title: Mettl3-/- mESCs replicate B [mESCs_Mettl3_KO_B_S12]

description:
Mettl3_KO_B_S12
processed data file: DESeq_mESCs.txt

source_name: Mettl3-/- mESCs

extract_protocol:
Total RNA was extracted using Trizol, followed by ethanol precipitation.
Polyadenylated RNA was purified using Dynabeads mRNA purification kit (Invitrogen, Cat #61006), followed by library preparation using ScriptSeq v2 RNA-seq Library Preparation Kit (Illumina) according to manufacturer’s instruction.

value: mouse embryonic stem cells

value: PolyA RNA-seq


title: Ythdf1/2/3-triple-KO mESCs replicate B [mESCs_Ythdf3_2_1_KO_B_S10]

status: Public on Jun 04 2020

type: SRA

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Ythdf3_2_1_KO_B_S10
processed data file: DESeq_mESCs.txt

library_source: transcriptomic

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed using cutadapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -q 20 -m 25).
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes.
Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output

molecule: total RNA

organism: Mus musculus

source_name: Ythdf1/2/3-triple-KO mESCs

growth_protocol: Maintenance of mESCs was conducted in in 500 mL of High-glucose DMEM (ThermoScientific), 15% USDA certified fetal bovine serum (FBS - Biological Industries), 1 mM L-Glutamine (Biological Industries), 1% nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Biological Industries), 1% Sodium-Pyruvate (Biological Industries), 10μg recombinant human LIF (Peprotech).

tag: strain background

tag: genotype

tag: cell type

tag: library strategy


title: Mettl3-/- mESCs replicate A [mESCs_Mettl3_KO_A_S11]

description:
Mettl3_KO_A_S11
processed data file: DESeq_mESCs.txt


title: 10e7_4e7b-PBMC

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

country: USA

institute: The University of Chicago

description:
Sample 10e7_4e7b, age 7
Measured on EPIC array

hyb_protocol: Illumina Infinium

scan_protocol: Illumina IScan

data_processing:
1.) Remove probes with SNPs whose MAF is >= 0.05 in Africans, Americans or Europeans. 2.) Remove cross hybridizing probes; remove probes on sex chromosomes; remove probes with a detection pvalue >= 0.01 in more than 25% of the samples. 3.) Samples 7804_4bab-CBMC, a60f_493d-CBMC, f86d_4016-PBMC failed QC and were removed from downstream analysis. 4.) Normalize methylated and unmethylated probe intensities separately with normalize.quantile.450k(<Methylset_Object>, method = "quantile1"); this is from ENmix package, version 1.14.0. 5.) Remove probe-type bias with preprocessSWAN from the minfi package, version 1.24.0. 6.) Calculate M-values as log2(Processed unmethylated intensity + 100) - log2(Processed methylated intensity + 100). M-values were used in all downstream analyses.
Normalized Beta-value, calculated as (Normalized methylated intensity + 100)/{(Normalized methylated intensity + 100) + (Normalized unmethylated intensity + 100)}. The offset of 100 was recommended by Du et al., 2010

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Human PBMCs at age 7

label_protocol: Illumina Infinium

extract_protocol: DNA for methylation studies was extracted from thawed CBMCs and PBMCs using the Qiagen AllPrep kit (QIAGEN, Valencia, CA)

tag: tissue

value: PBMCs

tag: age

value: age 7

tag: methylationplatenumber

tag: selfreportedrace

value: Black

tag: Sex

value: Male

tag: samplecollectionsite

value: Baltimore


title: PDIS9063-074

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
library strategy: RamDA-seq (random displacement amplification sequencing)
129 and CAST genomes by incorporating SNPs and indels into reference genome and transcriptome was created by Seqnature (Munger et al., 2014).
Bowtie (version 1.1.2) was used to align scRamDA-seq reads against the diploid transcriptome with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: ASEcount_G1_129.txt and ASEcount_G1_CAST.txt include read count data derived from 129 and CAST alleles, respectively, for each cell.

source_name: 129/CAST hybrid mESC

growth_protocol: The hybrid mouse ES cell line F1-21.6 (129Sv-Cast/EiJ, female), a kind gift from Prof. Joost Gribnau, were grown on either Laminin-511 (LN511, BioLamina, Stockholm, Sweden) in  Std medium (15% fetal bovine serum [FBS] [Gibco], 0.1 mM β-mercaptoethanol [Wako Pure Chemicals, Osaka, Japan], 1000U/ml of leukemia inhibitory factor [LIF, Wako Pure Chemicals, Osaka, Japan]). This cell line was previously described in (Jonkers et al., 2009).

extract_protocol:
Single cells were collected in 1 μL of cell lysis buffer (1 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher), and RNase-free water (TaKaRa)) in a 96-well PCR plate (BIOplastics). The cell lysates were denatured at 70 °C for 90 s and held at 4 °C until the next step. To eliminate genomic DNA contamination, 1 µL of genomic DNA digestion mix (0.5× PrimeScript Buffer, 0.2 U of DNase I Amplification Grade, 1: 5 000 000 ERCC RNA Spike-In Mix I (Thermo Fisher) in RNase-free water) was added to 1 µL of the denatured sample. The mixtures were agitated for 30 s at 2000 rpm using a ThermoMixer C at 4 °C, incubated in a C1000 thermal cycler at 30 °C for 5 min and held at 4 °C until the next step.
Library preparation for single-cell RamDA-Seq was performed as described previously (Hayashi et al., 2018).

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: PDIS9063-066


title: PDIS9063-065


title: 10e7_4e7b-CBMC

description:
Sample 10e7_4e7b, birth
Measured on EPIC array

source_name: Human cord blood at birth

value: Cord blood

value: birth


title: Ythdf1/2/3-triple-KO mESCs replicate A [mESCs_Ythdf3_2_1_KO_A_S9]

description:
Ythdf3_2_1_KO_A_S9
processed data file: DESeq_mESCs.txt


title: Ythdf3-/- mESCs replicate B [mESCs_Ythdf3_KO_B_S8]

description:
Ythdf3_KO_B_S8
processed data file: DESeq_mESCs.txt

source_name: Ythdf3-/- mESCs


title: 248d_4901-PBMC

description:
Sample 248d_4901, age 7
Measured on EPIC array


title: PDIS9063-064


title: Ythdf3-/- mESCs replicate A [mESCs_Ythdf3_KO_A_S7]

description:
Ythdf3_KO_A_S7
processed data file: DESeq_mESCs.txt


title: PDIS9063-063


title: Ythdf2-/- mESCs replicate A [mESCs_Ythdf2_KO_A_S5]

description:
Ythdf2_KO_A_S5
processed data file: DESeq_mESCs.txt

source_name: Ythdf2-/- mESCs


title: PDIS9063-068


title: 4bcf_414d-CBMC

description:
Sample 4bcf_414d, birth
Measured on EPIC array


title: PDIS9063-062


title: PDIS9063-067


title: 4bcf_414d-PBMC

description:
Sample 4bcf_414d, age 7
Measured on EPIC array


title: PDIS9063-060


title: Ythdf1-/- mESCs replicate B [mESCs_Ythdf1_KO_B_S4]

description:
Ythdf1_KO_B_S4
processed data file: DESeq_mESCs.txt

source_name: Ythdf1-/- mESCs


title: Ythdf2-/- mESCs replicate B [mESCs_Ythdf2_KO_B_S6]

description:
Ythdf2_KO_B_S6
processed data file: DESeq_mESCs.txt


title: Ythdf1-/- mESCs replicate A [mESCs_Ythdf1_KO_A_S3]

description:
Ythdf1_KO_A_S3
processed data file: DESeq_mESCs.txt


title: 0043_4ed8-CBMC

description:
Sample 0043_4ed8, birth
Measured on EPIC array


title: PDIS9063-058


title: PDIS9063-059


title: 0043_4ed8-PBMC

description:
Sample 0043_4ed8, age 7
Measured on EPIC array


title: Maf_cDKO

city: San Francisco

first: Ling-Lin

last: Pai

state: CA

address: 1550 4th Street

department: Psychiatry

institute: UCSF

data_processing:
Raw base cell files convered into FASTQ files using Cell Ranger V.2.
Transcriptome alignment to mm10 using Cell Ranger V.2.
Cell Ranger pipeline generated matrix data for WT and cDKO separately.
Combine the WT and cDKO matrix data sets
Filter out cells with either less than 500 total UMIs or over 20,000 total UMIs
Filter out cells with high mitochondrial contents
Seurat pipeline to LogNormalize the combined matrix data set
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Neonatal neocortical tissue

extract_protocol:
On the day of birth, the age-matched and gender-matched WT and Maf cDKO animals were harvested. Brain tissues were gently extracted from the skull, and neocortex (which includes the hippocampi) was dissected and placed in the freshly made HABG medium, HABG media was replaced by papain solution. We conducted papain treatment for 15 mins. After papain treatment, papain medium was replaced by HABG and tissues were tritrated up and down using large-bore pipette tips for 15-20 times. Cell suspesion with medium was placed still for 1 min before the supernatant was taken out for 300g 5 min centrifugation. After centrifugation, medium was discarded, and cell pellet was resuspended with fresh HABG. Cell suspension was filtered using MACS 30um cell strainer. Cell density was quantified using hemocytometer. Final cell concentration was optimized to 2000 cell/ul. Samples were transported to UCSF IHG core for 10X genomics singel-cell RNA sequencing library preparation (v2 kit).
Library preparation was following the 10X Chromium Single 3’ Reagent Kits Version 2 user manuals. The library preparation was conducted by the IHG core facility experts.

value: Neonatal neocortical tissue

value: Developing excitatory neuron and inhibitory neurons

value: Neonate (P0)

tag: strain

value: mixed strains:C57BL/6 and CD1


title: PDIS9063-056


title: f751_47a0-PBMC

description:
Sample f751_47a0, age 7
Measured on EPIC array

value: Female


title: WT mESCs replicate B [mESCs_WT_B_S2]

description:
WT_B_S2
processed data file: DESeq_mESCs.txt

source_name: WT mESCs

value: WT


title: WT


title: PDIS9063-055


title: WT mESCs replicate A [mESCs_WT_A_S1]

description:
WT_A_S1
processed data file: DESeq_mESCs.txt

value: mouse embryonic stem cells


title: mOC

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

country: China

institute: Third Military Medical University

library_source: genomic

data_processing:
FastQC software was used for reads quality evaluation.
Fastp software was used for reads filtering to get clean reads.
Hisat2 software was used for spliced mapping with mouse genome GRCm38.
Circos software was used for chromosomal mapping.
Stringtie software was used for counting of fragments and trimmed mean of M values (TMM) was used for normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited xls files include RPKM values for each Sample concerning mRNA, lncRNA and circRNA

source_name: Bone marrow

growth_protocol: BMMs were used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more.

extract_protocol:
Femurs and tibia were dissected from mice and flushed using complete medium to acquire whole bone marrow. The whole cells were cultured using alpha-MEM complete media for 24 h and the floating cells were collected for further treatment of M-CSF (50ng/mL) for 72 h to generate BMMs.
WGBS DNA  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before testing.

value: Bone marrow

value: post natal week 11


title: f751_47a0-CBMC

description:
Sample f751_47a0, birth
Measured on EPIC array


title: 248d_4901-CBMC

description:
Sample 248d_4901, birth
Measured on EPIC array


title: BMM


title: 3450_4e8e-PBMC

description:
Sample 3450_4e8e, age 7
Measured on EPIC array

value: PBMCs

value: age 7


title: PDIS9063-053


title: Effector_Th17_RNA_REP2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description: Splenic CD44low CD62Lhi CD4+ cells were stimulated under Th17 culture conditions (10 ng/ml IL-6, and 10 ng/ml IL-1β, 10 ng/ml IL-23, 10 µg/ml anti-IL-4 Ab, and 10 µg/ml anti-IFN-γ Ab) for 6 days in vitro.

