title: Rad21tev+1UGDOX24H_6DWASH_primary_neuron_culture Rep1


title: healthy control Patient5345 [NeuN-pos RNAseq]

status: Public on Feb 28 2021

type: SRA

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.positive_GeneCounts.csv
5345

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to hg38 whole genome using tophat2 (2.0.11) with argument “--library-type fr-firststrand"
Gene annotations were obtained from iGenome UCSC hg38. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: cortical neuronal nuclei

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
40ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (ribozero ribosomal RNA depletion), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library..

treatment_protocol: Isolation of nuclei was performed as previously described (Krishnaswami et al., 2016) with minor modifications. Briefly, 50-250mg of pre-frontal cortical grey matter was homogenised in homogenisation buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 1μM DTT, 1X Proteinase Inhibitor w/o EDTA (Roche), 0.4U μl-1 RNaseIn (ThermoFisher) 0.2U μl-1 Superasin (ThermoFisher), 1μM DAPI) and centrifuged through an iodixanol gradient (Sigma). Pelleted nuclei were washed and then stained with NeuN antibody (Abcam, ab190195) in staining buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher), NeuN antibody (1:200)) for one hour at 4oC. For negative controls antibody was excluded. Nuclei were then sorted on BD Fusion, and collected in wash buffer (PBS, 1%BSA, 0.2U/μl RNaseIn (Thermofisher)), before proceeding to downstream RNA extraction.

tag: disorder

value: healthy control

tag: age

tag: gender

value: Female


title: CdLS Patient764P [NeuN-neg RNAseq]

description:
RNA-seq of CdLS cortical neuronal nuceli
CdLS.NeuN.negative_GeneCounts.csv

source_name: cortical non-neuronal nuclei

value: CdLS


title: NipblHET primary dissociated cortical neuron Rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
The reads were aligned to mouse genome UCSC mm9 using Tophat2 with arguments  “--library-type fr-firststrand”
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

organism: Mus musculus

source_name: Primary dissociated cortical neuron

growth_protocol: Mouse cortices were dissected and dissociated from individual E17.5-E18.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 0.8 × 10^6 cells per well on 6-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and one third of the media in each well was replaced every 3 days. Cultures were treated with 5uM Cytosine β-D-arabinofuranoside (Ara-C, Sigma) from day 2-4.

extract_protocol:
Total RNA was obtained in parallel from dissociated cortical neurons at DIV10 with QIAshredder and RNeasy mini kit (Qiagen).
RNA-seq libraries were prepared from 600 ng of total RNA (RNA integrity number (RIN) >8.0) with TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina).

tag: genotype

value: Nipbl+/-


title: IN55-gRNA-unedited-3

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

description: Quantification_of_editing_reads_counts_and_frequency.xls

library_source: genomic

data_processing:
Library strategy: Amplicon-seq
High-throughput sequencing was performed on NOVA SEQ system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
The types and proportions of SNVS are analyzed using customized shell scripts
Genome_build: hg38

molecule: genomic DNA

source_name: Muscle-derived stem cells

extract_protocol:
The cells were trypsinized and collected, and genomic DNA was extracted using the TIANamp Genomic DNA Kit (TIANGEN)
Amplification primers containing Illumina forward and reverse adapters were used for a first round of PCR (PCR 1) amplifying the genomic region of interest. Unique Illumina barcoding primer pairs were  added to each sample in a secondary PCR reaction (PCR 2).

tag: tissue

value: Muscle

tag: passages

tag: treatment

value: IN55-gRNA untreated


title: NipblHET primary dissociated cortical neuron Rep2


title: IN45-Cas9-gRNA-cas9-1

value: IN45-Cas9-gRNA cas9 only


title: CdLS Patient380P [NeuN-neg RNAseq]

value: Male


title: IN55-gRNA-unedited-2


title: NipblHET primary dissociated cortical neuron Rep1


title: NipblWT primary dissociated cortical neuron Rep3

value: Nipbl+/+


title: NipblWT primary dissociated cortical neuron Rep2


title: Rad21tev+VEH24H_6DWASH_primary_neuron_culture Rep1

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Reads were mapped to mm9 whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Primary neuron

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 2.5 × 10e05 cells per well on 24-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and half of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding NLS-TEV at a multiplicity of infection of 1. AraC was added 2 days later. Following 10 days in culture either 100ug/ml doxycyline or carrier (water) were added and samples collected 7 days later

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
200ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (ribozero ribosomal RNA depletion), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library..

treatment_protocol: On DIV10 1ug/ml doxycycline or water (as indicated in each individual sample) was added to the cells for 24 hours, and samples collected 7 days following beginning of treatment

value: water


title: IN45-Cas9-gRNA-mock-1

value: IN45-Cas9-gRNA mock (pbs)


title: CdLS Patient2082 [NeuN-neg RNAseq]


title: NipblWT primary dissociated cortical neuron Rep1


title: healthy control Patient2308 [NeuN-neg RNAseq]

description:
RNA-seq of healthy control cortical neuronal nuceli
CdLS.NeuN.negative_GeneCounts.csv


title: IN55-gRNA-target-3

value: IN55-gRNA gRNA+Cas9


title: healthy control Patient4715 [NeuN-neg RNAseq]


title: healthy control Patient1739 [NeuN-neg RNAseq]


title: IN45-Cas9-gRNA-cas9-3


title: IN55-gRNA-mock-3

value: IN55-gRNA mock (pbs)


title: IN55-gRNA-target-1


title: Rad21tev+1UGDOX24H_6DWASH_primary_neuron_culture Rep2

value: doxycycline


title: healthy control Patient4788 [NeuN-neg RNAseq]


title: healthy control Patient5345 [NeuN-neg RNAseq]


title: healthy control Patient3011 [NeuN-neg RNAseq]


title: IN55-gRNA-cas9-3

value: IN55-gRNA cas9 only


title: IN55-gRNA-mock-1


title: IN55-gRNA-cas9-2


title: IN44-gRNA-unedited-3

value: IN44-gRNA untreated


title: IN55-gRNA-cas9-1


title: input DNA

city: Wuhan

first: Ying

last: Huang

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University

data_processing:
Reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Gallus_gallus-5.0 of ensembl using Bowtie2 v2.3.4.1
MACS2 (v2.1.1.20160309) was used for peak calling with parameters -B -p 1e-9, where chicken genome size is set to 1.2e9
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: bedGraph files were generated using MACS2

organism: Gallus gallus

source_name: ovary

growth_protocol: The primary granulosa cells were pre-cultured with Medium 199 (Gibco, USA) and 5% FBS (Gibco, USA) overnight (8h).

extract_protocol: The chromatin was obtained by cell lysis (50 mM HEPES, pH 7.5; 150 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; and proteinase inhibitors) and was followed by sonication (Sonics VCX130, USA) on ice for 6 min. DNA (1 μg) was used for the preparation of the Chromatin Immunoprecipitation Sequencing (ChIP-Seq) library by NEBNext UltraII DNA Library Prep Kit for Illumina (NEB, USA, E7645 and E7335), according to the manufacturer’s instructions. The ChIP DNA library was sent to Novogene Co., Ltd. (Beijing, China) for paired-end 150 bp sequencing on the Illumina Nova platform.

tag: breed

value: Hy-Line Brown

value: follicle

tag: cell type

value: granulosa

tag: chip antibody


title: IN55-gRNA-target-2


title: Rad21tev+etoh_24h_primary_neuron_culture Rep3

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_ETOH_24H_Rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 1 × 10e06 cells per well on 6-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and one third of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding ERt2-TEV at a multiplicity of infection of 3. AraC was added 2 days later, and 500nM 4-hydroxy tamoxifen or carrier (ethanol) were added for 24h or 72h after 10 days in culture.

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
200ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (polyA enrichment), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library.

treatment_protocol: On DIV10 500nM 4-hydroxy tamoxifen or ethanol (as indicated in each individual sample) was added to the cells for 24 hours.

value: ethanol


title: IN44-gRNA-unedited-1


title: IN44-gRNA-unedited-2


title: Rad21tev+etoh_24h_primary_neuron_culture Rep1

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_ETOH_24H_Rep1


title: IN55-gRNA-unedited-1


title: Rad21tev+4OHT_24h_primary_neuron_culture Rep3

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_4OHT_24H_Rep3

value: 4-hydroxy tamoxifen


title: IN44-gRNA-target-3

value: Muscle

value: IN44-gRNA gRNA+Cas9


title: IN44-gRNA-target-1


title: Rad21tev+VEH6h_7Dwash_primary_neuron_culture Rep3

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH7D_Rep3

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 1 × 10e06 cells per well on 6-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and one third of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding NLS-TEV at a multiplicity of infection of 3. AraC was added 2 days later, and 6h 100ng/ml doxycyline or carrier (water) were added and samples collected 24h or 7 days later

treatment_protocol: On DIV10 100ng/ml doxycycline or water (as indicated in each individual sample) was added to the cells for 6 horus, and samples collected 24 hours or 7 days later


title: Rad21tev+4OHT_24h_primary_neuron_culture Rep1

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_4OHT_24H_Rep1


title: Rad21tev+4OHT_24h_primary_neuron_culture Rep2

description:
RNA-seq of tamoxifen-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_4OHT_24H_Rep2


title: Rad21tev+VEH6h_7Dwash_primary_neuron_culture Rep1

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH7D_Rep1


title: Rad21tev+VEH6h_7Dwash_primary_neuron_culture Rep2

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH7D_Rep2


title: AT01_3

city: Hohhot

first: LiGe

last: Bao

address: Inner Mongolia Agricultural University, No. 306, Zhaowuda Road/Street

institute: College of Veterinary Medicine, Inner Mongolia Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt software was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases, we used HISAT2 software to map reads to the genome. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package-edgeR.
Genome_build: Rattus norvegicus(ftp://ftp.ensembl.org/pub/release-88/fasta/rattus_norvegicus)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample ...

