title: YN15_033_PanTro_NeuN

description: Protocol 1


title: YN14_056_PanTro_NeuN

status: Public on Dec 31 2019

type: SRA

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

description: Protocol 1

library_source: transcriptomic

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19, PanTro5, RheMac8 from UCSC)
Crossmap and Liftover tools were used to translate non-human priamte coordinates into human coordinates. Human reference was used for gene annotation and counting (gencode v19). Uniquely mapped reads were quantified using HTSeq python suite using high-scored orthologs' protein coding genes by exons.
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: tab separated files with raw counts

molecule: total RNA

organism: Pan troglodytes

source_name: brain

extract_protocol:
nuclear extraction protocol: Tissue isolated from Brodmann Area 46 from 27 healthy humans, 11 healthy chimpanzee and 15 healthy rhesus macaque.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separate nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNase inhibitors and incubated with mouse Alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit Alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
total RNA extraction protocol: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

tag: tissue

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

value: F

tag: age

tag: humanized age

tag: hemisphere

value: L

tag: pmi

tag: rin


title: YN16_043_PanTro_Olig2

description: Protocol 1


title: YN16_043_PanTro_NeuN

description: Protocol 1


title: Bud_RNA_Stage4_rep1

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

data_processing:
Adapter sequences and low quality base pairs from the paired-ends reads were trimmed using Trimmomatic v. 0.35 using the following parameters: “PE [read1.fastq] [read2.fastq] pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
RNA-seq reads for each sample were mapped to the reference transcriptome (from Hydra 2.0 Genome Project) using Bowtie v. 1.2 with the following parameters: “-X 2000 -a -m 200 -S --seedlen 25 -n 2 -v 3”.
Gene expression levels and read counts were obtained using RSEM v. 1.2.31 with the following parameters: “--paired-end --num-threads 8 --calc-ci”.
Batch effects were removed from gene expression levels (TPM) using “ComBat” function from “sva” package in R. The TPM values were smooth quantile normalized using “qsmooth” package in R.
Genome_build: Hydra 2.0 Genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Tab-delimited text file includes batch-corrected and smooth quantile normalized TPM values for all samples.

organism: Hydra vulgaris

growth_protocol: Hydra vulgaris polyps were used for the isolation of RNA. They were fed freshly hatched Artemia salina nauplii twice per week.  Animals were starved for at least 1 day before any tissue manipulation or RNA isolation was carried out.

extract_protocol:
Each isolated tissue was dissolved in Qiagen RNeasy buffer RLT (with 2-betamercaptoethanol added) within 3 minutes of isolation. The dissolved tissue was immediately used for total RNA isolation using Qiagen RNeasy kit according to manufacturer’s protocol. The total RNA for each sample was treated with DNase from TURBO DNA-free kit to remove any genomic DNA contamination. RNA quality was checked with Agilent Bioanalyzer and samples with RIN scores ≥9 were used for RNA-seq library preparation.
Multiplexed RNA-seq libraries were built using the Smart-seq2 protocol with slight modifications. Briefly, mRNA from total RNA in each sample was converted to full-length cDNA using poly-dT primer and reverse transcriptase. cDNA was amplified using appropriate number of PCR cycles based on the initial amount of total RNA and as recommended by the Smart-seq2 protocol. 20 ng full-length cDNA for each sample was converted to sequencing library by tagmentation with the Illumina Nextera kit. 8 cycles of PCR were used for library amplification. Libraries were multiplexed and sequenced as 43 bp Illumina paired-end reads.

treatment_protocol: For regeneration, 1 animal per sample (with two biological replicates) was bisected at the region 1 (R1) and region 2 (R2) border and allowed to undergo head regeneration for a specific period of time (0, 2, 4, 6, 12, 24, or 48 hours). Then the R2-R3 region of the animal of a sample was isolated for RNA extraction. For the budding experiment, the head region of buds from animals at various stages of budding (S1, S3, S4, S5, S6, S7, S8, or S10) was bisected and used for total RNA extraction. Tissues from tentacles, budding zone, body column, hypostome, and foot were harvested for RNA extraction.

value: developing bud


title: monocytes.raiv.2.ifna

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
CD11b+CD33+CD15neg cells
raiv.2.ifna_beta

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Rstudio

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

growth_protocol: PBMCs were cultured for 4 days in RMPI medium + 10% FBS

extract_protocol: Genomic DNA was extracted and purified from sorted CD11b+CD33+ cells using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

treatment_protocol: Cell were treated in vitro for 4 days with TNF-alpha (10 ng/mL), IFN-alpha (100 ng/mL), IFN-gamma (100 ng/mL) or control

tag: treatments

value: treatment with IFN-alpha


title: YN06_108_PanTro_NeuN

description: Protocol 1

value: R


title: mononuclear cells of the spinal cord , Sample 155-5

city: shanghai

first: Niu

last: liman

address: Building No.5(West Area),No.280 South Chongqing Road

department: Shanghai Institute of Immunology,Department of Immunology and Microbiology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina bcl2fastq software was used for base-calling
STAR(2.5.3a) software was used for read alignment, parameter setting as follows:—twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated, and then normalized with TMM standard; DESeq2 software was used to filter differentially expressed genes, according to the standard that |log2(fold change)|>=1 and P value <=0.05
In processed data file, G1 refers to the mean value of Scr ctr group(2 biological repilcations) values; G2 refers to the mean value of normalized P155 group(2 biological repilcations) values;
Genome_build: mm10
Supplementary_files_format_and_content: seq_Processed data file of EAE -e.g. geo_submission_December 28.xlsx

organism: Mus musculus

source_name: mononuclear cells of the spinal cord

extract_protocol:
mononuclear cells of the spinal cord from EAE treated mouse were isolated using Percol™ gradient centrifugation, and washed twice with PBS,  total RNA was extracted with RNAiso Plus (Takara Bio) and purified with magnetic oligo (dT) beads after denaturation.  Purified mRNA samples were reverse transcribed into fragmented DNA samples and adenylated at the 3’ ends.
Adaptors were ligated to construct a library. DNA was quantified by Qubit (Invitrogen). After cBot cluster generation, DNA samples were then sequenced by an Illumina HiSeq X Ten SBS instrument from Genergy Bio (Shanghai).

treatment_protocol: P155 or Scr treatment was carried out every other day from the eighth day of EAE immunization.

tag: strain

tag: disease state

value: EAE mouse model

value: spinal cord

tag: cell type

value: mononuclear cells

tag: treatment


title: Bud_RNA_Stage3_rep2


title: Bud_RNA_Stage3_rep1


title: mononuclear cells of the spinal cord , Scr-5

value: Scramble microPEP(Scr)


title: mononuclear cells of the spinal cord , Sample 155-4


title: mononuclear cells of the spinal cord , Scr-4


title: Bud_RNA_Stage1_rep1


title: monocytes.raiv.2.c

description:
CD11b+CD33+CD15neg cells
raiv.2.c_beta

value: control


title: lncRNA and mRNA AD3_9m

city: BEIJING

first: MA

address: haidian

institute: peking university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The details of mRNA-seq, miRNA-seq, and circRNA-seq methods are described in Supplementary files.

tag: genotype


title: Bud_RNA_Stage4_rep2

tag: tissue


title: Neuro2A bioreplica 1

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

library_source: genomic

data_processing:
Library strategy: SSiNGLe-ILM
Only paired-end raw reads where read 1 started with 10G’s, read 2 started with 12T’s and each base of each read had Phred quality score >20 were selected.
Such reads were then aligned to the GRCh37/hg19 or GRCm38/mm10 assemblies of human or mouse genomes respectively using BWA-MEM (Version 0.7.12) with default settings. Only pairs of reads where both reads 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
Pairs of reads where fraction of T’s in the 20-base 5’ upstream sequence in the read 2 alignment was >40% were removed from the downstream analyses.
A single-strand break was defined as the first base after 12 T’s in the read 2.
Genome_build: hg19 for human and mm10 for mouse
Supplementary_files_format_and_content: bed.gz files containing coordinates of single-strand breaks

growth_protocol: Human chronic myeloid leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2. Mouse neuroblastoma (N2a) and human cervical carcinoma HeLa cell lines were obtained from National Infrastructure of Cell Line Resource. N2a cells were cultured in MEM/EBSS (HyClone), supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2. HeLa cells were cultured following at the same condition as K562 cells.

