nucleotides

tag: is it control sample?

value: yes (rescue of C6orf203 silencing)


title: ISH1&2_induction_rep3


title: Clarke_Bulk-Stim_Donor-31_ST_CD103pos


title: ChIPseq_H3K79me3_WT1

tag: strain


title: ChIPseq_H3K79me1_KO2


title: C6orf203_rescued_B [1163_7]


title: Clarke_Bulk_Donor-18_TIL_CD103pos

source_name: Tumor


title: Clarke_Bulk_Donor-4_NIL_CD103neg

source_name: Non-involved lung


title: ChIPseq_H3K79me1_KO1


title: C6orf203_silenced_C [1162_8]

source_name: transgenic 293 cells expressing in the tet-inducible manner  miRNAs silencing endogenous copy of C6orf203 gene

value: no


title: control_induction_rep1

description: Gene expression after 1-week chemical induction in the roots of control plants

source_name: control with chemical induction

value: control with chemical induction


title: Arabidopsis_thaliana_COL_Rep1_15


title: isp-1(qm150);ctb-1(qm189) switched to klf-1 RNAi at L4 stage biological rep 1

tag: Stage


title: ChIPseq_H3K79me1_WT2


title: ISH1_induction_rep2

description: Gene expression after 1-week chemical induction in the roots of ISH1-ind plants

source_name: ISH1 with chemical induction

value: ISH1 with chemical induction

tag: tissue


title: C6orf203_rescued_A [1163_5]


title: ISH1_non-induction_rep3

description: Gene expression in the roots of ISH1-ind plants

source_name: ISH1 without chemical induction

value: ISH1 without chemical induction


title: C6orf203_silenced_B [1162_6]


title: control_non-induction_rep3

description: Gene expression in the roots of control plants

source_name: control without chemical induction

value: control without chemical induction


title: Clarke_Bulk_Donor-22_NIL_CD103pos


title: ChIPseq_H3K79me1_WT1


title: C6orf203_silenced_A [1162_4]


title: ISH1_induction_rep1


title: ISH1&2_induction_rep2


title: Clarke_Bulk_Donor-14_NIL_CD103pos


title: monkey_Oo_R2

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

country: China

institute: Chinese Academy of Sciences

description: small RNA-seq of crab-eating monkey oocyte detected by CAS-seq with single oocyte, biological replicate 1

data_processing:
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs, rRNAs, sn/snoRNAs and tRNAs successively. The reads that couldn’t be mapped to these known small RNAs were used to predict piRNAs, endo-siRNAs and xiRNAs successively. For the reads that could be mapped to multiple genome loci, we used the program reallocate (http://www.smallrnagroup-mainz.de/software.html) to apportion the read counts of multiply mapped sequences according to their local transcription level calculated by uniquely mapped sequences within 5 kb flanking regions. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: sequence of miRNA, endo-siRNA, piRNA and their expression (RPM) in each sample were provided

organism: Macaca fascicularis

source_name: single oocyte

extract_protocol: cDNA library construction strategies of Illumina TruSeq, our CAS-seq and our previous 10ng-seq were utilized. Details were in the online method of our article.

value: single oocyte

tag: rna input

tag: library construction method

value: CAS-seq

tag: spike-in

value: Adult


title: monkey_Oo_R1


title: Clarke_Bulk_Donor-30_NIL_CD103neg


title: Clarke_Bulk_Donor-11_NIL_CD103pos


title: control_induction_rep2


title: parental_C [293_3]

source_name: parental Flp-In T-REx-293 cells

value: yes


title: parental_A [293_1]


title: ISH1_non-induction_rep2


title: control_induction_rep3


title: Clarke_Bulk_Donor-18_TIL_CD103neg

value: Lymphocyte


title: Clarke_Bulk_Donor-26_TIL_CD103pos


title: HEK293_1ng_R3

description: small RNA-seq of HEK293 cell lines  detected by CAS-seq with 1ng input of total RNA, technical replicate 3

source_name: HEK293 cell line

value: HEK293 cell line

value: 1ng input of total RNA


title: Clarke_Bulk_Donor-26_TIL_CD103neg


title: Clarke_Bulk_Donor-23_TIL_CD103pos


title: HEK293_1ng_R2

description: small RNA-seq of HEK293 cell lines  detected by CAS-seq with 1ng input of total RNA, technical replicate 2


title: ISH2_non-induction_rep1

description: Gene expression in the roots of ISH2-ind plants

source_name: ISH2 without chemical induction

value: ISH2 without chemical induction

value: root


title: SHU00238-4

first: Rui

last: Chen

address: Nanchen Road 383

institute: Shanghai University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C and 60 rpm on Affymetrix GeneChip miRNA Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: HCT116 cell line

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: HCT116 cells cultivate at 37 ℃ under constant temperature and humidity, keeping the concentration of CO2 at 5%.

extract_protocol: Exosomal RNAs were extracted by the miRNeasy Serum/Plasma Advanced Kit according to the manufacturer's instructions.

treatment_protocol: Add 1 μM SHU00238 into HCT-116 cells and cultivate with the normal cells at the same condition for 48 hours.

value: Human colorectal


title: parental_B [293_2]

value: transcriptome (C6orf203)

value: embrionic kidney (PubMed ID:886304)

value: 293 - ATCC  number CRL-1573

value: > ~100 nucleotides


title: Clarke_Bulk_Donor-24_TIL_CD103pos


title: ISH2_induction_rep1

description: Gene expression after 1-week chemical induction in the roots of ISH2-ind plants

source_name: ISH2 with chemical induction

value: ISH2 with chemical induction


title: SHU00238-1


title: HEK293_1ng_R1

description: small RNA-seq of HEK293 cell lines  detected by CAS-seq with 1ng input of total RNA, technical replicate 1

value: no


title: SHU00238-2


title: control_non-induction_rep2

value: control without chemical induction


title: SHU00238-3


title: Clarke_Bulk_Donor-28_TIL_CD103neg


title: Control-4


title: ISH1_non-induction_rep1

value: ISH1 without chemical induction


title: Control-3


title: Clarke_Bulk_Donor-24_TIL_CD103neg


title: ISH1&2_non-induction_rep1

description: Gene expression in the roots of ISH1&2 plants

source_name: ISH1&2 without chemical induction

value: ISH1&2 without chemical induction


title: ISH2_induction_rep3


title: GH3254: 1h Cort rep#1 GR ChIP-seq

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Library DR

department: LRBGE

institute: NIH

data_processing:
RTA 2.4.6 was used for Basecalling and Bcl2fastq 2.17 were used for demultiplexing.
Alignment was performed by Bowtie2 2.2.6 software with the mm10 reference genome.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Peaks were called using HOMER "findPeaks" function with -fdr 0.001 -F 6 -L 6 -tagThreshold 75
Genome_build: mm10

organism: Mus musculus

source_name: 33AP1C9 cells harboring stable integrations of a MMTV-pp7 reporter construct and expressing GFP-tagged PP7 coat protein

extract_protocol: Lysates were clarified from sonicated nuclei and GR/DNA complexes were isolated with antibody.

treatment_protocol: Cells were plated for experiments in phenol red free growth medium supplemented with 10% charcoal-dextran serum 48 hours before hormone treatment.  Cells were left untreated or induced with 600nM corticosterone for 0h, 1h, 12h.

tag: parental cell line

value: C127 cells

value: cell line derived from mouse mammary epithelial tissues

tag: treatment

value: Corticosterone

tag: concentration

tag: time

tag: antibody

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1006


title: ISH2_non-induction_rep2

tag: ecotype background

tag: genotype/variation


title: Clarke_Bulk_Donor-21_TIL_CD103pos

tag: cell type surface markers

tag: cell type

value: Lymphocyte

tag: donor #


title: GH3256: INPUT ChIP-seq

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1010


title: Clarke_Bulk_Donor-11_NIL_CD103neg


title: ISH2_induction_rep2

value: root

tag: age


title: Clarke_Bulk_Donor-21_TIL_CD103neg


title: GH3255: 12h Cort rep#1 GR ChIP-seq

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1008


title: Control-1

value: Human colorectal


title: Control-2


title: sperm, Famine F0_rep1

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

description: E.bw

data_processing:
Filtered reads were mapped to mouse reference genome mm10 by using BWA v0.6.2
Differentially methylated regions (DMRs) were identified using MEDIPS
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deepTools

source_name: sperm

extract_protocol:
Sperm were removed, incubated with lysis buffer at 55℃ for 3h under constant rotation, then extracted using TIANamp Genomic DNA Kit according to the manufacture's instructions. DNA was sheared by sonication and fragmented to a size of 100-500 bp, then immunoprecipitated with antibody against 5-mc, then purify immunoprecipitated DNA.
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)

