title: KO_DSS rep2

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

data_processing:
Library strategy: MeRIP-seq
Illumina Casava (1.8) software used for basecalling.
Data were aligned to the mm10 mouse genome assembly using Bowtie (v2.2.5) with the settings ‘--very-sensitive’.
Low quality mapped reads were removed using SAMtools (v1.3.1) with the settings ‘-q 30’.
Use the RNAcentral database to filter known rRNA sequences.
Peaks were called using MACS2 (v2.1.0) with the settings ‘--keep-dup 1 -q 0.05’, and further annotated by HOMER (v4.10)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools (v 3.3.0)

source_name: colon epithelial cell

extract_protocol:
Colons were removed from the sacrificed mice and cut open longitudinally. Feces were removed and mucus was lightly scraped off. Then, the colon tissues were washed with cold PBS three times, cut into small pieces and incubated with PBS supplemented with 5 mM EDTA, 1 mM DTT and 10 μM ROCK inhibitor (Y-27632; MedChemExpress, Monmouth Junction, NJ, USA) at 37℃ for 25 min with gentle shaking. Cell supernatant containing isolated epithelial cells was then centrifuged (500 × g, 5 min), and the pellet was used for total RNA isolation.
Methylated RNA immunoprecipitation(MeRIP) with specific m6A antibody and RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced on an Illumina HiSeq™ 2500 platform with 6G base PE150 reads.

treatment_protocol: 2.5% DSS treatment for 5 days and followed by 2 days normal water, and mice were sacrificed at day7

value: colon

value: Ythdf1 KO

tag: antibody


title: Chronic lymphocytic leukemia 4; from the CLL2O trial [2O_CLL004]

status: Public on May 06 2020

type: genomic

city: London

first: Jennifer

last: Edelmann

address: Charterhouse Square

department: Centre for Haemato-/Oncology

country: United Kingdom

institute: Barts Cancer Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4
affymetrix-array-type = GenomeWideSNP_6
program-name = Genotyping Console
program-version = 3.0.3190.24001
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for all samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 146 CD19-positive fractions, and 91 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: mononuclear cells CD19+

tag: cohort

value: treatment-naïve

tag: tp53 status

value: TP53 aberration

tag: atm status

value: no ATM deletion


title: WT_DSS input rep2

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype

value: WT


title: WT_DSS rep2


title: Chronic lymphocytic leukemia 6; from the CLL2O trial [2O_CLL006up]


title: KO_DSS input rep2


title: KO_DSS rep1


title: Chronic lymphocytic leukemia 3 paired normal; from the CLL2O trial [2O_CLL003pn]

value: mononuclear cells CD19-

value: not annotated


title: WT_DSS input rep1


title: WT_DSS rep1


title: Chronic lymphocytic leukemia 8 paired normal; from the CLL2O trial [2O_CLL008pn]


title: Chronic lymphocytic leukemia 3; from the CLL2O trial [2O_CLL003]

value: relapsed


title: Chronic lymphocytic leukemia 5; from the CLL2O trial [2O_CLL005]


title: KO_DSS input rep1


title: Chronic lymphocytic leukemia 2 paired normal; from the CLL2O trial [2O_CLL002pn]


title: Chronic lymphocytic leukemia 2; from the CLL2O trial [2O_CLL002]


title: Chronic lymphocytic leukemia 1 paired normal; from the CLL2O trial [2O_CLL001pn]


title: BM_LTHSC_RNA-Seq_Rep1

city: PHILADELPHIA

first: Kai

last: Tan

state: PA

address: 3501 CIVIC CENTER BLVD.

country: USA

institute: Children's Hospital of Philadelphia

data_processing:
Sequencing reads were aligned to the mouse genome ( mm9 ) using Tophat. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses.
The Ensembl database (release 66 ) was used as the source of gene annotation. FPKM values were calculated by cufflinks. The featureCounts function of the Subread package was used to extract both gene-level and transcript-level read counts. Differential expression analysis was performed using the edgeR algorithm at gene-level and Ebseq at transcript-level.
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

source_name: 6-8 week-old bone marrow hematopoietic stem cells

extract_protocol:
5 stages of hematopoietic stem and progenitor cells were sorted from mouse embryos or adult bone marrow. Total RNA samples were isolated using Rneazy Micro Kit (Qiagen).
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit for Qubit and the size distribution was assessed using High Sensitivity DNA Kit for Bioanalyzer. Libraries were sequenced on Illumina HiSeq2500 in paired-end mode with the read length of 100 nt.

value: Adult bone marrow

tag: age

value: 6-8 week-old

value: bone marrow hematopoietic stem cells


title: FL_LTHSC_RNA-Seq_Rep1

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

value: Fetal liver

value: Embryonic day 14.5

value: fetal liver hematopoietic stem cells


title: Chronic lymphocytic leukemia 1; from the CLL2O trial [2O_CLL001]


title: FL_LTHSC_RNA-Seq_Rep2


title: PreHSC_RNA-Seq_Rep3

source_name: Embryonic day 10.5 major arteries PreHSC

value: AGM

value: Embryonic day 10.5

value: major arteries PreHSC


title: PreHSC_RNA-Seq_Rep1


title: BM_LTHSC_RNA-Seq_Rep2


title: PreHSC_RNA-Seq_Rep2


title: HE_RNA-Seq_Rep2

source_name: Embryonic day 10.5 major arteries hemogenic endothelium

value: major arteries hemogenic endothelium


title: HMDM M0 rep48

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Base calling was done by RTA v1.18
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp, 2) read was uniquely mapped
Genome_build: hg19
Supplementary_files_format_and_content: macrophage_allele_specific_expression.txt contains allele-specific read counts generated for each ASE SNP in HMDM and M1-polarized HMDM samples.

molecule: polyA RNA

source_name: Macrophage

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected using BD VACUTAINER® CPT™ Cell Preparation Tubes with Sodium Citrate. The freshly isolated PBMC were plated (6-well plates, 3x10^6 cells per well, or 24-well plates, 1x10^6 cells per well) (BD PrimariaTM cell culture plates, BD Biosciences, Bedford, MA), allowed to adhere (overnight), washed with RPMI-1640 and cultured in macrophage culture media (20% FBS in RPMI 1640 media with 100 ng/ml human M-CSF) (300-25, Peprotech, Rocky Hill, NJ) for 7 days to induce macrophage differentiation as we described. (PMID: 25904599, 28882870).

extract_protocol:
RNA samples were extracted using All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 300 ng input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Modification of protocol include (1) fragmentation time is decreased from 8 to 6 min to ensure libraries were > 100 bp long and (2) PCR amplification is limited to 12 cycles. To minimize lane and batch effects in RNA-Seq experiments, barcoded libraries were mixed and pooled in equimolar (2 nmol/L) amounts and diluted to 4 pmol/L for cluster formation on a single flow cell lane, followed by 100 bp paired-end sequencing on Illumina’s HiSeq 2500.

treatment_protocol: Macrophage polarization was obtained by removing culture medium at Day 6 and culturing cells for an additional 18-20 hour in 10% FBS in RPMI 1640 media with 50 ng/ml M-CSF for M0 control as the unstimulated macrophages, or the above media supplemented with 20 ng/ml IFN-gamma (R&D, Minneapolis, MN) and 100 ng/ml lipopolysaccharide (LPS; Sigma-Aldrich, St. Louis, MO) for M1 polarization.

value: PBMC derived macrophage (HMDM)

tag: race

value: Caucasian

tag: Sex

value: Female

tag: disease state

value: Healthy subject


title: HMDM M1 rep46

value: M1-polarized HMDM


title: HMDM M0 rep47


title: sgControl_Trametinib02uM.RNA-seq.rep2

city: stanford city

first: Or

last: Gozani

state: California

address: 371 Serra Mall, Room 208A Stanford, CA 94305-5020

department: Department of Biology

institute: Stanford University

data_processing:
RNA-seq data processing, low-quality and adapter-containing reads were trimmed using trim-galore package under paired-end mode, any reads shorter than 50 bp were removed.
The remaining trimmed sequences were mapped to the reference genome (mm10) with hisat2 (5) under default settings.
We used htseq-count to count the mapped reads number on every mm10 Refseq transcript.
Differential gene expression analysis was performed with DESeq2 software.
Genome_build: mm10
Supplementary_files_format_and_content: txt:reads_counts

source_name: KPCR cells

growth_protocol: Cell lines were established from trametinib-resistant PDAC tumors (hereto referred to as KPCR cells).

extract_protocol:
Total RNA was extracted from KPCR cells (n = 3) (sgControl + Trametinib 0.2µM, sgSETD5 + Trametinib 0.2µM, or DMSO + Trametinib 0.2µM, UNC0638 0.6 µM + RGFP966 0.6µM + Trametinib 0.2µM) using Trizol reagent.
Total RNA was subjected to polyA selection using Dynabeads mRNA purification kit. 20 ng polyA RNA was utilized for library generation using SMARTer Stranded RNA-seq kit.

treatment_protocol: KPCR cells were treated with sgSetD5 or Hdac3 and G9a inhibitor.

value: KPCR cells


title: UNC0638.06uM_RGFP966.06uM_Trametinib02uM.RNA-seq.rep1

tag: treatment

value: Hdac3 and G9a inhibitor


title: sgSetd5_Trametinib02uM.RNA-seq.rep1

value: Setd5 KD


title: sgSetd5_Trametinib02uM.RNA-seq.rep3


title: UNC0638.06uM_RGFP966.06uM_Trametinib02uM.RNA-seq.rep3


title: sgControl_Trametinib02uM.RNA-seq.rep3


title: UNC0638.06uM_RGFP966.06uM_Trametinib02uM.RNA-seq.rep2


title: sgSetd5_Trametinib02uM.RNA-seq.rep2


title: sgControl_Trametinib02uM.RNA-seq.rep1


title: DMSO_Trametinib02uM.RNA-seq.rep3


title: HMDM M1 rep48


title: HE_RNA-Seq_Rep1


title: HMDM M0 rep46


title: DMSO_Trametinib02uM.RNA-seq.rep2


title: Endo_RNA-Seq_Rep2

source_name: Embryonic day 10.5 major arteries endothelium

value: major arteries endothelium


title: DMSO_Trametinib02uM.RNA-seq.rep1


title: HMDM M1 rep47


title: HMDM M0 rep45


title: Smoked_NRF_F1Brain_rep8

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Sequencing data from RNASeq libraries was aligned using Novoalign.
Aligned splice junction were converted to genomic coordinates and low quality and non-unique reads were further parsed using SamTranscriptomeParser (USeq; v8.8.8) under default settings.
Stranded differential expression analysis was calculated with the USeq program DefinedRegionDifferentialSeq, which utilizes DESeq2 and the reference mm10.

source_name: Brain

extract_protocol:
Qiangen AllPrep Universal Kit was utilized to extrad RNA from mouse brains.
RNA extracted from F1 frontal cortices was subjected to Illumina TruSeq Stranded RNA kit with Ribo-Zero Gold library preparation and subsequently sequenced on a Hi-Seq 2500 using 50 Cycle-Single Read Sequencing v4. Eight samples were sequenced per lane for a minimum of 25-million reads per sample.

value: Brain

value: NRF-/-

value: smoked


title: HMDM M1 rep43

value: Male


title: HMDM M0 rep44


title: Smoked_NRF_F1Brain_rep7


title: HMDM M0 rep42


title: Smoked_NRF_F1Brain_rep4


title: HMDM M0 rep43


title: Cycle 18 PER1 BAC

city: Durham

first: Tim

last: Reddy

state: North carolina

address: CIEMAS, Room 2347 101 Science Drive

institute: Duke university

description: BAC DNA

library_source: genomic

data_processing:
FASTQs files were aligned to the human genome reference assembly hg38 with bowtie2 (version 2.3.4.3), using the --sensitive option and requiring a MAPQ of at least 30 and properly paired.
All alignments were deduplicated using Picard (MarkDuplicates, version 2.14.0)
Three replicates for each sample were merged using samtools (version 1.9)
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs with observed read counts were generated with bamCoverage (deeptools, version 3.0.1) and normalized with scalers reported from CRADLE; bigwigs with corrected read counts were generated from CRADLE; We calculated Gibbs free energy measurement based on Gibbs fee energy value reported by Protozanova et al.  (Protozanova E, Yakovchuk P, Frank-Kamenetskii MD: Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol 2004, 342(3):775-785.)