extract_protocol:
Cells were crosslinked with formaldehyde in vivo, fragmented with MNase and used for genomic DNA extraction.
Samples were prepared according to the SSiNGLe-ILM protocol. Briefly, nuclei were isolated from cells crosslinked in vivo with formaldehyde and subjected to MNase treatment to fragment DNA to 150-500bp. The genomic DNA was then isolated after cross-link reversal and subjected to polyA-tailing using terminal transferase to tag positions of endogenous single-strand DNA breaks (products of MNase fragmentation would not be tailed under these conditions). The polyA-tailed single-strand DNA molecules were then used as templates for 2nd strand DNA synthesis with a chimeric 5’-DNA-RNA-3’ oligonucleotide followed by polyC-tailing of the 2nd strand DNA. The resulting polyA- and polyC-tailed double-strand DNA molecules were used for Illumina sequencing library construction using PCR with oligonucleotides containing appropriate adaptors at their 5’ ends.

treatment_protocol: For drug treatments, 1-2 million cells were seeded at 1 million cells per ml of medium per well in 24- (1ml media) or 6-well (2-3 ml) plates. After 16 hours, the following chemicals were added separately: 0.1% DMSO, 0.5mM H2O2, 1μM imatinib (Abmole Bioscience Inc, M3241), 0.0462µM romidepsin (Abmole Bioscience Inc, M2007), 1μM talazoparib (Abmole Bioscience Inc, M1732), 1μM SN-38 (Abmole Bioscience Inc, M3016), 40μM 10074-G5 (Sigma, 475957), 1μM YM-155 (Abmole Bioscience Inc, M2342) and 100μM etoposide (Abmole Bioscience Inc, M2326) and incubated for 6, 12, 24, 36 or 48 hours. All drugs (with exception of H2O2) were dissolved in DMSO, concentration of which was kept at 0.1% in all treatments. All treatments were done in two biological replicas for SSiNGLe-ILM. The following treatments were performed on separate batch of cells for SSiNGLe-SMS: DMSO, etoposide, SN-38, romidepsin, imatinib and talazoparib for 6, 12, 24 (with the exception of imatinib), 36 and 48 hours. For the Nt.BbvCI experiments, hydrogen peroxide treatment was done only for 6 hours and un-treated cells grown under the same conditions were used as controls.

tag: cell line

value: neuroblastoma  cell line


title: Neuro2A bioreplica 3


title: lncRNA and mRNA AD1_9m


title: circRNA AD3_9m


title: lncRNA and mRNA AD2_9m


title: circRNA AD2_9m


title: lncRNA and mRNA WT3_9m

value: wild type


title: circRNA AD1_9m


title: circRNA WT2_9m


title: circRNA WT1_9m


title: lncRNA and mRNA WT1_9m


title: lncRNA and mRNA AD3_6m


title: SW620_Mock_rep2

first: Marian

middle: L.

last: Waterman

state: CA

address: Rm B251 Medical Sciences I, School of Medicine

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz

data_processing:
Adapter sequences and low quality base pairs from the 5’ and 3’ ends of the paired-ends reads were trimmed using Trimmomatic v. 0.35 (Bolger et al, 2014) using the following parameters: “PE read1.fastq read2.fastq pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
Reads from the host (mouse) and the graft (human) were classified and separated using Xenome (Conway et al, 2012).
Reads for each sample were mapped to the reference transcriptome (GENCODE v. 28 for human and v. M18 for mouse) using Bowtie v. 1.2 (Langmead et al, 2009) with the following parameters: “-X 2000 -a -m 200 -S --seedlen 25 -n 2 -v 3”.
Gene expression levels and read counts were obtained using RSEM v. 1.2.31 (Li & Dewey, 2011).
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values of host (mouse) and graft (human).

source_name: Xenograft (mouse caecum)

growth_protocol: Cell lines were cultured in Dulbecco’s Modification of Eagle’s Medium (DMEM, Hyclone) or RPMI-1640 (Hyclone) supplemented with 10% Fetal Bovine Serum (Atlas Biologicals), 1% Penicillin/Streptomycin (Mediatech), and 2mM Glutamine (Mediatech).

extract_protocol:
Mouse caecums were excised and rinsed with PBS prior to flash freezing in liquid nitrogen. Tissue was fragmented using a mortar and pestle, and approximately 1 mg tissue was collected into Precellys (Bertin) tubes with TRIzol. Following tissue homogenization, RNA was extracted from cells using TRIzol (Invitrogen) and DirectZol RNA Extraction Kit following the manufacturer’s instructions (Zymo Research). RNA quality was checked with Agilent Bioanalyzer. Samples with RNA Integrity Number (RIN) scores ≥ 9 were used for RNA-seq library construction.
RNA-seq libraries were built using the Smart-seq2 protocol (Picelli et al, 2014) with modifications according to (Serra et al, 2018).

treatment_protocol: dnLEF1 cell lines were prepared as previously described (Pate et al, 2014). LRP6 knockout (LRP6KO) cell lines were created by co-transfecting cell lines with 3 μg LRP6 CRISPR and 300 ng eGFP-Puro using BioT transfection reagent (Bioland Scientific, B01). After selection with Puromycin, cells were sorted for LRP6 knockdown using flow cytometry (anti-human LRP6-APC, R&D Systems MAB1505). Immuno-deficient NSG mice (Jackson labs) were anaesthetized with 300μl of 100mg/kg ketamine/10mg/kg xylazine. The surgical site was shaved and cleaned with ethanol. After an incision was made, the caecum was drawn out and washed with sterile PBS. Cells (5*10^5) were injected in the caecum wall at six to eight sites using a Hamilton syringe (Hamilton 80301), three to four injections per side. The peritoneal wall and skin were sutured separately, the former with resorbable sutures, the latter with nylon. 5mg/kg carprofen was injected as an analgesic. Mice health was monitored for 28 days prior to harvest.

tag: transduction

value: Mock lentiviral transduction


title: Bud_RNA_Stage1_rep2


title: SW620_Mock_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: circRNA WT3_9m

value: brain


title: circRNA AD3_6m


title: circRNA AD2_6m


title: SW620_LRP6KO_rep2

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz

value: LRP6 knock-out using CRISPR/Cas9 transfection


title: SW620_Mock_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: SW620_LRP6KO_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: lncRNA and mRNA AD2_6m


title: Neuro2A bioreplica 2


title: circRNA WT3_6m


title: SW620_LRP6KO_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: circRNA AD1_6m


title: SW620_dnLEF1_rep2

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz

value: Dominant negative LEF1 using lentiviral transduction


title: lncRNA and mRNA WT2_6m


title: lncRNA and mRNA WT2_9m


title: SW620_dnLEF1_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: lncRNA and mRNA WT3_6m


title: SW620_Cas9_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz

tag: transfection

value: Mock CRISPR/Cas9 transfected and sorted cells


title: SW620_Cas9_rep2

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: SW620_dnLEF1_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: circRNA WT1_6m


title: SW480_Mock_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: SW620_Cas9_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: SW480_Mock_rep2