tag: strain

value: ICR

value: sperm of F0 males

value: 12 wk of age

tag: stress

value: famine


title: ISH1_induction_rep3

value: ISH1 with chemical induction

tag: tissue


title: ISH2_non-induction_rep3

value: ISH2 without chemical induction


title: sperm, Famine F0_rep2

description: E.bw


title: Clarke_Bulk_Donor-29_TIL_CD103neg


title: GH3253: untreated rep#1 GR ChIP-seq

value: untreated

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1004


title: sperm, control F0_rep1

description: C.bw

value: control


title: Clarke_Bulk_Donor-9_NIL_CD103neg


title: ISH1&2_non-induction_rep2

value: ISH1&2 without chemical induction


title: Slc10a1-KO-20months-rep1

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

data_processing:
Clean mRNA-seq reads were aligned to the mouse reference genome (GRCm38) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene-level read count for each Sample

source_name: Liver

extract_protocol: Freshly isolated livers were immediately frozen and stored in liquid nitrogen until use. mRNA was extracted using Trizol regent (Invitrogen) following the manufacturer’s instructions. For mRNA-seq analysis, mRNA was isolated with Dynabeads® mRNA Purification Kits (Invitrogen), fragmented in 5x first strand buffer(Invitrogen) at 95°C for 5 min, and reverse-transcribed using SuperScript® II Reverse Transcriptase (Invitrogen). After the first strand was synthesized, Second Strand Buffer (Invitrogen), RNase H (New England Biolabs), dNTPs, and DNA polymerase I (TaKaRa) were added to the second-strand synthesis reaction for 2.5 h at 16°C, and cDNA was purified with Agencourt AMPure XP beads (Beckman). Libraries were constructed with a NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs), PCR products were purified using AMPure XP beads. RNA libraries were quantified by Qubit 1.0 (Invitrogen) and analyzed with an Agilent 2100 bioanalyzer(Agilent) for size distribution, and were sequenced with the Illumina Hiseq-2500 platform.

value: Liver

value: 20 months

tag: genotype

tag: gender

value: male


title: WT-20months-rep2

value: wild type


title: 1ng_mouseTestis_CAS-seq-2E_R3

data_processing:
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs, rRNAs, sn/snoRNAs and tRNAs successively. The reads that couldn’t be mapped to these known small RNAs were used to predict piRNAs, endo-siRNAs and os-piRNAs successively. For the reads that could be mapped to multiple genome loci, we used the program reallocate (http://www.smallrnagroup-mainz.de/software.html) to apportion the read counts of multiply mapped sequences according to their local transcription level calculated by uniquely mapped sequences within 5 kb flanking regions. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: The expression of piRNA sequences and piRNA clusters (RPM) in each group of samples were provided.

source_name: small RNA-seq of mouse testis detected by CAS-seq-2E with 1ng input of total RNA, technical replicate 1

value: testis

tag: rna input

value: 1ng input of total RNA

tag: library construction method

value: CAS-seq-2E(CAS-seq with modification)

tag: spike-in

value: no

value: 8 weeks old, male mice

tag: molecule subtype

value: small RNA in length of 17-40 nt


title: Slc10a1-KO-20months-rep2


title: 1ng_mouseTestis_CAS-seq-2E_R2

source_name: small RNA-seq of mouse testis detected by CAS-seq-2E with 1ng input of total RNA, technical replicate 2


title: WT-20months-rep3


title: Slc10a1-KO-20months-rep3


title: sperm, control F0_rep2

description: C.bw

value: ICR

value: sperm of F0 males

value: 12 wk of age


title: 1ng_mouseTestis_CAS-seq-2E_R1


title: Clarke_Bulk_Donor-11_TIL_CD103neg

source_name: Tumor

value: Lymphocyte


title: Clarke_Bulk_Donor-20_TIL_CD103pos


title: Clarke_Bulk_Donor-20_TIL_CD103neg


title: Slc10a1-KO-8weeks-rep6

value: 8 weeks


title: 1ng_mouseTestis_CAS-seq_ComparisonWithCASseq2E_R3

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA,  to compare with CAS-seq-2E, technical replicate 3

value: CAS-seq


title: Slc10a1-KO-8weeks-rep5


title: Clarke_Bulk_Donor-16_NIL_CD103pos

source_name: Non-involved lung


title: Clarke_Bulk_Donor-3_NIL_CD103neg


title: Slc10a1-KO-8weeks-rep4


title: control_non-induction_rep1

value: control without chemical induction

value: root


title: WT-20months-rep1

value: Liver

value: 20 months


title: 1ng_mouseTestis_CAS-seq_ComparisonWithCASseq2E_R1

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA,  to compare with CAS-seq-2E, technical replicate 1


title: Obese myeloma, Rep5

city: Houston

first: Jing

last: Yang

address: 7455 Fannin St

department: Lymphoam & Myeloma

institute: UT MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Obese myeloma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: CD138+ cells directly isolated from myeloma patients

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit according to the protocol provided with the kit. Quality control was performed with Agilent

tag: subject status

value: newly diagnosed myeloma patient

tag: obesity

value: obese patients (BMI > 30 kg/m2)

value: bone marrow aspirate

value: CD138+ malignant plasma cells


title: Clarke_Bulk_Donor-13_TIL_CD103neg


title: Obese myeloma, Rep3


title: 1ng_mouseTestis_CAS-seq_R3

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA, technical replicate 3

value: testis

value: 1ng input of total RNA

value: no


title: Slc10a1-KO-8weeks-rep3

value: male


title: Slc10a1-KO-8weeks-rep2


title: ISH1&2_non-induction_rep3

tag: ecotype background

value: ISH1&2 without chemical induction


title: Obese myeloma, Rep1


title: Obese myeloma, Rep2


title: Obese myeloma, Rep4


title: 1ng_mouseTestis_CAS-seq_R2

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA, technical replicate 2

value: 8 weeks old, male mice

value: small RNA in length of 17-40 nt


title: Normal weight myeloma, Rep4

source_name: Normal weight myeloma

value: normal weights (BMI < 25 kg/m2)


title: 1ng_mouseTestis_CAS-seq_ComparisonWithCASseq2E_R2

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA,  to compare with CAS-seq-2E, technical replicate 2

value: CAS-seq


title: 1ng_mouseTestis_CAS-seq_R1

source_name: small RNA-seq of mouse testis detected by CAS-seq with 1ng input of total RNA, technical replicate 1


title: Clarke_Bulk_Donor-17_TIL_CD103neg

value: Lymphocyte


title: WT-8weeks-rep4

value: 8 weeks

value: wild type


title: Slc10a1-KO-8weeks-rep1

value: Liver


title: Clarke_Bulk_Donor-6_NIL_CD103neg


title: 10ng_mouseTestis_10ng-seq_R3

source_name: small RNA-seq of mouse testis detected by 10ng-seq with 10ng input of total RNA, technical replicate 3

value: 10ng input of total RNA


title: 10ng_mouseTestis_10ng-seq_R2

source_name: small RNA-seq of mouse testis detected by 10ng-seq with 10ng input of total RNA, technical replicate 2


title: Clarke_Bulk_Donor-14_TIL_CD103neg


title: Clarke_Bulk_Donor-22_TIL_CD103pos


title: Normal weight myeloma, Rep2

value: newly diagnosed myeloma patient


title: Clarke_Bulk_Donor-8_NIL_CD103pos


title: Clarke_Bulk_Donor-24_NIL_CD103neg


title: Clarke_Bulk_Donor-28_TIL_CD103pos


title: 200ng_mouseTestis_TruSeq_R3

source_name: small RNA-seq of mouse testis detected by TruSeq with 200ng input of total RNA, technical replicate 3

value: 200ng input of total RNA

value: TruSeq


title: Normal weight myeloma, Rep3

value: bone marrow aspirate

value: CD138+ malignant plasma cells


title: Slc10a1-KO-4weeks-rep3

value: 4 weeks


title: WT-8weeks-rep1

value: male


title: Clarke_Bulk_Donor-27_TIL_CD103pos


title: Slc10a1-KO-4weeks-rep2


title: WT-8weeks-rep3


title: 200ng_mouseTestis_TruSeq_R1

source_name: small RNA-seq of mouse testis detected by TruSeq with 200ng input of total RNA, technical replicate 1

value: testis

value: no


title: Normal weight myeloma, Rep1


title: 200ng_mouseTestis_TruSeq_R2

source_name: small RNA-seq of mouse testis detected by TruSeq with 200ng input of total RNA, technical replicate 2

value: 8 weeks old, male mice

value: small RNA in length of 17-40 nt


title: WT-8weeks-rep2

source_name: Liver


title: 10ng_mouseTestis_10ng-seq_R1

source_name: small RNA-seq of mouse testis detected by 10ng-seq with 10ng input of total RNA, technical replicate 1


title: Clarke_Bulk_Donor-26_NIL_CD103pos


title: 4ug_mouseTestis_afterOxidization_R3

source_name: small RNA-seq of mouse testis after NaIO4 oxidization, biological replicate 3

value: 11/12 of 4ug total RNAs extracted from mouse testis

value: CAS-seq

value: 1.8 × 10-6 pmole spike-in

value: mouse testis

value: 18.5 days old

tag: Sex


title: 4ug_mouseTestis_afterOxidization_R4

source_name: small RNA-seq of mouse testis after NaIO4 oxidization, biological replicate 4