molecule: other

source_name: BAC

extract_protocol: Purified PER1 BAC (CH17-212C17; chr17:7981103-8192310) was harvested from E. coli using standard protocols. Following DNA shearing using the Covaris S2 system, the BAC DNAs were size-selected using solid phase reversible immobilization (SPRI) beads. STARR-seq insert libraries were prepared using the NEBNext DNA Library Prep Master Mix kit and 50 ng of template DNA. Adapted DNAs were enriched in triplicate reactions via 3, 6, 12, or 18 cycles of PCR using the NEB Q5 PCR kit. The resulting libraries were characterized on the Agilent Tape Station prior to 50-cycles of paired-end sequencing on the Illumina MiSeq platform.

tag: bac id

tag: protocol

value: Fragments generated by randoming shearing PER1 BAC library were amplified with 18 PCR cycles


title: Smoked_NRF_F1Brain_rep6


title: HMDM M1 rep42


title: YAMC with IFNγ treatment, biological rep3

type: RNA

city: Chicago

first: Fangyi

last: Liu

state: IL

address: 2430 N Halsted St

department: Center for Intestinal and Liver inflammation Research

institute: Stanley Manne Children's Research Institute

hyb_protocol: Biotin labeled RNA were hibridized overnight with a GeneChip® miRNA 4.0 array cartridge. The protocol provided by Affymetrix was followed.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G . The protocol provided by Affymetrix was followed.

data_processing:
After annotation with the mouse miRNA database 4.0, the expressions of a total of 3196 miRNAs/cartridge were acquired. For each treatment, three biological replicates were performed. A two-fold change with P<0.05 compared to a control was used as the cutoff for differential miRNA expression.
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: YAMC with IFNγ treatment

label_protocol: RNA was labeled with Biotin using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix) using a protocol provided by the manufacturer.

growth_protocol: YAMC cells were maintained in RPMI 1640 medium containing 5% heat-inactivated fetal bovine serum, 5 U/ml mouse IFNγ, 100 unit/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin, and 5 ng/ml selenous acid at 33°C as permissive conditions in a water-saturated atmosphere incubator with 5% CO2. Cells were cultured under non-permissive conditions (IFNγ-free and 37°C) for at least 24 h before IFNγ stimulation.

extract_protocol: Total RNAs were extracted from cells using miRNeasy Mini Kit supplied by Qiagen according to protocol provided by the manufacturer.

treatment_protocol: YAMC cells were treated with 100ng/ml IFNγ at 37℃ for 12h before harvast.

value: Conditionally-immortalized young adult mouse colonocyte (YAMC)

value: 100ng/ml IFNγ for 12 h


title: HMDM M0 rep41


title: Endo_RNA-Seq_Rep1

value: AGM

value: Embryonic day 10.5


title: HMDM M1 rep41

value: Caucasian


title: HMDM M1 rep40


title: Cycle 12 PER1 BAC

description: BAC DNA

value: Fragments generated by randoming shearing PER1 BAC library were amplified with 12 PCR cycles


title: Smoked_NRF_F1Brain_rep2


title: YAMC with IFNγ treatment, biological rep2


title: YAMC w/o IFNγ treatment, biological rep3

source_name: YAMC w/o IFNγ treatment

value: none (control)


title: YAMC w/o IFNγ treatment, biological rep2


title: Cycle 3 PER1 BAC

description: BAC DNA

value: Fragments generated by randoming shearing PER1 BAC library were amplified with 3 PCR cycles


title: HMDM M1 rep45

value: M1-polarized HMDM

value: Female

value: Healthy subject


title: Cycle 6 PER1 BAC

description: BAC DNA

value: Fragments generated by randoming shearing PER1 BAC library were amplified with 6 PCR cycles


title: HMDM M1 rep44


title: YAMC w/o IFNγ treatment, biological rep1


title: YAMC with IFNγ treatment, biological rep1


title: Smoked_NRF_F1Brain_rep3

value: Brain


title: Smoked_NRF_F1Brain_rep5

value: NRF-/-


title: HMDM M0 rep40

value: PBMC derived macrophage (HMDM)


title: HMDM M1 rep39

value: Male


title: Control_NRF_F1Brain_rep6

value: control


title: Control_NRF_F1Brain_rep7


title: HMDM M0 rep39


title: Smoked_NRF_F1Brain_rep1

value: smoked


title: Control_NRF_F1Brain_rep5


title: HMDM M1 rep38


title: Control_NRF_F1Brain_rep4


title: HMDM M0 rep37


title: HMDM M0 rep38


title: HMDM M1 rep37


title: Control_NRF_F1Brain_rep1


title: Control_NRF_F1Brain_rep3


title: Control_NRF_F1Brain_rep8


title: HMDM M1 rep36


title: Control_WT_F1Brain_rep6

value: C57BL/6J wild type


title: HMDM M0 rep36


title: Control_WT_F1Brain_rep5


title: Control_WT_F1Brain_rep4


title: HMDM M0 rep35


title: HMDM M1 rep35


title: Control_WT_F1Brain_rep3


title: DRG neurons, biological replicate 4

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

description: Gene expression data from cultured embryonic sensory (DRG) neurons

hyb_protocol: Affymetrix Rat Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA. Hybridization was performed for 16 hrs at 45oC.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data were analyzed using the oligo package (from Bioconductor) in R. Data were background corrected, normalized with quantile normalization, log-transformed (log2 scale), and summarized into probesets using the Robust Multichip Analysis (RMA) method.

label: biotin

organism: Rattus norvegicus

source_name: DRG culture

label_protocol: cDNA was generated using the Affymetrix WT Plus Kit using 250 ng of total RNA.

growth_protocol: DRGs were harvested from E15 embryos and cultured for 9 days.

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: DRG neurons were purified in culture with treatment of Ara-C. Neurons were grown defined culture media including NGF for 9 days following isolation.

value: Sprague Dawley

value: dorsal root ganglion neurons

tag: developmental stage

value: embryonic


title: Control_NRF_F1Brain_rep2


title: DRG neurons, biological replicate 5


title: HMDM M1 rep34

value: Caucasian


title: HMDM M0 rep34


title: Control_WT_F1Brain_rep1


title: SCG neurons, biological replicate 3

source_name: SCG culture

growth_protocol: SCGs were harvested from P1-2 pups and cultured for 6 days.

treatment_protocol: SCG neurons were purified in culture with treatment of Ara-C. Neurons were grown defined culture media including NGF for 6 days following isolation.

value: superior cervical ganglion neurons


title: HMDM M1 rep33


title: Smoked_WT_F1Brain_rep7


title: DRG neurons, biological replicate 6


title: DRG neurons, biological replicate 2


title: DRG neurons, biological replicate 3


title: SCG neurons, biological replicate 2


title: Smoked_WT_F1Brain_rep6


title: HMDM M0 rep33


title: SCG neurons, biological replicate 4


title: HMDM M1 rep32


title: Smoked_WT_F1Brain_rep5


title: HMDM M0 rep32


title: Control_WT_F1Brain_rep2


title: Smoked_WT_F1Brain_rep4


title: HMDM M1 rep31


title: Smoked_WT_F1Brain_rep3


title: Injured sciatic nerve (7dpi), biological replicate 1

description: Gene expression data from sciatic nerve

source_name: sciatic nerve

extract_protocol: Total RNA was extracted using Trizol followed by the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Treatment (injured) and control (uninjured) sciatic nerves were harvested from young rats. Nerves were frozen in liquid nitrogen prior to storage at -800C. Nerves were then homogenized with a Dounce homogenizer and total RNA was then extracted.

value: sciatic nerve

value: male

value: 6 weeks postnatal

value: Injured sciatic nerve (7dpi)


title: SCG neurons, biological replicate 1


title: Injured sciatic nerve (7dpi), biological replicate 4

description: Gene expression data from sciatic nerve


title: Contralateral control uninjured sciatic nerve (7 dpi), biological replicate 4

description: Gene expression data from sciatic nerve

value: uninjured


title: HMDM M0 rep31

value: Healthy subject


title: Injured sciatic nerve (7dpi), biological replicate 3

description: Gene expression data from sciatic nerve


title: Injured sciatic nerve (7dpi), biological replicate 2

description: Gene expression data from sciatic nerve


title: Smoked_WT_F1Brain_rep2

value: Brain


title: HMDM M1 rep30

value: M1-polarized HMDM

value: Female


title: Contralateral control uninjured sciatic nerve (7 dpi), biological replicate 3

description: Gene expression data from sciatic nerve


title: Smoked_WT_F1Brain_rep1


title: HMDM M0 rep30

value: PBMC derived macrophage (HMDM)


title: HMDM M0 rep29

value: Male


title: Smoked_NRF_F1brain_rep8

data_processing:
For genome wide DNA methylation analysis, sequence data from RRBS libraries was aligned to the mouse mm10 genome using the Bismark pipeline with special attention to RRBS specific issues, as noted in the Bismark User Guide and the Bismark RRBS Guide. Only CpGs where read coverage was greater than 8 for at least 4 biological replicates were considered “scoreable” for downstream analysis. Only CpGs with more than 5% change in methylation relative to control samples were classified as differentially methylated.
When considering DMRs, only regions greater than 50 base-pairs in length with 3 or more scorable CpGs were analyzed. Then, one third of the CpGs within each analyzed region needed to be differentially methylated in order for a given region to be under consideration as a DMR.
Finally, qualifying regions were classified as bonafide DMRs if there was more than 5% change in methylation relative to control samples.
Genome_build: mm10
Supplementary_files_format_and_content: bed format. Score represents the DNAme level of the given genomic loci in a particular sample.

extract_protocol:
Qiangen AllPrep Universal Kit was utilized to extrad DNA from tissues (Sperm or Brain).
Following DNA extraction, Bioo Scientific NEXTflex Bisulfite Library Prep Kit for Illumina Sequencing was used for library preparation. To maximize coverage, we employed two separate restriction digests with MspI and TaqαI. Following digestion, products were pooled, and Klenow Fragment was utilized to create 3’A overhangs. DNA was subsequently purified with Zymo DNA Clean and Concentrate Columns followed by ligation of Methylated Illumina PE Adapters and Ampure purification with SPRI beads. Purified products were Sodium Bisulfite Converted using ZymoResearch EZ DNA Methylation Gold Kit, and libraries were amplified over 20 cycles using Platinum Taq DNA polymerase, followed by a final Ampure purification and confirmation of library size range on a 2% agarose gel.  DNA was submitted to the Huntsman Cancer Institute High Throughput genomic core for sequencing on a Hi-Seq 2500 using 50 cycle-single read chemistry. Four to six samples were sequenced per lane for a minimum of 35-million reads per sample.