organism: Rattus norvegicus

source_name: Fibroblast-like synoviocytes

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Rat synovial tissues

value: Fibroblast-like synoviocytes

tag: treated

value: treated by 10^-7M TCDCA


title: IN55-gRNA-mock-2


title: IN44-gRNA-mock-3

value: IN44-gRNA mock (pbs)


title: IN44-gRNA-mock-2


title: AT01_2


title: IN44-gRNA-mock-1


title: Rad21tev+DOX6h_7Dwash_primary_neuron_culture Rep2

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX7D_Rep2


title: Rad21tev+DOX6h_7Dwash_primary_neuron_culture Rep3

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX7D_Rep3


title: IN44-gRNA-cas9-3

value: IN44-gRNA cas9 only


title: AT1_3

value: treated by 10^-6M TCDCA


title: Rad21tev+DOX6h_7Dwash_primary_neuron_culture Rep1

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX7D_Rep1


title: IN44-gRNA-cas9-2


title: Rad21tev+ VEH6h_24hwash_primary_neuron_culture Rep2

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH24H_Rep2

value: water


title: Rad21tev+etoh_24h_primary_neuron_culture Rep2

description:
RNA-seq of ethanol-treated Rad21-Tev primary neuron transduced with ERT2-TEV
Rad21Tev24_GeneCounts.csv
TEV_ETOH_24H_Rep2


title: AT01_1


title: Rad21tev+VEH_6h_24hwash_primary_neuron_culture Rep3

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH24H_Rep3


title: AT1_1


title: IN44-gRNA-target-2


title: AT10_3

value: treated by 10^-5M TCDCA


title: AT10_2


title: FCA2

value: untreated group


title: Rad21tev+VEH6h_24hwash_primary_neuron_culture Rep1

description:
RNA-seq of vehicle-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_VEH24H_Rep1


title: Rad21tev+DOX6h_24hwash_primary_neuron_culture Rep3

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX24H_Rep3

value: doxycycline


title: Rad21tev+DOX6h_24hwash_primary_neuron_culture Rep2

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX24H_Rep2


title: Rad21tev+ DOX6h_24hwash_primary_neuron_culture Rep1

description:
RNA-seq of doxycycline-treated Rad21-Tev primary neuron transduced with NLS-TEV
Rad21Dox1D7D_GeneCounts.csv
TEV_DOX24H_Rep1


title: Stretch_RASAG_Day_11

city: Heverlee

first: Adrian

last: Ranga

state: Flanders

address: Celestijnenlaan 200F - Room 03.349

department: Mechanical Engineering

country: Belgium

institute: KU Leuven

data_processing:
Raw sequencing data was demultiplexed using the mkfastq pipeline of CellRanger 3.0.2.
Alignment, barcode assignment and UMI quantification was performed using the count pipeline of CellRanger 3.0.2 and mapped to the hg38 genome
Genome_build: hg38
Supplementary_files_format_and_content: processed raw count text file was generated from the Seurat object on R, and contains the raw count of each gene for every cell that remained after the QC step
Supplementary_files_format_and_content: metadata text file was generated from the Seurat object on R, and contains the metadata of each cell that remained after the QC step

source_name: Human iPSC derived neural tube organoids

growth_protocol: single iPSCs were embedded in PEG hydrogels with a stiffness of 2 kPa and grown on top of elastomeric membranes connected to mechanical stretching devices. The cells were kept in neurobasal medium for 11 days with media changes every 2 days after the first 3 days.

extract_protocol:
PEG gels were detached from elastomeric membranes and dissociated using TrypLE for 6 to 7 minutes at 37 degrees Celsius and with mechanical agitation. This process also dissociated the embedded organoids into single cells. The TrypLE was neutralized using DMEM with 20% FBS. The single cells were spun down and washed twice with PBS before filtering and loading into the 10X Genomics Chromium Single Cell 3' Kit.
Library preparations for the scRNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were accessed using LUNA dual fluorescence cell counter (Logos Biosystems) and a targeted cell recovery of 6000 cells was aimed for all the samples. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3 user guide; CG00052 Rev B), and at the different check points, the library quality was accessed using Qubit  (ThermoFisher) and Bioanalyzer (Agilent). With a sequencing coverage targeted for 50,000 reads per cell, single cell libraries were sequenced either on Illumina’s NovaSeq 6000 or NovaSeq 500 platforms using paired-end sequencing workflow and with recommended 10X; v3 read parameters (28-8-0-91 cycles).

treatment_protocol: Rock inhibitor (Y-27632) was supplemented to the media for the first 3 days to help increase survival. From day 3 to 5 a treatment of retinoic acid (RA) and smoothened agonist (SAG) are supplemented to the media. During this treatment period, stretched samples (samples 1 and 3) underwent an equibiaxial stretch that increased the surface area of the membrane by 100%.

tag: tissue/cell type

tag: experimental time

value: Day 11

value: Treated with RA and SAG

tag: stretch state

value: stretched


title: AT10_1


title: FCA3


title: No_Stretch_RASAG_Day_11

value: Human iPSC derived neural tube organoids

value: unstretched


title: FCA1


title: AT1_2


title: IN44-gRNA-cas9-1

description: Quantification_of_editing_reads_counts_and_frequency.xls

value: Muscle


title: WT2: WT M-MDSC rep2

status: Public on Feb 27 2021

city: Shanghai

first: Jiawei

last: Li

address: 180 Fenglin Road

institute: Fudan University Zhongshan Hospital

data_processing:
Data were filtered to get clean reads with Seqtk.
RNA-seq reads were aligned to the GRCm38.p4 (mm9) genome assembly using Hisat2 (version 2.0.4) with default parameters.
After Hisat2 comparison, the number of Fragments of each gene were counted with Stringtie (version: 1.3.0), and then nor alized using TMM (trimmed mean of M values).  Finally, using perl script to calculate the FPKM value of each gene.
Genome_build: GRCm38.p4 (mm9)
Supplementary_files_format_and_content: gene expression excel

source_name: bone marrow

extract_protocol:
Sorted fresh MDSC cells were put in Trizol reagent and total RNA was harvested. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Myeloid-derived suppressor cells

tag: strain

value: mTOR WT


title: WT1: WT M-MDSC rep1


title: WT3: WT M-MDSC rep3


title: ESTn_vnx_d13_8

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

data_processing:
Sequencing was performed using a NextSeq 500 sequencer (Illumina) and the NextSeq 500/550 High Output Kit version 2.5 (75 cycles).
Bcl2fastq (version 2.19.0.316) was used to base call and demultiplex raw bcl files into FASTQ files.
Quality control reports were generated using FastQC (version 0.11.5).
Reads were mapped to the mouse reference genome (GRCm38.p6, release 15) using STAR (version 2.6.0b).
Read counts were compiled into an expression matrix using featureCounts (version 1.6.1).
Genome_build: GRCm38.p6, release 15
Supplementary_files_format_and_content: CountTable.xlsx: count data per sample plus gene annotation

molecule: polyA RNA

source_name: neural embryonic stem cells

growth_protocol: Murine embryonic stem cells (ES-D3, ATCC) were maintained on polystyrene 35 mm plates in a humidified atmosphere at 37 °C and 5% CO2, and passaged every two to three days.

extract_protocol:
Eight samples per condition were fixated in QIAzol and kept at −80 °C until further use. Samples were homogenised using the QIAshredder and subsequently purified with the RNeasy microarray tissue kit according to manufacturer’sprotocol. The Qubit was used to determine the RNA concentration and the Bioanalyzer to determine the quality of the samples.
Samples were further processed for Next Generation Sequencing according to the Illumina TruSeq Stranded mRNA protocol.

treatment_protocol: Neural differentiation was performed as described in Theunissen et al. (2011, Toxicol. Sci. 122, 437–447). Stem cells were differentiated for three days to form an embryonic body (EB) before being exposed to either 2 μM of FLX or 90 μM of VNX, from day 3 to day 7 or 13 of their differentiation.

value: neural embryonic stem cells

tag: time

value: day 13

value: 90 uM venlafaxine

tag: replicate


title: ESTn_vnx_d13_7


title: ESTn_vnx_d13_2


title: ESTn_vnx_d13_3


title: ESTn_vnx_d13_1


title: ESTn_vnx_d13_5


title: RAW264.7 macrophages, LPS activated, 13-HDHEA treatment, replicate 3

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

label: biotin

source_name: RAW264.7 macrophages, LPS activated (1.0 µg/mL), 13-HDHEA treatment (5.0 µM)

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: RAW264.7 macrophages (American Type Culture Collection, Teddington, UK) were cultured in DMEM containing 10% FCS and 1% penicillin and streptomycin (P/S) at 37 °C in a 5% CO2 humidified incubator. For the incubations 2 mL of 250.000 cells/mL were seeded and incubated for 24h in 6-wells plates.

extract_protocol: RNA was isolated using Qiagen RNeasy Micro Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: At the day of the experiment, medium of the adherent cells was discarded and replaced by fresh medium containing a vehicle (0.1% EtOH in medium), 5.0 µM 13-HDHEA (13-hydroxydocosahexaenoyl ethanolamide), 5.0 µM 16-HDHEA (16-hydroxydocosahexaenoyl ethanolamide)or a combination of 13-HDHEA (2.5 µM )and 16-HDHEA (2.5 µM). During the incubations the final concentration of EtOH was preserved at 0.1% in DMEM. After 30 min. pre-incubation with vehicle or the endocannabinoids, the macrophages were stimulated with 1.0 µg/mL LPS. This was achieved by adding 20 µL of 100 µg/mL LPS (10% PBS in medium) to cells. Control incubations without LPS were treated with 20 µL 10% PBS in medium instead of the LPS. Cells were harvested after 24h.