title: Clarke_Bulk_Donor-20_NIL_CD103neg

source_name: Non-involved lung

tag: cell type surface markers

value: Lymphocyte


title: Clarke_Bulk_Donor-23_NIL_CD103pos

tag: cell type


title: Clarke_Bulk_Donor-26_NIL_CD103neg

tag: donor #


title: 4ug_mouseTestis_afterOxidization_R2

source_name: small RNA-seq of mouse testis after NaIO4 oxidization, biological replicate 2

tag: age


title: mouse_Oo_singleOo_R3

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 3

source_name: single oocyte

value: single oocyte

tag: strain

value: 8 to 10 weeks old, female mice


title: 4ug_mouseTestis_beforeOxidization_R4

source_name: small RNA-seq of mouse testis before NaIO4 oxidization, biological replicate 4

value: 1/12 of 4ug total RNAs extracted from mouse testis

value: 1.7 × 10-7 pmole spike-in


title: Clarke_Bulk_Donor-8_TIL_CD103pos

source_name: Tumor


title: Clarke_Bulk_Donor-27_TIL_CD103neg


title: mouse_Oo_singleOo_R2

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 2


title: 4ug_mouseTestis_beforeOxidization_R3

source_name: small RNA-seq of mouse testis before NaIO4 oxidization, biological replicate 3


title: Clarke_Bulk_Donor-25_TIL_CD103neg

description: Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)


title: Slc10a1-KO-4weeks-rep1

value: Liver


title: WT-4weeks-rep1

value: 4 weeks

value: wild type


title: WT-4weeks-rep2

value: male


title: WT-4weeks-rep3


title: mouse_Oo_singleOo_R1

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 1

value: no


title: 4ug_mouseTestis_afterOxidization_R1

source_name: small RNA-seq of mouse testis after NaIO4 oxidization, biological replicate 1


title: Input_WT_ZT8_rep4

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 100 bp) were aligned to mouse reference genome mm9 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling was performed using MACS (v1.4.2) with the default cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

extract_protocol:
Please see article for methodological details
ChIP–seq samples were sequenced using the Illumina HiSeq 2000 .

tag: strain background

tag: treatment

value: BMAL1 WT

tag: time point

value: liver

tag: chip antibody


title: Wip1SH + ATMi (AT_SH_2)

city: Nice

first: Dmitry

last: Bulavin

address: 28 Av Valomdrose

country: France

institute: IRCAN

description:
Wip1SH + ATMi
replicate 2

data_processing: The data were normalized using quantile normalization

source_name: HCT116 cell line with Wip1 depleted by shRNA, ATM inhibitor

label_protocol: Biotinylated cRNA were prepared with the Illumina totalPrep-96 RNA Amplification Kit

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% FCS treated with or without 10 uM ATMi for 3 days (the inhibitor was changed every day)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: genotype/variation

value: ATM inhibitor


title: 4ug_mouseTestis_beforeOxidization_R1

source_name: small RNA-seq of mouse testis before NaIO4 oxidization, biological replicate 1

tag: rna input

tag: library construction method

value: CAS-seq

tag: spike-in

tag: tissue

value: small RNA in length of 17-40 nt


title: mouse_Oo_singleOo_R6

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 6


title: mouse_Oo_singleOo_R5

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 5


title: Clarke_Bulk_Donor-23_NIL_CD103neg


title: 4ug_mouseTestis_beforeOxidization_R2

source_name: small RNA-seq of mouse testis before NaIO4 oxidization, biological replicate 2

value: mouse testis

tag: molecule subtype


title: Clarke_Bulk_Donor-22_TIL_CD103neg


title: mouse_Oo_singleOo_R4

description: small RNA-seq of mouse oocyte detected by CAS-seq with single oocyte, biological replicate 4


title: 30ng_mouseTestis_afterOxidization_R3

value: 30ng total RNAs extracted from mouse testis

value: 1.5 × 10-8 pmole spike-in

value: 18.5 days old

tag: Sex


title: 30ng_mouseTestis_afterOxidization_R4


title: Clarke_Bulk_Donor-21_NIL_CD103pos

tag: cell type surface markers

value: Lymphocyte


title: Clarke_Bulk_Donor-24_NIL_CD103pos

tag: cell type


title: Input_RE_ZT8_rep4

value: BMAL1 Liver-RE


title: Input_WT_ZT20_rep2


title: 30ng_mouseTestis_afterOxidization_R2


title: WT + ATMi (AT_3)

description:
WT + ATMi
replicate 3

source_name: HCT116 cell line, ATM inhibitor

value: WT


title: Wip1SH (SH_2)

description:
Wip1SH
replicate 2

source_name: HCT116 cell line with Wip1 depleted by shRNA

value: Untreated


title: Wip1SH + ATMi (AT_SH_1)

description:
Wip1SH + ATMi
replicate 1


title: Input_WT_ZT8_rep1


title: Wip1SH + ATMi (AT_SH_3)

description:
Wip1SH + ATMi
replicate 3


title: mouse_Oo_1ng_R3

description: small RNA-seq of mouse oocyte detected by CAS-seq with 1ng input of total RNA, technical replicate 3

value: single oocyte

value: 1ng input of total RNA

value: 8 to 10 weeks old, female mice


title: WT + ATMi (AT_1)

description:
WT + ATMi
replicate 1


title: WT (WT_2)

description:
WT
replicate 2

source_name: HCT116 cell line


title: Clarke_Bulk_Donor-21_NIL_CD103neg

tag: donor #


title: mouse_Oo_1ng_R2

description: small RNA-seq of mouse oocyte detected by CAS-seq with 1ng input of total RNA, technical replicate 2

value: no

tag: age


title: WT (WT_3)

description:
WT
replicate 3


title: Wip1SH (SH_3)

description:
Wip1SH
replicate 3


title: Wip1SH (SH_1)

description:
Wip1SH
replicate 1


title: WT (WT_1)

description:
WT
replicate 1


title: Input_RE_ZT8_rep3


title: WT + ATMi (AT_2)

description:
WT + ATMi
replicate 2


title: Input_WT_ZT20_rep4

value: BMAL1 WT


title: Input_RE_ZT20_rep4

value: liver


title: 30ng_mouseTestis_afterOxidization_R1

tag: strain

value: male


title: Clarke_Bulk_Donor-19_TIL_CD103neg


title: 30ng_mouseTestis_beforeOxidization_R4

value: CAS-seq


title: Clarke_Bulk_Donor-20_NIL_CD103pos


title: Input_RE_ZT20_rep3

tag: strain background


title: mouse_Oo_1ng_R1

description: small RNA-seq of mouse oocyte detected by CAS-seq with 1ng input of total RNA, technical replicate 1


title: 30ng_mouseTestis_beforeOxidization_R3

value: small RNA in length of 17-40 nt


title: Bmal1_WT_ZT8_rep4

tag: treatment

value: anti-BMAL1  antibody (Abcam ab93806)


title: mouse_Oo_10ng_R2

description: small RNA-seq of mouse oocyte detected by 10ng-seq with 10ng input of total RNA, technical replicate 1

value: 10ng input of total RNA


title: mouse_Oo_10ng_R1


title: Input_KO_ZT8_rep1

value: BMAL1 KO

tag: time point


title: Clarke_Bulk_Donor-19_NIL_CD103neg


title: humanTestis_rabbit-IgG-IP_output

source_name: the output of rabbit-IgG-IP experiment for human testis

value: testis

value: 200 μl of the cell lysis derived from 20 mg human testis

value: CAS-seq-2E(CAS-seq with modification)

value: 1 × 10-9 pmole spike-in

value: Adult


title: Clarke_Bulk_Donor-7_TIL_CD103neg

value: Lymphocyte


title: 30ng_mouseTestis_beforeOxidization_R1

value: 30ng total RNAs extracted from mouse testis

value: 1.5 × 10-8 pmole spike-in

value: mouse testis

value: 18.5 days old


title: 30ng_mouseTestis_beforeOxidization_R2


title: Bmal1_WT_ZT20_rep4

value: BMAL1 WT

value: liver

tag: chip antibody


title: Clarke_Bulk_Donor-7_TIL_CD103pos


title: humanTestis_AGO2-IP_output

source_name: the output of human AGO2-IP experiment for human testis


title: Bmal1_WT_ZT8_rep1


title: Clarke_Bulk_Donor-12_NIL_CD103pos


title: mouse_oocyte_afterOxidization_R2

source_name: small RNA-seq of mouse oocyte after NaIO4 oxidization, biological replicate 2

value: 14/15 of the RNAs extracted from 30 mouse oocytes

value: CAS-seq

value: 9.3 × 10-10 pmole spike-in

value: mouse oocyte

value: 8 to 10 weeks old

value: female


title: Clarke_Bulk_Donor-18_NIL_CD103pos


title: humanTestis_HILI-IP_output

source_name: the output of human HILI-IP experiment for human testis

value: testis

value: 200 μl of the cell lysis derived from 20 mg human testis

value: small RNA in length of 17-40 nt


title: Bmal1_RE_ZT8_rep4

value: BMAL1 Liver-RE

value: anti-BMAL1  antibody (Abcam ab93806)