value: NRF-/-

tag: tag

value: Smoked


title: Smoked_NRF_F1brain_rep7


title: HMDM M1 rep28


title: Injured sciatic nerve (3dpi), biological replicate 3

description: Gene expression data from sciatic nerve

value: Sprague Dawley

value: Injured sciatic nerve (3dpi)


title: Contralateral control uninjured sciatic nerve (7 dpi), biological replicate 2

description: Gene expression data from sciatic nerve


title: Injured sciatic nerve (3dpi), biological replicate 4

description: Gene expression data from sciatic nerve


title: DRG neurons, biological replicate 1

value: dorsal root ganglion neurons

value: embryonic


title: Smoked_NRF_F1brain_rep4


title: Smoked_NRF_F1brain_rep5


title: Injured sciatic nerve (3dpi), biological replicate 2

description: Gene expression data from sciatic nerve

value: sciatic nerve


title: HMDM M0 rep28

value: Caucasian


title: Smoked_NRF_F1brain_rep3


title: Injured sciatic nerve (3dpi), biological replicate 1

description: Gene expression data from sciatic nerve

value: male

value: 6 weeks postnatal


title: Contralateral control uninjured sciatic nerve (7 dpi), biological replicate 1

description: Gene expression data from sciatic nerve

value: uninjured


title: HMDM M0 rep27

value: Healthy subject


title: HMDM M1 rep29


title: Smoked_NRF_F1brain_rep2

value: Brain


title: Smoked_NRF_F1brain_rep1


title: HMDM M0 rep26


title: Contralateral control uninjured sciatic nerve (3 dpi), biological replicate 4

description: Gene expression data from sciatic nerve


title: Smoked_NRF_F1brain_rep6


title: Contralateral control uninjured sciatic nerve (3 dpi), biological replicate 2

description: Gene expression data from sciatic nerve


title: Control_NRF_F1brain_rep8

value: Control


title: HMDM M1 rep25

value: M1-polarized HMDM

value: Female


title: Contralateral control uninjured sciatic nerve (3 days post injury [dpi]), biological replicate 1

description: Gene expression data from sciatic nerve


title: Control_NRF_F1brain_rep6


title: Control_NRF_F1brain_rep7


title: HMDM M1 rep26

value: Male


title: CRC0262LMX0B03202TUMR01000

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by Bioconductor lumi pipeline with loess normalization

source_name: CRC PDX

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V4 arrays

growth_protocol: Tumor were collected upon surgical resection and stored in liquid nitrogen

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

tag: patient id

tag: mutational status

value: QuadWT

tag: cetuximab response

value: PR

tag: response 3wks

tag: response 6wks

value: chronic


title: HMDM M0 rep25

tag: cell type

value: PBMC derived macrophage (HMDM)


title: HMDM M1 rep24


title: CRC0327LMX0B03204TUMR01000

value: NT


title: Control_NRF_F1brain_rep5

tag: tissue

tag: strain

value: NRF-/-


title: HMDM M1 rep23

tag: age


title: Control_NRF_F1brain_rep4


title: Control_NRF_F1brain_rep3


title: HMDM M0 rep23

tag: race


title: Control_NRF_F1brain_rep2


title: HMDM M1 rep22

tag: Sex


title: HMDM M0 rep22

tag: disease state


title: Control_NRF_F1brain_rep1


title: CRC0327LMX0B03205TUMR01000

tag: treatment


title: Control_WT_F1brain_rep8


title: Control_WT_F1brain_rep7

value: C57BL/6J wild type


title: HMDM M0 rep24

value: Caucasian


title: CRC0219LMX0B03210TUMR01000


title: HMDM M0 rep21


title: CRC0322LMX0A03209TUMR09000


title: CRC0327LMX0B03209TUMR01000


title: CRC0322LMX0A03204TUMR01000


title: Control_WT_F1brain_rep5


title: CRC0327LMX0B03202TUMR01000

value: acute


title: HMDM M1 rep20


title: CRC0322LMX0A03207TUMR05000


title: CRC0322LMX0A03202TUMR01000


title: Control_WT_F1brain_rep4


title: CRC0322LMX0A03208TUMR09000


title: CRC0115LMX0b03204R01000 72H

value: SD


title: HMDM M0 rep20


title: Control_WT_F1brain_rep3


title: HMDM M1 rep19


title: Contralateral control uninjured sciatic nerve (3 dpi), biological replicate 3

description: Gene expression data from sciatic nerve

value: Sprague Dawley

value: sciatic nerve

value: male

value: 6 weeks postnatal

value: uninjured


title: HMDM M0 rep19

value: Healthy subject


title: Control_WT_F1brain_rep2

value: Brain

value: Control


title: HMDM M1 rep21

value: M1-polarized HMDM

value: Female


title: CRC0115LMX0b03203R01000 48H

value: QuadWT


title: HMDM M1 rep18


title: Control_WT_F1brain_rep1


title: CRC0115LMX0b03202R01000 24H


title: HMDM M1 rep17

value: Male


title: CRC0327LMX0B03211TUMR01000

value: PR

value: chronic


title: HMDM M0 rep17

value: PBMC derived macrophage (HMDM)

value: Caucasian


title: HMDM M0 rep18


title: Smoked_WT_F1brain_rep6

value: C57BL/6J wild type

value: Smoked


title: CRC0098LMX0b03204R01000 48H

value: acute


title: CRC0115LMX0b03201R01000 PHY

value: SD

value: NT


title: CRC0098LMX0b03201R01000 24H


title: Smoked_WT_F1brain_rep5


title: Smoked_WT_F1brain_rep7


title: CRC0069LMX0A03202TUMR01000


title: HMDM M1 rep16


title: HMDM M0 rep16


title: CRC0185LMX0B03211TUMR01000


title: Control_WT_F1brain_rep6


title: Smoked_WT_F1brain_rep4


title: Smoked_WT_F1brain_rep8


title: CRC0185LMX0B03206TUMR01000


title: Smoked_WT_F1brain_rep3


title: HMDM M1 rep14


title: Smoked_WT_F1brain_rep2


title: CRC0185LMX0B03207TUMR01000


title: HMDM M0 rep14


title: CRC0185LMX0B03203TUMR01000


title: Control_WT_F1sperm_rep5

source_name: Sperm

value: Sperm


title: HMDM M1 rep13

value: Healthy subject


title: HMDM M0 rep15


title: CRC0185LMX0B03212TUMR01000


title: Control_WT_F1sperm_rep6


title: HMDM M1 rep27


title: HMDM M0 rep13


title: HMDM M1 rep15


title: Control_WT_F1sperm_rep3


title: HMDM M1 rep12


title: Control_WT_F1sperm_rep4


title: CRC0219LMX0A03202TUMR01000


title: Control_WT_F1sperm_rep2


title: HMDM M0 rep12


title: CRC0219LMX0A03203TUMR01000


title: Control_WT_F1sperm_rep1


title: HMDM M1 rep11


title: CRC0219LMX0A03210TUMR01000


title: Smoked_WT_F1sperm_rep7


title: Smoked_WT_F1sperm_rep6


title: HMDM M1 rep10


title: Smoked_WT_F1sperm_rep5


title: Smoked_WT_F1brain_rep1

value: Brain


title: HMDM M0 rep10


title: HMDM M1 rep9


title: CRC0219LMX0A03211TUMR01000


title: CRC0179LMX0A03201TUMR01000

value: SD-PR


title: Smoked_WT_F1sperm_rep2


title: CRC0219LMX0B03205TUMR01000


title: Smoked_WT_F1sperm_rep3


title: CRC0219LMX0A03204TUMR05000


title: CRC0219LMX0B03202TUMR01000


title: CRC0219LMX0B03209TUMR01000


title: HMDM M0 rep9


title: Smoked_WT_F1sperm_rep1


title: HMDM M0 rep11


title: Smoked_NRF_sperm_rep9

value: NRF-/-


title: HMDM M0 rep8

value: Female


title: HMDM M1 rep7

value: M1-polarized HMDM


title: Smoked_WT_F1sperm_rep4


title: Smoked_NRF_sperm_rep7


title: HMDM M1 rep6


title: HMDM M0 rep7


title: HMDM M0 rep6


title: CRC0179LMX0A03202TUMR01000

value: QuadWT


title: Smoked_NRF_sperm_rep5


title: Smoked_NRF_sperm_rep8


title: HMDM M1 rep5


title: HMDM M0 rep5


title: HMDM M1 rep4


title: Smoked_NRF_sperm_rep3


title: CRC0179LMX0A03205TUMR01000


title: Smoked_NRF_sperm_rep6


title: Smoked_NRF_sperm_rep2


title: CRC0246LMX0B03203TUMR01000

value: PR


title: CRC0246LMX0B03204TUMR01000


title: HMDM M0 rep4


title: Smoked_NRF_sperm_rep4


title: CRC0246LMX0B03209TUMR01000

value: chronic


title: HMDM M0 rep3

value: PBMC derived macrophage (HMDM)


title: HMDM M1 rep3

value: Caucasian


title: HMDM M1 rep1

value: Male


title: HMDM M1 rep2


title: CRC0262LMX0B03211TUMR05000


title: Smoked_WT_Recovery3_sperm_rep8

value: C57BL/6J wild type

value: Smoked


title: Smoked_WT_Recovery3_sperm_rep10


title: Smoked_WT_Recovery3_sperm_rep7


title: CRC0262LMX0B03209TUMR01000


title: CRC0262LMX0A03204TUMR01000

value: acute


title: CRC0262LMX0A03207TUMR01000


title: CRC0262LMX0B03207TUMR09000

value: NT


title: CRC0262LMX0B03205TUMR01000


title: CRC0262LMX0A03211TUMR01000


title: CRC0252LMX0A03211TUMR01000


title: Smoked_NRF_sperm_rep1

value: Sperm


title: Smoked_WT_Recovery3_sperm_rep5


title: CRC0252LMX0B03210TUMR01000


title: HMDM M0 rep2

value: Healthy subject


title: CRC0262LMX0A03201TUMR09000


title: CRC0252LMX0B03201TUMR01000


title: HMDM M0 rep1


title: CRC0252LMX0B03208TUMR01000


title: Smoked_WT_Recovery3_sperm_rep9


title: Smoked_WT_Recovery3_sperm_rep6


title: CRC0252LMX0B03205TUMR01000


title: iMac_AUX_ni_rep2

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: CRG

data_processing:
Reads were aligned using STAR (outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -sjdbOverhang 100 –outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
Gene expression was quantified using STAR (--quantMode GeneCounts)
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files used for browser exploration data

source_name: Leukaemia cell line

growth_protocol: B and CEBPA induced cells were grown in RPMI medium

extract_protocol:
Cells were collected by centrifugation and RNA was extracted using the miRNeasy mini kit (Qiagen).
Libraries were constructed using the ribozero depletion kit and Illumina TruSeq Stranded total RNA Library Preparation Kit.