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: 100ng_afterOxidation_R1

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

data_processing:
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome of mouse (mm10) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs. The left ones that could be mapped to mouse testis piRNA clusters downloaded from piRNA cluster database were annotated as piRNAs. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Synthesized spike-ins (Genepharma, Shanghai, China) were phosphorylated by T4 Polynucleotide Kinase (Takara, Japan) and pooled, with a final concentration of 10^-9 μM.  The spike-in mixture was added to each sample before processing by NaIO4 oxidization. The following RNA oligos were used as spike-ins:  sp1: 5’-/5Phos/rArArCrUrUrCrArGrGrGrUrCrArGrCrUrUrGrCrCrG-3’  sp2: 5’-/5Phos/rCrCrUrGrGrArCrUrArGrUrCrGrUrCrArGrCrArUrU-3’  sp3: 5’-/5Phos/rUrArCrCrCrGrUrArArUrCrUrUrCrArUrArArUrCrCrGrArG-3’  sp1Me: 5’-/5Phos/rArArCrUrUrCrArGrGrGrGrArArGrCrUrUrGrCrCmG-3’  sp2Me: 5’-/5Phos/rCrCrUrGrGrArCrUrArGrUrCrGrUrCrArGrUrGrUmU-3’  sp3Me: 5’-/5Phos/rUrArCrCrCrGrUrArArUrArGrUrCrArUrArArUrCrCrGrAmG-3’
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: sequence of miRNA, endo-siRNA, piRNA and their expression (RPM) in each sample were provided

source_name: 100 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 1

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

tag: strain background

value: 4 months old

tag: Sex

value: male

value: testis

tag: time point

value: after NaIO4 oxidization

tag: rna input

value: 100 ng input of total RNA

tag: library construction method

tag: spike-in

tag: molecule subtype

value: small RNA in length of 17-40 nt


title: lncRNA and mRNA WT1_6m

tag: age


title: 50ng_afterOxidation_R2

source_name: 50 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 2

value: 50 ng input of total RNA


title: 100ng_afterOxidation_R2

source_name: 100 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 2


title: SW480_Mock_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: SW480_dnLEF1_rep3

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: 50ng_afterOxidation_R1

source_name: 50 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 1


title: SW480_dnLEF1_rep2

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: lncRNA and mRNA AD1_6m

tag: strain


title: 10ng_afterOxidation_R2

source_name: 10 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 2

value: 10 ng input of total RNA


title: 10ng_afterOxidation_R1

source_name: 10 ng of total RNA derived from mouse testis, after NaIO4 oxidization, technical replicate 1


title: SW480_dnLEF1_rep1

description:
Mouse_TPM.txt.gz
Human_TPM.txt.gz


title: RT9

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

description: all 9 samples FPKM values.xlsx

data_processing:
Illumina bcl2fastq version 2.18.0.12 software used for basecalling.
TopHat version 2.1.1 was used to align the raw FASTQ files to the human reference genome using parameters --library-type fr-firststrand; --keep-fasta-order; -G
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters --library-type fr-firststrand; -g
Cuffmerge version 2.2.1 was used to merge the transcript abundances together
Cuffdiff version 2.2.1 was used to identify differentially expressed genes using parameters --library-type fr-firststrand
Genome_build: GRCh37 Release 25
Supplementary_files_format_and_content: Excel (tab-delimited) file containing all samples (column headers) with genes (rows) showing intensity values (FPKM)

growth_protocol: 16HBE14o- cells were cultured in Minimum Essential Modified Eagle's Medium (Invitrogen) with 10% fetal bovine serum in a humidified incubator at 37°C in 5% CO2 in 6-well plates and allowed to grow to 70-80% confluence prior to the start of the experiments.

extract_protocol: Total RNA containing the small ncRNA fraction was isolated using miRNeasy kit (Qiagen, 217004) RNA concentrations were calculated based on the absorbance at 260 nm. RNA samples were stored at -70°C until use.

treatment_protocol: Pharmacological induction of ER stress and activation of the UPR :  cells were treated with the compounds for the time periods specified: calpain inhibitor I (ALLN; 100 μM, Sigma, A6185);  Tunicamycin (Tm; 2.5 μg/ml, Sigma, T7765)  Control cells were treated respectfully with Dimethyl Sulfoxide (DMSO; < 0,5% v/v, Sigma, D2650).

value: normal immortalized human cells

value: Tunicamycin 9h


title: circRNA WT2_6m


title: 100ng_beforeOxidation_R1

description: Data20190226_RPI91_100ng_beforeOxidation

source_name: 100 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 1

value: before NaIO4 oxidization


title: 100ng_beforeOxidation_R2

description: Data20190226_RPI92_100ng_beforeOxidation

source_name: 100 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 2


title: RT6

description: all 9 samples FPKM values.xlsx

value: Tunicamycin 6h


title: 50ng_beforeOxidation_R1

source_name: 50 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 1


title: RT2

description: all 9 samples FPKM values.xlsx

value: Tunicamycin 2h


title: RT4

description: all 9 samples FPKM values.xlsx

value: Tunicamycin 4h


title: 10ng_beforeOxidation_R1

source_name: 10 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 1


title: 10ng_beforeOxidation_R2

source_name: 10 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 2


title: RA9

description: all 9 samples FPKM values.xlsx

value: ALLN 9h


title: RA6

description: all 9 samples FPKM values.xlsx

value: ALLN 6h


title: RA2

description: all 9 samples FPKM values.xlsx

value: ALLN 2h


title: A485_2_RNASeq

city: Boston

first: Beth

last: Zucconi

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB 164

department: Medicine

institute: Brigham & Women's Hospital

description:
mRNA
2-22_A485_RNASeq
2-22_228 column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_228.deseq.xls

data_processing:
QC with RseQC.
Align with STAR.
Batch Correction with Combat.
Expression Matrix with Cufflinks.
Differential expression with DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuff_Isoform_Counts.csv: Comma-separated text file.
Supplementary_files_format_and_content: *.deseq.xls: Excel files include base mean counts and the fold change relative to DMSO controls.

source_name: Androgen dependent prostate cancer cell line

extract_protocol:
Trizol prep with DNase digestion.
NEB prep.

treatment_protocol: LNCaP cells were divided into 4 different drug treatment groups (including control) and were treated with I-CBP112 and/or A-485 for 24 h.

value: LNCaP-FGC


title: ICBP112_2_RNASeq

description:
mRNA
2-22_ICBP112_RNASeq
2-22_112 column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_112.deseq.xls

value: Androgen dependent prostate cancer cell line


title: DMSO_2_RNASeq

description:
mRNA
2-22_DMSO_RNASeq
2-22_DMSO column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv

value: DMSO


title: RA4

description: all 9 samples FPKM values.xlsx

value: ALLN 4h


title: ICBP112A485_1_RNASeq

description:
mRNA
12-17_ICBP112A485_RNASeq
12-17_2x column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_2x.deseq.xls

value: ICBP112 and A485


title: RA0

description: all 9 samples FPKM values.xlsx

value: no stress


title: Carmil3-KO rep1

first: Xiaojing

last: Ma

address: Dongchuan Rd. 800

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows: 1) Remove the adaptor-polluted reads (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out); 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie/Bowtie2 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12. TopHat, specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again.
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Per Million Mapped Fragments) was then calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes FPKM values for each Sample

source_name: 4T1 cells

growth_protocol: 4T1 control cells and Carmil3 KO single cell derived clones were cultured in six-well plate under an atmosphere of 5% CO2 at 37℃ and tested mycoplasma-free, maintained in DMEM (GIBCO) supplemented with 10% fetal bovine serum (GIBCO)and 100 μg/ml penicillin/streptomycin (GIBCO).