title: mouse_oocyte_afterOxidization_R1

source_name: small RNA-seq of mouse oocyte after NaIO4 oxidization, biological replicate 1


title: humanTestis_HIWI-IP_output

source_name: the output of human HIWI-IP experiment for human testis

value: CAS-seq-2E(CAS-seq with modification)

value: 1 × 10-9 pmole spike-in

value: Adult


title: Clarke_Bulk_Donor-5_TIL_CD103pos

value: Lymphocyte


title: humanTestis_IP_input

source_name: the input of IP experiments for human testis

value: 80 μl of the cell lysis derived from 20 mg human testis

value: no


title: mouse_oocyte_beforeOxidization_R1

source_name: small RNA-seq of mouse oocyte before NaIO4 oxidization, biological replicate 1

value: 1/15 of the RNAs extracted from 30 mouse oocytes

value: 6.7 × 10-11 pmole spike-in


title: Bmal1_WT_ZT20_rep2

value: BMAL1 WT

value: liver


title: Bmal1_RE_ZT8_rep3


title: Clarke_Bulk_Donor-17_NIL_CD103neg

source_name: Non-involved lung


title: human_Oocyte_afterOxidization_R3

source_name: small RNA-seq of human oocyte after NaIO4 oxidization, biological replicate 3

value: 14/15 of the RNAs extracted from 10 human oocytes

value: CAS-seq

value: 1 × 10-8 pmole spike-in

value: human oocyte


title: Clarke_Bulk_Donor-5_TIL_CD103neg

source_name: Tumor


title: human_Oocyte_afterOxidization_R2

source_name: small RNA-seq of human oocyte after NaIO4 oxidization, biological replicate 2

value: small RNA in length of 17-40 nt


title: Clarke_Bulk_Donor-13_NIL_CD103pos


title: Bmal1_RE_ZT20_rep4

value: BMAL1 Liver-RE


title: human_Oocyte_afterOxidization_R1

source_name: small RNA-seq of human oocyte after NaIO4 oxidization, biological replicate 1


title: Clarke_Bulk_Donor-4_NIL_CD103pos


title: mouse_oocyte_beforeOxidization_R2

source_name: small RNA-seq of mouse oocyte before NaIO4 oxidization, biological replicate 2

value: mouse oocyte

value: 8 to 10 weeks old

value: female


title: human_Oocyte_beforeOxidization_R3

source_name: small RNA-seq of human oocyte before NaIO4 oxidization, biological replicate 3

value: 1/15 of the RNAs extracted from 10 human oocytes

value: Adult


title: Bmal1_KO_ZT8_rep1

value: BMAL1 KO

value: anti-BMAL1  antibody (Abcam ab93806)


title: Clarke_Bulk_Donor-16_NIL_CD103neg

value: Lymphocyte


title: human_Oocyte_beforeOxidization_R2

source_name: small RNA-seq of human oocyte before NaIO4 oxidization, biological replicate 2


title: Bmal1_RE_ZT20_rep3


title: CD24Mid_45-U-Neg_7

city: Bath

first: Adele

last: Murrell

address: The Avenue

department: Biology and Biochemistry

country: United Kingdom

institute: University of Bath

data_processing:
100BP reads were trimmed to 50BP and aligned to the NCBIM37.67 transcriptome using Bowtie version 0.12.8 using parameters as recommended by MMSeq guidelines
Gene expression estimates were calculated using the MMSeq workflow
Genome_build: NCBIM37.67 (transcriptome)
Supplementary_files_format_and_content: MMSeq gene expression estimates (FPKM)

source_name: Small intestine epithelium

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

tag: sample group

tag: antibodies

value: Anti-CD24 (Biolegend), anti-CD45 D Pharmingen Cat. No. 553080, Ulex europaeus agglutinin I (UEA)(custom conjugation)


title: Clarke_Bulk_Donor-15_TIL_CD103neg


title: CD24Neg_45-U-Neg_8


title: CD24Neg_45-U-Neg_6


title: humanOocyte_HIWI3-IP_output

source_name: the output of human HIWI3-IP experiment for human oocyte

tag: rna input

value: 20 μl of oocyte lysis derived from 31 oocytes

value: CAS-seq with modification

value: 5 × 10-11 pmole spike-in


title: human_Oocyte_beforeOxidization_R1

source_name: small RNA-seq of human oocyte before NaIO4 oxidization, biological replicate 1

tag: library construction method

value: CAS-seq


title: Clarke_Bulk_Donor-14_NIL_CD103neg


title: Clarke_Bulk_Donor-5_NIL_CD103pos


title: humanOocyte_HIWI-IP_output

source_name: the output of human HIWI-IP experiment for human oocyte

tag: spike-in


title: Relb-/-Nfkb2-/- 6h TNF replicate 2

city: New Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Marg

department: Infection and immunity

country: India

institute: National Institute of Immunology

description: SAMPLE 20

hyb_protocol: illumina standard direct hybridization protocol

scan_protocol: By using illumina Bead Array Reader version 3.7.9.27572

data_processing: The raw data was extracted from illumina's Genome studio software and the same used to check the quality of data. The data were normalized using quantile normalisation method.

source_name: Mouse embryonic fibroblasts

label_protocol: Biotinylated cRNA were prepared with TargetAmpTM- Nano labelling Kit for illumina Expression Beadchip

growth_protocol: Mouse embryonic fibroblasts were cultured in complete DMEM media with 10% BCS and passaged by trypsinizing every third day.

extract_protocol: Total RNA was isolated using  RNeasy Kit (QIAGEN) and on column DNase digestion was performed according to manufacturer protocol. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: Mouse embryonic fibroblasts were treated at 90% confluency with recombinant tumor necrosis factor (10 ng/ml)

value: Mouse embryonic fibroblasts

tag: genotype

value: TNF


title: CD24Mid_45-U-Neg_5


title: CD24Neg_45-U-Neg_4


title: humanOocyte_Ago4-IP_output

source_name: the output of human Ago4-IP experiment for human oocyte

tag: tissue

value: human oocyte

tag: molecule subtype

value: small RNA in length of 17-40 nt


title: Relb-/-Nfkb2-/- 6h TNF replicate 1

description: SAMPLE 19


title: Nfkb2-/- 6h TNF replicate 2

description: SAMPLE 16


title: humanOocyte_Ago3-IP_output

source_name: the output of human Ago3-IP experiment for human oocyte


title: monkey_Oo_R5

description: small RNA-seq of crab-eating monkey oocyte detected by CAS-seq with single oocyte, biological replicate 1

source_name: single oocyte

value: single oocyte

value: no


title: Relb-/-Nfkb2-/- untreated replicate 1

description: SAMPLE 17

value: untreated


title: Clarke_Bulk_Donor-12_NIL_CD103neg

tag: cell type surface markers


title: Clarke_Bulk_Donor-13_TIL_CD103pos

tag: cell type


title: humanOocyte_Ago2-IP_output

source_name: the output of human Ago2-IP experiment for human oocyte


title: monkey_Oo_R4


title: CD24Mid_45-U-Neg_3


title: Relb-/-Nfkb2-/- untreated replicate 2

description: SAMPLE 18


title: CD24Neg_45-U-Neg_2


title: Clarke_Bulk_Donor-12_TIL_CD103neg

tag: donor #


title: CD24Mid_45-U-Neg_1


title: Nfkb2-/- untreated replicate 2

description: SAMPLE 14


title: Nfkb2-/- untreated replicate 1

description: SAMPLE 13


title: Clarke_Bulk_Donor-11_TIL_CD103pos


title: humanOocyte_Ago1-IP_output

source_name: the output of human Ago1-IP experiment for human oocyte

tag: age


title: humanOocyte_rabbit-IgG-IP_output

source_name: the output of rabbit-IgG-IP experiment for human oocyte


title: Clarke_Bulk_Donor-9_NIL_CD103pos

source_name: Non-involved lung


title: monkey_Oo_R3

tag: strain


title: Nfkb2-/- 6h TNF replicate 1

description: SAMPLE 15


title: monkey_Oo_R6


title: Clarke_Bulk_Donor-8_NIL_CD103neg


title: humanOocyte_IP_input

source_name: the input of IP experiments for human oocyte


title: FiveInput

data_processing:
Illumina sequencing reads were demultiplexed and aligned against the mm9 genome assembly using BWA.
DiffBind package was used to quantitatively compare reads within peaks in Cd24a_Mid and CD24a_Neg cells
Read coverage around TSS was calculated using ‘GenomicRanges’ and ‘Rsamtools’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: Mouse gut