tag: cell line

value: macrophages

tag: experimentid

tag: preincubation (30min) with

value: 5.0 uM 13-HDHEA (13-hydroxydocosahexaenoyl ethanolamide)

tag: lps activated (1.0 ug/ml)

value: yes


title: RAW264.7 macrophages, LPS activated, vehicle treatment, replicate 2

source_name: RAW264.7 macrophages, LPS activated (1.0 µg/mL), vehicle treatment (0.1% EtOH)

value: vehicle (0.1% EtOH)


title: ESTn_vnx_d13_4

tag: tissue


title: L_W22_37R3 (reanalysis)

city: Ames

first: Stephen

middle: H

last: Howell

state: Iowa

address: 1111 WOI Road

department: Plant Sciences Institute Department of Genetics, Development and Cell Biology

country: USA

institute: Iowa State University

description: re-analysis of GSM4669870

data_processing:
Sequencing data were filtered with SOAPnuke (v1.5.2, github.com/BGI-flexlab/SOAPnuke) by removing reads (1) containing sequencing adapters, (2) in which more than 20% of the bases have a quality score less than 5 or (3) in which 5% or more of the bases are unknown (represented by N).  Clean reads were stored in FASTQ format and mapped to the reference maize B73 genome using HISAT2 (v2.0.4, http://www.ccb.jhu.edu/software/hisat/index.shtml). And then used for quality control, visualization of the alignment, new transcript prediction. Bowtie2 (v2.2.5, http://bowtiebio.sourceforge.net/%20Bowtie2%20/index.shtml) was used to align the clean reads to the reference coding gene set (transcripts (cDNA), plants.ensembl.org/info/website/ftp/index.html).
After alignment with the reference genome, rMATS (Shen et al., 2014) (v3.2.5, http://rnaseq-mats.sourceforge.net) was used to detect AS of the samples. Five major types of alternative splicing were detected including exon skipping (ES), intron retention (IR), mutually exclusive exons (MXE), alternative 5’ donor sites (A5SS) or alternative 3’ acceptor sites (A3SS).  rMATS is a statistical method for robust and flexible detection of differential AS from replicate RNA-Seq data. rMATS uses a likelihood-ratio test to calculate the P value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. First, the IncLevel1 (denoted as ψ, Inclusion Level) and IncLevel2 from two conditions is calculated as such: ψ = (I/LI) / (I/LI + S/LS). where: ψ = Inclusion Level (IncLevel1), I = number of reads mapped to the exon inclusion isoform (IC_SAMPLE_1), S = number of reads mapped to the exon skipping isoform (SC_SAMPLE_1), LI = effective length of the exon inclusion isoform ( IncFormLen), LS = effective length of the exon skipping isoform (SkipFormLen). IncLevelDifference =  IncLevel1 - IncLevel2.  rMATS uses a likelihood-ratio test to calculate the P value for the difference in the mean ψ values between two sample groups. The false discovery rate (FDR) was obtained by using Benjamini Hochberg method, and the threshold of |Δψ| > 5% and FDR ≤1% were used to judge the alternative splicing.
Supplementary_files_format_and_content: Alternative splicing events in W22 in response to increased MDTs (20 DAG).csv  : tab-delimited csv files include count values for alternative splicing events in samples for 20 DAG plants
Supplementary_files_format_and_content: Alternative splicing events in W22 in response to increased MDTs (27 DAG).csv: tab-delimited csv files include count values for alternative splicing events in samples for 27 DAG plants
Supplementary_files_format_and_content: Differential alternative splicing events in W22 in response to increased MDTs (20 DAG).xlsx: tab-delimited xlsx files include count values for differential alternative splicing (DAS) events in samples for 20 DAG plants
Supplementary_files_format_and_content: Differential alternative splicing events in W22 in response to increased MDTs (27 DAG).xlsx: tab-delimited xlsx files include count values for differential alternative splicing (DAS) events in samples for 27 DAG plants

organism: Zea mays

source_name: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 3

growth_protocol: Seeds of maize W22 were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition. The performance of plants under these conditions was monitored by a robot, equipped with various sensors, that travels from chamber to chamber (Bao et al., 2019).  The temperature and light cycles were offset by 40 min from chamber to chamber to allow the robot to enter the different chambers at the same time of virtual day. The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  Plant performance was assessed at three different stages of vegetative growth, V4, V5 and V13-R1 stages (He et al., 2010), with the most extensive analysis carried out at the mid vegetative stages (V4 and V5).  The stages are defined by the leaf numbers visible in the collars.  For example, the V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

extract_protocol:
RNA was extracted from small samples (0.1 g) of leaf lamina (avoiding the midrib) obtained from the middle of the first fully expanded leaves. The samples were taken in triplicate, one sample from each of three different plants, in the two chambers set for the same conditions.  The samples obtained from the plants in the two different chambers were taken at the same time of virtual day, because the temperature and light cycles are offset to allow for sampling at the same time of day. The samples were separately ground to a powder in liquid nitrogen, and RNA was isolated using a Plant RNeasy Mini Kit and treated with DNase (Qiagen, www.qiagen.com/us/) according to the manufacturer’s instructions. RNA quality and quantity were determined by the UV absorbance spectra, gel electrophoresis and Agilent 2000 BioAnalyzer (http://www.agilent.com).
For RNAseq analysis, poly A RNA was isolated from the purified RNA using oligo(dT)-attached magnetic beads and fragmented at elevated temperature with NEBNext RNA fragmentation buffer (New England BioLabs).  cDNA library construction, sequencing, and primary bioinformatics analysis were performed by BGI Tech Solutions Co., Ltd. (Beijing Genomic Institute (www.genomics.org.cn, BGI)) as follows:  First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis.  cDNA ends were repaired by A-Tailing followed by adding RNA Index Adapters. The cDNA fragments were amplified by PCR, and the products purified by Ampure XP Beads (Beckman Coulter).  The products were validated for quality control using an Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized using splint oligos (Diegelman and Kool, 2000). The single strand circular DNAs (ssCir DNAs) were amplified with phi29 (Blanco et al., 1989) to make DNA nanoballs (DNBs) (Porreca, 2010).  DNBs were loaded into the patterned nanoarray and single end 50 base reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Seeds of maize W22 were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition.  The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  The V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

tag: ecotype

value: leaf

tag: Stage

value: V5 stage

tag: condition

value: maximum daily temperature 37°C


title: L_W22_37R1 (reanalysis)

description: re-analysis of GSM4669868

source_name: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 1


title: ESTn_vnx_d7_7

value: day 7

tag: treatment


title: RAW264.7 macrophages, no LPS, replicate 3

source_name: RAW264.7 macrophages, not activated (no LPS; PBS only), vehicle treatment (0.1% EtOH)

tag: cell type

value: no


title: L_W22_35R2 (reanalysis)

description: re-analysis of GSM4669866

source_name: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 2

value: maximum daily temperature 35°C


title: RAW264.7 macrophages, LPS activated, 16-HDHEA treatment, replicate 2

source_name: RAW264.7 macrophages, LPS activated (1.0 µg/mL), 16-HDHEA treatment (5.0 µM)

value: 5.0 uM 16-HDHEA (16-hydroxydocosahexaenoyl ethanolamide)


title: RAW264.7 macrophages, LPS activated, vehicle treatment, replicate 3


title: RAW264.7 macrophages, LPS activated, 16-HDHEA treatment, replicate 3


title: L_W22_33R3 (reanalysis)

description: re-analysis of GSM4669864

source_name: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 3

value: maximum daily temperature 33°C


title: RAW264.7 macrophages, LPS activated, 13-HDHEA treatment, replicate 1


title: RAW264.7 macrophages, LPS activated, 13-HDHEA treatment, replicate 2


title: RAW264.7 macrophages, no LPS, replicate 2


title: RAW264.7 macrophages, LPS activated, combined 13-HDHEA + 16-HDHEA treatment, replicate 3

source_name: RAW264.7 macrophages, LPS activated (1.0 µg/mL), combined 13-HDHEA  (2.5 µM) and 16-HDHEA (2.5 µM) treatment

value: 2.5 uM 13-HDHEA (13-hydroxydocosahexaenoyl ethanolamide) + 2.5 uM 16-HDHEA (16-hydroxydocosahexaenoyl ethanolamide)


title: RAW264.7 macrophages, LPS activated, combined 13-HDHEA + 16-HDHEA treatment, replicate 1


title: RAW264.7 macrophages, LPS activated, combined 13-HDHEA + 16-HDHEA treatment, replicate 2


title: RAW264.7 macrophages, LPS activated, vehicle treatment, replicate 1


title: RAW264.7 macrophages, LPS activated, 16-HDHEA treatment, replicate 1


title: RAW264.7 macrophages, no LPS, replicate 1


title: L_W22_33R2 (reanalysis)

description: re-analysis of GSM4669863

source_name: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 2


title: ESTn_vnx_d7_8


title: L_W22_37R2 (reanalysis)

description: re-analysis of GSM4669869

source_name: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 2


title: L_W22_35R3 (reanalysis)

description: re-analysis of GSM4669867

source_name: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 3


title: ESTn_vnx_d7_6


title: L_W22_35R1 (reanalysis)

description: re-analysis of GSM4669865

source_name: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 1


title: E_W22_35R3 (reanalysis)

description: re-analysis of GSM4669843

source_name: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 3

value: V4 stage


title: L_W22_33R1 (reanalysis)