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4T1 cells

value: Carmil3 knockout

value: mammary tumor cells


title: Carmil3-KO rep2


title: ICBP112A485_2_RNASeq

description:
mRNA
2-22_ICBP112A485_RNASeq
2-22_2x column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_2x.deseq.xls


title: WT rep2

value: wild type


title: A485_1_RNASeq

description:
mRNA
12-17_A485_RNASeq
12-17_228 column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_228.deseq.xls


title: P2: HOTAIRM1 siRNA replicate 2

city: La Jolla

first: Michael

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

data_processing:
Kallisto – transcript quantification
Sleuth – gene differential expression analysis/gene normalized abundance measurements
HISAT2 - alignment of sequencing reads
edgeR - differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: .xls, TPM values, sleuth output, edgeR output

source_name: Caki-1 cells

extract_protocol:
Rneasy Mini kit
NEBNext Ultra II directional library kit

value: Caki-1 cells

tag: genotype/variation

value: HOTAIRM1 siRNA


title: Carmil3-KO rep3

tag: cell type


title: DMSO_1_RNASeq

description:
mRNA
12-17_DMSO_RNASeq
12-17_DMSO column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv

tag: treatment


title: 50ng_beforeOxidation_R2

source_name: 50 ng of total RNA derived from mouse testis, before NaIO4 oxidization, technical replicate 2

value: 4 months old

value: male

value: testis

value: before NaIO4 oxidization

value: 50 ng input of total RNA

value: small RNA in length of 17-40 nt


title: input DNA_2

data_processing:
ChiLin pipeline.
QC with FastQC.
Align with Bowtie.
Peak calling by MACS2.
Pearson correlation with wigCorrelate; %overlap between replicates determined.
Peaks annotated with HOMER after removal of blacklisted regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Chromatin shearing followed by p300 immunoprecipitation.
Swift Biosciences Accel-NGS 2S

value: LNCaP-FGC

value: Androgen dependent prostate cancer cell line

tag: chip antibody


title: RNA151215RH_10236_A46biop_post_etoh

city: Portland

first: Nicole

last: Walter

state: OR

address: 3181 SW Sam Jackson Park Road

department: Behavioral Neuroscience

institute: Oregon Health & Science University

data_processing:
Reads were aligned to NCBI assembly MF5 (accession GCA_000364345.1) using STAR version 2.5.2b (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax = 2 and outFilterMultimapNmax = 1.
Using HTSeq version 0.6.1p1 (Anders et al., 2015) and the MF5 GTF annotation file (33,107 genes) read counts were summarized at the gene level.
Generalized linear models, using DESeq2 (Love et al., 2014), were used to detect differential expression using paired analyses
The complete RNAseq dataset for this cohort of animals included 38 samples. However, only 32 were used in the paired analysis (before v. after). The other 6 were sham controls (no before samples). This is explained in the manuscript. Keeping the dataset complete would allow others to do subsequent analyses using the sham control animal (after) samples.
Genome_build: MF5 (Macaca_fascicularis_5.0)
Supplementary_files_format_and_content: Supplemental Table 1.xlsx reports transcripts per million gene x sample

organism: Macaca fascicularis

source_name: Area 46

extract_protocol: Libraries without strand orientation were prepared using the TruSeq RNA Sample Preparation Kit version 2 (Illumina). Libraries were sequenced according to specification on a HiSeq 2500 (Illumina) at the Oregon Health and Science University Massively Parallel Sequencing Shared Resource. PolyA-selected libraries were multiplexed four per lane, yielding an average of 44 million total single-end reads per sample.

tag: cohort

value: Cyno 13

tag: tissue

value: brain (prefrontal cortical area 46)


title: RNA151215RH_10235_A46biop_post_etoh


title: WT rep1

tag: cell line

tag: genotype


title: RNA151215RH_10234_A46biop_post_etoh


title: RNA171120RH_10232_A46biop_post_etoh


title: RNA151215RH_10233_A46biop_post_etoh


title: input DNA_1

value: DMSO


title: RNA151215RH_10230_A46biop_post_etoh


title: Miami0001_Control_Olig2_human

description:
Protocol 1
GSM2874016

source_name: brain

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

value: M

tag: humanized age

tag: hemisphere

value: R

tag: pmi

tag: rin


title: RNA151215RH_10229_A46biop_post_etoh


title: ICBP112_1_RNASeq

description:
mRNA
12-17_ICBP112_RNASeq
12-17_112 column in Cuff_Isoform_Counts.csv file.
processed data file: Cuff_Isoform_Counts.csv
processed data file: DMSO_vs_112.deseq.xls


title: RNA151215RH_10227_A46biop_post_etoh


title: AN16799_Control_Olig2_human

description:
Protocol 1
GSM2874015

tag: age


title: RNA151215RH_10225_A46biop_post_etoh


title: AN10090_Control_Olig2_human

description:
Protocol 1
GSM2874013


title: AN03398_Control_Olig2_human

description:
Protocol 1
GSM2874011

value: F

value: L


title: RNA140430RH_10205_A46biop_post_etoh

value: Cyno 9


title: RNA151215RH_10226_A46biop_post_etoh


title: RNA140430RH_10204_A46biop_post_etoh


title: RNA140430RH_10207_A46biop_post_etoh


title: X4615_Control_Olig2_human

description:
Protocol 1
GSM2874010


title: X3590_Control_Olig2_human

description:
Protocol 1
GSM2874008


title: AN15240_Control_Olig2_human

description:
Protocol 1
GSM2874014


title: X3602_Control_Olig2_human

description:
Protocol 1
GSM2874009


title: WT rep3

value: 4T1 cells

value: wild type

tag: cell type

value: mammary tumor cells


title: RNA140430RH_10201_A46biop_post_etoh

tag: treatment


title: RNA140430RH_10203_A46biop_post_etoh


title: X3586_Control_Olig2_human

description:
Protocol 1
GSM2874007


title: RNA140430RH_10202_A46biop_post_etoh


title: X1541_Control_Olig2_human

description:
Protocol 1
GSM2874005


title: RNA140430RH_10200_A46biop_post_etoh


title: X1539_Control_Olig2_human

description:
Protocol 1
GSM2874004


title: RNA140430RH_10199_A46biop_post_etoh


title: RNA151215RH_10231_A46biop_post_etoh


title: RNA140430RH_10198_A46biop_post_etoh


title: AN05483_Control_Olig2_human

description:
Protocol 1
GSM2874012


title: X1532_Control_Olig2_human

description:
Protocol 1
GSM2874002


title: RNA140430RH_10206_A46biop_post_etoh


title: RNA140430RH_10197_A46biop_post_etoh


title: RNA151215RH_10236_A46biop_pre_etoh


title: X1530_Control_Olig2_human

description:
Protocol 1
GSM2874001


title: X1529_Control_Olig2_human

description:
Protocol 1
GSM2874000


title: RNA151215RH_10233_A46biop_pre_etoh


title: X3545_Control_Olig2_human

description:
Protocol 1
GSM2874006


title: RNA151215RH_10232_A46biop_pre_etoh


title: X1526_Control_Olig2_human

description:
Protocol 1
GSM2873997


title: RNA151215RH_10230_A46biop_pre_etoh


title: X1527_Control_Olig2_human

description:
Protocol 1
GSM2873998


title: X1528_Control_Olig2_human

description:
Protocol 1
GSM2873999


title: RNA151215RH_10229_A46biop_pre_etoh


title: X1524_Control_Olig2_human

description:
Protocol 1
GSM2873995


title: Ezh2-KO & Ezh1-heterozygousKO Sample 4

type: RNA

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: EZH2-KO & EZH1-hetKO 4 vs. WT1

hyb_protocol: Manufacturer's protocol (Agilent)

scan_protocol: Scan Protocol: GE2_107_Sep09 Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: EZH2-KO & EZH1-hetKO 4

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

extract_protocol: Total RNA was isolated from kidneys using RNAlater (ThermoFisher Scientific) and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: strain

value: embryonic day 17.5

value: Mouse Kidneys

value: EZH2-KO & EZH1-hetKO

value: control


title: Miami0002_Control_NeuN_human

description:
Protocol 1
GSM2873977

value: NeuN


title: Ezh2-KO & Ezh1-WT Sample 3

description: EZH2-KO & EZH1-WT 3 vs. WT1

source_name: EZH2-KO & EZH1-WT 3

value: EZH2-KO & EZH1-WT


title: Control wildtype Kidney Pair 4

description: WT4 vs. WT1


title: RNA151215RH_10234_A46biop_pre_etoh

tag: cohort

value: Cyno 13

value: brain (prefrontal cortical area 46)