extract_protocol:
Genomic DNA was phenol-chlorofom extracted.
Illumina libraries were prepared before the pull-down using 1-3 micrograms of sonicated genomic DNA.  Libraries were prepared using a ‘with-bead’ procedure (Fisher et al. 2011) or with the TruSeq DNA sample preparation kit (Illumina) following manufacturer’s instructions. Adaptor modified genomic DNA was then immunoprecipitated following (Weber et al. 2007).  Input and pull-down material was whole genome amplified as previously described (Schmidt et al. 2009) except that samples were amplified with 10 PCR cycles, ran on 2% EX agarose gels (LifeTechnologies), size selection of 300 to 500bp fragments with the MinElute gel extraction kit (Qiagen), further amplified with 7 PCR cycles and purified with AMPURE XP beads.  This procedure was also done for amplification with TruSeq reagents. Libraries were qualified and quantified by Bioanalyzer and submitted for sequencing by the CI Genomics core facility.
hmeDIP-seq

tag: antibody

value: No antibody


title: Clarke_Bulk_Donor-10_TIL_CD103neg

source_name: Tumor


title: DH55 Shoot after salt treatment_rep1

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
The tagged libraries were sequenced using a HiSeq 2500 (Illumina Inc.).
Trimmomatic (Bolger et al., 2014) was used to discard low-quality reads, trim adaptor sequences, trim low quality nucleotides at the beginning or end of the read (PHRED33 quality score of less than 3), and discard short reads (under 21 nt).
The retained high-quality reads were mapped to the C. sativa reference genome and transcripts available in the NCBI C. sativa release 100 (JFZQ00000000.1, Kagale et al., 2014) using STAR (Dobin et al, 2012)
For each gene, normailization for library size was performed by dividing the counts by the library size following the method described by Anders and Huber, 2010 to yield CPM
Further normalization was performed using DESeq to approximate a negative binomial distribution.
The differential expression analysis of digital gene expression data software (edgeR) was used to calculate expression changes between libraries (Chen et al., 2014).  The Biological Coefficient of Variation (BCV) value was set to 2 according to the software's instructions.  Expression changes were said to be significant if the multiple test corrected p-value and the false discovery rate (FDR) were ≤ 0.05 and the absolute value of  log 2 CPM was higher than 1.
Genome_build: C. sativa release 100 (JFZQ00000000.1)
Supplementary_files_format_and_content: MS Excel spreadsheet with the genes as rows and the samples as columns.  Each replicate is its own column.

organism: Camelina sativa

source_name: Shoot

growth_protocol: Camelina sativa cv. DH55 seeds were sown in soil-less potting mixture (Stringham, 1971) in 10 x 10 x 8 cm square pots.  Plants were grown in a controlled growth chamber (16 h light/8 h dark, 20/17°C) supplemented with halogen lights.   Bacteria were cultured for 24 h in tryptic soy broth (TSB) containing 100 μg ml−1 ampicillin for wild-type strains or 100 μg ml−1 ampicillin and 10 μg ml−1 tetracycline for the acdS mutant strains (Ali et al., 2012). Bacterial cultures were centrifuged at 4,000 x g and re-suspended to an OD600nm = 0.50 ± 0.02 in 0.03 M MgSO4.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen Inc.)
cDNA libraries were prepared using the TruSeq Stranded mRNA and Total RNA Library Prep kits with TruSeq LT indexed adaptors (Illumina Inc.).

treatment_protocol: Salt Treatment:  NaCl solutions at 192 mM were prepared to obtain a solution with an electrical conductivitie (EC) of 15 dSm-1 at 20°C. 50 ml of tap water (EC 1,248 µSm-1) was applied daily to each pot and replaced with 50 ml of saline solution (EC 15 dSm-1) 7 days after sowing.  The accumulation of salt in the pots was controlled by draining and the EC of the drained water was measured weekly.  Bacterial Treatment: Soil was inoculated with either 2 ml of PGPB or 2 ml of 0.03 M MgSO4 (control and transgenic plants) at the time of sowing and again one week after sowing.  Shoot matter was harvested 21 days after the initial salt treatment just before the plants began to bolt.

tag: infraspecific name

tag: developmental stage

value: 28 days after planting

tag: treatment

value: salt treatment

value: whole shoot


title: FiveBound

tag: sample group

value: anti 5-hmC rabbit polyclonal (Active Motif, 39791)


title: 2-4hours_human_GVoocyte_R4

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after 2-4 hour cell culture, biological replicate 4

value: human GV oocyte

value: Adult


title: FourBound


title: Clarke_Bulk_Donor-9_TIL_CD103pos

value: Lymphocyte


title: DH55 Shoot expressing acdS under RolD promoter after salt treatment_rep3

tag: expressing

value: expressing acdS under RolD promoter


title: 2-4hours_human_GVoocyte_R2

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after 2-4 hour cell culture, biological replicate 2

tag: rna input

value: CAS-seq


title: FourInput


title: DH55 Shoot after salt treatment_rep3


title: DH55 Shoot after salt treatment_rep2


title: Clarke_Bulk_Donor-7_NIL_CD103pos


title: DH55 Shoot expressing acdS under RolD promoter after salt treatment_rep2


title: EightBound


title: Clarke_Bulk_Donor-1_NIL_CD103neg


title: 2-4hours_human_GVoocyte_R3

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after 2-4 hour cell culture, biological replicate 3

tag: library construction method


title: OneBound


title: OneBoundp2


title: overNight_human_GVoocyte_R3

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after overnight cell culture, biological replicate 3

tag: spike-in


title: SevenBound


title: DH55 Shoot expressing acdS under 35S promoter after salt treatment_rep2

value: expressing acdS under 35S promoter


title: DH55 Shoot expressing acdS under 35S promoter after salt treatment_rep3


title: Clarke_Bulk_Donor-8_TIL_CD103neg


title: Clarke_Bulk_Donor-6_TIL_CD103pos


title: overNight_human_GVoocyte_R4

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after overnight cell culture, biological replicate 4


title: overNight_human_GVoocyte_R2

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after overnight cell culture, biological replicate 2


title: SixBound


title: DH55 Shoot expressing acdS under 35S promoter after salt treatment_rep1


title: Clarke_Bulk_Donor-7_NIL_CD103neg


title: SixBoundp2


title: overNight_human_GVoocyte_R1

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after overnight cell culture, biological replicate 1


title: human_GVoocyte_totalRNA_5oocyte

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with total RNA derived from 5 GV-oocytes

value: 1ng input of total RNA derived from 5 GV oocytes


title: DH55 Shoot after 8R6 exposure and salt treatment_rep2

value: 8R6 exposure and salt treatment


title: human_GVoocyte_totalRNA_10oocyte

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with total RNA derived from 10 GV-oocytes

value: 1ng input of total RNA derived from 10 GV oocytes

value: small RNA in length of 17-40 nt


title: DH55 Shoot after 8R6 exposure and salt treatment_rep3


title: TwoBound


title: DH55 Shoot after 8R6 exposure and salt treatment_rep1


title: Clarke_Bulk_Donor-6_TIL_CD103neg


title: DH55 Shoot expressing acdS under RolD promoter after salt treatment_rep1


title: Clarke_Bulk_Donor-6_NIL_CD103pos


title: Clarke_Bulk_Donor-3_TIL_CD103pos


title: Clarke_Bulk_Donor-9_TIL_CD103neg


title: human_morula_R3_withSpikeIn

source_name: small RNA-seq of human morula-embryo detected by CAS-seq with single embryo, biological replicate 3, with synthetic spike-in

value: single oocyte

value: 5 × 10-10 pmole spike-in

value: human morula embryo


title: human_morula_R2_withSpikeIn

source_name: small RNA-seq of human morula-embryo detected by CAS-seq with single embryo, biological replicate 2, with synthetic spike-in


title: Clarke_Bulk_Donor-3_TIL_CD103neg


title: Hippocampus, 1 Gy Proton irradiation, biol rep 1

city: Portland

first: Soren

last: Impey

state: OR

address: 3181 SW Sam Jackson Park Rd, LBRB Rm 709

department: Dept of Pediatric

institute: OHSU

description: 5hmC DIP-Seq of 1 Gy irradiated hippocampal tissue

data_processing:
Library strategy: 5hmC DIP-Seq
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Reads were trimmed to 44 bases (first 4 bases were discared, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to mm9 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
Peaks were called in all samples and merged to create a common set of regions to analyze. Aligned sequnce tags in these regions were counted for each sample to create a count matrix for enriched regions.
Genome_build: mm9
Supplementary_files_format_and_content: There are two supplementary files per sample.  The *.bw files are UCSC bigWig format and represent the aligned tag density for each sample in a set of merged peaks from the whole experiment (all four samples).  The *_MergedPeakCounts.txt files are un-normalized tag counts for each merged peak region (suitable for count based tools such as DESeq2).

source_name: Hippocampus

extract_protocol:
Qiagen All-prep DNA/RNA kit
Libraries were made using Illumina TrueSeq DNA Sample Prep Kits.

treatment_protocol: Mice were exposed to 0 Gy (sham) or 1 Gy of Proton radiation.