description: re-analysis of GSM4669862

source_name: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 1


title: ESTn_flx_d13_8

value: neural embryonic stem cells

value: 2 uM fluoxetine


title: ESTn_flx_d13_5

value: day 13


title: ESTn_flx_d13_7


title: ESTn_vnx_d7_5

value: 90 uM venlafaxine


title: L_W22_31R3 (reanalysis)

description: re-analysis of GSM4669861

source_name: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 3

value: maximum daily temperature 31°C


title: E_W22_31R3 (reanalysis)

description: re-analysis of GSM4669837

source_name: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 3


title: E_W22_31R1 (reanalysis)

description: re-analysis of GSM4669835

source_name: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 1


title: E_W22_33R1 (reanalysis)

description: re-analysis of GSM4669838

source_name: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 1


title: L_W22_31R1 (reanalysis)

description: re-analysis of GSM4669859

source_name: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 1


title: E_W22_37R3 (reanalysis)

description: re-analysis of GSM4669846

source_name: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 3


title: E_W22_33R2 (reanalysis)

description: re-analysis of GSM4669839

source_name: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 2


title: L_W22_31R2 (reanalysis)

description: re-analysis of GSM4669860

source_name: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 2


title: ESTn_vnx_d7_2

source_name: neural embryonic stem cells


title: ESTn_vnx_d7_3


title: E_W22_37R2 (reanalysis)

description: re-analysis of GSM4669845

source_name: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 2


title: Z56065

city: Suzhou

first: Qiu

last: Chen

address: 199 Renai Road

institute: Soochow University

data_processing:
Removelow quality tags
Remove tags with 5'primer contaminants
Remove tags without 3'primer
Remove tags without insertion
Remove tags with polyA and shorter than18nt
Supplementary_files_format_and_content: We use miRDeep2 (for animals) to predict novel miRNA by  exploring the characteristic hairpin structure of miRNAprecursor.   Piano is used to predict piRNAs. This algorithm is based on the Support Vector  Machine (SVM) algorithm and transposon interaction information.

source_name: seminal plasma

extract_protocol:
miRNeasy Serum/Plasma Advanced Kit
1)Filter small RNA: separate18-30nt RNA segment by PAGEgel.  2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3'  end of selectedsmall RNAs from step1.  3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is  cross-linked to the 3'adapter of RNAs and excessive free 3'adapter.  4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The  connection (5' adaptor) will be attached to the 5' end only, but it is not c onnected to  the 3'adaptor or RT primer hybrid chain.This greatly reduces self-ligation.  5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand  cDNA.  6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with  both3'and5'adaptor.
7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to  eliminate primer-dimer and other by products.  8)Library quantitative and pooling cyclization.

tag: gender

value: male

tag: sperm symptoms

value: astheno-teratospermia

tag: population

value: Han population

value: seminal plasma


title: E_W22_37R1 (reanalysis)

description: re-analysis of GSM4669844

source_name: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 1

value: leaf

value: maximum daily temperature 37°C


title: M48529


title: ESTn_flx_d13_2


title: E_W22_35R2 (reanalysis)

description: re-analysis of GSM4669842

source_name: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 2


title: Z59095

value: Asthenospermia


title: E_W22_35R1 (reanalysis)

description: re-analysis of GSM4669841

source_name: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 1

value: maximum daily temperature 35°C


title: ESTn_vnx_d7_1

value: day 7


title: E_W22_33R3 (reanalysis)

description: re-analysis of GSM4669840

source_name: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 3

value: maximum daily temperature 33°C


title: ESTn_flx_d7_8


title: ESTn_flx_d13_6


title: E_W22_31R2 (reanalysis)

description: re-analysis of GSM4669836

source_name: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 2


title: ESTn_flx_d13_4


title: C45043


title: ESTn_flx_d7_5


title: X74546


title: C95886

value: teratospermia


title: F65654


title: W58194


title: ESTn_flx_d13_1


title: L97940

value: normal


title: T02958


title: S55153


title: L31752


title: ESTn_flx_d7_6

value: neural embryonic stem cells


title: ESTn_flx_d7_4

value: 2 uM fluoxetine


title: X48288


title: Z91085


title: ESTn_flx_d7_1


title: ESTn_flx_d7_3


title: Z00061


title: ESTn_flx_d7_2


title: OE9

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

description: cultivars "Compound raceme"; flower

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000188115.4_SL3.0
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Tomato flower

growth_protocol: Tomatoes grow naturally in the greenhouse

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and paired end 150 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: cultivar

value: Compound raceme

value: flower


title: S64271


title: ESTn_con_d13_6

value: day 13

value: control


title: D92304

value: male


title: Mtb K -> LCMV + αIFNAR3 TCR

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

description: Chromium Single Cell VDJ library v1

data_processing:
mkfastq (Cell Ranger 5.0.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 5.0.0) was used to generate the filtered UMI matrix with default parameters
Seurat (4.0.0) was used to filter (cutoffs as follows: 1. number of genes per cell, at least 200 and 6000 at most; 2. percentage of mitochondrial counts per cell, 5% at most), normalize (LogNormalize function with default parameters) and scale the UMI matrix (ScaleData function regressing the variables mitochondrial gene percentage and number of UMIs per cell).
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Whole_Processed_annotations.tsv : meta data
Supplementary_files_format_and_content: Whole_Processed_normalized_counts.tsv : log-normalized counts
Supplementary_files_format_and_content: Whole_Processed_umi_counts.tsv : UMI count data matrix

source_name: Lung infiltrating CD45+ Immune cells

extract_protocol:
To create a single-cell suspension, each lung was chopped into small pieces, and incubated in RPMI supplemented with 1.3 mM EDTA at 37℃ on a shaking incubator for 30 min. After the incubation, the small fragments were incubated again in complete medium solution containing 0.1% collagenase type II (Worthington Biochemical, Lakewood, NJ, USA) for 1h. The single-cell suspensions were then filtered through a 40-μm cell nylon mesh strainer, treated with RBS lysis buffer (Gibco) for 3 min, and washed twice with RPMI containing 2% FBS. Lymphocytes from trachea lymph nodes were mashed through a 70- μm cell strainer (BD Falcon), and red blood cell (RBC) lysis was performed using ACK lysing buffer (Gibco Laboratories). For CD45.2+ cell enrichments, suspensions of pulmonary cells were enriched by two-step magnetic cell sorting. Briefly, lung cells were incubated with CD45.2-FITC antibody (Miltenyi Biotec) and washed out. Then, cells were incubated with Anti-FITC microbeads (Miltenyi Biotec) and separated by sequential passage through LS MACS column (Miltenyi Biotec). The positive fraction was mostly composed of CD45.2+ cells.
Single-cell sequencing libraries were prepared by using Chromiun 10X Genomics platform with a ChromiumTM Next GEM Single Cell 5’ Library & Gel Bead Kit (10X genomics) and ChromiumTM Single Cell V(D)J Enrichment Kit, mouse T cell (10X genomics) according to the manufacturer’s instructions.

treatment_protocol: Mice were exposed to Mtb K in the calibrated inhalation chamber of an airborne infection apparatus for 60 min delivering a predetermined dose (Glas-Col, Terre Haute, IN, USA) including approximately 200 to 300 viable bacteria. At 14 days post Mtb K infection, some of these mice were also infected intraperitoneally (i.p.) with 2x10^5 PFU of LCMV Armstrong (Arm) 53b. To blockade type I IFN receptor, 250 ug of anti-IFNAR1 (MAR1-5A3, Bio X cell) or Mouse IgG1 isotype control (MOPC-21, Bio X cell) was administrated to Mtb K infeted mice at 13, 15, and 17 days post Mtb infection by intraperitoneally injetion

tag: strain

value: Lung infiltrating CD45+ Immune cells

tag: genotype

value: alpha-IFNAR1 antibody (MAR1-5A3)


title: ESTn_con_d13_5

tag: time

tag: replicate


title: Mtb K -> LCMV + αIFNAR2 GEX

description: Chromium Next GEM Single Cell 5p RNA library v1.1


title: ESTn_con_d13_8


title: Mtb K -> LCMV + αIFNAR1 BCR

description: Chromium Single Cell VDJ library v1


title: ESTn_con_d13_4


title: ESTn_con_d13_7


title: Mtb K -> LCMV GEX

value: Isotype control antibody


title: CK2_3

description: cultivars "Compound raceme"; bud

source_name: Tomato bud

value: bud


title: OE30

description: cultivars "Compound raceme"; flower


title: Mtb K -> LCMV BCR

description: Chromium Single Cell VDJ library v1


title: ESTn_con_d13_2


title: Mtb K TCR

description: Chromium Single Cell VDJ library v1


title: CK2_1

description: cultivars "Compound raceme"; bud


title: CK2_2

description: cultivars "Compound raceme"; bud


title: Mtb K GEX


title: OE1

description: cultivars "Compound raceme"; flower


title: CK1_3

description: cultivars "monomaker"; bud

value: monomaker


title: Mtb K BCR

description: Chromium Single Cell VDJ library v1


title: ESTn_con_d7_7


title: CK1_1

description: cultivars "monomaker"; bud


title: ESTn_con_d13_1


title: Naïve TCR

description: Chromium Single Cell VDJ library v1


title: CK1_2

description: cultivars "monomaker"; bud


title: Naïve GEX


title: Mtb K -> LCMV TCR

description: Chromium Single Cell VDJ library v1


title: ESTn_con_d7_8


title: VMB_LRRK2_knockout_3_Ribo-seq

city: Berkeley

first: Jungwoo Wren

state: CA

address: Barker Hall, Room 416

department: Molecular and Cell Biology

institute: UC Berkeley

description: LRRK2 knockout 3

data_processing:
Library strategy: Ribo-seq
Illumina Casava 1.8 software used for basecalling.
Sequences were processed and trimmed using Greg Hannon's fastx_toolkit setup and rRNA depleted, aligned following a protocol from Ingolia NT. Nature Protocols (2012).  Tophat (2.0.11) with Bowtie2 (2.2.2) was used.
Counted reads were processed by DESeq (1.20), and translation efficiency was calculated.
(LRRK2 knockout set 1 ribosome profiling data are aligned reads as the original fastq became unavailable to access)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with DESeq processed expression levels and translation efficiency

source_name: LRRK2 knockout

extract_protocol:
Mouse brain samples; samples were dissected and frozen in dry ice, and homogenized and processed.
Libraries were prepared for sequencing using previously published ribosome profiling protocol.