title: RNA171120RH_10226_A46biop_pre_etoh

tag: tissue


title: Ezh2-KO & Ezh1-WT Sample 4

description: EZH2-KO & EZH1-WT 4 vs. WT1

source_name: EZH2-KO & EZH1-WT 4


title: Ezh2-KO & Ezh1-homozygousKO Sample 2

description: EZH2-KO & EZH1-homoKO 2 vs. WT1

source_name: EZH2-KO & EZH1-homoKO 2

value: EZH2-KO & EZH1-homoKO


title: RNA171120RH_10227_A46biop_pre_etoh


title: Ezh2-KO & Ezh1-homozygousKO Sample 3

description: EZH2-KO & EZH1-homoKO 3 vs. WT1

source_name: EZH2-KO & EZH1-homoKO 3


title: AN16799_Control_NeuN_human

description:
Protocol 1
GSM2873975

value: brain

value: Frozen Brain Tissue

value: Brodmann Area 46

value: M


title: X1525_Control_Olig2_human

description:
Protocol 1
GSM2873996

value: F

value: L


title: RNA140430RH_10206_A46biop_pre_etoh

value: Cyno 9


title: RNA140430RH_10204_A46biop_pre_etoh


title: AN15472_Control_NeuN_human

description:
Protocol 1
GSM2873974


title: RNA140430RH_10207_A46biop_pre_etoh


title: Ezh2-KO & Ezh1-homozygousKO Sample 4

description: EZH2-KO & EZH1-homoKO 4 vs. WT1

source_name: EZH2-KO & EZH1-homoKO 4


title: X1536_Control_Olig2_human

description:
Protocol 1
GSM2874003

value: R


title: RNA140430RH_10203_A46biop_pre_etoh


title: Miami0001_Control_NeuN_human

description:
Protocol 1
GSM2873976


title: SP4_RNA-seq_rep3

city: Wuhan

first: jin

last: jing

state: Hubei

address: Wuhan, Hubei Province, P.R.China

department: College of Life Sciences

institute: Wuhan University

data_processing:
Raw reads of ATAC-seq, ChIP-seq and RNA-seq were separately aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using Bowtie2, SOAP2 aligner and HISAT2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks of ATAC-seq and ChIP-seq were identified using the MACS and SICER
Genome_build: MSU7
Supplementary_files_format_and_content: bed file were generated by MACS, scores represent -10*log10(pvalue); wig files were generated using SICER, Scores represent probability；tab-delimited text files include RPKM values for each sample.

organism: Oryza sativa

source_name: Sterility male of WXS at uninucleate period

growth_protocol: The rice PTGMS line WXS (O. sativa ssp. indica) were grown in the paddy field of Wuhan University (30.35°N, 114.33°E), Wuhan, China, in summer. From 20 July to 30 August 2016, the average temperatures were? , with a 14h light/10 h dark photoperiod, which caused WXS male sterility (WXS(S)). When panicle length reached ~ 1 cm (before the stages of early premeiosis), half of the plants were transferred to growth chamber at an average temperature of 22°C with a 14h light/10h dark photoperiod and 77% relative humidity, ensuring the illumination, humidity values and other environment factors in the growth chamber close to the natural condition as far as possible, which could make WXS convert into male fertility (WXS(F))

extract_protocol:
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on the intact nuclei isolated by Plant Nuclei Isolation/Extraction Kit (CELLYTPN1, sigma) from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit. Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers. Total RNA of WXS was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Chromatin from panicle of WXS was immunoprecipitated with antibodies against H3K4me2 and H3K9ac. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
The genomic fragments of Tn5, RNA libraries and ChIP-ed DNA were separately prepared for sequencing using standard Illumina protocols

treatment_protocol: Young panicles were collected and were immediately frozen in liquid nitrogen. All collected samples were ground into fine powder for ChIP-seq, ATAC-seq and RNA-seq experiments.

tag: line

value: Wuxiang S (WXS)

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle

tag: period

value: uninucleate


title: RNA140430RH_10201_A46biop_pre_etoh


title: AN15240_Control_NeuN_human

description:
Protocol 1
GSM2873973

tag: nuclei

value: NeuN


title: AN10090_Control_NeuN_human

description:
Protocol 1
GSM2873972

tag: tissue preparation


title: AN03398_Control_NeuN_human

description:
Protocol 1
GSM2873970

tag: region


title: AN05483_Control_NeuN_human

description:
Protocol 1
GSM2873971

tag: sample id


title: SP4_RNA-seq_rep2

tag: genotype


title: RNA140430RH_10198_A46biop_pre_etoh


title: Ezh2-KO & Ezh1-heterozygousKO Sample 1

description: EZH2-KO & EZH1-hetKO 1 vs. WT1

source_name: EZH2-KO & EZH1-hetKO 1

value: embryonic day 17.5

value: Mouse Kidneys

value: EZH2-KO & EZH1-hetKO

value: control


title: RNA140430RH_10197_A46biop_pre_etoh

value: brain (prefrontal cortical area 46)


title: SP3_RNA-seq_rep1

source_name: Sterility male of WXS at meiosis period

value: meiosis


title: X3611_Control_NeuN_human

description:
Protocol 1
GSM2873968

value: brain

value: Frozen Brain Tissue

value: Brodmann Area 46

tag: gender

tag: humanized age


title: X3602_Control_NeuN_human

description:
Protocol 1
GSM2873967

value: M

tag: hemisphere

value: L

tag: pmi


title: SP4_RNA-seq_rep1


title: SP3_RNA-seq_rep3


title: SP3_RNA-seq_rep2


title: FP4_RNA-seq_rep3

source_name: Fertility male of WXS at uninucleate period


title: X4615_Control_NeuN_human

description:
Protocol 1
GSM2873969

tag: age

tag: rin


title: RNA140430RH_10200_A46biop_pre_etoh

tag: treatment

value: Cyno 9


title: X3586_Control_NeuN_human

description:
Protocol 1
GSM2873965


title: FP4_RNA-seq_rep2

value: Wuxiang S (WXS)


title: FP3_RNA-seq_rep3

source_name: Fertility male of WXS at meiosis period

value: photo-thermosensitive genic male sterile (PTGMS) rice line


title: X3590_Control_NeuN_human

description:
Protocol 1
GSM2873966


title: X3545_Control_NeuN_human

description:
Protocol 1
GSM2873964


title: FP3_RNA-seq_rep2

value: panicle


title: Ezh2-KO & Ezh1-heterozygousKO Sample 2

description: EZH2-KO & EZH1-hetKO 2 vs. WT1

source_name: EZH2-KO & EZH1-hetKO 2

tag: strain


title: FP3_RNA-seq_rep1


title: X1539_Control_NeuN_human

description:
Protocol 1
GSM2873961

value: F

value: R


title: X1540_Control_NeuN_human

description:
Protocol 1
GSM2873962

value: NeuN


title: X1541_Control_NeuN_human

description:
Protocol 1
GSM2873963


title: FP4_RNA-seq_rep1

value: uninucleate


title: W48_Lep1

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to rn6 or Macaca5 reference genome using hisat2 v2.1.0 with default parameters.
Gene expression for each sample was quantified using featureCounts(v 1.6.1) and  DEseq2(v 1.2.0).
Genome_build: rn6;Macaca_fascicularis_5.0
Supplementary_files_format_and_content: rat_all_normat.csv: abundance measurements(DESeq2, log2-transformed)
Supplementary_files_format_and_content: geneCounts_featureCounts_macaca.tab: abundance measurements(raw counts)