value: 1 Gy Proton irrdadiation

value: Hippocampus


title: Hippocampus, 1 Gy Proton irradiation, biol rep 2


title: Hippocampus, 0 Gy Proton irradiation, biol rep 2

description: 5hmC DIP-Seq of 0 Gy (sham) irradiated hippocampal tissue

value: 0 Gy Proton irradiation


title: Hippocampus, 0 Gy Proton irradiation, biol rep 1


title: human_morula_R1_withSpikeIn

source_name: small RNA-seq of human morula-embryo detected by CAS-seq with single embryo, biological replicate 1, with synthetic spike-in


title: Clarke_Bulk_Donor-5_NIL_CD103neg

data_processing:
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_Bulk_raw-counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_Bulk_TPM.txt contains Transcript per Million normalized counts

source_name: Non-involved lung

extract_protocol:
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method  with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were sonstructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).


title: human_2cell_R3_withSpikeIn

source_name: small RNA-seq of human 2cell-embryo detected by CAS-seq with single embryo, biological replicate 3, with synthetic spike-in

value: human 2cell embryo


title: Pool4B_Non_TRM

description:
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
Non_TRM_NormCov.bw

data_processing:
OMNI-ATAC-seq data were mapped against the human hg19 reference genome
Technical replicates were randomly downsampled to up to 30,000,000 total reads and then merged
Reads were mapped with boetie2, using Samtools to select uniquely mappable reads with (MAPQ >=30)
Tag align files were shifted by 4 or 5 bases to account for the TN5
Genome_build: hg19
Supplementary_files_format_and_content: Non_TRM_NormCov.bw contains tag density files in bigWig format
Supplementary_files_format_and_content: TIM3Pos_IL7Rneg_TRM_NormCov.bw contains tag density files in bigWig format

source_name: Human cancer tissue

growth_protocol: CD8+ cell types were isolated from human tissue and directly sorted by Flow cytometry into 50% FBS 50% PBS. No particular cell growth procedure was required.

extract_protocol:
OMNI-ATAC-seq was performed as described in Corces, et al., 2017 (PMC5623106) with minor variations
OMNI-ATAC-seq was performed as described in Corces, et al., 2017 (PMC5623106) with minor variations

value: Treatment naïve

tag: donor


title: Clarke_Bulk_Donor-3_NIL_CD103pos


title: Clarke_Bulk_Donor-2_NIL_CD103neg


title: human_2cell_R1_withSpikeIn

source_name: small RNA-seq of human 2cell-embryo detected by CAS-seq with single embryo, biological replicate 1, with synthetic spike-in

tag: tissue

value: Adult


title: human_2cell_R2_withSpikeIn

source_name: small RNA-seq of human 2cell-embryo detected by CAS-seq with single embryo, biological replicate 2, with synthetic spike-in

tag: molecule subtype


title: CRA_5

city: Zacatecas

first: María

middle: Fernanda

last: Romo García

state: Zacatecas

address: Alameda

country: Mexico

institute: IMSS

description: Gene expression after addition of 1ml RNAlater to human blood 4 ml samples

hyb_protocol: The dried sample was resuspended in 17 μL of nuclease-free water, Hyb Spike-In solution, 10× Gene Expression Blocking Agent and 2× Hi-RPM Hybridization Buffer and were Incubated at 100°C for 5 min. The mixture was hybridized to Agilent miRNA microarray  (G4870A) 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), then dried immediately.

scan_protocol: Arrays were scanned using an Agilent Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um . Dye channel was set to Green and Green PMT is set to 100%.

data_processing: The generated image files were analyzed using Agilent Feature Extraction Software (v 12.0.1.1). Using default parameters (protocol miRNA_1200_Jun14  and Grid: 070156_D_F_20141006 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CRA, whole blood

label_protocol: total RNA (100 ng) was placed in 1.5 mL microfuge tube. 2 μL of the CIP Master Mix was added  to each sample tube and Incubated at 37°C  for 30 min. to dephosphorylate the sample.posteriorly 2.8 μL of DMSO was added to each sample and Incubated at 100°C for 10 min.  4.5 μL of the Ligation Master Mix, wich contain Cy3 was added and incubated  for 2 hours.

extract_protocol: A sample of 500 µl of whole blood was mixed with 700 µl of Tri-Pure reagent (ROCHE, USA) well mixed in vórtex and left during 3 minutes at 25°C. Posteriorly 100 ul of Chloroform:Isoamyl alcohol 24:1 were added and centrifuged at 13,000xg for 15 minutes at 4°C. The aqueous phase was then transferred to a pre-filter column of Absolutely-miRNA RNA kit (Agilent) and the extraction continued performed as indicated in the manufacturer’s instructions. RNA was stored at -70°C until use

value: whole blood

tag: gender

value: female

tag: disease state

value: CRA


title: CRA_4


title: Clarke_Bulk_Donor-1_TIL_CD103pos

source_name: Tumor

tag: cell type surface markers

tag: cell type

value: Lymphocyte

tag: donor #


title: Pool3C_TIM3Pos_IL7Rneg_TRM

description:
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
TIM3Pos_IL7Rneg_TRM_NormCov.bw


title: ERA_4

source_name: ERA, whole blood

value: ERA


title: human_Oo_R3_withSpikeIn

data_processing:
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs, rRNAs, sn/snoRNAs and tRNAs successively. The reads that couldn’t be mapped to these known small RNAs were used to predict piRNAs, endo-siRNAs and xiRNAs successively. For the reads that could be mapped to multiple genome loci, we used the program reallocate (http://www.smallrnagroup-mainz.de/software.html) to apportion the read counts of multiply mapped sequences according to their local transcription level calculated by uniquely mapped sequences within 5 kb flanking regions. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: sequence of miRNA, endo-siRNA, piRNA and their expression (RPM) in each sample were provided

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 3, with synthetic spike-in

value: CAS-seq

value: human oocyte

tag: age


title: ERA_5


title: Pool3B_TIM3Pos_IL7Rneg_TRM


title: human_Oo_R2_withSpikeIn

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 2, with synthetic spike-in

value: small RNA in length of 17-40 nt


title: CCP+_5

source_name: CCP+, whole blood

value: CCP+


title: Clarke_Bulk_Donor-1_TIL_CD103neg


title: Clarke_Bulk_Donor-4_TIL_CD103pos


title: Clarke_Bulk_Donor-1_NIL_CD103pos


title: Pool3A_TIM3Pos_IL7Rneg_TRM


title: MS6671 PBT2 3

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
HiSeq 2500 ultra-high-throughput sequencing system was used for base-calling
Samples were uploaded to the Galaxy web platform (public server at usegalaxy.org), trimmed and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133; E. coli accession number: CP025401.1) using bowtie2 with default parameters
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0
Genome_build: LN824133; CP025401.1
Supplementary_files_format_and_content: Text files for each sample

organism: Klebsiella pneumoniae

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133; E. coli accession number: CP025401.1) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of PBT2 (7 µM for E. coli and 64 µM for K. pneumoniae).

tag: strain


title: Hela_1ng_BioR2

description:
small RNA-seq of Hela cell lines detected by CAS-seq with 1ng input of total RNA, biological replicate 2
small RNA in length of 17-40 nt

source_name: Hela cell line

extract_protocol: cDNA library construction strategies of Illumina TruSeq, our CAS-seq and our previous 10ng-seq were utilized. Details were in the online method of our article.

tag: cell line

value: Hela

value: 1ng input of total RNA

value: no


title: CRA_2

value: male


title: MS6671 PBT2 2


title: CRA_3


title: Hela_1ng_BioR1

description:
small RNA-seq of Hela cell lines detected by CAS-seq with 1ng input of total RNA, biological replicate 1
small RNA in length of 17-40 nt


title: Pool4A_Non_TRM

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

tag: treatment


title: human_Oo_R5

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 5

value: single oocyte


title: MS6671 PBT2 1


title: A549_1ng_BioR2

description:
small RNA-seq of A549 cell lines detected by CAS-seq with 1ng input of total RNA, biological replicate 2
small RNA in length of 17-40 nt

source_name: A549 cell line


title: MS6671 Control 3


title: CTRL_5

source_name: CTRL, whole blood

value: CTRL


title: human_Oo_R1_withSpikeIn

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 1, with synthetic spike-in

value: 5 × 10-10 pmole spike-in


title: human_Oo_R4

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 4

value: Adult


title: CCP+_3

value: whole blood


title: HEK293_1ug_R1

description: small RNA-seq of HEK293 cell lines  detected by TruSeq with 1ug input of total RNA, technical replicate 1

source_name: HEK293 cell line

value: HEK293 cell line

value: 1ug input of total RNA

value: TruSeq


title: MS6671 Control 2


title: CCP+_4

value: female


title: HEK293_1ug_R2

description: small RNA-seq of HEK293 cell lines  detected by TruSeq with 1ug input of total RNA, technical replicate 2


title: CTRL_3


title: human_Oo_R6

source_name: small RNA-seq of human oocyte detected by CAS-seq with single oocyte, biological replicate 6

value: CAS-seq


title: CTRL_4


title: MS6671 Control 1


title: CRA_1

value: CRA


title: ERA_3

value: ERA


title: HEK293_10ng_R3

description: small RNA-seq of HEK293 cell lines  detected by 10ng-seq with 10ng input of total RNA, technical replicate 1

value: 10ng input of total RNA


title: HEK293_10ng_R2

description: small RNA-seq of HEK293 cell lines  detected by 10ng-seq with 10ng input of total RNA, technical replicate 3


title: MAL_rep2

data_processing:
Reads of RNA-seq were mapped to the Sus scrofa genome (sus11.1) with STAR (v2.5.3a)
Gene differential expression analysis using DESeq2 (v1.20.0) based on the reads count file obtained by HTSeq (v0.9.1)
Genome_build: sus11.1
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each gene

organism: Sus scrofa

source_name: oocyte

growth_protocol: Porcine ovaries were obtained from a slaughterhouse and transported to the laboratory in 2 hr. Follicular fluid from 3–6 mm antral follicles were aspirated with an 19-gauge syringe. Cumulus oocyte complexes (COCs) with uniform cytoplasm and several layers

extract_protocol:
The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).
Libraries were constructed with TruSeq DNA library preparation kit (Illumina)

treatment_protocol: MAL treatment was to dilute MAL (original concentration 0.75 M) dissolved in DMSO in IVM medium to give a final concentration of 1 mM.