tag: brain region

value: ventral midbrain

tag: age

value: 3 months old

value: LRRK2 knockout


title: Naïve BCR

description: Chromium Single Cell VDJ library v1


title: ESTn_con_d7_6

value: day 7


title: ESTn_con_d7_1


title: ESTn_con_d7_5


title: VMB_wild-type_control_3_Ribo-seq

description: wild-type control 3

source_name: wild-type control

value: wild-type


title: RNA-Seq-p38α-floxed-Vav-cre-iPC-rep1

city: xiamen

first: cai

last: shaowei

address: fujian province xiamen city Xiang 'an area Xiang 'an south road 4221

institute: university

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using STAR version 2.7.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: In vitro-differentiated B cell

growth_protocol: Naïve B cells purified from mouse spleen were firstly cultured on NIH3T3 feeder cells overexpress CD40L, BAFF and IL-4 (referred as IL-4 feeder cells in the text) on 6 well plates at a density of 1*105 cells/well for 4 days, then the iGCB cells were transferred to new NIH3T3 feeder cells overexpress CD40L, BAFF and IL-21 (referred as IL-21 feeder cells) also at a density of 1*105 cells/well and cultured for another 4 days, induced plasma cells (referred as iPCs) were collected at indicated times for future analysis.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using Stranded mRNA-seq Lib Prep Kit for Illumina (Cat. RK20301; ABclonal). Paired-end sequencing was performed with Illumina HiSeq platform.

treatment_protocol: Naïve B cells cultured in the iPC differentiation system at day 2 were infected with retrovirus.

value: induced CD138+ plasma B cell

value: untreated


title: ESTn_con_d7_4

value: neural embryonic stem cells


title: ESTn_con_d0_7

value: day 0


title: ESTn_con_d7_2


title: RNA-Seq-p38α-floxed-Vav-cre-iPC-rep3


title: STR_wild-type_control_3_Ribo-seq

description: wild-type control 3

value: striatum


title: STR_LRRK2_knockout_1_mRNA-seq

description: LRRK2 knockout 1

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequences were processed and trimmed using Greg Hannon's fastx_toolkit setup and rRNA depleted, aligned following a protocol from Ingolia NT. Nature Protocols (2012).  Tophat (2.0.11) with Bowtie2 (2.2.2) was used.
Counted reads were processed by DESeq (1.20), and translation efficiency was calculated.
(LRRK2 knockout set 1 ribosome profiling data are aligned reads as the original fastq became unavailable to access)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with DESeq processed expression levels and translation efficiency


title: ESTn_con_d0_6

value: control


title: STR_LRRK2_knockout_3_Ribo-seq

description: LRRK2 knockout 3


title: STR_wild-type_control_2_mRNA-seq

description: wild-type control 2


title: RNA-Seq-p38α-floxed-Vav-cre-iPC-rep2


title: Input_2362

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

country: Spain

institute: Universitat Autonoma de Barcelona

description:
Input replicate 3
Total RNA

hyb_protocol: Biotinilated cDNA was hybridized at 48ºC to MouseRef-8 v2 expression beadchips (Illumina) for 16h before washing and analyzing according to manufacturer’s directions.

scan_protocol: Signal was detected using a Beadarray Reader (Illumina)

data_processing: Data was analyzed for differential expression using the GenomeStudio data analysis software (Illumina). Average normalization, the Illumina custom error model and multiple testing corrections using Benjamini and Hochberg False discovery rate were applied to the analysis. Only transcripts with a differential score >13 were considered.

label: Biotin

source_name: input, mice ID 2362

label_protocol: RNA was amplified using the Ovation SL WTA system (Nugen) prior to biotinilation according to the EncoreIL biotinilation kit (Nugen).

extract_protocol: RNA was extracted using the RNeasy micro kit (Qiagen)

value: All cells in the VN


title: IP_2364

description:
Immunoprecipitate replicate 3
Polysome RNA

source_name: immunoprecipitate, mice ID 2364

value: VGLUT2 neurons in the VN


title: RNA-Seq-p38α-floxed-iPC-rep2


title: STR_wild-type_control_1_mRNA-seq

description: wild-type control 1


title: STR_LRRK2_knockout_2_mRNA-seq

description: LRRK2 knockout 2


title: RNA-Seq-p38α-floxed-iPC-rep1

value: induced CD138+ non-plasma B cell


title: RNA-Seq-p38α-floxed-iPC-rep3


title: Input_2364

description:
Input replicate 4
Total RNA

source_name: input, mice ID 2364


title: IP_2303

description:
Immunoprecipitate replicate 1
Polysome RNA

source_name: immunoprecipitate, mice ID 2303


title: ESTn_con_d0_8

source_name: neural embryonic stem cells


title: ESTn_con_d0_4


title: Input_2303

description:
Input replicate 2
Total RNA

source_name: input, mice ID 2303


title: IP_2362

description:
Immunoprecipitate replicate 2
Polysome RNA

source_name: immunoprecipitate, mice ID 2362


title: RNA-Seq-p38α-floxed-Vav-cre-non-PC-rep3

value: induced CD138- non-plasma B cell


title: STR_LRRK2_knockout_2_Ribo-seq

description: LRRK2 knockout 2


title: RNA-Seq-p38α-floxed-Vav-cre-non-PC-rep1


title: STR_LRRK2_knockout_1_Ribo-seq

description: LRRK2 knockout 1


title: ESTn_con_d0_1


title: RNA-Seq-p38α-floxed-Vav-cre-non-PC-rep2


title: ESTn_con_d0_5


title: L-M3: mTOR-KO M-MDSC rep3

source_name: bone marrow

value: Myeloid-derived suppressor cells

value: mTOR knock-out


title: STR_wild-type_control_2_Ribo-seq

description: wild-type control 2


title: STR_wild-type_control_1_Ribo-seq

description: wild-type control 1


title: RNA-Seq-p38α-floxed-non-PC-rep1


title: STR_G2019S/D1994A_LRRK2_1_mRNA-seq

description: G2019S/D1994A LRRK2 1

value: G2019S/D1994A LRRK2 TG


title: L-M2: mTOR-KO M-MDSC rep2


title: STR_G2019S/D1994A_LRRK2_2_mRNA-seq

description: G2019S/D1994A LRRK2 2

value: 3 months old


title: PCI 10 weeks 1

city: Villingen-Schwenningen

first: Markus

last: Blaess

address: Jakob-Kienzle-Strasse 17

department: Institute of Precision Medicine

country: Germany

institute: Furtwangen University

description: recoverd, no obviouse disease

hyb_protocol: 250ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf, Germany) a Biorad MJ Thermal Cycler (Biorad, München, Germany). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina, San Diego, USA). Hybridization is performed according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina). Quantity of target used: 0.75 µg cRNA of each sample was hybridized on a Mouse-Ref-8 v2.0 Expression BeadChip (Illumina, San Diego, USA/Eindhoven, The  Netherlands) containing 25,697 probes for murine genome-wide  expression analysis and several control probes for sample- preparation, hybridisation, washing and staining quality Hybridization time:  20 h Volume:  15 µl Temperature:  58° C

scan_protocol: Scanning hardware : Illumina iScan array scanner; scanning software: iScan control software; spatial resolution (pixel space) 0.53 µm.

data_processing:
Data processing was performed using Genome Studio Software V2011.1 and R Package “lumi”. Raw data was subjected to average normalization (RSN, log2 signal transformation), quality control and background correction.
Bead types with detection values p < 0.01 in at least one sample (sham 3 d, sham 10 w, PCI 3 d, or PCI 10 w) were called ‘present’ and analyzed. Hierarchical clustering identified sample 9298740075_G as an outlier and was removed from further processing. Differentially expressed genes (DEG) with LFC=log2FC >1 for PCI vs. Sham at same time point for False Discovery Rate adjustment (FDR-adj.) were filtered. False Discovery Rate was adjusted at p-value <0.05 using the Welch-modified t-test.

source_name: 10 weeks after PCI_whole brain

label_protocol:
Label incorporation metho: Hybridized arrays were stained with 1 µg/µl Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe, Germany), washed dried and scanned immediately on a Illumina iScan array Reader.
Label used: Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe, German).

growth_protocol: All animal experiments were approved by the state authorities of Thuringia (UKJ-02-085-14) and were performed in accordance with animal welfare and the ARRIVE guidelines for reporting animal research. All efforts were made to minimize animal suffering and to reduce the number of animals used. Adult male C57BL6/J mice were kept in a 12 h light-/dark cycle in standard cages with free access to food and water.

extract_protocol: Total cellular RNA from murine brain biopsies were isolated according to standard totalRNA extraction procedures using QIAzol lysis reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.