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was extracted from snap-frozen liver samples using TRIzol (Life Technologies) according to the manufacturer’s instructions. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
the libraries were sequenced on an Illumina Hiseq X platform and 150 bp paired-end reads were generated sequencing libraries were generated using the rRNA- depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA)

value: liver


title: W48_Lep2


title: W48_WT2


title: W48_Lep3


title: W32_Lep2


title: W48_WT1


title: Control wildtype Kidney Pair 3

description: WT3 vs. WT1

value: embryonic day 17.5

value: Mouse Kidneys

value: control


title: Ezh2-KO & Ezh1-WT Sample 2

description: EZH2-KO & EZH1-WT 2 vs. WT1

source_name: EZH2-KO & EZH1-WT 2

value: EZH2-KO & EZH1-WT


title: W32_Lep1


title: X1528_Control_NeuN_human

description:
Protocol 1
GSM2873955

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19, PanTro5, RheMac8 from UCSC)
Crossmap and Liftover tools were used to translate non-human priamte coordinates into human coordinates. Human reference was used for gene annotation and counting (gencode v19). Uniquely mapped reads were quantified using HTSeq python suite using high-scored orthologs' protein coding genes by exons.
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: tab separated files with raw counts

extract_protocol:
nuclear extraction protocol: Tissue isolated from Brodmann Area 46 from 27 healthy humans, 11 healthy chimpanzee and 15 healthy rhesus macaque.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separate nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNase inhibitors and incubated with mouse Alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit Alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
total RNA extraction protocol: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

value: brain

value: Frozen Brain Tissue


title: X1526_Control_NeuN_human

description:
Protocol 1
GSM2873953

value: Brodmann Area 46


title: X1530_Control_NeuN_human

description:
Protocol 1
GSM2873957

value: M

value: L


title: X1525_Control_NeuN_human

description:
Protocol 1
GSM2873952


title: X1538_Control_NeuN_human

description:
Protocol 1
GSM2873960


title: X1524_Control_NeuN_human

description:
Protocol 1
GSM2873951


title: X1536_Control_NeuN_human

description:
Protocol 1
GSM2873959


title: Control wildtype Kidney Pair 2

description: WT2 vs. WT1


title: Ezh2-KO & Ezh1-WT Sample 1

description: EZH2-KO & EZH1-WT 1 vs. WT1

source_name: EZH2-KO & EZH1-WT 1


title: X1532_Control_NeuN_human

description:
Protocol 1
GSM2873958


title: X1529_Control_NeuN_human

description:
Protocol 1
GSM2873956


title: Ezh2-KO & Ezh1-homozygousKO Sample 1

description: EZH2-KO & EZH1-homoKO 1 vs. WT1

source_name: EZH2-KO & EZH1-homoKO 1

value: EZH2-KO & EZH1-homoKO


title: W48_WT3


title: FXN vs EMPTY (slide B)

city: Rome

first: Silvia

last: Gioiosa

address: Via dei Tizii,6

department: Supercomputing Applications and Innovation

country: Italy

institute: CINECA

description: frataxin-deficient lymphoblastoid cells derived from a FRDA patient stably reconstituted with wild type frataxin (FTX) vs frataxin-deficient lymphoblastoid cells derived from a FRDA patients stably reconstituted with an empty vector

hyb_protocol: Hybridization was performed in duplicate, with one dye swap. Microarray slides were incubated in a water bath at 42°C for an overnight in the dark.

scan_protocol: Each slide was scanned on the GenePix 4000B Microarray Scanner at the optimal wavelength for the Alexa555 (F532) and Alexa647 (F635) dyes.

data_processing: Flagged spots were filtered and systematic bias in the data was removed by applying dye-swap and printiploess intra-array normalization followed by inter-array quantile normalization.

label: Alexa647, Alexa555 dyes

label_protocol: Direct labelling of second strand (ss) cDNA was conducted according to manufacturer’s instructions (Invitrogen) with starting material of 5 µg of total RNA. Briefly, the amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. PCR purification kit (Qiagen) was used to remove unincorporated dNTPs, fluorescent dyes and primer. Alexa555- and Alexa647-labelled cDNA was then combined in one tube and evaporated almost to dryness. The combined labelled cDNAs were stored on ice protected from light until hybridization.

extract_protocol: Total RNA of HEK-293 and HEK-293 Flp-In was extracted and purified using TriZol reagent (Invitrogen). RNA quality and quantity was assessed using a Nanodrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis.

tag: condition

value: FRDA

label: Alexa-555, Alexa-647


title: X1527_Control_NeuN_human

first: Genevieve

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Protocol 1
GSM2873954

source_name: brain

tag: tissue


title: Control wildtype Kidney Pair 1

description: WT1 vs. WT1


title: W32_WT1


title: W16_Lep3


title: W16_Lep2


title: Input DNA

city: Memphis

first: Jinghui

last: Zhang

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
The reads were aligned to the human genome (GRCh37-lite) with bwa (v0.7.12).
The multiple mapped reads and duplicated reads were removed.
Fragment length was estimated based on cross correlation plot which is generated by SPP (v1.10.1).
MACS (v2.1.1.20160309) was used to call peaks for H3K27Ac ChIP-seq data.
The results were filtered against known false positive peaks using ENCODE black list.
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: Processed data were presented in bigwig format, to be visualized in  IGV (http://software.broadinstitute.org/software/igv/) or UCSC genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway).

source_name: Human T-ALL PDX

growth_protocol: The mononuclear cells (MNCs) isolated from the patient BM samples were engrafted into 5 irradiated NOG mice (3-4 week-old female mice, Beijing Vital River Laboratory Animal Technology Co., Ltd., Beijing, China) via intravenous (i.v.) injection. Weekly monitoring of peripheral appearance of leukemic cells (CD45+) was performed via flow cytometry analysis with retro-orbital bleeding. All the animal experiments were conducted under sterile conditions at Crown Bioscience SPF facility, and performed strictly under the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine for 5min. Sonicated DNA fragments with 100–300 bp were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with Anti-H3K27Ac antibody (ab4729, Abcam). After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB).

tag: host strain

value: NOG mice (3-4 week-old).

tag: host gender

value: female

tag: engrafted with

value: MNCs isolated from the patient BM sample

tag: sample type

value: T-ALL Patient Dirived Xenograft (PDX) sample

tag: chip antibody

value: none.


title: H3K27Ac ChIP-seq

value: H3K27Ac (ab4729, Abcam)


title: ATAC_Mono_BM_SteadyState_rep2

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description: ATAC-seq in bone marrow monocytes in steady state (mouse), replicate 2

data_processing:
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations and/or insufficient mapping quality) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Reads mapping in chrM were removed with a custom script and samtools view
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

source_name: Bone Marrow

extract_protocol:
20000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.

value: Bone Marrow

tag: cell type

value: Monocyte

tag: infection

value: Steady State


title: W16_Lep1

value: liver


title: ATAC_Mono_LP_Toxo_rep2

description: ATAC-seq in monocytes from the Small intestine lamina propria from T. gondii infected mice, replicate 2

source_name: Lamina Propria

value: Lamina Propria

value: Toxoplasma gondii infection


title: W16_WT1


title: W32_WT2


title: W32_WT3


title: W16_WT3


title: W16_WT2


title: MDA231-BrM MYC WT rep2

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

country: South Korea

institute: KAIST

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the National Center for Biotechnology Information (NCBI) Genome database (assembly ID: GRCh38).
STAR was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 2.5). To estimate gene expression levels, counts per million (CPM) mapped reads values were calculated for each sample. The CPM data were normalised using quantile normalisation in the R language environment (version 3.2.5).
Genome_build: GRCh38
Supplementary_files_format_and_content: 'quantile normalised Log2 CPM'

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 2 days.

extract_protocol:
Total RNAs were isolated using Qiazol (Qiagen, Valencia, CA) followed by chloroform extraction.
Total RNAs were subjected to enrichment of polyA+ RNA using Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). Strand-specific RNA-seq libraries were prepared from the polyA+ RNA. The RNA-seq libraries were sequenced using single-end methodology with a length of 50 nt (SE50) (two replicates each) using an Illumina nextseq500

tag: cell line

value: brain metastatic derivative of MDA-MB-231

tag: passage

tag: genotype

value: cMYC rescue


title: W8_WT1


title: W8_Lep3


title: W4_Lep2


title: W4_Lep1


title: W8_Lep2


title: W8_WT2


title: W8_WT3


title: W4_Lep3


title: W8_Lep1


title: MDA231-BrM VEC rep2

value: vector control


title: Ezh2-KO & Ezh1-heterozygousKO Sample 3

description: EZH2-KO & EZH1-hetKO 3 vs. WT1

source_name: EZH2-KO & EZH1-hetKO 3

value: embryonic day 17.5

value: Mouse Kidneys

value: EZH2-KO & EZH1-hetKO

value: control


title: W4_WT2


title: W4_WT3


title: MDA231-BrM MYC WT rep1


title: W4_WT1


title: MDA231-BrM VEC rep1


title: KO_CDM_4

city: Clemson

first: William

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

data_processing:
Illumina Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 20,000,000 read pairs with a 2 x 150 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (GCF_000001635.25_GRCm38.p6) using GSNAP.  Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.