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Six-day cultured Th17 cells generated from primary splenic CD4_T cells

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

value: Effector Th17


title: 8be9_46af-PBMC

description:
Sample 8be9_46af, age 7
Measured on EPIC array

value: Black

value: Baltimore


title: PDIS9063-052

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: Effector_Th2_RNA_REP2

description: Splenic CD44low CD62Lhi CD4+ cells were stimulated under Th2 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-4, and 10 µg/ml anti-IFN-γ Ab) for 6 days in vitro.

source_name: Six-day cultured Th2 cells generated from primary splenic CD4_T cells

value: Effector Th2


title: PDIS9063-051


title: B6N_3_hippocampus_Ribo

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: Ribosome protected RNA fragments

data_processing:
Forebrain RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM20 transcript reference.
Hippocampus RNA-seq was mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus RNA-seq and ribosome profiling reads were counted at the gene-level using featureCounts. The RNA-seq data was quantifified by counting reads overlapping exons and the ribosome profiling data was quantified by counting reads overlapping CDS regions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts for hippocampus RNA-seq and ribosome profiling samples.

source_name: Hippocampus

extract_protocol:
For forebrain samples, forebrains were isolated, and stored in RNAlater and frozen at -20C. Following ribosomal RNA depletion, the remaining RNA was purified, fragmented, and libraries were prepared using TruSeq Stranded Total RNA with RiboZero-Mouse (Illumina). mRNA libraries for the assessment of translational efficiency in the B6JN and B6JN-nTr20-/- hippocampus were prepared using the TruSeq v2 mRNA kit (Illumina). mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. Ribosome profiling libraries were generated from B6N and B6N-nTr20-/- hippocampi. Libraries were constructed as previously described (Ingolia et al., 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols and ribosome profiling libraries were prepared following the protocol described in Ingolia et al., 2012

value: Hippocampus

value: 8 weeks old

value: wild-type n-Tr20

tag: batch

value: Batch 4


title: B6N_nTr20_del_1_hippocampus_Ribo

description: Ribosome protected RNA fragments


title: B6N_nTr20_del_2_hippocampus_Ribo

description: Ribosome protected RNA fragments


title: 8be9_46af-CBMC

description:
Sample 8be9_46af, birth
Measured on EPIC array

value: Cord blood

value: birth

value: Female


title: 5f71_4c61-PBMC

description:
Sample 5f71_4c61, age 7
Measured on EPIC array

value: Male


title: pOC

value: Bone marrow

value: post natal week 11


title: Effector_Th1_RNA_REP2

description: Splenic CD44low CD62Lhi CD4+ were stimulated under Th1 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-12, and 1 µg/ml anti-IL-4 Ab) for 6 days in vitro.

source_name: Six-day cultured Th1 cells generated from primary splenic CD4_T cells

value: Effector Th1


title: B6N_2_hippocampus_Ribo

description: Ribosome protected RNA fragments


title: PDIS9063-049


title: 5f71_4c61-CBMC

description:
Sample 5f71_4c61, birth
Measured on EPIC array


title: B6N_1_hippocampus_Ribo

description: Ribosome protected RNA fragments


title: B6N_nTr20_del_3_hippocampus_RNA

description: poly(A) selected RNA

value: Batch 3


title: B6N_nTr20_del_3_hippocampus_Ribo

description: Ribosome protected RNA fragments


title: Effector_Th2_RNA_REP1


title: PDIS9063-054


title: a60f_493d-PBMC

description:
Sample a60f_493d, age 7
Measured on EPIC array

value: PBMCs

value: age 7

value: Black


title: B6N_nTr20_del_2_hippocampus_RNA

description: poly(A) selected RNA


title: 3450_4e8e-CBMC

description:
Sample 3450_4e8e, birth
Measured on EPIC array

value: Baltimore


title: Effector_Th1_RNA_REP1


title: a60f_493d-CBMC

description:
Sample a60f_493d, birth
Measured on EPIC array


title: PDIS9063-047

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: Ribo-seq Mettl3-/- mESCs replicate B

data_processing:
Library strategy: Ribo-seq
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were pre-processed by trimming their linker (sequence CTGTAGGCACCATCAAT) and polyA removal with cutadapt.
Reads were aligned to mouse genome version mm10 with Bowtie aligner (parameters -v -m 16 -p 8 --max), where only uniquely aligned reads where used for further analyses.
Per gene, for translation calculation, reads were counted in the coding region excluding 15 and 6 nucleotides from the beginning and end of each coding sequence (CDS), respectively (Ingolia et al. 2009; McGlincy and Ingolia 2017).
For each gene and sample, Ribo-seq RPKM values were calculated
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-seq RPKM

source_name: mouse embryonic stem cells

extract_protocol:
Cells were lysed in lysis buffer (20mM Tris 7.5, 150mM NaCl, 15mM MgCl2, 1mM dithiothreitol) supplemented with 0.5% triton, 30 U/ml Turbo DNase (Ambion) and 100μg/ml cycloheximide. The lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. Pellet was resuspended in Trizol and then RNA was isolated from cells using chloroform-based separation.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

treatment_protocol: For ribosome profiling cells were treated with Cycloheximide as previously described (McGlincy and Ingolia 2017; Ingolia et al. 2009).

tag: cell line

value: mouse embryonic stem cells (mESCs)


title: B6N_nTr20_del_1_hippocampus_RNA

description: poly(A) selected RNA

value: Hippocampus

value: 8 weeks old


title: Naive_CD4T_RNA_REP2

description: Splenic CD44low CD62Lhi CD4+ cells were sorted by cell sorter.

source_name: Primary splenic navie CD4 T cells

value: Nave CD4 T


title: PDIS9063-050


title: 85aa_4e0f-PBMC

description:
Sample 85aa_4e0f, age 7
Measured on EPIC array


title: Effector_Th17_RNA_REP1

value: Effector Th17


title: B6N_3_hippocampus_RNA

description: poly(A) selected RNA

value: wild-type n-Tr20


title: B6N_2_hippocampus_RNA

description: poly(A) selected RNA


title: 85aa_4e0f-CBMC

description:
Sample 85aa_4e0f, birth
Measured on EPIC array

value: Cord blood

value: birth

value: Male


title: B6N_1_hippocampus_RNA

description: poly(A) selected RNA


title: Spl9_naiveBC_9A_plus

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: Spl9 CD19CreI/+ naiveBC

data_processing:
Raw data was processed with Dropseq tools v1.12
reads were mapped to the genome using STAR (Dobin et al., 2013)
Gene models from Ensembl release GRCm38.87 were used
Counts were collapsed to molecules using the UMI tag (appended to the readID of each read)
Genome_build: GRCm38p5
Supplementary_files_format_and_content: Gene and sample wise UMI counts

source_name: Spleen

extract_protocol:
RNA was cleaned-up from the lysate (TCL buffer; Qiagen) using magnetic beads (GC Biotech) and mRNA was directly eluted in reverse transcription master mix.
bulk SCRB-seq (Soumillon et al., 2014; Parekh et al., 2016)

tag: individual

value: naive B cells

value: spleen


title: Spl9_GCB_9A_minus

description: Spl9 CD19CreI/+ GCB

value: germinal center (GC) B cells


title: PDIS9063-045


title: Spl9_PC_9A_plus

description: Spl9 CD19CreI/+ PC

value: plasma cells (PC)


title: PDIS9063-044


title: 917d_4410-PBMC

description:
Sample 917d_4410, age 7
Measured on EPIC array

value: PBMCs

value: age 7

value: Hispanic


title: f70a_47b0-PBMC

description:
Sample f70a_47b0, age 7
Measured on EPIC array

value: Black

value: Baltimore


title: 917d_4410-CBMC

description:
Sample 917d_4410, birth
Measured on EPIC array


title: PDIS9063-042

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: PDIS9063-048


title: PDIS9063-043


title: Spl8_GCB_8A_minus

description: Spl8 c-RelTG CD19CreI/+ GCB

value: c-RelTG CD19CreI/+


title: NIS-2_ChIP-seq

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

data_processing:
Basecalls performed using CASAVA version 1.8
For data analysis a dedicated pipeline was used (https://incpmpm.atlassian.net/wiki/spaces/PUB/pages/21758010/ChIP+Seq+on+Pipeline+Pilot). 12 million Runx3 IP and 7 million NIS sequences were aligned uniquely to the mouse genome (mm9) using bowtie version 1 ( paremeters:  -m 1  --phred33-quals -5 0 -3 0  --best -n 1 -l 28  --strata --solexa-quals -B 1 -S ).
Bound regions of merged biological replicates were detected using MACS2 (2.0.10).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing 13014 peaks detected by MACS2.

growth_protocol: Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions using in-house anti Runx3 Ab and 30x106 D1 cells in each ChIP-Seq replicate.

extract_protocol:
Cultured D1 cells were collected, fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 40ul of anti-Runx3 Ab were added to 15 mL of diluted, fragmented chromatin; Fragmented chromatin IP with NIS served as control. DNA was purified using QIAquick spin columns (QIAGEN).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel.

value: D1 dendritic cell line

tag: origin

tag: chip antibody

value: Rabbit non-immuned serum


title: PDIS9063-046


title: Naive_CD4T_RNA_REP1

value: Nave CD4 T


title: f70a_47b0-CBMC

description:
Sample f70a_47b0, birth
Measured on EPIC array

value: Cord blood

value: birth


title: Spl8_PC_8B_plus

description: Spl8 c-RelTG CD19CreI/+ PC


title: NIS-1_ChIP-seq


title: Runx3-3_ChIP-seq

value: Polyclonal rabbit anti-mouse Runx3


title: PDIS9063-041


title: Spl8_naiveBC_8A_plus

description: Spl8 c-RelTG CD19CreI/+ naiveBC

value: naive B cells

value: spleen


title: 1b47_432d-PBMC

description:
Sample 1b47_432d, age 7
Measured on EPIC array

value: Female


title: Spl7_PC_7B_plus

description: Spl7 c-RelTG CD19CreI/+ PC

value: plasma cells (PC)


title: Runx3-2_ChIP-seq


title: PDIS9063-038


title: PDIS9063-040


title: Runx3-1_ChIP-seq


title: Spl7_GCB_7A_minus

description: Spl7 c-RelTG CD19CreI/+ GCB

value: germinal center (GC) B cells


title: PDIS9063-037


title: a963_44d0-PBMC

description:
Sample a963_44d0, age 7
Measured on EPIC array

value: PBMCs

value: age 7

value: Male


title: PDIS9063-036

value: 129/CAST hybrid F1


title: a963_44d0-CBMC

description:
Sample a963_44d0, birth
Measured on EPIC array

value: Black

value: Baltimore


title: Spl7_naiveBC_7A_plus

description: Spl7 c-RelTG CD19CreI/+ naiveBC

value: c-RelTG CD19CreI/+


title: ESC-D12

city: Wuhan

first: Xuejiao

last: Sun

state: Hebei

address: Jiefang Avenue 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
By using Base Calling 0.11.4, FASTQ sequence data were derived from the RNA-sequencing data.
Sequenced reads were trimmed for adaptor sequences and  low-quality sequences using Cutadapt Version 1.2.1.
The transcriptome data were aligned to the reference genome using TopHat2.
With Cuffquant version 2.2.1, expression of mRNAs and lncRNAs was normalized and outputted. Fragments Per Kilo bases per Million fragments (FPKM) were calculated.
Hierarchical clustering was performed with R software
Genome_build: hg19_GRCh38
Supplementary_files_format_and_content: lncRNA.txt and mRNA.txt: abundance measurements

source_name: Embryonic stem cells

growth_protocol: Human ESCs were maintained on a layer of irradiated murine embryonic fibroblasts.