treatment_protocol: C/EBPa was induced with beta-estradiol; CTCF depletion was induced with auxin

tag: subclone

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: CEBPA+auxin

tag: time


title: iMac_AUX_ni_rep1


title: iMac_DMSO_ni_rep1

value: CEBPA+DMSO


title: Smoked_WT_Recovery3_sperm_rep3


title: Smoked_WT_Recovery3_sperm_rep4


title: Smoked_WT_Recovery3_sperm_rep2


title: CRC0252LMX0A03201TUMR01000


title: iMac_DMSO_LPS_rep2

value: CEBPA+DMSO+LPS


title: iMac_DMSO_ni_rep2


title: CRC0252LMX0A03206TUMR01000


title: Smoked_WT_Recovery2_sperm_rep10


title: iMac_DMSO_LPS_rep1


title: iMac_AUX_LPS_rep1

value: CEBPA+auxin+LPS


title: Smoked_WT_Recovery2_sperm_rep9


title: iMac_AUX_LPS_rep2


title: Smoked_WT_Recovery2_sperm_rep7


title: Smoked_WT_Recovery2_sperm_rep6


title: Smoked_WT_Recovery3_sperm_rep1


title: CRC0188LMX0A03206TUMR01000

value: QuadWT

value: SD-PR


title: Smoked_WT_Recovery2_sperm_rep8


title: CRC0188LMX0A03205TUMR01000


title: CRC0188LMX0A03202TUMR01000


title: CRC0188LMX0A03212TUMR01000

description: 9257631106_E_CRC0188_QuadWT_SD-PR_CRONICO

value: chronic


title: CRC0171LMX0B03210TUMR01000

description: 9257631099_K_CRC0171_QuadWT_SD-PR_CRONICO


title: CRC0171LMX0B03212TUMR01000

description: 9257631099_L_CRC0171_QuadWT_SD-PR_CRONICO


title: CRC0171LMX0B03204TUMR01000


title: Smoked_WT_Recovery2_sperm_rep3


title: CRC0188LMX0A03209TUMR01000

description: 9257631106_D_CRC0188_QuadWT_SD-PR_CRONICO


title: BLaER subclone, 168h_CTCF_AID_DMSO_RNAseq_rep1

source_name: Leukemia cell line (cultured)


title: BLaER subclone, 168h_CTCF_AID_AUX_RNAseq_rep1


title: BLaER subclone, 24h_CTCF_AID_AUX_RNAseq_rep2


title: BLaER subclone, 168h_CTCF_AID_AUX_RNAseq_rep2


title: BLaER subclone, 24h_CTCF_AID_AUX_RNAseq_rep1


title: Smoked_WT_Recovery2_sperm_rep2


title: BLaER subclone, 168h_CTCF_AID_DMSO_RNAseq_rep2


title: Smoked_WT_Recovery2_sperm_rep5


title: CRC0171LMX0B03201TUMR01000


title: Smoked_WT_Recovery2_sperm_rep1


title: Smoked_WT_Recovery2_sperm_rep4


title: BLaER subclone, 24h_CTCF_AID_DMSO_RNAseq_rep1


title: CRC0116LMX0B03206TUMR01000

value: PR


title: Smoked_WT_Recovery1_sperm_rep9


title: Smoked_WT_Recovery1_sperm_rep8


title: CRC0116LMX0B03212TUMR01000


title: BLaER subclone, B_CTCF_AID_RNAseq_rep1

value: Non-treated


title: Smoked_WT_Recovery1_sperm_rep7


title: BLaER subclone, 24h_CTCF_AID_DMSO_RNAseq_rep2


title: CRC0116LMX0B03204TUMR01000


title: BLaER cell line, 168h_RNAseq_rep2

tag: cell line

value: BLaER

value: CEBPA


title: BLaER subclone, B_CTCF_AID_RNAseq_rep2


title: CRC0098LMX0B03209TUMR01000


title: BLaER cell line, 144h_RNAseq_rep2


title: CRC0098LMX0B03205TUMR01000


title: Smoked_WT_Recovery1_sperm_rep5

value: C57BL/6J wild type

tag: tag

value: Smoked


title: HMDM M1 rep8

value: M1-polarized HMDM

value: Caucasian

value: Female


title: Smoked_WT_Recovery1_sperm_rep4

value: Sperm


title: CRC0098LMX0B03202TUMR01000

tag: patient id

value: NT


title: CRC0098LMX0B03208TUMR01000

tag: mutational status


title: BLaER cell line, 120h_RNAseq_rep2


title: BLaER cell line, 96h_RNAseq_rep2


title: BLaER cell line, 72h_RNAseq_rep2


title: CRC0246LMX0B03208TUMR01000

tag: cetuximab response


title: Smoked_WT_Recovery1_sperm_rep3


title: Smoked_WT_Recovery1_sperm_rep2


title: CRC0297LMX0B03211TUMR05000

tag: response 3wks


title: CRC0179LMX0A03208TUMR01000

description: 9269315012_C_CRC0179_QuadWT_SD-PR_CRONICO

tag: response 6wks


title: BLaER cell line, 48h_RNAseq_rep2


title: Smoked_WT_Recovery1_sperm_rep1


title: BLaER cell line, 18h_RNAseq_rep2


title: Smoked_WT_sperm_rep9


title: BLaER cell line, 9h_RNAseq_rep2


title: CRC0098LMX0B03203TUMR01000


title: Smoked_WT_Recovery1_sperm_rep6


title: Smoked_WT_sperm_rep7


title: BLaER cell line, B_RNAseq_rep2


title: CRC0297LMX0B03207TUMR01000

value: acute


title: BLaER cell line, 24h_RNAseq_rep2


title: BLaER cell line, 168h_RNAseq_rep1


title: Smoked_WT_sperm_rep8


title: BLaER cell line, 144h_RNAseq_rep1


title: BLaER cell line, 120h_RNAseq_rep1


title: CRC0297LMX0A03210TUMR05000


title: CRC0297LMX0B03206TUMR01000


title: CRC0297LMX0B03204TUMR01000


title: BLaER cell line, 96h_RNAseq_rep1


title: Smoked_WT_sperm_rep4


title: Smoked_WT_sperm_rep5


title: BLaER cell line, 72h_RNAseq_rep1


title: CRC0297LMX0A03208TUMR05000


title: Smoked_WT_sperm_rep2


title: Smoked_WT_sperm_rep1


title: CRC0297LMX0A03206TUMR01000


title: CRC0297LMX0A03212TUMR05000


title: CRC0297LMX0B03210TUMR05000


title: CRC0054LMX0B03202TUMR05000


title: CRC0297LMX0A03204TUMR01000


title: Control_NRF_sperm_rep10

value: NRF-/-

value: Control


title: CRC0054LMX0A03201TUMR01000

value: QuadWT


title: BLaER cell line, 24h_RNAseq_rep1


title: Control_NRF_sperm_rep9


title: CRC0095LMX0b04205R01000 CRONICO

value: SD


title: Control_NRF_sperm_rep8


title: BLaER cell line, 9h_RNAseq_rep1


title: BLaER cell line, 18h_RNAseq_rep1


title: Control_NRF_sperm_rep7


title: BLaER cell line, B_RNAseq_rep1


title: CRC0095LMX0b04206R01000 CRONICO

value: chronic


title: CRC0095LMX0b04204R01000 72H


title: BLaER cell line, 48h_RNAseq_rep1


title: CRC0095LMX0b04203R01000 48H


title: Control_NRF_sperm_rep5


title: ARID1A KO_IFNγ_Rep2_ATAC_Seq

city: Ann Arbor,

first: Jing

last: Li

state: MI

address: 500 S State St,

department: Surgery

institute: University of Michigan

data_processing:
The sequenced raw reads of each sample were aligned to the human reference genome GRCh38 using Novoalign.
BAM files were created using SAMtools, and removed for duplicated reads or mitochondria reads.
Reads were further filtered to identify nucleosome-free, open chromosomal regions.
MACS2 was used to call ATAC-seq peaks, from which differentially accessible regions were determined by limma and EdgeR.
The coverage tracks were generated using the program bam2wig.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig file indicating peak intensity at open chromosomal regions

source_name: OVCA429 Cells

growth_protocol: OVCA429 cells was cultured  as previously reported.

extract_protocol:
Cell nuclei were isolated and subjected to transposase for 30 minutes under active shaking (Buenrostro et al., 2013; Corces et al., 2017). Then, the purified tagged genomic DNA was amplified to generate illumine NGS library with Nextera DNA Sample Preparation Kit (Illumina, #FC-121-1030). The DNA size selection was done with Ampure beads (Beckman Coulter). The library was measured by bioanalyzer. Sequencing was performed by paired-end 50-mer sequencing in replicates at University of Michigan with HiSeq 2500 (Illumina).
Then, the purified tagged genomic DNA was amplified to generate illumine NGS library with Nextera DNA Sample Preparation Kit.

treatment_protocol: OVCA429 cells were treated with PBS or IFNg for 3 hours.

value: OVCA429 Cells

value: IFNγ 3h Rep2

tag: genotype/variation


title: ARID1A KO_IFNγ_Rep1_ATAC_Seq

tag: tissue

value: IFNγ 3h Rep1


title: Smoked_WT_sperm_rep6

tag: strain


title: ARID1A KO_PBS_Rep2_ATAC_Seq

value: PBS Rep2


title: ARID1A KO_PBS_Rep1_ATAC_Seq

value: PBS Rep1


title: Control_NRF_sperm_rep4


title: Control_NRF_sperm_rep2


title: Smoked_WT_sperm_rep3

value: C57BL/6J wild type

value: Smoked


title: Control_NRF_sperm_rep1


title: Control_NRF_sperm_rep6


title: CRC0179LMX0a03202RL01 72H

value: SD-PR


title: ARID1A WT_PBS_Rep2_ATAC_Seq

value: wild type


title: CRC0095LMX0b04201R01000 PHY


title: Control_WT_sperm_rep10

value: Sperm


title: CRC0095LMX0b04202R01000 24H


title: ARID1A WT_IFNγ_Rep2_ATAC_Seq


title: ARID1A WT_PBS_Rep1_ATAC_Seq


title: Control_NRF_sperm_rep3


title: ARID1A WT_IFNγ_Rep1_ATAC_Seq


title: Control_WT_sperm_rep9


title: Control_WT_sperm_rep8


title: Control_WT_sperm_rep6


title: Control_WT_sperm_rep7


title: Control_WT_sperm_rep5


title: Control_WT_sperm_rep4


title: Control_WT_sperm_rep3


title: MDA-MB-231 cell AKAP95 knockdown rescued

city: Charlottesville

first: Bi

last: Shi

state: Virginia

address: 1340 JPA Pinn Hall Room 6017

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
2 x 150 pair-end sequencing was performed using the HiSeq2500 (Illumina). RNA-seq read quality were checked by FASTQC software. 40-60 millions reads per sample were mapped to human and mouse reference genome (hg19 and mm9, respectively) using Tophat version v2.0.4. Transcript assembly was performed using HTseq v0.9.0. Assembled RNA-seq count files were imported into RStudio v1.2 software for analysis of differential expression with DESeq2 v3.8 package.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: count tables (read counts for transcripts)

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium plus 10% FBS. MEF were generated from E13.5 embryos and cultured in DMEM plus 10% FBS. 2 ug/mL puromycin or 20 ug/mL blasticidin were added into the medium when needed.

extract_protocol:
Zymo Direct-zol RNA Kits
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA librabry preparation with polyA selection

treatment_protocol: MDA-MB-231 cells were firstly infected with pLKO.1-Scr or pLKO.1-AKAP95 sh#1 lentiviral vector and selected with blasticidin. The AKAP95 knockdown (KD) MDA-MB-231 cells were futher rescued with pTripZ-empty or pTripZ-AKAP95 lentiviral vector. After selection with puromycin, the cells were cultured under the induction of doxycycline (10 ng/mL). MEF  AKAP95 het or KO cells were firstly infected with pWZL-blast-Myc retroviral vector and selected with blastcidin. The Myc-induced cells were further infected with pTripZ-AKAP95 serial lentiviral vectors and selected with puromycin. The BSDRPuroR cells were induced by 100 ng/mL of doxycycline.