tag: developmental stage

value: MII

value: MAL

value: oocyte


title: CCP+_2

value: CCP+


title: S. pneumoniae, Control_1

city: Leicester

first: Liam

middle: Alexander

last: Crawford

address: Adrian Building, University Road

department: Genetics and Genome Biology

institute: University of Leicester

description: Expression 4C10

data_processing:
RNA-seq fastq files were gently trimmed using Trimmomatic (ver. 0.30)
Read mapping to S. pneumoniae D39 genome (NC_008533) and to SpSL1 phage (KM882824), transcript abundance quantification and normalization, and differential expression analysis were carried out using Rockhopper software (ver. 2.0.2).
Genome_build: NC_008533
Genome_build: KM882824
Supplementary_files_format_and_content: tab-delimited text file includes normalized read values for each Sample

organism: Streptococcus pneumoniae

source_name: Bacterial Culture

growth_protocol: pneumococcal strains were grown in CAT-Galactose to mid-log phase (OD590 approximately 0.15)

extract_protocol:
10 ml of pneumococcal cells were added to phenol (5%)/ethanol (95%) and pelleted at 4000 rpm at 4 degrees. For RNA extraction pellets were resuspended in 50 μl TE (pH8) with 3 mg/ml lysozyme and incubated at 37°C for 20 mins to lyse cells. The Maxwell 16 LEV simplyRNA Cells kit (Promega) was then used along with a Maxwell 16 LEV instrument (Promega) for RNA extraction. RNA samples were processed with the ScriptSeq Complete Kit for bacteria (CamBio)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mid-log phase pneumooccla strains were treated with SpSL1 phage (MOI of 0.2)

tag: infection

value: control

tag: time


title: HEK293_10ng_R1

description: small RNA-seq of HEK293 cell lines  detected by 10ng-seq with 10ng input of total RNA, technical replicate 2

tag: rna input

tag: library construction method

value: no


title: S. pneumoniae, Control_2

description: Expression 4N10


title: MAL_rep1


title: control_rep3


title: S. pneumoniae, SpSL1, 90 Minutes

description: Expression 4A90

value: bacteriophage SpSL1

value: 90 Minutes


title: myb98_mature_ovule

city: Bei Jing

first: huang

last: jiaying

address: Yiheyuan Road

department: School of life science

institute: Peking University

description: We used myb98 ovule

data_processing:
Tophat (version 2.0.14) was used to align the clean reads with the A. thaliana genome in TAIR10 with default parameters.
Cuffdiff (version 2.2.1) (parameters: default) was used to calculate and normalize the differential expression levels of these two samples’ RNA using the FPKM values.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for two sample, wild-type and myb98

source_name: ovule

growth_protocol: All of the seeds were placed on half-strength Murashige and Skoog medium with or without resistance. The plates with seeds stay in 4℃ for 2 days, followed by growth (16 hr light/8 hr dark cycles) for 10 days in the incubator. Seedlings transferred into the soil grew in the greenhouse with LED lights (GPL production modules DR/W and DR/B/FR, Philips) under long-day conditions (16 hr light/8 hr dark) at 22°C ± 2°C.

extract_protocol:
Plant Total RNA Purification Kit (GeneMark, China).
Libraries were prepared according to Illumina's Hi-seq 2000  instructions accompanying the RNA Sample Kit.

treatment_protocol: The stamens of floral stage 12 flowers of the WT plants were emasculated. Ovules of about 50 emasculated pistils were manually collected under a stereomicroscope at 36HAE (hours after emasculated).

tag: developmetal stage

value: mature ovule

tag: genotype/variation


title: control_rep2


title: HEK293_1ng_BioR1

first: Ligang

last: Wu

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

description:
small RNA-seq of HEK293 cell lines  detected by CAS-seq with 1ng input of total RNA, biological replicate 1
small RNA in length of 17-40 nt

value: 1ng input of total RNA

tag: spike-in


title: CCP+_1

tag: tissue

value: whole blood

tag: gender


title: CTRL_2

tag: disease state

value: CTRL


title: control_rep1

tag: cell type


title: S. pneumoniae, SpSL1, 10 Minutes

description: Expression 4A10

value: 10 Minutes


title: ERA_1

value: female


title: ERA_2


title: S. pneumoniae, SpSL1, 50 Minutes

description: Expression 4A50

value: 50 Minutes


title: WT_mature_ovule

description: We used ms1 ovule which not be pollinated instead of real wild-type plants

value: wild-type


title: CTRL_1


title: MAL_rep3


title: X35KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11

status: Public on Jun 12 2019

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw .cel files were processed using fRMA parameters (median polish) after which batch effects were corrected using ComBat. BRB-Array tools (Biometric Research Branch Array Tools (http://brb.nci.nih.gov/BRB-ArrayTools/) was used for analyzing the transcript expression data and a two-sample t-test was used for statistical testing.

source_name: stomach

label_protocol: Gene expression analysis using the Affymetrix HG-U133_Plus_2 platform (Affymetrix, Santa Clara, CA, USA) was carried out according to standard operating procedures by the VIB MicroArray Facility of the KU Leuven.

extract_protocol: Total RNA was isolated from fresh frozen tumor samples using RNAbee (Tel Test Inc., Friendswood, TX, USA) following the standard extraction protocol recommended by the manufacturer. RNA concentration and quality were examined using a Nanodrop-1000 (Nanodrop Technologies, Wilmington, DE, USA).

value: Gastrointestinal stromal tumor

tag: imatinib naive/resistant

value: Imatinib-naïve


title: X27KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11

source_name: small intestine

value: Imatinib-resistant


title: X53KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X4KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X1KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X64KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X36KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X48KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11

source_name: duodenum


title: X42KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9


title: X105KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9


title: X14KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X8KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X89KIT17: Gastrointestinal stromal tumor, c-KIT mutation exon 17


title: X70KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X108KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9


title: X102KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X104KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X112KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X24KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: 2-4hours_human_GVoocyte_R1

source_name: small RNA-seq of human GV oocyte detected by CAS-seq with single GV oocyte after 2-4 hour cell culture, biological replicate 1

value: single oocyte

value: CAS-seq

value: human GV oocyte

tag: age

value: Adult

tag: molecule subtype

value: small RNA in length of 17-40 nt


title: ThreeBound

source_name: Mouse gut

tag: sample group

tag: antibody

value: anti 5-hmC rabbit polyclonal (Active Motif, 39791)


title: X54KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X73KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: X85KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9


title: WI-38 Proliferating Control 2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: WI-38  proliferating control

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program.
The reads were cleaned usning cutadapt program
The reads were aligned using STAR aligner (v2.4) using hg19 Ensembl v82 annotation database
Read counts were generated using featureCounts software
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: Lung

growth_protocol: Cultured in DMEM supplemented with 10% FBS (Gibco), 1% antibiotics, 1% antimycotics, and 1% NEAA (Invitrogen).