extract_protocol:
Total RNA was extracted from cells using the Trizol reagent (Invitrogen) according to the manusfacture's protocol. RNA quantity and  purity of total were confirmed using NanoDrop ND-2000 spectrophotometer (Thermo Fisher  Scientific), and RNA integrity was checked using Agilent Bioanalyzer 2100 system (Agilent). The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: ESCs were cultured using motor neuron (MN) differentiation medium containing DMEM/F12, Neurobasal medium, N2, B27, ascorbic acid, Glutamax and penicillin/streptomycin. The medium was additionally supplemented with chemical compounds: 3 μM CHIR99021 , 2 μM DMH-1  and 2 μM SB431542  for 6 days differentiated into neuroepithelial progenitors; 1 μM CHIR99021, 2 μM DMH-1, and 2 μM SB431542, 0.1 μM RA  and 0.5 μM Purmorphamine for 6 days differentiated into MN progenitors; 0.5 μM RA and 0.1μM Purmorphamine for 6 days differentiated into MNs.

value: ESC-derived motor neuron progenitors

tag: treatment

value: motor neuron induction

tag: time point

value: Day 12


title: ESC-D18

value: ESC-derived motor neurons

value: Day 18


title: PDIS9063-035

tag: strain background

value: Embryonic stem cell


title: ESC-D6

tag: cell type

value: ESC-derived neuroepithelial progenitors

value: Day 6


title: 0276_4d38-CBMC

description:
Sample 0276_4d38, birth
Measured on EPIC array

value: Cord blood

value: birth

value: Female


title: PDIS9063-034


title: Spl6_naiveBC_6A_plus

description: Spl6 c-RelTG CD19CreI/+ naiveBC

tag: genotype

value: naive B cells

value: spleen


title: Spl5_PC_5B_plus

description: Spl5 c-RelTG CD19CreI/+ PC

value: plasma cells (PC)

tag: tissue


title: DLD-1 cells transfected with original NA 2hr replicate3

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

description: Replicate 3

data_processing:
We used CASAVA 1.8.2 for the base calling (Illumina, San Diego, CA).
We used STAR aligner version 2.6.1c (Dobin et al., 2013, PMID: 23104886) with the default parameters to map RNA-Seq reads to human reference genome (GRCh38, obtained from Ensembl.org).
We counted the short-reads at the gene level using featureCounts 1.5.2 (Liao et al., 2014, PMID: 24227677). We used "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters.
Genome_build: Human reference genome GRCh38 (obtained from Ensembl.org, release 87).
Supplementary_files_format_and_content: Tab-limited text files have human gene IDs (Ensembl 87) as well as read counts from featureCounts.

source_name: DLD-1 cells

growth_protocol: The human colorectal cancer cell line DLD-1 was cultured in DMEM supplemented with heat-inactivated 10% FBS, antibiotics, and 2 mM GlutaMAX in 5% CO2 atmosphere at 37°C. From 75 to 100K of AID-tagged cells were plated on each well of 6-well plate dishes for RNA isolation. Cells at 85% of confluency were washed with PBS and lysed with RLT buffer.

extract_protocol:
RNAeasy Mini Kit (Qiagen). Extracted RNA was analyzed for 260/280 and RIN value on Bioanalyzer 2100 (Agilent).
TruSeq Standard Total RNA Library Prep Kit (Illumina, San Diego, CA) was used to generate RNA-Seq libraries for the Illumina-platforms. The libraries were prepared by the Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (Bethesda, MD) as per manufacture’s guideline using Ribo-Zero Gold.

treatment_protocol: All AID-tagged cell lines were treated with 1 mM auxin (I5148, Sigma Aldrich) for nucleoporins loss for 0hrs or 2/3hrs

value: original

tag: agent


title: 00d1_4cde-PBMC

description:
Sample 00d1_4cde, age 7
Measured on EPIC array

source_name: Human PBMCs at age 7

value: PBMCs

tag: age

value: age 7

tag: methylationplatenumber

value: Black

value: Male

value: Baltimore


title: PDIS9063-032

source_name: 129/CAST hybrid mESC

value: 129/CAST hybrid F1


title: 1b47_432d-CBMC

description:
Sample 1b47_432d, birth
Measured on EPIC array

source_name: Human cord blood at birth

tag: selfreportedrace

tag: Sex


title: Spl6_PC_6B_plus

description: Spl6 c-RelTG CD19CreI/+ PC

value: c-RelTG CD19CreI/+


title: Spl5_GCB_5A_minus

description: Spl5 c-RelTG CD19CreI/+ GCB

value: germinal center (GC) B cells


title: PDIS9063-030

value: Embryonic stem cell


title: 0276_4d38-PBMC

description:
Sample 0276_4d38, age 7
Measured on EPIC array

tag: samplecollectionsite


title: 00d1_4cde-CBMC

description:
Sample 00d1_4cde, birth
Measured on EPIC array


title: 62c5_4d11-PBMC

description:
Sample 62c5_4d11, age 7
Measured on EPIC array


title: Spl6_GCB_6A_minus

description: Spl6 c-RelTG CD19CreI/+ GCB


title: DLD-1 cells transfected with original NA 2hr replicate2

description: Replicate 2


title: 62c5_4d11-CBMC

description:
Sample 62c5_4d11, birth
Measured on EPIC array


title: Spl5_naiveBC_5A_plus

description: Spl5 c-RelTG CD19CreI/+ naiveBC


title: DLD-1 cells transfected with original NA 2hr replicate1

description: Replicate 1


title: PDIS9063-033


title: Spl4_PC_4B_plus

description: Spl4 CD19CreI/+ PC


title: PDIS9063-028


title: 6e19_401d-PBMC

description:
Sample 6e19_401d, age 7
Measured on EPIC array


title: Spl4_GCB_4A_minus

description: Spl4 CD19CreI/+ GCB


title: DLD-1 cells transfected with original and treated with Auxin for 2hr replicate1

description: Replicate 1

value: Auxin


title: 6e19_401d-CBMC

description:
Sample 6e19_401d, birth
Measured on EPIC array

value: Cord blood


title: DLD-1 cells transfected with original and treated with Auxin for 2hr replicate2

description: Replicate 2


title: Spl4_naiveBC_4A_plus

description: Spl4 CD19CreI/+ naiveBC


title: PDIS9063-026


title: f665_4e1b-PBMC

description:
Sample f665_4e1b, age 7
Measured on EPIC array


title: DLD-1 cells transfected with NUP50-NeonGreen-AID replicate3

description: Replicate 3


title: Spl3_PC_3B_plus

description: Spl3 CD19CreI/+ PC


title: PDIS9063-029


title: a389_4c79-PBMC

description:
Sample a389_4c79, age 7
Measured on EPIC array


title: PDIS9063-024


title: DLD-1 cells transfected with original and treated with Auxin for 2hr replicate3

description: Replicate 3


title: DLD-1 cells transfected with NUP50-NeonGreen-AID replicate1

description: Replicate 1


title: f665_4e1b-CBMC

description:
Sample f665_4e1b, birth
Measured on EPIC array

value: birth


title: Spl3_naiveBC_3A_plus

description: Spl3 CD19CreI/+ naiveBC


title: Spl2_PC_2B_plus

description: Spl2 CD19CreI/+ PC


title: a389_4c79-CBMC

description:
Sample a389_4c79, birth
Measured on EPIC array

value: Female


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 9hr replicate3

description: Replicate 3


title: DLD-1 cells transfected with NUP50-NeonGreen-AID replicate2

description: Replicate 2


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 9hr replicate2

description: Replicate 2


title: 9df6_44a2-PBMC

description:
Sample 9df6_44a2, age 7
Measured on EPIC array


title: PDIS9063-027


title: PDIS9063-021


title: PDIS9063-023


title: PDIS9063-022


title: 9df6_44a2-CBMC

description:
Sample 9df6_44a2, birth
Measured on EPIC array


title: Spl2_GCB_2A_minus

description: Spl2 CD19CreI/+ GCB


title: 7804_4bab-PBMC

description:
Sample 7804_4bab, age 7
Measured on EPIC array


title: PDIS9063-020


title: PDIS9063-025


title: Spl2_naiveBC_2A_plus

description: Spl2 CD19CreI/+ naiveBC

value: naive B cells


title: Spl3_GCB_3A_minus

description: Spl3 CD19CreI/+ GCB

value: spleen


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 9hr replicate1

description: Replicate 1


title: PDIS9063-019


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 3hr replicate3

description: Replicate 3


title: Spl16_PC_16B_plus

description: Spl16 c-RelTG CD19CreI/+ PC

value: plasma cells (PC)


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 3hr replicate2

description: Replicate 2


title: 7804_4bab-CBMC

description:
Sample 7804_4bab, birth
Measured on EPIC array


title: Spl16_GCB_16A_minus

description: Spl16 c-RelTG CD19CreI/+ GCB


title: debb_4963-PBMC

description:
Sample debb_4963, age 7
Measured on EPIC array


title: PDIS9063-018


title: Spl16_naiveBC_16A_plus

description: Spl16 c-RelTG CD19CreI/+ naiveBC


title: DLD-1 cells transfected with NUP50-NeonGreen-AID and treated with Auxin for 3hr replicate1

description: Replicate 1


title: Spl15_PC_15B_plus

description: Spl15 c-RelTG CD19CreI/+ PC


title: debb_4963-CBMC

description:
Sample debb_4963, birth
Measured on EPIC array


title: PDIS9063-017


title: PDIS9063-016


title: Spl15_GCB_15A_minus

description: Spl15 c-RelTG CD19CreI/+ GCB


title: a55c_472f-CBMC

description:
Sample a55c_472f, birth
Measured on EPIC array

value: Mixed (>1 race)