extract_protocol:
Livers were removed and stored at -80 degrees C. RNA was extracted from each treatment group (n=4) using Trizol.
Libraries were prepared using NEB Next Ultra RNA Library Prep kit.

treatment_protocol: WT and Cyp2b-null mice were fed either a normal chow diet (ND) or choline-deficient, L-amino acid-defined high fat diet (CDAHFD, 0.1% methionine and 62% fat) for 8 weeks.

tag: diet

tag: Sex

value: male


title: MDA231-BrM shMYC rep2

value: cMYC knockdown


title: KO_CDM_3

value: choline-deficient, L-amino acid-defined high fat diet (CDAHFD, 0.1% methionine and 62% fat)


title: MDA231-BrM shMYC rep1


title: KO_CDM_2


title: KO_CDM_1


title: 27-IX-16-4-8-190 [MS_321]

city: Fort Pierce

first: Joshua

last: Voss

state: FL

address: 5600 N US Highway 1

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

data_processing:
Data processing was completed using the analysis pipeline available on GitHub:
https://github.com/mstudiva/tagseq-modified-scripts
Genome_build: concatenated M. cavernosa (https://github.com/mstudiva/Mcav-Annotated-Transcriptome.git) and Symbiodinium Clade C (ftp://marchanon:anon@rc-ns-ftp.its.unc.edu/CladeC_Symbiodinium_transcriptome.zip) transcriptomes
Supplementary_files_format_and_content: tab-delimited text file containing gene counts per sample and isogroup annotations

organism: Montastraea cavernosa

tag: site

value: EFGB

tag: depth

value: shallow

tag: time

value: twelve


title: 5-V-16-1-2 [MS_319]

value: WFGB

value: mesophotic


title: MDA231-BrM shCntr rep1

value: nontargeting shRNA


title: MDA231-BrM shCntr rep2


title: EB 7013 [MS_318]


title: KO_NDM_4

value: normal chow

value: liver

tag: strain


title: 26-IX-16-4-4-120 [MS_320]


title: KO_NDM_3

tag: tissue


title: 4-V-16-1-8-60 [MS_317]

value: six


title: KO_NDM_1


title: KO_NDM_2


title: EB 7015 [MS_316]


title: Muscle_8d_WT#2

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Whole tissue

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cel sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: mTreg24 TCR-tg- (B6)

value: skeletal muscle

value: Whole tissue

tag: age

value: 6-8 weeks


title: Muscle_8d_WT#3


title: 26-IX-16-4-3-121 [MS_314]


title: Muscle_8d_Tg#3

value: mTreg24 TCR-tg+ (B6)


title: 26-X-14-2-9 [MS_315]


title: WT_CDM_3

value: wild type (WT)

value: male


title: WT_CDM_1

value: choline-deficient, L-amino acid-defined high fat diet (CDAHFD, 0.1% methionine and 62% fat)


title: 26-IX-16-1-2-178 [MS_312]


title: Tg+.spleen.Treg.uninjured#2

source_name: Vβ8+ Tregs

value: mTreg24 TCR-tg+ Foxp3 GFP+ (B6)

value: spleen

value: VBeta8+ Tregs


title: WT.spleen.Treg#2

source_name: Tregs

value: mTreg24 TCR-tg- Foxp3 GFP+ (B6)

value: Tregs


title: Muscle_8d_Tg#2


title: Muscle_8d_Tg#1


title: EB 200 [MS_313]

value: EFGB

value: mesophotic


title: WT_CDM_2

value: liver


title: WT_NDM_4

value: normal chow


title: Tg+.spleen.Treg.injured#2


title: 4-V-16-1-9-192 [MS_311]

value: six


title: WT_NDM_3


title: 26-IX-16-3-1-180 [MS_309]

value: WFGB

value: twelve


title: WT_NDM_2


title: Muscle_8d_WT#1

value: mTreg24 TCR-tg- (B6)

value: skeletal muscle

value: Whole tissue

value: 6-8 weeks


title: 27-IX-16-4-1-188 [MS_310]

value: shallow


title: WT.muscle.Treg#2


title: WT_CDM_4

value: choline-deficient, L-amino acid-defined high fat diet (CDAHFD, 0.1% methionine and 62% fat)

value: wild type (WT)

value: male


title: 4-V-16-4-2-177 [MS_308]


title: Tg+.muscle.Treg#2

value: mTreg24 TCR-tg+ Foxp3 GFP+ (B6)

value: VBeta8+ Tregs


title: 26-IX-16-1-3-179 [MS_307]


title: WT_NDM_1


title: KO_CDF_4

value: female


title: Tg+.spleen.Treg.uninjured#1

value: spleen


title: 25-X-14-1-9 [MS_306]


title: 27-IX-16-4-9-169 [MS_305]

value: EFGB


title: Tg+.spleen.Treg.injured#1


title: KO_CDF_3

value: liver


title: KO_CDF_1


title: EB 57 [MS_304]

value: mesophotic


title: WT.muscle.Treg#1

value: mTreg24 TCR-tg- Foxp3 GFP+ (B6)

value: Tregs


title: 5-V-16-1-5 [MS_303]

value: WFGB


title: KO_NDF_4

value: normal chow


title: Tg+.muscle.Treg#1

value: skeletal muscle


title: KO_NDF_3


title: 26-IX-16-2-3-69 [MS_300]

value: transplant

value: twelve


title: 4-V-16-2-1 [MS_298]

value: shallow


title: KO_NDF_2


title: EB 187 [MS_299]


title: 4-V-16-2-7-57 [MS_301]

value: six


title: 25-X-14-1-8 [MS_302]


title: WT_CDF_2

value: choline-deficient, L-amino acid-defined high fat diet (CDAHFD, 0.1% methionine and 62% fat)

value: wild type (WT)


title: KO_NDF_1


title: WB 118 [MS_297]


title: WT_CDF_3


title: WT.spleen.Treg#1

value: 6-8 weeks


title: KO_CDF_2

value: female


title: 4-V-16-1-2 [MS_296]


title: WT_CDF_4


title: WT_CDF_1


title: WB 1014 [MS_295]


title: WT_NDF_4


title: WT_NDF_3


title: S353_5_muMT_3

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_5_muMT_3_S5

data_processing:
Basecalling was performed using RTA 2.4.11
bcl files were converted to fastq using CASAVA 1.8.2
For protein coding genes, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Count tables were generated using featureCounts v1.6.2.
For Transposable elements, Fastq files were mapped to the Gencode mouse genome Release M21 (GRCm38.p6) using the STAR aligner v2.7.1a with standard settings.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files of raw counts

extract_protocol:
bulk RNA extracted from the whole tissue: RNA was extracted from hippocampal lysates using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
for WT and MAVS-KO ICV-Veh and ICV-STZ mice: Total RNA library preparation and sequencing (500ng 2x125bp). RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (kapabiosystems) in accordance with the manufacturer’s instructions. Briefly, 500ng of total RNA was used for ribosomal depletion and fragmentation. Depleted RNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 9 cycles). Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent 2100), and were sequenced on an Illumina HiSeq2500 sequencer (v2 chemistry for Rapid Run) using 2 x 125bp cycles.
muMT and WT mice: Library preparation and RNAseq for WT and muMT mice were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina NextSeq 500 System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit – Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).

tag: strain background

tag: genotype/variation

tag: treatment

value: untreated

value: hippocampus


title: WT_NDF_1

value: liver


title: WT_NDF_2


title: 26-IX-16-1-1-176 [MS_292]

value: mesophotic


title: 4-V-16-4-5-180 [MS_291]


title: 26-IX-16-4-5-119 [MS_290]


title: S353_4_muMT_1

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_4_muMT_1_S4


title: sc5000

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

description: 5000-cells sample of normal liver cells

data_processing:
fastq files were aligned with Cell Ranger 2.2
Genome_build: hg38
Supplementary_files_format_and_content: UMI matrices of the 1000, 2000, 5000 and 10000 cells samples.