tag: cell types

value: Cancer cell line

tag: genotype

value: human MDA-MB-231 cancer cell line

value: AKAP95 shRNA and rescued with pTripZ-AKAP95


title: MDA-MB-231 cell AKAP95 knockdown

value: AKAP95 shRNA


title: MDA-MB-231 cell Scr

value: scramble shRNA


title: Control_WT_sperm_rep2

value: Control


title: CRC0179LMX0a03205RL01 PHI

value: QuadWT

value: NT


title: CRC0179LMX0a03206RL01 24H

value: acute


title: Control_WT_sperm_rep1


title: MEF Akap95-KO Myc Tripz-YF rep2

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: Akap95 KO MEF cells

value: Akap95 KO MEF with Myc and pTripZ-AKAP95 YF overexpression


title: CRC0102LMX0b03209R01000 CRONICO

value: PR

value: chronic


title: CRC0179LMX0a02202RL01

value: SD-PR


title: CRC0096LMX0a03207R01000 CRONICO


title: MEF Akap95-KO Myc Tripz-YF rep1


title: CRC0059LMX0b04204R01000 72H

description: 5688887027_H_CRC0059_PIK3CA(H1047R)_PR_ACUTO


title: CRC0179LMX0a03204RL01 48H


title: CRC0179LMX0a03208RL01 CRONICO

description: 6898368023_B_CRC0179_QuadWT_SD-PR_CRONICO


title: CRC0059LMX0b04203R01000 48H

description: 5688887027_G_CRC0059_PIK3CA(H1047R)_PR_ACUTO


title: MEF Akap95-KO Myc Tripz-WT rep2

value: Akap95 KO MEF with Myc and pTripZ-AKAP95 WT overexpression


title: CRC0059LMX0b04202R01000 24H

description: 5688887027_F_CRC0059_PIK3CA(H1047R)_PR_ACUTO


title: MEF Akap95-KO Myc Tripz-YS rep2

value: Akap95 KO MEF with Myc and pTripZ-AKAP95 YS overexpression


title: CRC0059LMX0a03209R01000 CRONICO

description: 5688887027_I_CRC0059_PIK3CA(H1047R)_PR_CRONICO


title: MEF Akap95-KO Myc Tripz-WT rep1


title: CRC0102LMX0b03201R01000 PHI


title: Kidney tissue_rep5

city: Hengyang

first: Shuangquan

address: Changsheng Road, Xiangxiang District

institute: University of South China

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (the yield is >1.65 μg and the specific activity is >9.0 pmol Cy3 per μg cRNA) was fragmented at 60°C for 30 minutes following the manufacturers instructions using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). On completion of the fragmentation reaction, hybridize at 65°C for 17 hours After hybridization, microarrays were washed.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Extract data using Agilent Feature Extraction Software

organism: Oryctolagus cuniculus

source_name: Kidney tissue_rep5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by Purify the labeled/amplified RNA and labeled cRNA QC.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000.

extract_protocol: Cryopulverization of Kidney tissue using the Biopulverizer and homogenization using the Mini-Bead-Beater-16 . RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA was quantified and quality monitored  using a NanoDrop-1000 spectrophotometer and  the Baseline-ZERO DNase(EPICENTRE, Cat. Nos. DB0711K).

value: Kidney tissue

tag: gender

value: male

tag: group

value: syphilis combined with diabetes


title: CRC0102LMX0b03206R01000 48H

tag: treatment


title: CRC0102LMX0b03205R01000 72H


title: CRC0059LMX0b04201R01000 PHI

description: 5688887027_E_CRC0059_PIK3CA(H1047R)_PR_NT


title: CRC0076LMX0b04208R01000 CRONICO


title: Kidney tissue_rep1

source_name: Kidney tissue_rep1

value: control


title: MEF Akap95-KO Myc Tripz-YS rep1


title: CRC0076LMX0b04203R01000 48H


title: Kidney tissue_rep4

source_name: Kidney tissue_rep4


title: CRC0102LMX0b03203R01000 24H


title: Kidney tissue_rep2

source_name: Kidney tissue_rep2

value: normal


title: Kidney tissue_rep6

source_name: Kidney tissue_rep6


title: CRC0076LMX0b04201R01000 72H


title: Kidney tissue_rep3

source_name: Kidney tissue_rep3


title: MEF Akap95-KO Myc Tripz-vec rep2

value: Akap95 KO MEF with Myc and pTripz-empty vector overexpression


title: BRAFV600E F/+;Lyve1-Cre/+ Liver, rep 2

city: Worcester

first: Chinmay

last: Trivedi

state: MA

address: 368 Plantation St, AS7-1047

department: Medicine

institute: University of Massachusetts Medical School

description: Gene expression data from BRAFV600E E11.5 liver

hyb_protocol: 3ug of cDNA were hybridized for 16 hours at 45ºC on GeneChip Mouse Exon 1.0 ST arrays. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw microarray .cel files were imported and processed using Transciptome Analysis Console version 4.0.

source_name: BRAFV600E F/+;Lyve1-Cre/+ mouse embryonic liver at E11.5

label_protocol: Fragmented and biotinylated cDNA were prepared using the GeneChip WT PLUS Reagent Kit according to the Affymetrix protocol from 100ng total RNA.

extract_protocol: Total RNA was extracted from embryonic liver samples using Qiagen Rneasy Kit according to the manufacturer's instructions.

value: embryonic liver

tag: age

value: BRAFV600E F/+;Lyve1-Cre/+


title: CRC0076LMX0b04202R01000 24H

value: QuadWT

value: acute


title: MEF Akap95-KO Myc rep1

value: Mouse embryonic fibroblasts

value: Akap95 KO MEF cells

value: Akap95 KO MEF with Myc overexpression


title: MDA-MB-231_siCon

city: Taipei

first: Ji-Lin

last: Chen

state: Taiwan

address: No.201, Sec. 2, Shipai Rd.,, Beitou District

country: Taiwan

institute: VGHTPE

description:
Gene expression data from control MDA-MB-231 cells
H0102-050-231-shLUC_(HG-U133_Plus_2).rma-Signal

hyb_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on a Affymetrix Genechip scanner.

data_processing:
Gene-expression data were generated using the Affymetrix Human Genome U133 Plus 2.0 Array.
affymetrix-algorithm-param-apt-program-name=Expression Console
affymetrix-algorithm-param-apt-version=1.3.1.187

source_name: Human breast cancer cells

growth_protocol: MDA-MB-231 cells were grown in Dulbecco's Modified Eagle Medium supplement with 10% FBS, 2 mM l-glutamine, 0.1 mM non-essential amino acids and 1% penicillin/streptomycin in a 5% CO2 atmosphere at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231 cells were transfected with siRNAs against KMO (L-009897-01) or control (D-001810-10) using DharmaFECT Transfection Reagent for 48 h.

tag: cell type

value: triple-negative breast cancer (TNBC) cell line

value: transfected with siRNA against control


title: MDA-MB-231_siKMO

description:
Gene expression data from KMO-knockdown MDA-MB-231 cells
H0102-051-231-shK421_(HG-U133_Plus_2).rma-Signal

label_protocol: According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

tag: cell line

value: transfected with siRNA against KMO


title: MEF Akap95-Het Myc rep2

value: Akap95 Het MEF cells

value: Akap95 Het MEF with Myc overexpression


title: MEF Akap95-Het Myc rep1


title: CRC0096LMX0b03206R01000 72H

value: PR


title: MEF Akap95-KO Myc rep2


title: CRC0076LMX0b04205R01000 PHI

value: NT


title: BRAFV600E F/+;Lyve1-Cre/+ Liver, rep 3


title: MEF Akap95-KO Myc Tripz-vec rep1


title: BM_LTHSC_H3K4me3_Rep2

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting
Uniquely mapped reads from both ChIPed and input DNA were used to compute a normalized signal for each 200 bp bin across the genome
ChIP-Seq peaks were called by MACS using default parameter setting
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: 6-8 week-old bone marrow hematopoietic stem cells

extract_protocol:
5 stages of hematopoietic stem and progenitor cells were sorted from mouse embryos or adult bone marrow. ChIP reactions were performed using 20,000 FACS-sorted cells. Iped and Input DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

value: Adult bone marrow

value: 6-8 week-old

tag: chip antibody

value: H3K4me3 (07-473, Millipore)

value: bone marrow hematopoietic stem cells


title: Oil and Pathogen Spleen 3 Low

city: Ocean Springs

middle: L

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to the Paralichthys olivaceus genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: Paralichthys olivaceus genome (NCBI genome ID 10840)
Supplementary_files_format_and_content: XLSX files including TPM expression values

organism: Paralichthys lethostigma

source_name: Oil and Pathogen Spleen 3 Low

growth_protocol: All organisms were kept at 15 ppt salinity, 22 degrees C, and dissolved oxygen greater than 5 ppm

extract_protocol:
Qiagen RNeasy kit using manufacturer's protocols
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: Oil-exposed organisms were placed into tanks with oiled sediment for 8 days.  Vibrio-exposed organisms were removed from their tanks on day 7, placed into V. anguillarum contaminated tanks for 1 hour, and then placed back into their original tanks.

tag: oil in sediment concentration

tag: vibrio anguillarum concentration

value: spleen


title: CRC0096LMX0b03203R01000 24H

source_name: CRC PDX

tag: patient id

tag: mutational status

value: QuadWT

tag: cetuximab response


title: Oil and Pathogen Spleen 1 Low

source_name: Oil and Pathogen Spleen 1 Low


title: BRAFV600E F/+;Lyve1-Cre/+ Liver, rep 1

value: embryonic liver

tag: genotype/variation

value: BRAFV600E F/+;Lyve1-Cre/+


title: BRAFV600E F/+ Liver, rep 3

description: Gene expression data from Control E11.5 liver

source_name: BRAFV600E F/+ mouse embryonic liver at E11.5

tag: tissue

value: BRAFV600E F/+


title: CRC0096LMX0b03205R01000 48H

tag: response 3wks

tag: response 6wks

value: acute


title: JS181107

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCh38 genome using STAR aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph track. Bedgraph files represent different numbers of T to C mutations identified: TC.0 = 0 mutations, TC.1 = 1 mutation, TC.2 = 2 mutations, etc.

source_name: immortalized 293Ts

growth_protocol: 293T cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: s4U plus and minus cells had their media replaced with growth media supplemented with 500 uM s4U or left unsupplemented, respectively. Cells were incubated with s4U for 2h.

tag: genotype

value: DCP2 KO

value: immortalized 293Ts

tag: s4u feed

value: Yes


title: JS181114

value: No


title: JS181108


title: CRC0096LMX0b03202R01000 PHI


title: BRAFV600E F/+ Liver, rep 2


title: CRC0096LMX0a03205R01000 48H


title: CRC0096LMX0a03204R01000 24H


title: CRC0096LMX0a03203R01000


title: CRC0096LMX0a03206R01000 72H


title: BM_LTHSC_H3K4me3_Rep1

tag: strain


title: Pathogen Only Spleen 2 Low

source_name: Pathogen Only Spleen 2 Low

value: 0 mg/kg


title: BRAFV600E F/+ Liver, rep 1


title: JS181113

value: Wild Type


title: Oil and Pathogen Spleen 2 Low

source_name: Oil and Pathogen Spleen 2 Low


title: BM_LTHSC_H3K4me1_Rep2

value: H3K4me1 (ab8895, Abcam)


title: JS181102


title: JS181101


title: Pathogen Only Spleen 1 Low

source_name: Pathogen Only Spleen 1 Low


title: BM_LTHSC_H3K27me3_Rep2

value: Adult bone marrow

value: H3K27me3 (07-449, Millipore)


title: BM_LTHSC_H3K4me1_Rep1

value: 6-8 week-old


title: BM_LTHSC_H3K27me3_Rep1

value: bone marrow hematopoietic stem cells


title: Control Spleen 3 Low

source_name: Control Spleen 3 Low

value: 0 cfu/mL

value: spleen


title: Oil Only Spleen 1 Low

source_name: Oil Only Spleen 1 Low


title: OVCA429+IFNg-8H+GSK-126.2

data_processing:
The sequenced raw reads of each sample were aligned to the human reference genome GRCh 38 using HISAT2 .
The transcriptome was self-merged to allow processing with StringTie
Different conditions were compared using ballgown R package, Limma.
Other methods also were used to validate it.
Genome_build: GRCh 38
Supplementary_files_format_and_content: Excel File with gene expression values

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).
The Illumina Ribo-Zero Gold rRNA Removal Kit (Cat# MRZG126) was used for RNA-sequencing library preparation for RNA-sequencing. Sequencing was performed by paired-end 50-mer sequencing in replicates at the University of Michigan sequencing core facility with HiSeq 4000 (Illumina). The sequenced raw reads of each sample were aligned to the human reference genome GRCh 38 .

treatment_protocol: WT and KO cells were treated with interferon for indicated time points.