title: a55c_472f-PBMC

description:
Sample a55c_472f, age 7
Measured on EPIC array

value: PBMCs


title: PDIS9063-015


title: Spl15_naiveBC_15A_plus

description: Spl15 c-RelTG CD19CreI/+ naiveBC


title: DLD-1 cells transfected with NUP153-NeonGreen-AID replicate2

description: Replicate 2


title: DLD-1 cells transfected with NUP153-NeonGreen-AID replicate1

description: Replicate 1


title: DLD-1 cells transfected with NUP153-NeonGreen-AID replicate3

description: Replicate 3


title: PDIS9063-014


title: 85bc_4369-PBMC

description:
Sample 85bc_4369, age 7
Measured on EPIC array

value: age 7


title: Spl14_PC_14B_plus

description: Spl14 c-RelTG CD19CreI/+ PC


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 8hr replicate3

description: Replicate 3


title: 85bc_4369-CBMC

description:
Sample 85bc_4369, birth
Measured on EPIC array

value: Black


title: Spl14_GCB_14A_minus

description: Spl14 c-RelTG CD19CreI/+ GCB


title: ac8a_4da4-PBMC

description:
Sample ac8a_4da4, age 7
Measured on EPIC array


title: PDIS9063-013


title: PDIS9063-011


title: PDIS9063-010


title: ac8a_4da4-CBMC

description:
Sample ac8a_4da4, birth
Measured on EPIC array


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 8hr replicate2

description: Replicate 2


title: Spl14_naiveBC_14A_plus

description: Spl14 c-RelTG CD19CreI/+ naiveBC


title: Spl13_PC_13B_plus

description: Spl13 c-RelTG CD19CreI/+ PC


title: PDIS9063-009


title: 849c_424f-PBMC

description:
Sample 849c_424f, age 7
Measured on EPIC array


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 2hr replicate3

description: Replicate 3


title: Spl13_GCB_13A_minus

description: Spl13 c-RelTG CD19CreI/+ GCB


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 8hr replicate1

description: Replicate 1


title: 6a32_47fc-PBMC

description:
Sample 6a32_47fc, age 7
Measured on EPIC array


title: 849c_424f-CBMC

description:
Sample 849c_424f, birth
Measured on EPIC array


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 2hr replicate2

description: Replicate 2


title: Spl12_PC_12B_plus

description: Spl12 CD19CreI/+ PC


title: PDIS9063-008


title: DLD-1 cells transfected with GAP1-NeonGreen-AID replicate3

description: Replicate 3


title: 6a32_47fc-CBMC

description:
Sample 6a32_47fc, birth
Measured on EPIC array


title: DLD-1 cells transfected with GAP1-NeonGreen-AID replicate2

description: Replicate 2


title: Spl13_naiveBC_13A_plus

description: Spl13 c-RelTG CD19CreI/+ naiveBC


title: PDIS9063-006


title: Spl12_GCB_12A_minus

description: Spl12 CD19CreI/+ GCB


title: c327_4fff-PBMC

description:
Sample c327_4fff, age 7
Measured on EPIC array

value: Male


title: PDIS9063-005


title: c327_4fff-CBMC

description:
Sample c327_4fff, birth
Measured on EPIC array

value: Baltimore


title: PDIS9063-004

value: 129/CAST hybrid F1


title: PDIS9063-003


title: Spl11_PC_11B_plus

description: Spl11 CD19CreI/+ PC


title: 9ea6_469e-PBMC

description:
Sample 9ea6_469e, age 7
Measured on EPIC array


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 8hr replicate3

description: Replicate 3


title: Spl11_GCB_11A_minus

description: Spl11 CD19CreI/+ GCB


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 8hr replicate2

description: Replicate 2


title: 9ea6_469e-CBMC

description:
Sample 9ea6_469e, birth
Measured on EPIC array


title: PDIS9063-007


title: DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 2hr replicate1

description: Replicate 1


title: 8119_45f3-PBMC

description:
Sample 8119_45f3, age 7
Measured on EPIC array


title: ESC

description: ESC

value: Embryonic stem cells

value: untreated

value: Day 0


title: PDIS9063-002

value: Embryonic stem cell


title: Spl11_naiveBC_11A_plus

description: Spl11 CD19CreI/+ naiveBC


title: ChIP-seq-delS1-4-L1-PolII-rep2

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
The ChIP-seq analysis workflow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012) with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Deeptools (Ramírez et al., Nucleic Acids Research, 2016) was applied for the generation of bedGraph files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph of ChIP-seq.

source_name: Mammary gland

growth_protocol: Mouse mammary tissues were harvested at day one of lactation (L1), and day 6 and day 18 of pregnancy (p6 and p18).

extract_protocol:
Mammary tissues from specific stages during pregnancy and lactation were harvested, and stored at -80°C. The frozen-stored tissues were ground into powder in liquid nitrogen. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-1081), GR (Thermo Fisher Scientific, PA1-511A), H3K27ac (Abcam, ab4729), H3K4me3 (Millipore, 17-614), NFIB (Santa Cruz Biotechnology, sc-5567), and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

tag: Stage

value: Lactation day 1

value: Mammary gland

tag: chip-antibody

value: RNA polymerase II (Abcam, ab5408)


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 8hr replicate1

description: Replicate 1

tag: cell line

value: Auxin


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 2hr replicate3

description: Replicate 3


title: ChIP-seq-delS1-4-L1-PolII-rep1


title: Spl10_GCB_10A_minus

description: Spl10 CD19CreI/+ GCB

tag: individual

value: germinal center (GC) B cells

value: spleen


title: ChIP-seq-delS1-4-L1-H3K4me3-rep2

value: H3K4me3 (Millipore, 17-614)


title: 8119_45f3-CBMC

description:
Sample 8119_45f3, birth
Measured on EPIC array

value: Cord blood

value: birth

value: Female


title: DLD-1 cells transfected with GAP1-NeonGreen-AID replicate1

description: Replicate 1

tag: time point


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 2hr replicate1

description: Replicate 1


title: Spl10_naiveBC_10A_plus

description: Spl10 CD19CreI/+ naiveBC

value: naive B cells


title: Spl12_naiveBC_12A_plus

description: Spl12 CD19CreI/+ naiveBC


title: ChIP-seq-delS1-4-L1-H3K4me3-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate3

description: Replicate 3

value: AID-NeonGreen-TPR


title: Spl1_PC_1B_plus

description: Spl1 CD19CreI/+ PC

value: plasma cells (PC)


title: ChIP-seq-delS1-4-L1-H3K27ac-rep2

value: H3K27ac (Abcam, ab4729)


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate2

description: Replicate 2


title: Spl1_GCB_1A_minus

description: Spl1 CD19CreI/+ GCB


title: ChIP-seq-delS1-4-L1-H3K27ac-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate1

description: Replicate 1


title: ChIP-seq-delS1-4-L1-GR-rep2

value: GR (Thermo Scientific, PA1-511A)


title: Ovary_PND46_60_rep6

type: RNA

city: Montreal

first: Oceane

last: Albert

state: Quebec

address: 3655 Promenade Sir William Osler, McIntyre Medical Sciences Bldg, Room 107

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

description: Gene expression after perinatal exposure to BFR mixture

hyb_protocol: … hybridized on arrays using the SurePrint G3 Rat Gene Expression 8x60K microarray kit (Agilent Technologies) as per manufacturer’s instructions

scan_protocol: Arrays were read on an Agilent SureScan Microarray Scanner G2600D.

data_processing: The resulting data were analyzed using GeneSpring version 14.9 (Agilent Technologies). Data were normalized using percentile shift normalization to the 75th percentile.

organism: Rattus norvegicus

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 6

label_protocol: RNA (100 ng) was labeled with Cy3 using the Agilent One Color Low Input Quick Amp kit and …

extract_protocol: RNA was extracted from entire ovaries using the Qiagen RNEasy® Mini Kit (Qiagen, Toronto, ON). Briefly, frozen ovaries were pulverized to a thin powder using a chilled mortar and pestle, placed in 1 mL of RLT buffer supplemented with ß-mercaptoethanol and mechanically disrupted using a rotor-stator homogenizer (Polytron PT10-35GT, Kinematica Inc) at 20 000 rpm for 20 s. Homogenates were further processed with a QIAshredder column (Qiagen), and RNA was isolated as per the manufacturer's instructions. RNA quality was measured using a NanoDrop 2000 Spectrophotometer (Thermo Fisher), with 260/280 and 260/230 absorbance ratios comprised between 1.9-2.1 and 2.0-2.2, respectively.

treatment_protocol: Virgin female Sprague Dawley rats aged 6-7 weeks were purchased from Charles River Laboratories (St-Constant, QC, Canada) and acclimated for two weeks on control diet. Females were fed a diet supplemented with a commercial mixture of BFRs for a minimum of one week prior to mating and until weaning at postnatal day (PND) 21. This mixture was composed of PBDEs (52.1 % DE-71, 0.4% DE-79 and 44.2% BDE-209) and a mixture of hexabromocyclododecane (HBCD: 3.3%) representative of the proportion of BFRs found in domestic dust in Boston, MA (Allen 2008, Stapleton 2008). The rats followed a diet formulated to contain 0; 0.75; 250 or 750 mg of a BFR mixture per kg in order to deliver 0; 0.06; 20 and 60 mg/kg body weight (bw)/day, assuming a food consumption of 80 g/kg bw/day. Female offspring were sacrificed at PND46. The ovaries were removed, weighed, and stored at -80°C for gene expression analysis.

value: BFR mixture

tag: dose

value: 60 mg/kg/day

tag: gender

value: Ovary

value: 46 days


title: Spl10_PC_10B_minus

description: Spl10 CD19CreI/+ PC

tag: genotype

tag: cell type


title: Spl1_naiveBC_1A_plus

description: Spl1 CD19CreI/+ naiveBC

tag: tissue


title: DLD-1 cells transfected with GAP1-NeonGreen-AID and treated with Auxin for 2hr replicate2

description: Replicate 2

tag: agent


title: Std-3

data_processing:
All reads were aligned to the reference genome (GRCm38) using HISAT (v.2.1.0)
The software HTSeq (Anders et al., 2015) was used in calculating gene-wise unique molecular identifier (UMI) counts which were converted into transcript counts after collision probability correction (Grün et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: umi_counts.txt includes read count data for each sample.

source_name: C57BL6/J WT  mESC_Std

growth_protocol: WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 coated dish under either Std  (StemSure D-MEM [Wako Pure Chemicals, Osaka, Japan], 15% of fetal bovine serum, 0.1 mM β-mercaptoethanol, 1x MEM nonessential amino acids [Wako Pure Chemicals], a 2 mM L-alanyl-L-glutamine solution [Wako Pure Chemicals], 1000 U/mL LIF [Wako Pure Chemicals], 20 mg/ mL gentamicin [Wako Pure Chemicals]), 2i (Std + 1 µM PD0325901 [CS-0062, Chem Scene], 3 µM CHIR99021 [034-23103, Wako Pure Chemicals]) or PD-MK (Std medium + 1 µM PD0325901 [CS-0062, Chem Scene], 4 µM MK-2206 2HCl [S1078, Selleck Chemicals, Houston TX]) medium.

extract_protocol:
RNA was extracted from either Std/LN511, 2i/LN511 or PDMK/LN511 conditioned cells at 70% confluency in a well of a 6-well plate using RNeasy Plus Mini (Qiagen).
Bulk RNA-Seq was performed by CEL-Seq2 method (Hashimshony et al., 2016) with total RNA amounts were used the range of 30-60 ng.