extract_protocol:
Total RNA was extracted using TriPure (Roche)
RiboRNA depletion was done using RiboRNA depletion nano kit (Qiagen), cDNA synthesis was made with Ovation RNA-seq System V2 (NuGEN), Library prep was made with TruSeq ChIP Sample Preparation Kit (Illumina), Hiseq PE Cluster Kit (Illumina) and Hiseq SBS Kit (Illumina) was used for clustering and sequencing

tag: cell line

value: Human Diploid Lung Fibroblast

value: Lung

tag: treatment

value: Proliferating cells

tag: passages


title: WI-38 Proliferating Control 1

description: WI-38  proliferating control


title: WI-38 Replicative Exhaustion 2

description: WI-38  replicative senescence

value: Replicative exhaustion


title: X2KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9

source_name: colon


title: WI-38 Replicative Exhaustion 1

description: WI-38  replicative senescence


title: WI-38 IR+ 2

description: WI-38 IR-induced senescence

value: 10 Gy of ionizing radiation exposure


title: X77KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9


title: X78KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: WI-38 IR- 2

description: WI-38 control

value: Control


title: WI-38 IR+ 1

description: WI-38 IR-induced senescence


title: X58KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11


title: A549_1ng_BioR1

city: Shanghai

description:
small RNA-seq of A549 cell lines detected by CAS-seq with 1ng input of total RNA, biological replicate 1
small RNA in length of 17-40 nt

tag: rna input

value: 1ng input of total RNA

value: no


title: WI-38 IR- 1

description: WI-38 control


title: WI-38 Dox+ 2 Repeat

description: WI-38 doxorubicin-induced senescence

value: Treated with 2 µg/mL Dox (Sigma) for 24 h


title: WI-38 Dox+ 1 Repeat

description: WI-38 doxorubicin-induced senescence


title: X71KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11

value: Gastrointestinal stromal tumor


title: X44KIT9: Gastrointestinal stromal tumor, c-KIT mutation exon 9

value: Imatinib-resistant


title: WI-38 Dox- 1 Repeat

description: WI-38 control


title: WI-38 Dox- 2 Repeat

description: WI-38 control


title: HEK293_1ng_BioR2

description:
small RNA-seq of HEK293 cell lines  detected by CAS-seq with 1ng input of total RNA, biological replicate 2
small RNA in length of 17-40 nt

tag: library construction method


title: pnet_81_h3k27ac

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing: ChIP-seq reads were aligned to the reference genome (hg19) using BWA 0.7.10. Reads with mapping scores <10 were discarded, and those aligned to the same position and strand were only counted once. Density signals were calculated by igvtools, and converted to bigWigs with bedGraphToBigWig. Peaks were called with HOMER 4.6, using parameters -style histone -L 0.  Genome_build: hg19

extract_protocol:
30-μm sections from frozen samples with >90% tumor enrichment were collected in microtubes, washed in phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde for 5 min, and quenched with 0.125 M glycine for 5 min at room temperature. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 40 min in a Covaris E210 instrument (duty cycle 20%; intensity 8; cycles per burst 200).
Soluble chromatin (5 µg) was immunoprecipitated with 10 μg H3K4me2 (Millipore 07-030) or H3K27ac (Active Motif 39133) antibodies (Ab). ChIP-seq libraries were constructed by end repair (Epicentre ER0720) of precipitated DNA, base extension with Klenow fragment (New England Biolabs M0212L), and ligation (New England Biolabs M220S) of Y-form sequencing adapters (Illumina), followed by 14 cycles of PCR. Between enzymatic steps, fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter).

tag: chip antibody

tag: pnet subtype


title: pnet_80_h3k27ac


title: X39KIT11: Gastrointestinal stromal tumor, c-KIT mutation exon 11

value: Imatinib-naïve


title: VUB03-20qdup

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.26.1) of Bioconductor. Expression values are represented on a log2-scale.

source_name: human embryonic stem cell line VUB03, undifferentiated, 20q11.21 duplication

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).

growth_protocol: Undifferentiated cells were cultured on mitomycin-inactivated CF1 mice embryonic fibroblasts at 5% CO2 at 37°C in knock-out Dulbecco’s Modified Eagle Medium (Invitrogen) containing 20% knock-out serum replacement (Invitrogen), 2 mmol/l L-glutamine (Invitrogen), 1% non-essential amino acids (NEAA; Invitrogen), 0.1 mmol/l β-mercaptoethanol (Sigma-Aldrich) and 4 ng/ml human recombinant basic fibroblast growth factor (bFGF; Invitrogen).

extract_protocol: RNeasy Mini kit (Qiagen), protocol as provided by the manufacturer.

value: VUB03 subline

value: human embryonic stem cell

value: female

tag: developmental stage

value: hESC

tag: differentiation stage

value: undifferentiated

tag: karyotype


title: VUB07

source_name: human embryonic stem cell line VUB07, undifferentiated, no chromosomal aberrations

tag: gender

value: normal


title: VUB02

source_name: human embryonic stem cell line VUB02, undifferentiated, no chromosomal aberrations

tag: cell type

value: male


title: VUB03

source_name: human embryonic stem cell line VUB03, undifferentiated, no chromosomal aberrations


title: VUB07-20qdup

source_name: human embryonic stem cell line VUB07, undifferentiated, 20q11.21 duplication

value: VUB07 subline


title: pnet_70_h3k27ac


title: VUB02-20qdup

source_name: human embryonic stem cell line VUB02, undifferentiated, 20q11.21 duplication

value: VUB02 subline


title: pnet_75_h3k27ac


title: VUB01-20qdup

source_name: human embryonic stem cell line VUB01, undifferentiated, 20q11.21 duplication

value: VUB01 subline


title: Blood_nc_rep1

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

description:
Sample name: RJ-NC
Gene expression, biological replicate 1 of 4

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quatified using Agilent Feature Extraction Software (version A.8.5.1.1)

data_processing: The data were quantile normalized using software R

source_name: Peripheral Blood, healthy volunteer, replicate 1

label_protocol: Standard Agilent protocol

extract_protocol: Total RNA extracted using Trizol following the manufacture's instructions.

tag: disease state

value: healthy control

tag: tissue

value: whole blood

value: 45 years


title: VUB01

source_name: human embryonic stem cell line VUB01, undifferentiated, no chromosomal aberrations


title: Blood_44_rep2

description:
Sample name: RJ-44
Gene expression, biological replicate 2 of 4

source_name: Peripheral Blood, gastric carcinoma, replicate 2

value: gastric carcinoma

tag: age

value: 44 years


title: Blood_46_rep4

description:
Sample name: RJ-46
Gene expression, biological replicate 4 of 4

source_name: Peripheral Blood, gastric carcinoma, replicate 4

value: 46 years


title: pnet_77_h3k27ac


title: pnet_56_h3k27ac


title: pnet_46_h3k27ac


title: pnet_61_h3k27ac


title: pnet_136_h3k27ac


title: pnet_31_h3k27ac


title: pnet_131_h3k27ac


title: pnet_42_h3k27ac


title: T47D_HA_GATA3_wt_repl2 [RNA-seq]

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

data_processing:
Strand-specific libraries were generated with the KAPA Stranded RNA-seq Library Preparation Kit (KAPA biosystems, KR0934) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to hg38 using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: hg38
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Strand-specific libraries were generated with the KAPA Stranded RNA-seq Library Preparation Kit (KAPA biosystems, KR0934).

value: Breast cancer cell line

tag: plasmid

value: HA_GATA3_wt plasmid


title: T47D_EV_repl2 [RNA-seq]

value: control plasmid


title: T47D_EV_repl1 [RNA-seq]


title: T47D_HA_GATA3_TR1_repl1 [RNA-seq]

value: HA_GATA3_TR1 plasmid


title: T47D_HA_GATA3_TR2_repl2 [RNA-seq]

value: HA_GATA3_TR2 plasmid


title: T47D_HA_GATA3_TR2_repl1 [RNA-seq]


title: T47D_HA_GATA3_TR1_repl2 [RNA-seq]


title: MCF7_aGATA3

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (v1.5) and MACS (v1.4) peak caller. Only peaks called by both algorithms were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: filtered.intersect files contain peaks called by both peak calling algorithms in bed format

extract_protocol:
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect the HA-tag (25mg, 05-904, Millipore) and GATA3 (10 mg, sc-268, Santa Cruz) with 100 ml Protein A magnetic beads (Thermo Scientific).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

value: aGATA3 (sc-268, Santa Cruz)


title: pnet_14_h3k27ac


title: T47D_HA_GATA3_TR2_aHA_siFOXA1_rep1

value: aHA (05-904, Millipore)

tag: sirna


title: T47D_HA_GATA3_TR2_aHA_siNT_rep2

tag: cell line

value: siNT


title: Blood_45_rep3

description:
Sample name: RJ-45
Gene expression, biological replicate 3 of 4

source_name: Peripheral Blood, gastric carcinoma, replicate 3


title: T47D_HA_GATA3_TR2_aHA_siNT_rep1


title: T47D_HA_GATA3_TR1_aHA_siNT_rep1


title: T47D_HA_GATA3_TR1_aHA_siFOXA1_rep2


title: T47D_HA_GATA3_wt_aHA_siFOXA1_rep1


title: T47D_HA_GATA3_wt_aHA_siNT_rep2


title: T47D_HA_GATA3_wt_aHA_siFOXA1_rep2


title: T47D_HA_GATA3_wt_repl1 [RNA-seq]


title: T47D_EV_aHA_siNT_rep2


title: T47D_EV_aHA_siFOXA1_rep1


title: T47D_EV_aHA_siFOXA1_rep2


title: Blood_39_rep1

description:
Sample name: RJ-39
Gene expression, biological replicate 1 of 4

source_name: Peripheral Blood, gastric carcinoma, replicate 1

value: 39 years


title: T47D_HA_GATA3_TR2_aHA_siFOXA1_rep2


title: T47D_HA_GATA3_TR2_aHA_rep2