value: OVCA429 Cells

tag: treatment

value: IFNg 8h+GSK126 Rep2

value: wild type


title: OVCA429+IFNg-8H+GSK-126.1

value: IFNg 8h+GSK126 Rep1


title: OVCA429+IFNg-8H+DMSO2

value: IFNg 8h+DMSO Rep2


title: OVCA429+IFNg-8H+DMSO1

value: IFNg 8h+DMSO Rep1


title: OVCA429+GSK-126.2

value: GSK126 Rep2


title: Control Spleen 2 Low

source_name: Control Spleen 2 Low


title: Oil Only Spleen 2 Low

source_name: Oil Only Spleen 2 Low


title: Control Spleen 1 Low

source_name: Control Spleen 1 Low


title: BM_LTHSC_H3K27ac_Rep1

tag: age

value: H3K27ac (ab4729, Abcam)


title: Oil and Pathogen Liver 3 Low

source_name: Oil and Pathogen Liver 3 Low

value: liver


title: OVCA429+DMSO2

value: DMSO Rep2


title: OVCA429+GSK-126.1

value: GSK126 Rep1


title: OVCA429+DMSO1

value: DMSO Rep1


title: BM_LTHSC_Input_Rep1

value: Adult bone marrow

tag: cell type


title: AC17+IFNg-8H2

value: AC17 Cells

value: IFNg 8h Rep2


title: Oil and Pathogen Liver 2 Low

source_name: Oil and Pathogen Liver 2 Low


title: AC17+IFNg-8H1

value: IFNg 8h Rep1


title: Pathogen Only Liver 3 Low

source_name: Pathogen Only Liver 3 Low

value: 0 mg/kg


title: Oil and Pathogen Liver 1 Low

source_name: Oil and Pathogen Liver 1 Low


title: AC17+PBS2

value: PBS Rep2


title: FL_LTHSC_H3K4me1_Rep2

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

value: Fetal liver

value: Embryonic day 14.5

value: H3K4me1 (ab8895, Abcam)

value: fetal liver hematopoietic stem cells


title: FL_LTHSC_H3K4me1_Rep1


title: Pathogen Only Liver 2 Low

source_name: Pathogen Only Liver 2 Low


title: FL_LTHSC_H3K4me3_Rep2

value: H3K4me3 (07-473, Millipore)


title: FL_LTHSC_H3K4me3_Rep1


title: BM_LTHSC_H3K27ac_Rep2

source_name: 6-8 week-old bone marrow hematopoietic stem cells

value: 6-8 week-old

value: bone marrow hematopoietic stem cells


title: Pathogen Only Liver 1 Low

source_name: Pathogen Only Liver 1 Low

value: liver


title: AC17+PBS1

value: PBS Rep1


title: Oil Only Liver 3 Low

source_name: Oil Only Liver 3 Low

value: 0 cfu/mL


title: FL_LTHSC_H3K27me3_Rep1

value: H3K27me3 (07-449, Millipore)


title: OVCA429+IFNg-8H2

value: OVCA429 Cells

value: wild type


title: BM_LTHSC_Input_Rep2

value: Adult bone marrow


title: FL_LTHSC_H3K27ac_Rep1

value: H3K27ac (ab4729, Abcam)


title: Oil Only Liver 2 Low

source_name: Oil Only Liver 2 Low


title: FL_LTHSC_H3K27ac_Rep2


title: OVCA429+IFNg-8H1

value: IFNg 8h Rep1


title: Oil Only Liver 1 Low

source_name: Oil Only Liver 1 Low


title: OVCA429+PBS2

value: PBS Rep2


title: FL_LTHSC_Input_Rep1

value: Fetal liver


title: Control Liver 1 Low

source_name: Control Liver 1 Low

value: 0 mg/kg


title: FL_LTHSC_Input_Rep2

value: Embryonic day 14.5


title: TOV21G-8h-2

data_processing:
The sequenced raw reads of each sample were aligned to the human reference genome GRCh 38 using STAR, HISAT2 .
The transcriptome was self-merged to allow processing with StringTie
Different conditions were compared using ballgown R package, Limmar.
Other methods also were used to validate it.
Genome_build: GRCh 38
Supplementary_files_format_and_content: Excel File with gene expression values

growth_protocol: OVCA429 cells was cultured as previously reported.

value: IFNg 8h Rep2

value: ARID1A mut


title: OVCA429+PBS1


title: Control Liver 2 Low

source_name: Control Liver 2 Low


title: PreHSC_H3K4me3_Rep2

source_name: Embryonic day 10.5 major arteries PreHSC

value: AGM

value: Embryonic day 11.5

value: H3K4me3 (07-473, Millipore)

value: major arteries PreHSC


title: FL_LTHSC_H3K27me3_Rep2

value: fetal liver hematopoietic stem cells


title: Oil and Pathogen Spleen 2 High

source_name: Oil and Pathogen Spleen 2 High

value: spleen


title: TOV21G-2h-1

value: IFNg 2h Rep1


title: Oil and Pathogen Spleen 1 High

source_name: Oil and Pathogen Spleen 1 High


title: TOV21G-8h-1


title: TOV21G-2h-2

value: IFNg 2h Rep2


title: PreHSC_H3K4me3_Rep1


title: TOV21G-2


title: PreHSC_H3K4me1_Rep1

value: H3K4me1 (ab8895, Abcam)


title: Oil and Pathogen Spleen 3 High

source_name: Oil and Pathogen Spleen 3 High


title: Pathogen Only Spleen 2 High

source_name: Pathogen Only Spleen 2 High


title: PreHSC_H3K4me1_Rep2


title: Pathogen Only Spleen 3 High

source_name: Pathogen Only Spleen 3 High


title: PreHSC_H3K27me3_Rep1

value: H3K27me3 (07-449, Millipore)


title: AC17 (ARID1A KO)-8h-2

source_name: AC17 (ARID1A KO)-8h-2

value: AC17 Cells


title: TOV21G-1

value: PBS Rep1


title: PreHSC_H3K27ac_Rep2

value: H3K27ac (ab4729, Abcam)


title: Pathogen Only Spleen 1 High

source_name: Pathogen Only Spleen 1 High

value: 0 mg/kg


title: Oil Only Spleen 3 High

source_name: Oil Only Spleen 3 High

value: 0 cfu/mL


title: Oil Only Spleen 2 High

source_name: Oil Only Spleen 2 High


title: AC17 (ARID1A KO)-8h-1

source_name: AC17 (ARID1A KO)-8h-1

value: IFNg 8h Rep1


title: PreHSC_H3K27ac_Rep1


title: AC17 (ARID1A KO)-2h-2

source_name: AC17 (ARID1A KO)-2h-2


title: PreHSC_Input_Rep2


title: AC17 (ARID1A KO)-2h-1

source_name: AC17 (ARID1A KO)-2h-1


title: Control Spleen 3 High

source_name: Control Spleen 3 High


title: PreHSC_Input_Rep1


title: AC17 (ARID1A KO)-2

source_name: AC17 (ARID1A KO)-2

value: PBS Rep2


title: PreHSC_H3K27me3_Rep2

value: AGM


title: Control Spleen 2 High

source_name: Control Spleen 2 High


title: AC17 (ARID1A KO)-1

source_name: AC17 (ARID1A KO)-1


title: Control Spleen 1 High

source_name: Control Spleen 1 High


title: HE_H3K4me3_Rep1

source_name: Embryonic day 10.5 major arteries hemogenic endothelium

value: Embryonic day 10.5

value: major arteries hemogenic endothelium


title: HE_H3K4me1_Rep2


title: Oil and Pathogen Liver 3 High

source_name: Oil and Pathogen Liver 3 High

value: liver


title: HE_H3K4me3_Rep2

value: H3K4me3 (07-473, Millipore)


title: OVCA429-8h-1

value: OVCA429 Cells

value: wild type


title: HE_H3K4me1_Rep1


title: OVCA429-2h-2

value: IFNg 2h Rep2


title: Oil and Pathogen Liver 1 High

source_name: Oil and Pathogen Liver 1 High


title: OVCA429-8h-2

value: IFNg 8h Rep2


title: JS1902_01

source_name: immortalized 293Ts

value: Wild Type

value: immortalized 293Ts

value: Yes


title: OVCA429-2


title: Oil Only Spleen 1 High

source_name: Oil Only Spleen 1 High

value: spleen


title: HE_H3K27me3_Rep2

value: H3K27me3 (07-449, Millipore)


title: HE_H3K27me3_Rep1


title: Pathogen Only Liver 2 High

source_name: Pathogen Only Liver 2 High

value: 0 mg/kg


title: OVCA429-1

value: PBS Rep1


title: OVCA429-2h-1

value: IFNg 2h Rep1


title: Pathogen Only Liver 3 High

source_name: Pathogen Only Liver 3 High


title: small intestine, uninfected 5-day old 129sv wild type mouse (scRNA-seq)

city: St. Louis

first: Siyuan

last: Ding

state: MO

address: 425 S. Euclid Ave., MPRB, Rm 9220

department: Molecular Microbiology

institute: Washington University in St. Louis

description: scRNA-seq of mouse small intestine

data_processing:
10X 3' v3 Gene Expression Library
Single-Cell 3'
2x101 HiSeq with Index
Paired End with Index
The .csv is the processed format imported into JMP for further analysis.
The .jmp file was generated by JMP Pro 14 for visualization
Genome_build: Mouse (mm9)
Supplementary_files_format_and_content: csv file reports abundance measurements; jmp file for visualization.

source_name: small intestine

extract_protocol:
Small intestinal tissues were harvested from three mice pooled together, using a standard EDTA-DTT protocol to strip off the loosely attached epithelial cells and lymphocytes in between
10X 3' v3 Gene Expression Library kit was used for library construction

value: small intestine

value: 5 day old


title: HE_H3K27ac_Rep1

city: PHILADELPHIA

institute: Children's Hospital of Philadelphia

value: AGM

value: Embryonic day 10.5

value: H3K27ac (ab4729, Abcam)

value: major arteries hemogenic endothelium


title: ENDO_H3K4me3_Rep2

source_name: Embryonic day 10.5 major arteries endothelium

value: H3K4me3 (07-473, Millipore)

value: major arteries endothelium


title: Pathogen Only Liver 1 High

source_name: Pathogen Only Liver 1 High

value: liver


title: Oil and Pathogen Liver 2 High

source_name: Oil and Pathogen Liver 2 High


title: ENDO_H3K4me1_Rep2

value: H3K4me1 (ab8895, Abcam)


title: ENDO_H3K27me3_Rep2


title: ENDO_H3K4me1_Rep1


title: Oil Only Liver 3 High

source_name: Oil Only Liver 3 High

value: 0 cfu/mL


title: Oil Only Liver 2 High

source_name: Oil Only Liver 2 High


title: Control Liver 1 High

source_name: Control Liver 1 High


title: Oil Only Liver 1 High

source_name: Oil Only Liver 1 High


title: Control Liver 2 High

source_name: Control Liver 2 High


title: Control Liver 3 High

source_name: Control Liver 3 High


title: Oc rep4

city: Montpellier Cedex 5

first: Anne

last: Blangy

address: 1919 route de Mende

department: CRBM CNRS UMR 5237

country: France

institute: Montpellier Cell Biology Research Center

data_processing:
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to Mus musculus genome GRCm38, from iGenome downloaded on the 2017-07-13 using Bowtie 2 and TopHat 2
Cufflinks v2.1.1 was used to assembls aligned RNA-Seq reads into transcripts, estimate their abundances, and test for differential expression and regulation transcriptome-wide.
DESeq2 R package Release 2.13 was used to estimate variance-mean dependence in count data from the high- throughput sequencing and to test for differential expression between Mo, Oc and Dc based on a model using the negative binomial distribution
Genome_build: Mus musculus genome GRCm38
Supplementary_files_format_and_content: Txt file,  including test_id: A unique identifier describing the gene being tested; gene_id: The gene_id being tested; sample1: first group in the comparison; sample2: second group in the comparison; mean_1, mean_2: the mean of the normalized counts in each group; log2FoldChange : log2 fold change estimates after shrinkage (When count values are too low to allow an accurate estimate of the log fold change, the value is “shrunken” towards zero to avoid that these values, which otherwise would frequently be unrealistically large, dominate the top-ranked log fold changes.); pvalue: uncorrected p-value of the test statistic; padj : p value adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR); significant: can be either yes (padj <= 0.05) or no (padj > 0.05)