tag: strain background

value: Embryonic stem cell

tag: culture condition

value: standard (Std) medium


title: ChIP-seq-delS1-4-L1-GR-rep1

value: Lactation day 1

value: Mammary gland


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate-old1

description: Replicate old1


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate-old2

description: Replicate old2


title: Std-1


title: Std-2


title: ChIP-seq-delS1-4-L1-STAT5A-rep2

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 8hr replicate-old3

description: Replicate old3

value: Auxin


title: Ovary_PND46_60_rep5

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 5

tag: age


title: ChIP-seq-delS1-4-L1-STAT5A-rep1


title: ChIP-seq-delS1-2-L1-H3K27ac-rep2


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 8hr replicate-old2

description: Replicate old2


title: PD03-MK-2

source_name: C57BL6/J WT  mESC_PD03-MK

value: Akt/MAPK signal-inhibitor containing medium (PD-MK)


title: ChIP-seq-delS1-2-L1-H3K27ac-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 8hr replicate-old1

description: Replicate old1


title: DLD-1 cells transfected with AID-NeonGreen-TPR replicate-old3

description: Replicate old3


title: Ovary_PND46_60_rep2

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 2

value: Female


title: Ovary_PND46_20_rep5

source_name: Ovary RNA, 46 days, 20 mg/kg/day, replicate 5

value: 20 mg/kg/day


title: Ovary_PND46_60_rep3

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 3


title: PD03-MK-1


title: ChIP-seq-delS1-2-L1-GR-rep2


title: Ovary_PND46_20_rep4

source_name: Ovary RNA, 46 days, 20 mg/kg/day, replicate 4


title: Ovary_PND46_60_rep4

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 4


title: Ovary_PND46_20_rep3

source_name: Ovary RNA, 46 days, 20 mg/kg/day, replicate 3


title: 2i-3

source_name: C57BL6/J WT mESC_2i

value: 2i containing medium


title: Ovary_PND46_60_rep1

source_name: Ovary RNA, 46 days, 60 mg/kg/day, replicate 1


title: ChIP-seq-delS1-2-L1-GR-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate3

description: Replicate 3

source_name: DLD-1 cells

value: AID-NeonGreen-TPR


title: Ovary_PND46_20_rep2

source_name: Ovary RNA, 46 days, 20 mg/kg/day, replicate 2


title: PD03-MK-3


title: ChIP-seq-delS1-2-L1-STAT5A-rep2


title: 2i-1


title: ChIP-seq-delS1-2-L1-STAT5A-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate2

description: Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate1

description: Replicate 1


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate-old3

description: Replicate old3


title: ChIP-seq-delS4-L1-H3K27ac-rep2

value: H3K27ac (Abcam, ab4729)


title: Ovary_PND46_0.06_rep5

source_name: Ovary RNA, 46 days, 0.06 mg/kg/day, replicate 5

value: 0.06 mg/kg/day


title: st5_H4K16ac_rep5

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
ChIP-seq: Data processing was done using the bioRxiv. 2018, DOI: 10.1101/407312 pipeline. The DNA-mapping followed by the ChIp-seq pipeline were used. The default parameters were used.
Genome_build: dm6
Supplementary_files_format_and_content: ChIP-seq: bigwig normalized to Input, 1x coverage using bamCompare from deepTools, chrX was excluded for scalefactor calculation

organism: Drosophila melanogaster

source_name: blastoderm embryos nc14

growth_protocol: D. melanogaster flies were maintained  in standard Drosophila medium at 25oC.

extract_protocol:
ChIPseq: Dechorionated embryos were fixed using 0.1% Formaldehyde for 15min at RT. After fixation, they were hand picked for the desired developmental stage and frozen at -80oc until further use. Nuclei were isolated using short covaris sonication followed by chromatin digestion using Micrococcal nuclease and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II

tag: strain

value: w- OR

value: blastoderm embryos nc14

tag: technique

value: Mnase-ChIP-seq

tag: antibody

value: anti-H4K16ac(Merck Milipore, 07-329)


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate-old2

description: Replicate old2


title: DLD-1 cells transfected with AID-NeonGreen-TPR and treated with Auxin for 2hr replicate-old1

description: Replicate old1


title: ChIP-seq-delS4-L1-STAT5A-rep2

source_name: Mammary gland

tag: strain/background

tag: genotype/variation

tag: Stage


title: ChIP-seq-delS4-L1-H3K27ac-rep1

tag: chip-antibody


title: 2i-2

value: Embryonic stem cell


title: ChIP-seq-delS4-L1-STAT5A-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD & Auxin 2hr replicate3

description: Replicate 3

tag: cell line

value: ActinomycinD & Auxin

tag: time point


title: ChIP-seq-delS2-L1-H3K27ac-rep2

value: Lactation day 1


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD & Auxin 2hr replicate2

description: Replicate 2


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD & Auxin 2hr replicate1

description: Replicate 1


title: ChIP-seq-delS2-L1-H3K27ac-rep1

value: Mammary gland


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD 2hr replicate3

description: Replicate 3

value: ActinomycinD


title: st5_H4K16ac_rep1


title: st5_H4K16ac_rep2


title: st5_Input_rep5


title: st5_H4K16ac_rep3


title: st5_H4K16ac_rep4


title: st5_Input_rep4


title: ChIP-seq-delS2-L1-STAT5A-rep2

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: Ovary_PND46_20_rep1

source_name: Ovary RNA, 46 days, 20 mg/kg/day, replicate 1

value: BFR mixture

tag: dose

tag: gender

value: Ovary

value: 46 days


title: Ovary_PND46_0.06_rep1

source_name: Ovary RNA, 46 days, 0.06 mg/kg/day, replicate 1

value: Female


title: Ovary_PND46_0.06_rep3

source_name: Ovary RNA, 46 days, 0.06 mg/kg/day, replicate 3


title: Ovary_PND46_0_rep2

source_name: Ovary RNA, 46 days, 0 mg/kg/day, replicate 2

value: 0 mg/kg/day


title: Ovary_PND46_0.06_rep2

source_name: Ovary RNA, 46 days, 0.06 mg/kg/day, replicate 2


title: Ovary_PND46_0_rep4

source_name: Ovary RNA, 46 days, 0 mg/kg/day, replicate 4


title: Ovary_PND46_0_rep5

source_name: Ovary RNA, 46 days, 0 mg/kg/day, replicate 5


title: st5_Input_rep3


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD 2hr replicate2

description: Replicate 2

tag: genotype

value: AID-NeonGreen-TPR


title: Ovary_PND46_0_rep3

source_name: Ovary RNA, 46 days, 0 mg/kg/day, replicate 3

tag: tissue


title: ChIP-seq-delS2-L1-STAT5A-rep1


title: DLD-1 cells transfected with AID-NeonGreen-TPR ActinomycinD 2hr replicate1

description: Replicate 1

tag: agent


title: st5_Input_rep2


title: DLD-1 cells transfected with AID-HA-GANP1 replicate3

description: Replicate 3


title: LM-PCR, Sample 4

city: Stanford

first: Mark

middle: A

last: Kay

address: 269 Campus Drive

institute: Stanford University

description:
Demultiplex as described in README.txt
provirus_sites_w_abundance.txt

data_processing:
For ligation-mediated PCR, BBMap v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence. BBMap BBDuk was used to filter out reads for which there was amplification into the provirus from the 5' LTR and trim overlapping reads of primer read-through. BBMap demuxbyname was used to complete demultiplexing of technical replicates using the Read 1 linker-unique sequences, allowing for a hamming distance of 3. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 2500, filtering for uniquely mapped and properly matched read pairs. UMI-tools dedup was used to deduplicate aligned reads using the --ignore-umi flag. For each read pair, we required that they maintain the correct predicted orientation: the LTR junction read is ?upstream? of the breakpoint read if aligned to the + strand, or "downstream" if aligned to the - strand. Read 2 LTR junction positions were clustered within 20bp to generate a set of consensus junctions. Clonal abundance was computed as the depth-normalized number of unique breakpoints for each junction after clustering breakpoint positions within 5bp, scaled to the maximum number of breakpoints in any sample. We required that consensus sites be recovered in both technical replicates associated with a biological replicate and have at least two unique breakpoints to be accepted. A set of population-wide consensus sites was generated by repeating junction clustering across all technical replicates.
For inverse PCR, BBTools v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence and extract barcodes. In Read 1, barcodes were extracted while discarding all remaining sequence up to the reconstituted AseI/NdeI restriction site (excluding the last two, non-consensus bases). BBTools BBDuk was then used to filter out reads for which there was amplification into the provirus from the 3' LTR and trim primer read-through. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 3850, filtering for uniquely mapped and properly matched read pairs. Consensus sites were generated by clustering Read 2 LTR junction positions within 20bp and technical replicates were subsequently merged. Inverse PCR consensus sites were mapped back to provirus consensus sites, requiring that iPCR and LM-PCR LTR junctions be mapped to opposite strands and overlap at their LTR junction positions by not more than 10bp using bedtools v2.28.0 intersect.
Processing of normalization (DNA barcodes) and expression (RNA barcodes) reads were carried out in an identical manner. Forward and reverse reads were merged using BBTools v38.60 BBMerge while filtering low quality reads and error-correcting overlapping regions. UMI-toolsv1.0.0 extract was used to extract barcodes. Unique barcodes were collapsed and counted.
The set of accepted barcodes were those that had at least five normalization reads in both of a pair of technical replicates, and two mapping reads at a single site by inverse PCR. A barcode was definitively assigned to a site if at least 90% of the total reads for that barcode mapped to the site, with fewer than 2.5% mapping to a secondary locus.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: provirus_sites_w_abundance.txt: Provirus sites and number of unique breakpoints for each from LM-PCR sequencing
Supplementary_files_format_and_content: barcodes_norm_expr_raw_counts.txt: Raw normalization and expression counts for each mapped barcode
Supplementary_files_format_and_content: mapped_barcodes.txt: Genomic locations of mapped barcodes
Supplementary_files_format_and_content: README.txt: Python regex and sequences for genomic DNA extraction, barcode extraction, and demultiplexing of LM-PCR data

source_name: HAP1 cells

growth_protocol: HAP1 cells infected with a lentivirus-encoded dual Tet-ON expression system and targeted with barcoded AAV library were grown in complete IMDM supplemented with 7ug/mL blasticidin S-hydrochloride.

extract_protocol:
Genomic DNA was extracted from frozen cell pellets of 12e6 cells using the GeneJET Genomic DNA Purification Kit in two technical replicates for every biological replicate.   Total RNA was extracted using the Monarch Total RNA MiniPrep kit from samples frozen in 1X Protection Buffer, including in-column DNase I treatment, in two technical replicates for every biological replicate. 2ug of RNA was reverse transcribed with RNase H treatment in a 21ul reaction using the Superscript III First Strand cDNA Synthesis Kit with oligo(dT) primers.
Ligation-mediated PCR (LM-PCR) to map provirus sites was performed as previously described (Sherman et al., Mol Ther Methods Clin Dev, 2016; PMID: 28344990) except that 5 cycles of linear amplification plus 7 cycles of exponential amplification were used in the second round of PCR and primers were adapted to standard Illumina sequencing primers. Samples with different indexes were pooled together and sequenced on an Illumina MiSeq using 2x300bp paired-end reads.
For inverse PCR to map integrated barcodes, 4ug genomic DNA was digested in a 200ul reaction with 1X NEB Buffer 3.1, 134U AseI (NEB), and 134U NdeI (NEB). Digests were purified through a Monarch PCR & DNA Cleanup Kit column. 3 x 600ng purified digested DNA was self-ligated with 2800U high concentration T4 DNA Ligase (NEB) and incubated at 4ºC overnight in a volume of 400ul. Final PCR template was obtained by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. DNA pellets were dissolved in 30ul water and 5ul of each sample was used as template to amplify fragments containing both an integrated barcode and genomic DNA adjacent to the 5? LTR of the corresponding provirus site. iPCR was performed over two rounds in 12 independent reactions, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of second round PCR products were pooled and cleaned up using 0.8X Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina NextSeq 500 using 2x150bp paired-end reads.
PCR to measure normalized barcode expression was performed over two rounds in 10 independent reactions using 100ng genomic DNA or 1.68ul cDNA, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of the second round PCR products were pooled and cleaned up using 1.2X (normalization) or 1X (expression) Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina HiSeq4000 using 2x100bp paired-end reads.