treatment_protocol: Experimental sepsis was induced by the standardized and established PCI model as described previously . In brief, PCI mice received an intraperitoneal injection of human fecal slurry (diluted 1:4 in saline solution, 3 µl/g B.W.) with a 21-gauge cannula. Control mice were injected with 100µl of 0.9 M saline solution. Mice were closely monitored and the Clinical Severity Score (CSS) was assessed as described previously. To avoid premature death due to acute severe peritonitis, mice were systemically treated with antibiotics. PCI mice received the first subcutaneous (s.c.) injection of the beta-lactam antibiotic meropenem (650µl, 1mg/ml) when the CSS reached a point value of 3. To increase long-time survival after PCI, meropenem was s.c. injected b.i.d. for 7 days and one time per day at the following three days. Thereafter, enrofloxacin (Baytril 2,5%, Bayer AG, Germany) was added to the sugared drinking water (saccharose solution 2,5%) in a final concentration of 2 mg/ml until the end of the experiment. Both, PCI and control animals received equal amounts of antibiotic treatment

value: male

value: 12-14 weeks

tag: sepsis

value: 10 weeks after PCI

tag: meropenem

value: s.c. 10 days

tag: enrofloxacin

value: trinking water 9 weeks

value: mouse whole brain


title: SHAM 3 days 4

description: no Sepsis

source_name: Sham 3 days_whole brain

value: Sham 3 days

value: s.c. 3 days

value: no

tag: tissue


title: RNA-Seq-p38α-floxed-non-PC-rep2

value: untreated


title: PCI 3 days 4

description: acute Sepsis

source_name: 3 days after PCI_whole brain

value: 3 days after PCI


title: SHAM 3 days 3

description: no Sepsis


title: PCI 10 weeks 4

description: recoverd, no obviouse disease


title: SHAM 10 weeks 2

description: no Sepsis

source_name: Sham 10 weeks_whole brain

value: Sham 10 weeks


title: PCI 3 days 3

description: acute Sepsis


title: RNA-Seq-p38α-floxed-Vav-cre-iGCB-rep2

value: induced germinal center B cell


title: SHAM 3 days 2

description: no Sepsis


title: L-M1: mTOR-KO M-MDSC rep1

value: Myeloid-derived suppressor cells


title: PCI 3 days 2

description: acute Sepsis


title: STR_G2019S_LRRK2_1_mRNA-seq

description: G2019S LRRK2 1

source_name: G2019S LRRK2

value: striatum

value: G2019S LRRK2 TG


title: RNA-Seq-p38α-floxed-non-PC-rep3

value: induced CD138- non-plasma B cell


title: RNA-Seq-p38α-floxed-Vav-cre-iGCB-rep1


title: STR_G2019S_LRRK2_2_mRNA-seq

description: G2019S LRRK2 2

value: 3 months old


title: STR_Non-transgenic_control_3_mRNA-seq

description: Non-transgenic control 3

source_name: Non-transgenic control

value: wild-type


title: RNA-Seq-p38α-floxed-iGCB-rep2


title: STR_Non-transgenic_control_2_mRNA-seq

description: Non-transgenic control 2


title: STR_Non-transgenic_control_1_mRNA-seq

description: Non-transgenic control 1


title: STR_G2019S/D1994A_LRRK2_2_Ribo-seq

description: G2019S/D1994A LRRK2 2

value: G2019S/D1994A LRRK2 TG


title: Z76358

source_name: seminal plasma

value: male

value: Asthenospermia

value: Han population

value: seminal plasma


title: RNA-Seq-p38α-floxed-Vav-cre-p38α-iPC-rep1

value: induced  plasma B cell

value: overexpression of p38alpha using retrovirus


title: STR_G2019S_LRRK2_2_Ribo-seq

description: G2019S LRRK2 2


title: RNA-Seq-p38α-floxed-Vav-cre-BLIMP1-iPC-rep1

value: overexpression of BLIMP1 using retrovirus


title: STR_G2019S_LRRK2_1_Ribo-seq

description: G2019S LRRK2 1


title: Control_siRNA_rep2

city: Irvine

first: Michael

last: Parsons

address: 4101 Natural Sciences II

institute: University of California, Irvine

data_processing:
Reads were aligned to hg19 genome with HISAT2 (v2.0.5). Gene expression was quantified using the “featureCount” function of the Rsubread package (v1.28.1) to count read overlap with RefSeq genes. Genes with greater than one read across all four samples were submitted to DESeq2 (v1.18.1) to identify genes differentially expressed across conditions (absolute(log2(foldchange)) > 1, adjusted p-value < 0.05).
tab-delimited text file containing the output from DESeq2 indicating the foldchange and significance of each gene between the SOX9 and control siRNA conditions
hg19
Genome_build: mm10

source_name: PANC-1 cell line

growth_protocol: PANC-1 cells were grown in DMEM supplemented with 10% FBS at 37C with 5% CO2 and passaged at 70-80% confluency.

extract_protocol:
PANC-1 cells were transfected in 24-well plates with either 25 nM of control siRNA (Dharmacon catalog # D-001210-03-05) or 25 nM of SOX9 siRNA (Dharmacon catalog # M-021507-00-0005) using Lipofectamine 3000 (Thermo). After 48 hours, transfected PANC-1 cells were pooled and harvested, two replicates from each siRNA condition, and total RNA was isolated using a Qiagen RNeasy kit. RNA-seq libraries were created using the Illumina TruSeq Stranded Total RNA Sample Prep Kit. RNA-seq libraries were pooled and sequenced on the Illumina HiSeq 2000 to a minimum depth of 60 million 2x100 bp reads per library.
Illumina TruSeq Stranded Total RNA Sample Prep Kit

value: Pancreatic ductal adenocarcinoma cell

tag: cell line

tag: chip antibody

value: untreated

tag: sirna treatment

value: Control siRNA (Dharmacon catalog # D-001210-03-05)


title: Control_siRNA_rep1

tag: cell type


title: RNA-Seq-p38α-floxed-iGCB-rep1

source_name: In vitro-differentiated B cell

value: induced germinal center B cell

tag: treatment


title: RNA-Seq-p38α-floxed-Vav-cre-Vector-iPC-rep1

value: overexpression of Vector using retrovirus


title: SHAM 10 weeks 4

description: no Sepsis

tag: gender

value: 12-14 weeks

value: Sham 10 weeks

value: s.c. 10 days

value: trinking water 9 weeks

value: mouse whole brain


title: PCI 10 weeks 3

description: recoverd, no obviouse disease

value: male

value: 10 weeks after PCI


title: SOX9_siRNA_rep1

value: SOX9 siRNA (Dharmacon catalog # M-021507-00-0005)


title: PCI 3 days 1

description: acute Sepsis

value: 3 days after PCI

value: s.c. 3 days

value: no


title: SHAM 10 weeks 1

description: no Sepsis


title: PCI 10 weeks 2

description: recoverd, no obviouse disease


title: SHAM 3 days 1

description: no Sepsis

value: Sham 3 days


title: SHAM 10 weeks 3

description: no Sepsis


title: WT_3

city: Freiburg

first: Christian

last: Smolka

state: Baden Württemberg

address: Breisacher Strasse 33

department: Department of Cardiology and Angiology I

institute: Heart Center Freiburg University

description: Gene expression data from male, 6 months old, untreated mice

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645. Arrays were washed and stained using the Affymetrix wash and stain kit as described by the manufacturer.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software Version 4.0 and standard settings.
CEL-files were processed with Partek Genomics Suite software using standard settings with Anova.

source_name: untreated wildtype

label_protocol: We used the Affymetrix WT Plus kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: All mice were kept under a 12h/12h light/dark cycle in a specific pathogen-free animal facility with standard diet and water available ad libitum.

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

treatment_protocol: Samples from male, 6 months old, untreated mice were used.

tag: strain background

value: wildtype

value: 6 months

tag: Sex

value: liver


title: STR_G2019S/D1994A_LRRK2_1_Ribo-seq

description: G2019S/D1994A LRRK2 1

tag: strain

value: striatum

value: 3 months old

tag: genotype

value: G2019S/D1994A LRRK2 TG


title: RNA-Seq-p38α-floxed-Vector-iPC-rep1

value: induced  plasma B cell

value: overexpression of Vector using retrovirus


title: SOX9_siRNA_rep2

value: Pancreatic ductal adenocarcinoma cell

value: untreated


title: WT_1

value: male


title: miR-100_4

source_name: global microRNA-100 overexpressing mice

value: global miR-100 overexpression using CMV-Cre deleter ( Tg(CMV-cre)1Cgn/J) crossed to miR-100flox/flox, both on C57BL/6J background, Cre positive miR100flox/+ were selected and backcrossed to eliminate the Cre transgene and then further crossed to homozygosity


title: WT_4


title: STR_Non-transgenic_control_2_Ribo-seq

description: Non-transgenic control 2

value: wild-type


title: miR-100_3


title: KO-AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f-Hg

city: College Station

first: Robert

middle: S.

last: Chapkin

state: TX

address: 373 Olsen Blvd.

department: College of Agriculture and Life Sciences

institute: Texas A&M

data_processing:
For the mapping of reads to transcripts and cells, sample demultiplexing, barcode processing, and unique molecular identifier (UMI) countings were performed using the 10x Genomics pipeline CellRanger v.2.1.0 with default parameters.
Genome_build: mm10

source_name: colon

growth_protocol: The mouse genotypes used in this study include: tamoxifen inducible - Lgr5-EGFP-CreERT2 X Tomatof/f (WT, control), AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f (KO). Male mice (n=5 per genotype, 8-10 weeks of age) were intraperitoneally injected with 2.5 mg of tamoxifen (Sigma, T5648) dissolved in corn oil (25 mg/ml) once a day, for four consecutive days. Mice were maintained on an AIN-76A, semi-purified diet (Research Diets, D12450B), fed ad libitum and housed on a 12 h light-dark cycle. For all experiments, littermate controls were cohoused with the KO mice.