source_name: Bone marrow

growth_protocol: Bone marrow cells were extracted from long bones of C57BL/6J mice 6 to 8 weeks of age nd cultured in α-minimal essential medium (α-MEM, Lonza) containing 10% Fetal Bovine Serum (FBS, BioWest), heat inactivated at 56°C for 30 minutes, 2 mM glutamine (Lonza) and 100 U/mL penicillin and streptomycin (Lonza), 3 x 107 cells per 150 mm dishes at 37°C, 5.5% CO2, in a humidified incubation for 24 hours. Non-adherent cells were then collected and used to differentiate the three myeloid cell types. For bone marrow macrophages (Mo) and osteoclasts (Oc), non-adherent cells were then plated 5 x 106 cells per 10-cm plate in the same medium containing 100 ng/ml Macrophage colony-stimulating factor (M-CSF, Miltenyi) for 5 days. Cells were then detached using Accutase (SIGMA), washed in PBS and resuspended in Roswell Park Memorial Institute (RPMI) medium: SILAC RPMI 1640 (Lonza) supplemented with 10% dialyzed FBS (Life Technologies), 2.4 mM L-Prolin (SIGMA), 2 mM glutamine (Lonza) and 100 U/mL penicillin/streptomycin (Lonza). For Mo, cells were then plated 0.8 x 105 cell per well in 24 well plates in RPMI medium supplemented with 30 ng/ml M-CSF and with the L-enantiomers amino acids Lys (0.4 mM) and Arg (0.8 mM) (SIGMA). For Oc, cells were plated 1 x 105 cell per well in 24 well plates in RPMI medium supplemented with 30 ng/ml M-CSF and 50 ng/ml Receptor Activator of NF-κB Ligand (RANKL, Miltenyi) and with L amino acids as above. For immature dendritic cells (Dc), cells were plated 4x105 cells per well in 24 well plates in RPMI medium supplemented with 20 ng/ml Granulocyte Macrophage Colony Stimulating Factor (GM-CSF, Miltenyi) and with L amino acids as above. All media were changed every other day for 8 to 10 days. Following differentiation, Oc cultures were incubated with 120 µl per well Accutase (SIGMA), for a few minutes to remove mono-nucleated cells. Then all cultures were rinsed once with PBS and processed for RNA extraction. The experiment was performed 4 times.

extract_protocol:
Total RNA was extracted and purified using RNeasy Mini Kit and QIAshredder spin columns (QIAGEN) according to manufacturer’s instructions, 8 wells for Dc, 12 well for Mo and 4 wells for Dc, to obtain around 10 µg of RNA. RNA concentration was measured using a Nanodrop UV-visible spectrophotometer (Thermo Scientific) and RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies). Lysates were stored at -80°C until RNAseq analysis. For each RNAseq analysis, Oc, Dc and Mo RNA samples derived from the same mouse,and the experiment was done four times with four independent mouse bone marrow extractions.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit

value: osteoclasts

value: 6 to 8 weeks


title: Mo rep3

value: bone marrow macrophages


title: Dc rep4

value: immature dendritic cells


title: Oc rep3


title: Dc rep3


title: Oc rep2


title: 5EU 60 min HS replicate 5

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

country: Germany

institute: MPI

description: 5EU-labeled RNA

data_processing:
Direct RNA nanopore sequencing data preprocessing of synthetic RNAs. Direct RNA nanopore sequencing reads were obtained for each of the samples (Supplementary Table 1).  FAST5 files were base-called using Guppy 3.1.5 (Oxford Nanopore Technologies) with the following parameters: guppy_basecaller -c rna_r9.4.1_70bps_hac.cfg. Direct RNA nanopore sequencing reads were mapped with GraphMap 0.5.2 46 to the synthetic RNA reference sequence with the following parameters: graphmap align --evalue 1e-10. Further data processing was carried out using the R/Bioconductor environment.
Direct RNA nanopore sequencing data preprocessing of human K562 cells. Direct RNA nanopore sequencing reads were obtained for each of the samples (Supplementary Table 1).  FAST5 files were base-called using Guppy 3.1.5 (Oxford Nanopore Technologies) with the following parameters: guppy_basecaller -c rna_r9.4.1_70bps_hac.cfg. Direct RNA nanopore sequencing reads were mapped with Minimap2 2.10 47 to the GRCh38/hg38 genome assembly (Human Genome Reference Consortium) with the following parameters: minimap2 -ax splice -k14 --secondary=no. Samtools 1.3.1 48 was used to quality filter SAM files, whereby alignments with MAPQ smaller than 20 (-q 20) were skipped. Further data processing was carried out using the R/Bioconductor environment and custom python scripts.
RNA-seq data preprocessing and antisense bias correction. Paired-end 75 base reads with additional 6 base reads of barcodes were obtained for each of the samples (Supplementary Table 1).  Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin and Gingeras 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. We used a spike-in (RNAs) normalization strategy essentially as described (Schwalb, Michel et al. 2016) to allow observation of antisense bias ratio  (ratio of spurious reads originating from the opposite strand introduced by the reverse transcription reaction). Read counts (kij) for spike-ins were calculated using HTSeq (Anders, Pyl et al. 2015). The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38) in addition to the sum of the coverage of non-evident fragment parts (entire fragment). The number of transcribed bases (tbj) or read counts (kj) for all features (RefSeq-TUs) were corrected for antisense bias cj as follows using the parameter calculated as described above. RPKs were calculated upon antisense bias corrected read counts (kj) falling into the region of a RefSeq-TU divided by its length in kilobases. Coverages were calculated upon antisense bias corrected number of transcribed bases (tbj) falling into the region of a RefSeq-TU divided by its length in bases.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

source_name: K562 erythroleukemia cells

growth_protocol: Human K562 erythroleukemia cells were obtained from DSMZ (Cat. # ACC-10). K562 cells were cultured antibiotic-free in accordance with the DSMZ Cell Culture standards in RPMI 1640 medium (Thermo Fisher Scientific) containing 10 % heat inactivated fetal bovine serum (FBS) (Thermo Fisher Scientific), and 1x GlutaMAX supplement (Thermo Fisher Scientific) at 37 °C in a humidified 5 % CO2 incubator. Cells used in this study display the phenotypic properties, including morphology and proliferation rate, that have been described in literature. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen). Biological replicates were cultured independently.

extract_protocol:
Direct RNA nanopore sequencing library kit (SQK-RNA001, Oxford Nanopore Technologies)
Nanopore: Total RNA was extracted from K562 cells using QIAzol (Quiagen) according to manufacturer’s instructions. Poly(A) RNA was purified from 1 mg of total RNA using the µMACS mRNA Isolation Kit (Milteny Biotec) following the manufacturer’s protocol. The quality of poly(A) RNA selection was assessed using the TapeStation System (Agilent). Poly(A) selected RNAs were subsequently subjected to direct RNA nanopore sequencing library preparation (SQK-RNA001, SQK-RNA002, Oxford Nanopore Technologies) following manufacturer’s protocol with 1000 ng input. All libraries were sequenced on a MinION Mk1B (MIN-101B) for 48 h, unless reads sequenced per second stagnated dramatically.
RNA-seq: Total RNA was extracted from K562 cells using QIAzol according to manufacturer’s instructions except for the addition of 150 ng RNA spike-in mix 25 together with QIAzol. To isolate polyA RNA from 75 µg of total RNA, two subsequent rounds of purification by Dynabeads Oligo (dT)25 (invitrogen) were performed. Purification based on manufacturer’s instructions was performed twice, using 1 mg of Dynabeads Oligo (dT)25 beads for the first round and 0.5 mg for the second round of purification. The quality of polyadenylated RNA selection was assessed using RNA ScreenTape on a TapeStation (Agilent). Sequencing libraries were prepared using the NuGEN Ovation Universal RNA-seq kit according to manufacturer’s instructions. Fragments were amplified by 10 cycles of PCR, and sequenced on an Illumina NextSeq 550 in paired-end mode with 75 bp read length.

treatment_protocol:
Nanopore: K562 cells were kept at low passage numbers (<6) and at optimal densities (3x10^5 - 8x10^5) during all experimental setups. Per biological replicate, K562 cells were diluted 24 h before the experiment was performed (Supplementary Table 1). Per 5EU 60 min sample (6 replicates), cells were incubated at 37 °C, 5 % CO2 for 1 h after a final concentration of 500 µM 5-Ethynyluridine (5EU, Jena Bioscience) was added. Per 5EU 24 h sample (3 replicates), cells were incubated at 37 °C, 5% CO2 for 24 h. 5EU was added 3 times during the 24h incubation, i.e. every 8 hours (0h, 8h, 16h) at a final concentration of 500 µM. Control samples were not labeled (3 replicates). Per 5EU 60 min HS (heat shock) sample (5 replicates), cells were incubated at 42 °C for 5 min (until cell suspension reached 42 °C), and then 5EU was added at a final concentration of 500 µM. Further, heat shock treatments were performed in a water bath (LAUDA, Aqualine AL12) at 42 °C. for 1 h. Temperature was monitored by thermometer. To avoid transcriptional changes by freshly added growth medium, fresh growth medium was added 24 h prior to heat shock treatments 45. Exactly after the labeling duration, cells were centrifuged at 37 °C and 1,500 x g for 2 min.
RNA-seq: Two biological replicates of K562 cells were diluted 24 h before the experiment was performed. Per replicate, 3.6 x 107 cells in growth medium were labeled at a final concentration of 500 µM 4-thio-uracil (4sU, Sigma-Aldrich), and incubated at 37 °C, 5 % CO2 for 5 min. Exactly after 5 min of labeling, cells were harvested at 37 °C and 1,500 x g for 2 min.

tag: method protocol

value: Direct RNA nanopore sequencing

tag: cell line

value: K562 erythroleukemia cells

tag: treatment condition


title: ENDO_H3K27ac_Rep2

first: Kai

last: Tan

address: 3501 CIVIC CENTER BLVD.