treatment_protocol: Expression samples were treated with either 100ng/mL or 0ng/mL doxycycline prior to extraction.

tag: target site

value: Doxycycline-inducible provirus


title: st5_Input_rep1

value: w- OR


title: LM-PCR, Sample 3


title: ChIP-seq-delS1-L1-H3K27ac-rep2

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq-delS1-L1-H3K27ac-rep1


title: LM-PCR, Sample 2


title: ChIP-seq-delS1-L1-STAT5A-rep2


title: ChIP-seq-delS1-L1-STAT5A-rep1


title: st3-4_Input_rep2

source_name: preblastoderm embryos nc9-13

value: preblastoderm embryos nc9-13

value: Mnase-ChIP-seq


title: LM-PCR, Sample 1


title: DLD-1 cells transfected with AID-HA-GANP1 and treated with Auxin for 3hr replicate3

description: Replicate 3

value: Auxin


title: DLD-1 cells transfected with AID-HA-GANP1 and treated with Auxin for 3hr replicate2

description: Replicate 2


title: ChIP-seq-WT-p6-H3K27ac-rep2

value: wild-type

value: Pregnancy day 6


title: DLD-1 cells transfected with AID-HA-GANP1 and treated with Auxin for 3hr replicate1

description: Replicate 1


title: st3-4_H4K16ac_rep2

value: anti-H4K16ac(Merck Milipore, 07-329)


title: Ovary_PND46_0_rep1

source_name: Ovary RNA, 46 days, 0 mg/kg/day, replicate 1


title: ChIP-seq-WT-L1-H3K4me3-rep3

value: Lactation day 1

value: Mammary gland

value: H3K4me3 (Millipore, 17-614)


title: DLD-1 cells transfected with AID-FLAG-NXF1 replicate3

description: Replicate 3


title: DLD-1 cells transfected with AID-HA-GANP1 replicate1

description: Replicate 1


title: ChIP-seq-WT-L1-H3K4me3-rep2


title: st3-4_Input_rep3


title: DLD-1 cells transfected with AID-HA-GANP1 replicate2

description: Replicate 2


title: DLD-1 cells transfected with AID-FLAG-NXF1 replicate2

description: Replicate 2


title: Neg control PAO1 rep 4

city: Leuven

first: Cedric

last: Lood

address: Kasteelpark Arenberg 20 - box 2460

department: Division of Animal and Human Health Engineering

country: Belgium

institute: KU Leuven

data_processing:
Raw reads quality control performed with trimmomatic, seqtk, and fastqc
Alignment to reference genome using TopHat2 with stranded (filename includes .str) and non-stranded depending on sample
Read counts using HTSeq-count
Normalization of counts within the triplicates of a given condition using TPM
Host DGE comparing late infection with no infection was performed as described in Blasdel et al. 2018 (Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer)
Genome_build: Pseudomonas aeruginosa PAO1 with accession number NC_002516.2, and PA5oct denovo assembled genome (see related publication)
Supplementary_files_format_and_content: Phage PA5oct count tables and normalization in xlsx format, host DGE count tables and normalization in xlsx format

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1 growing exponentially in LB

growth_protocol: LB exponential growth

extract_protocol:
Organic extraction
truseq stranded mRNA

treatment_protocol: Viral infection as described in Blasdel et al. 2018, Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer

tag: infection time

value: 0 min


title: st3-4_H4K16ac_rep1


title: ChIP-seq-WT-L1-H3K4me3-rep1


title: st3-4_H4K16ac_rep3


title: ChIP-seq-WT-L1-NFIB-rep2

value: NFIB (Santa Cruz Biotechnology, sc-5567)


title: st3-4_Input_rep1


title: ChIP-seq-WT-p6-H3K27ac-rep1


title: DLD-1 cells transfected with AID-FLAG-NXF1 and treated with Auxin for 2hr replicate3

description: Replicate 3

source_name: DLD-1 cells


title: Neg control PAO1 rep 2


title: Neg control PAO1 rep 1


title: DLD-1 cells transfected with AID-FLAG-NXF1 and treated with Auxin for 2hr replicate2

description: Replicate 2


title: DLD-1 cells transfected with AID-FLAG-NXF1 and treated with Auxin for 2hr replicate1

description: Replicate 1


title: DLD-1 cells transfected with AID-FLAG-NXF1 replicate1

description: Replicate 1


title: Hs-578T cells - MEK5DD rep1

city: New Orleans

first: Matthew

last: Burow

state: Louisiana

address: 1430 Tulane Ave

institute: Tulane University School of Medicine

description:
GSF1149-Burow-RNA11_S11
Hs-578T-MEK5DD_p8_11

data_processing:
Demultiplexing of the reads was performed with bcl2fastq
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17.  Reads were further trimmed for partial adapters using custom perl scripts.
Reads were mapped to GRCh38 using Tophat2 (version 2.1.1)
Mapped reads were counted using custom perl scripts with Gencode v23 as the reference annotation.
R (version 3.3.1) and DESeq2 (version 1.12.4) were used to perform differential expresison analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file of RPKM values for each Sample

extract_protocol: When cells were 70% confluent, RNA was harvested from the breast cancer cells using the RNAEasy kit (Qiagen). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.

tag: cell type

value: triple negative breast cancer cells

tag: treatment


title: Neg control PAO1 rep 3


title: Pdk3_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC .
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides.  Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl rat genome version rn6 (version 94) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.26.0. Only genes with a minimum fold change of +- 2 (log2 = +-1), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: rn6
Supplementary_files_format_and_content: library size normalized counts

source_name: neonatal cardiomyocytes

growth_protocol: Cardiomyocytes were cultured in DMEM/F12 (Gibco) supplemented with 5% horse serum, L-glutamine, Na-pyruvate, penicillin and streptomycin at 37 °C and 5% CO2

extract_protocol:
For RNA-seq analysis, total RNA was isolated from rat neonatal cardiomyocytes using the miRNeasy Mini Kit (Qiagen).
1µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

treatment_protocol: Cardiomyocytes were transfected with adenovirus vectors encoding mock (control) or Pdk3

value: neonatal cardiomyocytes

tag: developmental stage

tag: transfection


title: 50 nM, replicate 2

city: Marburg

first: Victor

last: Sourjik

state: Hessen

address: Karl-von-Frisch-Straße 10

department: Systems and Synthetic Microbiology

institute: Max Planc Institute for Terrestrial Microbiology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated. The number of reads falling in the gene of this meta-transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: SacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Saccharomyces cerevisiae

source_name: haploid yeast mating type MATa

growth_protocol: Strain yAA95 was grown in a glass-flask at 30°C and 200 rpm shaking with SD medium composed of yeast nitrogen base (YNB, Formedium) with complete supplement mix (CSM, Formedium) and 2% glucose.

extract_protocol:
Frozen cell pellets were re-suspended in 500 µl ProtK buffer (100 mM Tris/Cl pH 7.9, 150 mM NaCl, 25 mM EDTA, 1% SDS) with freshly added 100 µg/ml Proteinase K (ThermoFisher). 500 µl glass beads were added and cells were disrupted by strong vortexing for 5 minutes. The resulting lysate-glass bead mixture was incubated for 60 minutes at 37°C. The RNA was isolated by 25:24:1 aqua-phenol:chloroform:isoamyl alcohol (Carl Roth) extraction followed by a chloroform extraction and precipitated with ethanol. The RNA pellet was washed once with 75% ethanol, re-suspended in water and treated with RNase-free DNaseI (Roche Life Science) according to the manufacturer’s protocol. Prior to library construction, the RNA was depleted of ribosomal RNAs with the Ribo-Zero Gold rRNA Removal Kit (Illumina) and reverse-transcribed with random hexamers
Multiplexed library preparation of total RNA and deep sequencing with IlluminaHiSeq 2000 technology with a read length of 50 bases was performed at EMBL gene core facility (Heidelberg, Germany).
Directional RNA-Seq

treatment_protocol: At mid-exponential phase (OD600 approximately 0.5), pheromone stimulation was initiated by transferring aliquots of the cell suspension into separate flasks with prepared stock solutions of synthetic alpha-pheromone (Sigma). After incubation for 60 minutes cells were harvested by transferring 5 ml of suspension into 15-ml tubes containing 5 ml ice and mixed to immediately cool down the suspension. Further steps were carried out on ice or at 4°C. After centrifugation and removal of supernatant, cell pellets were re-suspended in ice-cold water and transferred to 2-ml Eppendorf tubes. After another centrifugation step the supernatant was carefully removed and the cell pellets were stored at -20°C until further processing.

tag: strain

value: yAA95 (ura3::pAA35(PFUS1-Ubi(I)-sfGFP-TFUS1 :URA3) bar1delta::kanMX6 mfalpha1delta::SpHIS3 mfalpha2delta::hphNT1 arg4delta::klTRP1)

value: alpha-pheromone, 50 nM

tag: time

value: 60 min

tag: replicate


title: Hs-578T cells - ERK5ko rep2

description:
GSF1149-Burow-RNA10_S10
Hs-578T-ERK5-ko_p9_10


title: 20 nM, replicate 2

value: alpha-pheromone, 20 nM


title: ChIP-seq-WT-L1-NFIB-rep1

tag: strain/background

tag: genotype/variation

tag: Stage

tag: chip-antibody


title: Pdk3_1


title: Hs-578T cells - ERK5ko rep1

description:
GSF1149-Burow-RNA9_S9
Hs-578T-ERK5-ko_p8_9

tag: cell line


title: 10 nM, replicate 2

value: alpha-pheromone, 10 nM


title: Mock_2

value: Mock


title: 5 nM, replicate 2

value: alpha-pheromone, 5 nM


title: Hs-578T cells - MEK5DD rep2

description:
GSF1149-Burow-RNA12_S12
Hs-578T-MEK5DD_p9_12


title: 500 nM, replicate 2

value: alpha-pheromone, 500 nM


title: Hybrid_verbena_rep_3

city: Sesto Fiorentino

first: Giovanni

last: Bacci

state: FI

address: via Madonna del Piano, 6

department: Department of Biology

country: Italy

institute: University of Florence

description:
overall_collapsed.tsv
Hybrid_raw_counts.tsv

data_processing:
Basecalls and demultiplexing performed using bcl2fastq2 version 2.20
Trimming performed using StreamingTrim algorithm version 1.0 (with a quality threshold of 20)
Reads quantification with SALMON version 1.1
Normalization and analyses conducted using DESeq2 version 1.18
Genome_build: ASM696v1 (Sinorhizobium meliloti 1021); ASM34606v1 (Sinorhizobium meliloti 2011); ASM14779v3 (Sinorhizobium meliloti AK83)
Supplementary_files_format_and_content: Stats file generated by bcl2fastq2; raw count files are tab separated matrices reporting SALMON quantification

organism: Sinorhizobium meliloti

source_name: Bacterial culture

growth_protocol: Overnight cultures of S. meliloti, grown in M9-succinate medium at 30°C at 130 rpm were diluted to an OD600 of 0.05 in 5 ml of M9-succinate and incubated untill an OD of 0.4 was reached.