extract_protocol:
Subsequently, following transfer to chilled PBS-/-, crypts were mechanically separated from the connective tissue by vigorous vortexing. Cell suspensions were then filtered through a 40-µm mesh and Tomato-expressing cells (includes GFP+/Tom+ as well as GFP negative/Tom+) were collected using a MoFlo Astrios Cell Sorter (Beckman Coulter) or a Bio-Rad S3e Cell Sorter. Tomato positive cells represent colonic stem cells and their progeny.
Single cell GEMs (Gel bead in EMulsion) and sequencing libraries were prepared using the 10x Genomics Chromium Controller in conjunction with the single-cell 3′ v3 kit. The cDNA synthesis, barcoding, and library preparation were then carried out according to the manufacturer’s instructions.

treatment_protocol: Two weeks post tamoxifen injection, colons were removed, washed with cold PBS without calcium and magnesium (PBS-/-), everted on a disposable mouse gavage needle (Instech Laboratories) and incubated in 15 mM EDTA in PBS-/- at 37°C for 35 min.

value: colonic stem cells

value: Ahr-/-


title: miR-100_1


title: WT_2


title: STR_Non-transgenic_control_1_Ribo-seq

description: Non-transgenic control 1


title: STR_Non-transgenic_control_3_Ribo-seq

description: Non-transgenic control 3


title: miR-100_2


title: KO-AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f-H5


title: Hepatocyte LSKO Zn

city: Rochester

first: Zijuan

last: Liu

state: MI

address: 318 Meadow Brook Rd, Rochester, MI 48309

department: Biology

institute: Oakland University

data_processing:
Quality/Adapter Trimming; Trimmomatic; Version 0.36
Read alignment; hisat2; Version 2.1.0
Read counting (raw); HTSeq-Count; Version 0.11.2
Differential Expression Analysis; DESeq2; Version 1.28.1
Genome_build: GRCm38.96
Supplementary_files_format_and_content: *.txt; Weight-normalized read counts;

source_name: Liver

growth_protocol: Hepatocytes were cultured in serum-free basal medium (DMEM/F-12, 10 μM dexamethasone and 1% penicillin/streptomycin).

extract_protocol:
Cells were lysed in Trizol reagent and transferred to RNAse free tubes for processing. Using the Qiagen RNeasy Mini Kit (#74104), RNA was extracted and then cleaned using the Monarch RNA Cleanup Kit (#T2050S) from New England BioLabs. Total RNA was quantified and sent to GENEWIZ for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols at GENEWIZ

treatment_protocol: The primary hepatocytes were incubated for 24 hours in serum-free basal medium with an added 2 μM of manganese chloride, ferrous chloride, sodium selenite, and zinc chloride, respectively.

value: Liver

value: post-natal week 8

value: Alb-cre(+/+);Slc39a8(F/F) = (LSKO)


title: Hepatocyte LSKO Fe


title: SOX9_ChIP_rep2

data_processing:
Reads were aligned to hg19 with Bowtie2 (v2.2.5) in --local mode following TruSeq adapter removal and quality filtering with fastx toolkit (v0.0.14). Following alignment, reads with mapping score < MAPQ30, reads aligning to the mitochondria, and duplicate reads were removed with SAMtools (v1.3.1). ChIP-seq replicates were combined and peaks were called on this joint file with MACS2 (v2.1.1.20160309) using “callpeak”. Peaks with q-value >10^-3 were removed.
tab-delimited Excel file containing the peak calls from MACS2
hg19
Genome_build: mm10

extract_protocol:
Approximately 2.0 X 10^8 cells were crosslinked in 11% formaldehyde and stopped with 2.5 M glycine before being washed in 1X PBS, lysed, and sonicated for 35 minutes in a Bioruptor at 4C to achieve a fragment size of approximately 200 bp. An input fraction was set aside and the rest of the lysate was then incubated with 10 ug anti-SOX9 (AB5535, Millipore) overnight at 4C. Antibody-bound chromatin was then purified using Protein G Dynabeads (Thermo) and crosslinking was reversed overnight at 65C. ChIP-seq libraries were created using the Illumina TruSeq DNA Sample Prep Kit and quantified using Quant-iT PicoGreen dsDNA assay (Invitrogen). ChIP-seq libraries were pooled and sequenced on the Illumina HiSeq to a minimum depth of 59 million, 1x50bp reads per library.
Illumina TruSeq DNA Sample Prep Kit

value: SOX9 (Millipore, AB5535)


title: KO-AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f-H3


title: SBF_12

city: Utrecht

last: den Hertog

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Well numbers (X001-X384) in *.TranscriptCounts.tsv refer to well numbers of the 384-well plate in the following order: A1 to A24 - B1 to B24 - until P24.
The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded.
During sequencing, Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell
The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases. Read 1 was not used for quantification.
Genome_build: zV9 Danio Rerio
Supplementary_files_format_and_content: cell specific barcodes are specified in the file “cel-seq2_barcodes.csv”
Supplementary_files_format_and_content: transcriptCounts.tsv

organism: Danio rerio

source_name: CHT

extract_protocol:
Cells were sorted into 384 well plates. All wells underwent Cel-Seq2 protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hematopoietic stem and progenitor cells

tag: developmental stage

tag: sort day


title: Hepatocyte LSKO Se

tag: age

value: Sodium Selenite


title: SOX9_ChIP_rep1


title: SBF_11


title: Hepatocyte LSKO Mn


title: Hepatocyte LSKO rep2


title: WT-Lgr5-EGFP-CreERT2 X Tomatof/f-Lg


title: WT-Lgr5-EGFP-CreERT2 X Tomatof/f-L5


title: SBF_10


title: Hepatocyte LSKO rep1


title: KO-AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f-H4


title: pbl19/pPBL19C3A-GFP-HA transgenic plants

city: Guangzhou

first: yujia

address: No. 132, Huan East Road, Panyu District, Guangzhou City

department: School of life science

institute: sun yet-sen university

data_processing:
libraries were sequenced using an BGISEQ-500 platform
clean data were aligned to the Arabidopsis TAIR10 genome by HISAT
Data were filtered using the following specifications: Trimmomatic (version: 0.36),parameter setting: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Rosette of Arabidopsis

extract_protocol:
Total RNA was extracted from 28- day-old WT and pbl19/pPBL19-PBL19C3A-GFP-HA with using the RNAiso Plus reagent (Takara Bio, Japan).
RNA libraries were prepared for sequencing using BGISAQ-500 with 150 bp paired-end reads and data analysis were carried out by the Beijing Genomics institution

tag: ecotype

value: Rosettes

value: Four-week-old

value: pbl19/pPBL19-PBLC3A-GFP-HA transgenic plants (in the background of pbl19 null mutant)


title: WT


title: WT-Lgr5-EGFP-CreERT2 X Tomatof/f-L4


title: Hepatocyte WT rep1

value: Slc39a8(F/F) = (wild type)


title: SBF_8


title: KO-AhRf/f X Lgr5-EGFP-CreERT2 X Tomatof/f-H2


title: Hepatocyte WT rep2


title: SBF_7


title: SBF_9


title: Td DMSP3-8H

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

country: Japan

institute: Tokyo Dental College

hyb_protocol: cRNA was hybridized to a 15K 60-mer oligomicroarray (Treponema denticola custom Microarray 8x16K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction 12.0.3.1(Agilent Technologies).

data_processing: The fluorescent intensity data extracted from the raw images were imported into Agilent Feature Extraction 12.0.3.1 (Agilent Technologies).  After per chip normalization (Shift to 75 percentile) and per gene normalization (mean of control samples) were performed with GeneSpring 13.1.1.

organism: Treponema denticola

source_name: Major surface protein deficient mutant, replicate 2

label_protocol: The cRNA was amplified, labeled using Low Input Quick Amp WT Labeling Kit according to the manufacturer's instructions.

growth_protocol: T. denticola ATCC 35405 and DMSP3  were inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 day (to an absorbance at 660 nm of approximately 0.4-0.6).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen)  according to the manufacturer's instructions.

treatment_protocol: Td 35405     T. denticola ATCC 35405 grown in medium containing 10% serum  Td DMSP3     T. denticola DMSP3 grown in medium containing 10% serum

value: Major surface protein deficient mutant


title: MS_2W_2_Fat_ATAC

status: Public on Feb 26 2021

city: Wuhan

first: Shuhong

last: Zhao

address: No.1,Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: individual 2

data_processing:
The clean data was obtained after removing reads with adapter contamination or low quality.
After checking and trimming the adapter with Cutadapt (version 1.14), the ATAC-Seq reads were mapped to pig susScr11.1 genome using Bowtie2 (version 2.3.4.1).
Low MAPQ reads (less than 25) and duplicated reads of mapped BAM files were removed with SAMTools v1.2 and Picard v1.126.
The narrow peaks and the bedgraph files of -log10(p-value) signal tracks for each replicate were called individually with MACS2 v2.1.0 (-g genome.size -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits) following the guide of ENCODE project ATAC-seq pipeline. It was download at https://github.com/kundajelab/atac_dnase_pipelines.
The narrow peaks were filtered with the cutoff for P<1E-05. The bigwig files of -log10(p-value) signal tracks were generated with MACS2 v2.1.0 and bedGraphToBigWig command based on bedgraph files from the previous step.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bigwig files of signal tracks and bed files of narrow peaks for each sample.