tag: chip antibody


title: HE_Input

source_name: Embryonic day 10.5 major arteries hemogenic endothelium


title: Mo rep4


title: 5EU 60 min HS replicate 4

description: 5EU-labeled RNA


title: Oc rep1


title: ENDO_H3K4me3_Rep1


title: Dc rep2


title: ENDO_Input_Rep1


title: ENDO_Input_Rep2


title: Mo rep1


title: ENDO_H3K27me3_Rep1

value: H3K27me3 (07-449, Millipore)


title: cytosol replicate2

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
cutadapt
trimmomatic
fastqc
STAR mapping
HTSeq counts
DESeq normalization
Genome_build: GRCm38

source_name: cytosol replicate2

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: cytosol


title: Mo rep2


title: cytosol replicate1

source_name: cytosol replicate1


title: FC2P23

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

data_processing:
The demultiplexed fastq files generated using 10x CellRanger software (version 2.2.0)
Reads were mapped to the cellranger mm10-1.2.0 genome and counted with complementary annotation. Read processing, cells and barcodes quality control was performed using dropEst pipeline (Version: 0.8.3.) as described (Petukhov, V. et al. Genome Biol. 19,
Clean up cells and genes related to mesenchymal cell populations performed with MAST (Finak, G. et al. Genome Biol. 16, 278 (2015)) by identification of DE genes. Committed, mature, myelin forming oligodendrocytes were removed.
RNA-velocity analysis of samples separately using original deterministic approach of velocyto.R (La Manno, G. et al. Nature 560, 494–498 (2018ic
For integration UMI-counts matrices were taken additionally filtered out cells with less than 300 genes or 2,5*104 molecules. We derived 50 PCs matrix from linearly scaled total molecule counts and cell-cycle difference regressed; Seurat 3.0 CCA-alignment
Astro-ependymal and neuronal putative cells clusters were subseted. Spliced UMIs count matrix of integrated dataset was inputted in pySCENIC pipeline with default setting; regulons AUC scores matrix were derived (Aibar, S. et al. Nat. Methods 14, 1083–1nt
Regulons network was analysed and visualized with Gephi (Bastian, M., Heymann, S. & Jacomy, M. Gephi: An Open Source Software for Exploring and Manipulating Networks. (2009))
Large “bridge-cells” and immature neurons populations were redistributed to definitive cell populations by applying combination of two methods: Leiden network clustering algorithm (Traag, V. A., Waltman, L. & van Eck, N. J. Sci. Rep. 9, 5233 (2019)) a–1nt
Spliced molecules matrix was used to estimate pseudotime order and branching probabilities for cells from subgraph of glial line and "bridge" cells to confirm trajectories. For that purpose we used probabilistic approach Palantir (Setty, M. et al. Nat. Bi
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: rds R data files include Seurat 3 object with cells from all origines for each Sample

source_name: Hypothalamus

extract_protocol:
Single-cell RNA-seq were conducted in mice on a C57BL/6J background before sexual maturation during embryonic and postnatal days E15.5-P23. Postnatal mice (P10, P23) were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold
Cell were resuspended in PBS and concentrated up to 50-560 cells/μl. 33 μl of the solution form above together with 1 μl of lymphocyte suspension as spike-ins  were added to the Reverse transcription mix. All following procedures: cDNA synthesis, librald

value: wild type

value: Hypothalamus

tag: libbatch


title: 5EU 60 min HS replicate 2

description: 5EU-labeled RNA


title: 5EU 24 h replicate 3

description: 5EU-labeled RNA

value: 5EU, 24 h (8 h intervals)


title: 5EU 60 min HS replicate 1

description: 5EU-labeled RNA


title: 5EU 60 min HS replicate 3

description: 5EU-labeled RNA


title: migrasome replicate 2

source_name: migrasome replicate 2

value: migrasome


title: migrasome replicate 1

source_name: migrasome replicate 1


title: ENDO_H3K27ac_Rep1

source_name: Embryonic day 10.5 major arteries endothelium

value: AGM

value: Embryonic day 10.5

value: H3K27ac (ab4729, Abcam)


title: ENDO_Input_Rep3

value: major arteries endothelium


title: FC2P10


title: Dc rep1


title: 5EU 24 h replicate 2

description: 5EU-labeled RNA


title: TS-3

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Briefly, the robust microarray analysis (RMA) algorithm was used for background correction, intra- and inter-microarray normalization, and expression signal calculation. Once the absolute  expression signal for each gene (i.e., the signal value for each probe set)  was calculated in each microarray, a method [called significance analysis of  microarray (SAM)] was applied to calculate significant differential  expression and find the gene probe sets that characterized the highly  metastatic samples. The method uses permutations to provide robust  statistical inference of the most significant genes and provides P values  adjusted to multiple testing using false discovery rate (FDR).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: wild-type E15 cochlea

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Cochleas dissected from E15 mouse embryos

extract_protocol: Meis2 mutant embryos were distinguished from wild-type embryos by PCR genotyping. Total RNA was extracted from cochlear tissue using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). cDNA synthesis and amplification was performed using the WT Expression Kit (Ambion).

treatment_protocol: not applicable

value: whole cochlea


title: MEIS_KO-2

source_name: Meis2 ko E15 cochlea

value: Meis2 ko


title: TS-2


title: 5EU 60 min replicate 3

description: 5EU-labeled RNA

value: 5EU, 60 min


title: Control replicate 1

description: RNA


title: 5EU 60 min replicate 4

description: 5EU-labeled RNA


title: 5EU 60 min replicate 5

description: 5EU-labeled RNA


title: Control replicate 3

description: RNA


title: 5EU 24 h replicate 1

description: 5EU-labeled RNA


title: 5EU 60 min replicate 6

description: 5EU-labeled RNA


title: Control replicate 2

description: RNA


title: MEIS_KO-1


title: L2

city: Haikou

first: rui

last: xiong

address: Renmin Street

institute: Hainan University

description:
NL-VS-L2.filter.annot
Hylocereus undatus Britt

data_processing:
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000
raw reads is subjected to quality control (QC) that determine if a resequencing step is needed
After QC,transcriptome de novo assembly was carried out with short reads assembling program – Trinity
The rRNA removed high quality clean reads were mapped to the reference transcriptome using short reads alignment tool Bowtie2
We will proceed with downstream analysis including gene expression, basic and deep analysis
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: excel files include gene id,gene length,expression,RPKM,log2 Ratio,P-value,FDR…

organism: Selenicereus undatus

source_name: 2 cm of tissue around the thorn seat

growth_protocol: The plant material is 'Jindu No.1' red meat pitaya, which is located in Enhong Agricultural Technology company of Dongfang city, Hainan province. The pitaya plants at one year growth status were selected to supplementary light in night. The lighting period was from January 1st to March 31. In the meantime, except for the different supplementary light conditions, the field management measures such as watering amount and fertilization amount are the same.

extract_protocol:
RNA was harvested using CTAB reagent
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, Then the enriched  mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into  cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I, RNase H, dNTP  and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired,  poly(A) added, and ligated to Illumina sequencing adapters.

tag: cultivar

value: Jindu No.1

tag: developmental stage

value: one week after the bud stage after light treatment

value: thorn seat of the stem

value: one year


title: L0

description:
NL-VS-L1.filter.annot
Hylocereus undatus Britt

value: no flowering after light treatment

tag: tissue


title: L1

description:
L0-VS-L1.filter.annot
Hylocereus undatus Britt

value: flower bud stage after light treatment


title: 5EU 60 min replicate 2

description: 5EU-labeled RNA

value: Direct RNA nanopore sequencing

value: K562 erythroleukemia cells


title: Iron_plus_A

city: East Lansing

first: Shicheng

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Data from RNA-seq were checked for quality control (QC), pre-trimming, using Fast QC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads were subjected to trimming of low-quality bases and removal of adapter sequences using Trimmomatic (v0.32) with a 4-bp sliding window when the read quality was below 15 (using the Phred64 quality scoring system) or read length was less than 50 bp. The trimming process improved the quality of the data as evidenced by comparing Fast QC reports pre- and post-trimming. Forward and reverse read pairs were aligned to the reference genome using Bowtie2 (v2.2.3) with the –S option to produce SAM files as output (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). The average percentage of reads aligned was 90%. SAM files were converted to BAM format, sorted by name using the –n option and converted back to SAM format using SAMTools. Aligned reads were then counted per gene feature in the E. anophelis NUHP1 genome using the HTSeq Python library. Specifically, counting was performed using the htseq-count function within the HTSeq suite of tools using the “–r” name and “–s” no options. Differential gene expression was calculated by normalizing the data utilizing the trimmed mean of M-values normalization method and filtering out genes that had <10 counts per million (CPM) within the edgeR package. Statistical analysis was performed in RStudio (v 0.98.1102) by the exact test with a negative binomial distribution for each set of conditions and testing for differential gene expression using edgeR. Differentially expressed genes were determined to be statistically significant based on an adjusted p < 0.05.
Genome_build: Elizabethkingia anophelis Ag1 (GCA_000240095.2)
Supplementary_files_format_and_content: HTSeq gene counts against the Elizabethkingia anophelis NUPH1 annotations; the gene IDs (e.g. EAAG1_000010) are searchable in a GFF file (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/240/095/GCF_000240095.2_ASM24009v3) as locus tags.

organism: Elizabethkingia anophelis

source_name: bacterial culture_iron_plus

growth_protocol: E. anophelis cultures were grown overnight in LB and OD600nm was adjusted to 0.1 by diluting the cells into 20 ml of LB supplemented with either 12 µM of FeCl3 or 200 µM of 2, 2-dipyridyl in 250 ml flasks. Cells were grown at 30°C with shaking (200 rpm) for 3 hours to a final OD of 0.2 or 0.5 for iron-depleted cultures or iron-replete ones, respectively.

extract_protocol:
Cells grown in log-phase were re-suspended in RNAlater and frozen immediately after being harvested. RNA was isolated using Trizol reagents following the manufacturer’s manual. Residual DNA in the samples was removed using Dnase I. The integrity of the RNA was analyzed using an Agilent bioanalyzer (Agilent Technologies).
The Ribo-Zero rRNA removal kit (Gram-negative bacteria, Epicentre) was used to remove the ribosomal RNA species (23S and 16S rRNA) from total RNA in samples. Library construction and sequencing were performed by Beijing Genomics Institute (BGI) using TruSeq RNA sample preparation v2 guide (Illumina).

tag: growth phase

value: Log

value: Plus iron supplement


title: FC3P02

value: wild type

value: Hypothalamus


title: FC1P10


title: 5EU 60 min replicate 1

description: 5EU-labeled RNA


title: EGF 72 replicate 2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

description:
tablecounts_raw.csv
D203T07

data_processing:
Raw sequencing reads were aligned on the human hg38 reference genome using the STAR mapper [7] (2.5.3a), up to the generation of a raw count table per gene (Gencode annotation v26). Expressed genes (TPM>=1 in at least one sample) have then been selected for downstream analysis. The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3) functions were applied to detect genes with differential expression between untreated and EGF samples. Genes with an adjusted pvalue < 0,05 and a log2 fold-change > 1 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: table of raw counts per gene

source_name: Basal breast cancer cells

extract_protocol:
MDA-MB-468 cells were grown to ~ 70% confluence on 140 cm2 dishes and treated with EGF (100 ng mL-1) for 72 h in biological duplicate. Untreated cells were used as an appropriate control. Whole cell extracts (~ 9 x 105 cells) were collected by centrifugation at 500 x g for 5 min at 4ºC and washed twice in ice-cold PBS1x. Total RNA were extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and subjected to DNase I treatment using the RNase-free DNase set (Qiagen).  The total RNA was then analyzed using Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer System to determine RNA concentration, qualify RNA Integrity Number (RIN) which was high with RIN = 10 for all samples and confirm removal of DNA contamination.  After quality control of RNA, the ERCC RNA Spike-In (Ambion) was added to RNA samples (RNA samples: RNA Spike-In control diluted at 1/100, 5:1).
RNA sequencing libraries were prepared from 1µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. The 4 libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche). Sequencing was carried out on the NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases) using a S1 flow cell in order to obtain around 35 million clusters (70 million raw paired-end reads) per sample

treatment_protocol: Cells were harvested by trypsinization. After adding media to stop trypsin, cells were centrifuged at 500 x g for 5 min at room temperature.

value: MDA-MB-468 cells

tag: passages

value: EGF (100 ng mL-1) for 72 h


title: EGF 72 replicate 3

description:
tablecounts_raw.csv
D203T08

growth_protocol: MDA-MB-468 cells were grown to ~ 70% confluence on 140 cm2 dishes and treated with EGF (100 ng mL-1) for 72 h in biological duplicate. Untreated cells were used as an appropriate control. Whole cell extracts (~ 9 x 105 cells) were collected by centrifugation at 500 x g for 5 min at 4ºC and washed twice in ice-cold PBS1x.


title: NL

description:
NL-VS-L0.filter.annot
Hylocereus undatus Britt

value: no flowering under no light


title: Iron_plus_B


title: FC2P02

tag: genotype


title: FC2P00


title: FC2E17


title: FC2E15


title: Iron_plus_C


title: Iron_minus_B

source_name: bacterial culture_iron_minus

value: Minus iron supplement


title: Iron_minus_A


title: Iron_minus_C