extract_protocol:
After incubation, cells were blocked with RNAprotect Bacteria (Qiagen) and total RNA was extracted using RNeasy Mini kits (Qiagen) from 0.5 ml of culture following the manufacturer’s instructions, including on column DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 uM of luteolin or one of the three alfalfa root exudates normalised to the total organic carbon present was added to each of the cultures and incubated for additiona 4 hours at 30°C with shaling at 130 rpm.

value: verbena root exudate


title: 1 nM, replicate 2

value: alpha-pheromone, 1 nM


title: Primary T Transfected rep3

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

institute: Villanova University

description: Processed Data Primary FPKM Trans 3

data_processing: Data processed using Excel, raw data normalized for FPKM and synthesized using vLookup function.

source_name: Primary T Lymphocyte

growth_protocol:
Jurkat and PC-3 cells, grown using RPMI 1640 media supplemented with 10% FBS and 1% P/S and passaged every 2 days (Jurkats) or 2-5 days (PC-3).
Primary T cells from healthy donors were purchased from Astarte Biologics and grown in X-VIVO™ 15 media following the manufacturer’s protocol for Human T Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific #11131D) of a 1:1 ratio of beads to cells. The culture media was also supplemented with IL-2 at 1 ng/µL to stimulate T cell growth.  Beads were replaced every 7-10 days during passaging, while IL-2 was added every 2-3 days.  Transfections of primary T cells followed the protocol that was optimized for the Jurkat T cells, with 2.75 uL Lipofectamine per 1 ug of pDNA in a 24-well plate.

extract_protocol:
Small sample of cells evaluated using flow cytometry for transfection efficiency at 24 hours post-transfection, and then the remaining sample was lysed and extracted according to the Qiagen RNeasy kit instructions.
Samples sent off for sequencing with BGI for mRNA sequencing.

treatment_protocol: Human T lymphocyte leukemia cells (Jurkat, clone E6-1, ATCC® TIB-152TM) were seeded in 24 well plates at a density of 2x10^5 cells/well in fetal bovine serum-containing Opti-MEMTM Reduced Serum Medium without phenol red(ThermoFisher Scientific Inc., Waltham, MA) immediately prior to transfection. Transfections with Lipofectamine® LTX were performed according to the manufacturer’s protocol using Lipofectamine LTX, Plus Reagent, and pEF-GFP. 2.75 µl Lipofectamine LTX, 1 µl Plus, and 1 µg pEF-GFP per 200,000 cell well for Jurkats and primary T cells, 1 µl Lipofectamine LTX, 0.5 µl Plus, and 500 ng pEF-GFP per 50,000 cell well for PC-3 cells.

value: Primary T Lymphocyte

value: pEF-GFP


title: MDA-MB-231 cells - ERK5ko rep2

description:
GSF1149-Burow-RNA4_S4
MDA-MB-231-ERK5-ko_p8_4


title: 0.25 nM, replicate 2

value: alpha-pheromone, 0.25 nM


title: PDX-3936

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2) (Lipson et al., J Comput Biol. 2006 Mar;13(2):215-28). The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: ER- PR- HER2- PDX

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols (Ruiz, C., et al., Proc Natl Acad Sci U S A, 2011. 108(29): p. 12054-9). All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Fresh tumor samples from xenografts were flash-frozen and maintaned at -80 degrees C.

extract_protocol: Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Ruiz et al, 2011). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

tag: tissue source

value: Patient derived xenograft

tag: tissue type

value: frozen tissue

tag: flow sort content

value: human tumor

source_name: Reference pooled 46XX

value: Normal female genome


title: 0 nM, replicate 2

value: yAA95 (ura3::pAA35(PFUS1-Ubi(I)-sfGFP-TFUS1 :URA3) bar1delta::kanMX6 mfalpha1delta::SpHIS3 mfalpha2delta::hphNT1 arg4delta::klTRP1)

value: untreated


title: PDX-3143

tag: tissue


title: Hybrid_verbena_rep_1


title: Mock_1

value: neonatal cardiomyocytes


title: Primary T Transfected rep2

description: Processed Data Primary FPKM Trans 2


title: MDA-MB-231 cells - ERK5ko rep1

description:
GSF1149-Burow-RNA3_S3
MDA-MB-231-ERK5-ko_p7_3

value: triple negative breast cancer cells


title: Hybrid_verbena_rep_2


title: MDA-MB-231 cells - MEK5DD rep1

description:
GSF1149-Burow-RNA5_S5
MDA-MB-231-MEK5DD_p10_5


title: PDX-3613

source_name: ER- PR- HER2+ PDX


title: Primary T Transfected rep1

description: Processed Data Primary FPKM Trans 1


title: 0.05 nm, replicate 2

value: alpha-pheromone, 0.05 nm

value: 60 min


title: 500 nM, replicate 1


title: PDX-0002


title: MDA-MB-231 cells -  parental control rep2

description:
GSF1149-Burow-RNA2_S2
MDA-MB-231_p30_2

source_name: MDA-MB-231_parental control

value: parental control


title: Hs-578T cells-  parental control rep2

description:
GSF1149-Burow-RNA8_S8
Hs-578T_p84_8

source_name: Hs-578T_parental control


title: Hybrid_luteolin_rep_2

value: luteolin


title: 100 nM, replicate 1

value: alpha-pheromone, 100 nM


title: MDA-MB-231 cells -  parental control rep1

description:
GSF1149-Burow-RNA1_S1
MDA-MB-231_p29_1


title: Hybrid_luteolin_rep_1


title: Primary T Untransfected rep1

description: Processed Data Primary FPKM Control 1

value: No plasmid


title: PDX-3277

source_name: ER+ PR+ HER2- PDX


title: Primary T Untransfected rep2

description: Processed Data Primary FPKM Control 2

value: Primary T Lymphocyte


title: 50 nM, replicate 1

value: alpha-pheromone, 50 nM


title: Hybrid_lodi_rep_1

value: lodi root exudate


title: Jurkat Transfected rep3

description: Processed Data Jurkat FPKM T3

source_name: Acute T Cell Leukemia

value: Jurkat E6-1

value: pEF-GFP


title: Primary T Untransfected rep3

description: Processed Data Primary FPKM Control 3


title: Hybrid_lodi_rep_3


title: 10 nM, replicate 1

value: alpha-pheromone, 10 nM


title: 15 nM, replicate 1

value: alpha-pheromone, 15 nM


title: PDX-4272

value: Patient derived xenograft

value: frozen tissue

value: human tumor

value: Normal female genome


title: Hybrid_lodi_rep_2


title: Jurkat Transfected rep2

description: Processed Data Jurkat FPKM T2


title: PDX-4849


title: Hybrid_camporegio_rep_3

value: camporegio root exudate


title: 20 nM, replicate 1

value: yAA95 (ura3::pAA35(PFUS1-Ubi(I)-sfGFP-TFUS1 :URA3) bar1delta::kanMX6 mfalpha1delta::SpHIS3 mfalpha2delta::hphNT1 arg4delta::klTRP1)

value: alpha-pheromone, 20 nM

value: 60 min


title: 5 nM, replicate 1

value: alpha-pheromone, 5 nM


title: D2S7.122916

city: Boston

first: Fenna

middle: Marie

last: Krienen

state: MA

address: 77 Ave Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

description:
single-nucleus gene expression data based on 3' transcript counts
adHumInt.raw.dge.txt.gz

data_processing:
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts

source_name: Human Postmortem Brain

extract_protocol:
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)

tag: platform

value: Dropseq

value: Neocortex; Temporal lobe


title: PDX-2277


title: PDX-2147


title: Jurkat Untransfected rep3

description: Processed Data Jurkat FPKM C3

value: No plasmid


title: 1 nM, replicate 1

value: alpha-pheromone, 1 nM


title: PDX-2665


title: D2S1.122216

value: Neocortex; PFC


title: Jurkat Untransfected rep2

description: Processed Data Jurkat FPKM C2

value: Jurkat E6-1


title: D2S2.122216

value: Neocortex; V1


title: PC-3 Transfected rep2

description: Processed Data PC3 FPKM T2_FPKM

source_name: Prostate Cancer Cells

value: pEF-GFP


title: Jurkat Transfected rep1

description: Processed Data Jurkat FPKM T1


title: D1S7.030717.pool1


title: Hybrid_camporegio_rep_1


title: D1S7.030717.pool2


title: BI006_marm028_Munchkin_Put_rxn2

description:
single-nucleus gene expression data based on 3' transcript counts
marm.str.int.10X.raw.dge.txt.gz

organism: Callithrix jacchus

source_name: Adult Marmoset Brain

value: Striatum; Putamen


title: BL225C_verbena_rep_2

description:
overall_collapsed.tsv
BL225C_raw_counts.tsv

value: verbena root exudate


title: Hybrid_blank_rep_2

value: no treatment


title: Jurkat Untransfected rep1

description: Processed Data Jurkat FPKM C1


title: PC-3 Transfected rep3

description: Processed Data PC3 FPKM T3_FPKM


title: Hybrid_blank_rep_1


title: BL225C_verbena_rep_1


title: PC-3 Transfected rep1

description: Processed Data PC3 FPKM T1_FPKM


title: BI006_marm028_Munchkin_caud_rxn2

value: Striatum; Caudate


title: D1S2.121616.2B


title: D1S2.121616.2C


title: Hybrid_camporegio_rep_2

value: camporegio root exudate


title: BL225C_luteolin_rep_3

value: luteolin


title: 0 nM, replicate 1

value: yAA95 (ura3::pAA35(PFUS1-Ubi(I)-sfGFP-TFUS1 :URA3) bar1delta::kanMX6 mfalpha1delta::SpHIS3 mfalpha2delta::hphNT1 arg4delta::klTRP1)

value: untreated


title: PC-3 Untransfected rep3

description: Processed Data PC3 FPKM C3_FPKM


title: BL225C_luteolin_rep_2


title: BI006_marm028_Munchkin_Put_rxn1


title: D1S2.121616.2A


title: BI006_marm028_Munchkin_NACC_rxn1

value: Striatum; Nucleus accumbens


title: D1S2.121616.1

value: Dropseq


title: PC-3 Untransfected rep2

description: Processed Data PC3 FPKM C2_FPKM


title: BL225C_lodi_rep_3

value: lodi root exudate


title: BL225C_luteolin_rep_1


title: BI006_marm028_Munchkin_NACC_rxn2


title: PC-3 Untransfected rep1

description: Processed Data PC3 FPKM C1_FPKM

value: No plasmid


title: BL225C_lodi_rep_2


title: D1S2.122316.BB


title: WI-38 siG3BP1D8B

first: Amr

last: Omer

state: QUEBEC

address: 3655, Promenade Sir-William-Osler

department: Biochemistry

data_processing:
RNA quantity and quality was assessed using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), and a Bioanalyser (Agilent Technology Inc).
The 4 RNA-seq libraries were sequenced on the Illumina NextSeq 500 platform. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the reference mouse genome version mm10 (GRCm38) using Tophat version 2.0.10.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression , either in TPM or FPKM values
DESeq2 version 1.22.1 was then used to normalize gene readcounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include Log2FoldChange, Log10pvalue, IfcMLE, IfcSE and padj values for each group (Control/muHuR-KO)

source_name: WI-38 Cells

growth_protocol: WI-38 Cells were grown in EMEM to 70% confluence and induced to senescence using 10 Gy irradiation. After 8 days cells were harvested.