organism: Sus scrofa

source_name: Fat

extract_protocol:
Approximately 5 mg of tissue samples was crushed into a fine powder in liquid nitrogen.The pulverized tissues were suspended in 1mL ice-cold PBS and were gently spun down. The cell pellet was re-suspended in 1 mL lysis buffer (50 mM HEPES with pH 7.5, 140 mM NaCl, 1mM EDTA with pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), followed by isolation of 50,000 nuclei using previously published protocol with minor modifications (Buenrostro et al., 2015). Then the transposition reaction mix (12.5 μL TD buffer, 10 μL ddH2O, and 2.5 μL TDE) was added to the isolated nuclei. The reaction system was incubated at 37 °C for 1 hour followed immediately by purification with the Qiagen MinElute PCR Purification Kit.
The transposed DNA fragments were amplified with the appropriate number of cycles as determined by qPCR. The amplified PCR products were quantified and sequenced using an Illumina Hiseq X ten PE150 platform.

tag: breed

value: Meishan

value: fat

value: 2 weeks


title: WT-Lgr5-EGFP-CreERT2 X Tomatof/f-L2

value: wild-type


title: ES_2W_1_Muscle_ATAC

description: individual 1

source_name: Muscle

value: Enshi Black

value: muscle


title: WT-Lgr5-EGFP-CreERT2 X Tomatof/f-L3

value: colonic stem cells


title: LW_2W_1_Fat_ATAC

description: individual 1

value: Large White


title: MS_2W_2_Liver_ATAC

description: individual 2

value: liver


title: Td DMSP3-7G

source_name: Major surface protein deficient mutant, replicate 1


title: Td 405-1A

source_name: Wild type, replicate 1

value: wild type


title: MS_2W_1_Fat_ATAC

description: individual 1


title: Td 405-11K

source_name: Wild type, replicate 2


title: ES_2W_1_Spleen_ATAC

description: individual 1

source_name: Spleen

value: spleen


title: LW_2W_2_Muscle_ATAC

description: individual 2


title: Duroc_2W_1_Spleen_ATAC

description: individual 1

value: Duroc


title: Duroc_2W_2_Liver_ATAC

description: individual 2


title: LW_2W_1_Liver_ATAC

description: individual 1


title: Duroc_2W_2_Heart_ATAC

description: individual 2

source_name: Heart

value: heart


title: LW_2W_1_Muscle_ATAC

description: individual 1


title: ES_2W_1_Heart_ATAC

description: individual 1


title: MS_2W_2_Muscle_ATAC

description: individual 2


title: ESTn_con_d0_3

city: Bilthoven

first: Jeroen

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

data_processing:
Sequencing was performed using a NextSeq 500 sequencer (Illumina) and the NextSeq 500/550 High Output Kit version 2.5 (75 cycles).
Bcl2fastq (version 2.19.0.316) was used to base call and demultiplex raw bcl files into FASTQ files.
Quality control reports were generated using FastQC (version 0.11.5).
Reads were mapped to the mouse reference genome (GRCm38.p6, release 15) using STAR (version 2.6.0b).
Read counts were compiled into an expression matrix using featureCounts (version 1.6.1).
Genome_build: GRCm38.p6, release 15
Supplementary_files_format_and_content: CountTable.xlsx: count data per sample plus gene annotation

source_name: neural embryonic stem cells

extract_protocol:
Eight samples per condition were fixated in QIAzol and kept at −80 °C until further use. Samples were homogenised using the QIAshredder and subsequently purified with the RNeasy microarray tissue kit according to manufacturer’sprotocol. The Qubit was used to determine the RNA concentration and the Bioanalyzer to determine the quality of the samples.
Samples were further processed for Next Generation Sequencing according to the Illumina TruSeq Stranded mRNA protocol.

value: neural embryonic stem cells

tag: time

value: day 0

value: control

tag: replicate


title: Duroc_2W_2_Muscle_ATAC

description: individual 2

tag: tissue


title: LW_2W_2_Fat_ATAC

description: individual 2


title: Duroc_2W_1_Heart_ATAC

description: individual 1


title: ES_2W_2_Fat_ATAC

description: individual 2


title: ES_2W_2_Muscle_ATAC

description: individual 2


title: MS_2W_2_Spleen_H3K4me3

description: individual 2

data_processing:
The clean data was obtained after removing reads with adapter contamination or low quality.
ChIP reads and Input reads were aligned to susScr11.1 genome with BWA v0.7.15.
Low MAPQ reads (less than 25) and duplicated reads of mapped bam files were removed with SAMTools v1.2 and Picard v1.126. Then the filtered bam file of each sample were used to call peak.
The narrow peaks and the bedgraph files of -log10(p-value) signal tracks for each replicate were generated with MACS2 v2.1.0 (-g genome.size -p 0.01 --nomodel --shift 0 --extsize n --keep-dup 1 -B --SPMR). The “n” for –extsize parameter were automatically calculated by the ENCODE ChIP-seq pipeline which was downloaded from GitHub website (https://github.com/kundajelab/chipseq_pipeline).
The narrow peaks were filtered with the cutoff for P<1E-05. The bigwig files of signal tracks were generated with MACS2 v2.1.0 and bedGraphToBigWig command based on bedgraph files from the last step.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bigwig files of signal tracks and bed files of narrow peaks for each sample.

extract_protocol:
The frozen issues were ground to a fine powder with liquid nitrogen and fixed with 1% formaldehyde at room temperature for 20 min. Nuclear lysates were fragmented by Covaris S220 (Adaptive Focused Acoustics®). For each tissue, 300 μg of chromatin and 3 μg of H3K4me3 (Millipore-04-745) and H3K27ac (Abcam, ab4729) antibodies were used for ChIP-seq analysis.
ChIP–Seq libraries were constructed following Illumina protocols with minor modifications (Illumina, San Diego, CA), and sequenced on an illumina Hiseq X ten PE150 platform.

tag: chip antibody

value: H3K4me3 (Millipore-04-745)


title: ES_2W_2_Liver_ATAC

description: individual 2


title: MS_2W_1_Spleen_H3K27ac

description: individual 1

value: Meishan

value: H3K27ac (Abcam, ab4729)


title: MS_2W_1_Spleen_H3K4me3

description: individual 1

value: 2 weeks


title: ES_2W_1_Fat_ATAC

description: individual 1

value: fat


title: Duroc_2W_1_Liver_ATAC

description: individual 1


title: MS_2W_2_Liver_H3K27ac

description: individual 2


title: MS_2W_2_Heart_H3K4me3

description: individual 2


title: Duroc_2W_1_Muscle_ATAC

description: individual 1


title: MS_2W_1_Heart_H3K27ac

description: individual 1


title: Duroc_2W_2_Fat_ATAC

description: individual 2


title: MS_2W_2_Heart_H3K27ac

description: individual 2


title: MS_2W_1_Fat_H3K4me3

description: individual 1


title: MS_2W_2_Fat_H3K27ac

description: individual 2


title: MS_2W_1_Fat_H3K27ac

description: individual 1


title: Duroc_2W_1_Fat_ATAC

description: individual 1


title: MS_2W_2_Spleen_H3K27ac

description: individual 2


title: MS_2W_2_Muscle_H3K27ac

description: individual 2


title: MS_2W_1_Muscle_H3K4me3

description: individual 1


title: MS_2W_1_Liver_H3K27ac

description: individual 1


title: mT3-2D-GFP FACS cells from WT tumors

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Raw reads were aligned to the mm9 reference genome with BWA and quantified into read counts with the annotation model (Partek E/M). All subsequent RNA-seq analyses were performed in R version 3.5.1. Read counts were variance-stabilized with the regularized log (rlog) function in the R/Bioconductor package DESeq2 version 1.20.0. Log fold-changes were computed on the rlog-transformed expression data, and genes with absolute log fold-changes greater than or equal to one were retained as significant.  FDR adjusted p-values below 0.05 were considered statistically significant.
Genome_build: mm9
Supplementary_files_format_and_content: Raw reads were aligned to the mm9 reference genome with BWA and the data is presented in the file "BWA-RAW10-FKPM-FOLD". Log fold-changes are presented in the file "FCResults"

source_name: Murine KPC FACS tumor cells

growth_protocol: Cells were grown in standard conditions and maintained in Dulbecco's Modified Eagle Medium (DMEM)(Fisher Scientific, # SH30022LS) supplemented with heat-inactivated fetal bovine serum (HI-FBS) to a final concentration of 10% and 2 mM L-glutamine

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen). RNA concentration and quality were assessed using an Agilent BioAnalyzer (RINs >7). Equal amounts of RNA from each corresponding group were combined as one sample (1 WT sample, 1 SCID sample, and 1 cell line).
Indexed, paired-end sequencing libraries were prepared from 1.0 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit (polyA cDNA synthesis) in the Genomics and Epigenomics Shared Resource (GESR) in the Lombardi Comprehensive Cancer Center at Georgetown University Medical Center.
Libraries were sequenced on an Illumina NextSeq550 using PE 75 bp (150 cycle) chemistry to a mean depth of 40M reads per sample

treatment_protocol: mT3-2D-GFP FACS cells were either grown in SCID mice or WT mice

value: Murine KPC cells

tag: original strain

tag: effect

value: Immunocompetent

tag: group (mouse strain)

value: Cells grown in C57BL/6 (WT) mice


title: MS_2W_1_Muscle_H3K27ac

description: individual 1

value: muscle


title: mT3-2D-GFP cell line

source_name: Murine KPC cell line

tag: cell type

value: Basal level


title: MS_2W_2_Muscle_H3K4me3

description: individual 2


title: MS_2W_1_Liver_H3K4me3

description: individual 1

value: liver


title: MS_2W_2_Fat_H3K4me3

description: individual 2


title: LW_2W_2_Thymus_H3K4me3

description: individual 2

source_name: Thymus

value: Large White

value: thymus


title: MS_2W_2_Liver_H3K4me3

description: individual 2


title: MS_2W_1_Heart_H3K4me3

description: individual 1

value: heart