extract_protocol:
Total RNA from cell extracts was isolated using TRIzo reagent (Invitrogen) according to the manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA treatment was accomplished using JetPrime as per manufacturers protocol. siRNA specific for G3BP1 (exon 4) (5'-UCAACAUGGCGAAUCUUGGTG-3'; siRNA ID # 126650) was obtained from Ambion. Control siRNA was obtained from Dharmacon (5'-AAGCCAAUUCAUCAGCAAUGG-3').

tag: cell type

value: Senescent Embryonic Lung Fibroblasts

tag: knockdown

value: G3BP1 siRNA


title: BI005_marm027_Spencer_NACC_rxn1


title: HS90d_1

city: Yangzhou

first: Jiasong

last: Meng

address: 48 east wenhui road

department: College of horticulture and  plant protection

institute: Yangzhou University

data_processing:
the NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
The de novo assembly with clean reads were performed using Trinity software to generate transcripts, which were further clustered by Tgicl to obtain non-redundant unigenes.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the  unigene and reads count mapped to this gene.
Genome_build: All-Unigene.fa
Supplementary_files_format_and_content: Text file includes HS_seeds at 30-60-90DAF_FPKM (Gene_id, HS30d_1_FPKM, HS30d_2_FPKM, HS30d_3_FPKM, HS60d_1_FPKM, HS60d_2_FPKM, HS60d_3_FPKM, HS90d_1_FPKM, HS90d_2_FPKM, HS90d_3_FPKM). The .fa file includes the assembled sequences of all transcripts.

organism: Paeonia lactiflora

source_name: seeds of 90 days after flower (90 DAF)

growth_protocol: Seeds of herbaceous peony 'Hangshao' were collected in peony germplasm resource garden of Yangzhou University, China (32°39′N, 119°42′E). It had been introduced to the garden and grown in the same eco-environmental and cultivation conditions for eight years. Due to the limited fruit and low oil extraction rate at early stage, the follicle were hand-collected in the 30 days after flowering (DAF) for the first time and at intervals of 15 days until full maturity (including 30, 45, 60, 75 and 90 DAF). Seeds used for tanscriptome sequencing were collected from the same strain at developing stages for 30, 60 and 90 DAF.

extract_protocol:
Nine seed samples from three stage (30, 60 and 90 DAF, with three biological replicates) were snap-frozen in liquid nitrogen and ground to a fine powder. Total RNA samples were extracted through Total RNA Isolation System (Takara, Japan) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Hangshao

value: seeds

tag: age

value: 90 days after flower (90 DAF)


title: marm023_V2_NewRef

description:
single-nucleus gene expression data based on 3' transcript counts
marm.ctx.int.DS.raw.dge.txt.gz

value: Neocortex; V2


title: WI-38 siCTLD8B

value: Scrambled Control


title: HS90d_2


title: HS90d_3


title: WI-38 siG3BP1D8A


title: Hybrid_luteolin_rep_3

tag: strain

tag: treatment


title: FFPE tumor tissue of renal leiomyosarcoma from Female

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

hyb_protocol: Hybridization was performed using CytoScan™ HD Array Kit according to the manufacturer's protocol. GeneChip was washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip was scanned using the GeneChip™ Scanner 3000 7G.

data_processing:
Computational analysis of the microarray data files was performed using Chromosome Analysis Suite software (Affymetrix).
cychp files are containing results from Chromosome Analysis Suite

label: biotin

source_name: FFPE tumor tissue, kidney

label_protocol: Labeling was performed by using CytoScan™ HD Array Kit according to the manufacturer's protocol.  Labeling was performed by using CytoScan™ HD Array Kit according to the manufacturer's protocol.

extract_protocol: Genomic DNA was extracted from the formalin-fixed, paraffin-embedded tumor tissue by using GeneRead DNA FFPE kit (Qiagen).The isolated DNA sample were stored at -20°C.

tag: Sex

value: Female

tag: status

value: deceased

value: FFPE tumor tissue, kidney


title: HS60d_3

source_name: seeds of 60 days after flower (60 DAF)

value: 60 days after flower (60 DAF)


title: BL225C_camporegio_rep_3

value: camporegio root exudate


title: marm023_Temp_merged

value: Neocortex; Temporal lobe


title: WI-38 siCTLD8A


title: HS60d_2


title: BL225C_camporegio_rep_2


title: marm023_S1_merged

value: Neocortex; S1


title: BI005_marm027_Spencer_NACC_rxn2

value: Striatum; Nucleus accumbens


title: BL225C_camporegio_rep_1


title: BL225C_lodi_rep_1

value: lodi root exudate


title: HS60d_1


title: marm023_Par_merged

value: Dropseq

value: Neocortex; Parietal Cortex


title: 40 nM SOP1812_24 h MIA PaCa2 cell line Rep3

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

description:
MIA PaCa2 cell line Rep3
0

data_processing:
Illumina run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software (v2.19).
Fastq files were pre-processed to remove adapter contamination and poor quality sequences using the program Trimmomatic (v0.36)
Duplication levels were estimated using JE-Suite50
Reads per transcript were counted using the program FeatureCounts51 (v1.4.6p5)
Genome_build: Mapped to a recent human genome build (UCSC hg38: https://genome.ucsc.edu/) using the RNA-seq alignment tool STAR (v2.5b: https://github.com/alexdobin/STAR)
Supplementary_files_format_and_content: Excel format, contains differential expression data for 6 h and 24 h SOP1812 exposure

source_name: pancreatic cancer

growth_protocol: MIA PaCa-2 cells were seeded in 100 mm plates (6 h = 2.5 × 10^6 cells/plate and 24 h = 1.0 × 10^6 cells/plate) and incubated overnight.

extract_protocol:
Total RNA was extracted from 2 - 4 x 10^6 cells using the RNeasy mini kit (Qiagen, cat no. 74104) and on-column DNase1 digestion (Qiagen, cat no. 79254)
RNA-seq libraries were generated using the KAPA mRNA Library HyperPrep Kit for Illumina Platforms.

treatment_protocol: Cells were treated with40 nM SOP1812 or vehicle (DMSO) for 6 h and 24 h

tag: source

value: ATCC cell line

value: pancreas ductal adenocarcinoma cell line


title: HS30d_3

source_name: seeds of 30 days after flower (30 DAF)

value: Hangshao

value: seeds

value: 30 days after flower (30 DAF)


title: 40 nM SOP1812_24 h MIA PaCa2 cell line Rep2

description:
MIA PaCa2 cell line Rep2
0


title: BL225C_blank_rep_2

source_name: Bacterial culture

value: no treatment


title: 40 nM SOP1812_24 h MIA PaCa2 cell line Rep1

description:
MIA PaCa2 cell line Rep1
0


title: marm023_A1_merged_corrected

value: Neocortex; A1


title: HS30d_2


title: BL225C_blank_rep_3


title: Hs-578T cells-  parental control rep1

description:
GSF1149-Burow-RNA7_S7
Hs-578T_p83_7

value: triple negative breast cancer cells

value: parental control


title: Untreated/control_24 h MIA PaCa2 cell line Rep3

description:
MIA PaCa2 cell line Rep3
0

value: Untreated/control_24 h


title: BL225C_blank_rep_1


title: AK83_verbena_rep_3

description:
overall_collapsed.tsv
AK83_raw_counts.tsv

value: verbena root exudate


title: MDA-MB-231 cells - MEK5DD rep2

description:
GSF1149-Burow-RNA6_S6
MDA-MB-231-MEK5DD_p11_6


title: marm022_S1_merged_corrected


title: Untreated/control_24 h MIA PaCa2 cell line Rep2

description:
MIA PaCa2 cell line Rep2
0


title: marm022_Par_sl10_pool3_merged


title: Untreated/control_24 h MIA PaCa2 cell line Rep1

description:
MIA PaCa2 cell line Rep1
0


title: AK83_verbena_rep_2


title: Input_st15_controlRNAi_3

data_processing:
ChIP-seq: Data processing was done using the snakePipes pipeline (https://doi.org/10.1093/bioinformatics/btz436). The DNA-mapping followed by the ChIP-seq pipeline were used. The default parameters were used.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: ChIP-seq: bigwigs log2 to Input, 1x coverage using bamCompare from deepTools, chrX was excluded for scalefactor calculation. Fragments below 140 bp were removed.

source_name: mixed stage 15 embryos

growth_protocol: D. melanogaster flies were maintained in standard Drosophila medium at 25oC.

extract_protocol:
ChIPseq: Dechorionated embryos were fixed using 1% Formaldehyde for 15min at RT. After fixation, they were hand picked for the desired developmental stage and frozen at -80oc until further use. Nuclei were isolated using short covaris sonication followed by chromatin digestion using Micrococcal nuclease and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II

treatment_protocol: Maternal RNAi using mat-a-Gal4 (Bloomington Stock number 7062).

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)

value: mixed stage 15 embryos

tag: technique

value: ChIP-seq

tag: chip antibody


title: marm022_Par_sl10_pool2_merged


title: AK83_verbena_rep_1


title: st15_H3_msl3RNAi_Rep2

description: processed data file: st15_H3_msl3RNAi_log2Input_min140_ext_rep2.bw

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 57261)

value: anti-H3 (Cell Signaling 2650S)


title: marm022_Par_sl10_pool1_merged

value: Dropseq

value: Neocortex; Parietal Cortex


title: 40 nM SOP1812_6 h MIA PaCa2 cell line Rep2

description:
MIA PaCa2 cell line Rep2
0

value: ATCC cell line

value: pancreas ductal adenocarcinoma cell line


title: AK83_luteolin_rep_3

value: luteolin


title: marm022_Temp_sl07_merged

value: Neocortex; Temporal lobe


title: HS30d_1

value: Hangshao

value: seeds

value: 30 days after flower (30 DAF)


title: Untreated/control_6 h MIA PaCa2 cell line Rep3

description:
MIA PaCa2 cell line Rep3
0

value: Untreated/control_6 h


title: 40 nM SOP1812_6 h MIA PaCa2 cell line Rep1

description:
MIA PaCa2 cell line Rep1
0


title: st15_H4K16ac_msl3RNAi_Rep2

description: processed data file: st15_H4K16ac_msl3RNAi_log2Input_min140_ext_rep2.bw

value: anti-H4K16ac (Millipore 07-329)


title: AK83_luteolin_rep_2


title: BI005_marm027_Spencer_Put_rxn2

value: Striatum; Putamen


title: Untreated/control_6 h MIA PaCa2 cell line Rep2

description:
MIA PaCa2 cell line Rep2
0


title: Input_st15_msl3RNAi_2


title: BI006_marm028_Munchkin_Caud_rxn1

value: Striatum; Caudate


title: BI005_marm027_Spencer_Caud_rxn2


title: st15_H4K16ac_controlRNAi_Rep3

description: processed data file: st15_H4K16ac_controlRNAi_log2Input_min140_ext_rep3.bw

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)

value: mixed stage 15 embryos


title: BI005_marm027_Spencer_Put_rxn1


title: AK83_lodi_rep_3

value: lodi root exudate