source_name: Parenchymal and non-parenchymal liver cells

extract_protocol:
Hepatocytes were isolated by a two-step collagenase perfusion. Animals were anesthetized (fentanyl 50ug/kg, midazolam 5mg/kg, medetomidine 500ug/kg, i.p.), immobilized in a supine position and the liver and portal vein exposed. The portal vein was cannulated with a 22G catheter and perfusion at 4ml/min with the buffers allowed to run to waste through an incision in the inferior vena cava. The liver was perfused with 10 ml of HBSS (Mg2+, Ca2+ free,10mM HEPES, pH7 ) followed by 25ml of HBSS containing EDTA ( 10mM HEPES pH7, 5mM EDTA). The EDTA was removed from the liver by perfusion with 10 ml of HBSS followed by digestion with 25 ml of HBSS containing collagenase ( 10mM HEPES, 1mM CaCl2, 0.5mg/ml collagenase IV, 0.01mg/ml collagenase 1A (Sigma)). The liver was then removed and the cells released by cutting the capsule and gentle agitation of the digested liver in stop buffer (HBSS, 10mM HEPES pH7, 5mM EDTA, 10mM citrate, 1% FBS) and passed through a 70µm filter. The cell suspension was spun at 30G min to pellet most of the hepatocyte fraction, the supernatant collected and remnant cells pelleted at 250xG. This cell pellet was washed once in stop buffer then re-suspended in 20% isotonic Percoll and overlaid on a layer of 80% isotonic Percoll and spun at 500G for 10 minutes. The cells at the interface of the two Percoll layers were collected and washed in PBS, re-suspended in PBS and counted using a cell counter (BioRad TC 20).
scRNA-seq libraries were prepared from 1000, 2000, 5000 and 10000 cells using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (10xGenomics). Libraries were prepared according to the manufacturer’s protocol.

value: normal liver

tag: cell number


title: sc2000

description: 2000-cells sample of normal liver cells

tag: cell type

value: Parenchymal and non-parenchymal liver cells


title: sc10k

description: 10000-cells sample of normal liver cells


title: 4-V-16-4-7 [MS_288]

value: WFGB


title: SAM28

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

data_processing:
The latest version of the human reference genome assembly (GRCh38), gene models, and associated gene annotation information in the form of a Gene Transfer Format (GTF) file were obtained from the ENSEMBL database (Version 90). X and Y chromosomes were excluded to avoid gender-specific effects.
Sequences of known human rRNAs, rRNA pseudogenes, tRNA pseudogenes, mitochondrial rRNAs (mt-rRNAs), mitochondrial tRNAs (mt-tRNAs), and mt-rRNA pseudogenes were obtained from the Ensembl database (Version 90, August 2017) using the biomaRt R package (Version 2.32.1). Known human tRNA sequences were obtained from the Ensembl database (Version 90, August 2017) using the Ensembl Perl API (Version 90). These sequences were then used to build a Bowtie2 index of contaminant sequences.
Adapter sequences and low-quality 5’ ending sequences were removed from raw sequencing reads using the Trimmomatic software (Version 0.36).
The impact of quality filtering was assessed using the FastQC software.
Following adapter removal, sequence reads were aligned to the index of known human rRNAs and tRNAs using Bowtie2 with its local alignment option. Reads that mapped to the index were removed, and those that did not were output to a FASTQ file for alignment to the reference genome.
Filtered reads were aligned to the reference transcriptome/genome using the HISAT2 splice-aware sequence aligner (Version 2.1.0)
For each sample, the quality of reference alignments was evaluated using the RSeQC software (Version 2.6.4)
Quantification was carried out on the gene level using the featureCounts function of the Subread software package (Version 1.5.3). Reads that overlapped with multiple genes or mapped to multiple locations on the reference genome were excluded. Known ribosomal, transfer, and mitochondrial RNA genes were removed from the final read count analysis dataset
Genome_build: GRCh38
Supplementary_files_format_and_content: abate_npj_2019_rnaseq_featurecounts.tab.gz contains read counts as assigned by Subread featureCounts (Version 1.5.3). Rows represent genes, and columns represent samples.

molecule: polyA RNA

source_name: RNA extracted from PBMCs after stimulation with F1/V vaccine antigen for 24 hours

extract_protocol:
Add 600ul Buffer RLT Plus (with 2ME) and vortex for 30 seconds. Transfer lysed cells to a gDNA Eliminator spin column that is sitting in a 2ml collection tube that is supplied   Centrifuge at 11,000 rpm for 30 seconds. Discard the column and save the flow-through.  Add 600ul of 70% ethanol to the flow-through and mix by pipetting. Transfer half of the sample into an RNeasy spin column which has a 2ml collection tube supplied. Close lid and centrifuge for 15 seconds at 11,000 rpm. Discard the flow-through into the waste bag on the bench and place the column onto the 2ml tube again. Transfer the other half of the sample into the RNeasy spin column and centrifuge once again for 15 seconds at 11,000 rpm. Add 700ul Buffer RW1 to the RNeasy spin column. Close lid and centrifuge for 15 seconds at 11,000 rpm and then discard the flow through. Add 500ul Buffer RPE to the RNeasy spin column. Close the lid and centrifuge for 15 seconds for 11,000 rpm and then discard the flow through. Add 500ul Buffer RPE to the RNeasy spin column again. Close lid and centrifuge for 2 minutes at 11,000 rpm. Remove spin column gently out of the centrifuge to avoid any splashing of buffer onto the column. Discard the flow through and centrifuge RNeasy spin column (without any buffer) for 1 min at 14,000 rpm (full speed) to further dry the membrane. Place the RNeasy spin column into a new 1.5ml collection tube (supplied with kit) and add 50ul of RNase-free water (supplied with kit) directly onto the middle of the spin column membrane (without touching membrane with tip).Close lid and centrifuge for 1 minute at 11,000 rpm to elute the RNA. Place RNA on ice and discard the RNeasy spin column.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 1 to 3ug of total RNA. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000, using single reads extending 50 bases.
Fragments were sequenced on an Illumina HiSeq-3000, using single reads extending 50 bases. Fourty-one libraries were multiplexed across 4 sequencing lanes with targeted coverage of 39 million reads per RNA-Seq library.

treatment_protocol: Stimulated PBMC with F1/V vaccine antigen for 24h. Wash once with PBS. Then transfer 5e6 – 1e7 cells into a 1.5ml snap top tube and centrifuge cells at 2000g for 5 minutes at room temperature. Remove supernatant completely, leaving cell pellet intact. Put cell pellet on ice and take samples to a dedicated RNA extraction laboratory.

tag: subject

value: SUBF

value: Day 14

value: Flagellin/F1/V 10 mug

value: peripheral blood mononuclear cells (PBMCs)


title: 26-X-14-1-8 [MS_286]

value: EFGB

value: shallow


title: 5-V-16-4-1-118 [MS_287]

value: six


title: sc1000

description: 1000-cells sample of normal liver cells


title: 5-V-16-4-5-121 [MS_289]


title: S353_2_WT_3

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_2_WT_3_S2

value: wild type


title: 25-X-14-2-3 [MS_285]


title: SAM16

value: SUBN

value: Day 28


title: SAM29

value: Day 0


title: Irf3/7-KO NT rep1

city: Dallas

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

institute: University of Texas Southwestern Medical Center

data_processing:
Blc2fastq2 Conversion software (Illumina) was used to generate de-multiplexed Fastq files.
Illumina reads were post-processed and aligned to the mouse mm9 assembly using Tophatprogram with default parameters in the DNAnexus.
Expression values were normalized as Fragments per Kilobase Million reads after correction for gene length (FPKM) in Cuffdiff version 1.06 in the DNAnexus
Genome_build: mm9

source_name: Bone Marrow-derived Dendritic cells (BMDCs)

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) cells were generated by flushing bone marrow cells from femurs and tibia of WT or indicated knockout (KO) mice, depleting red blood cells using ACK lysis buffer, and resuspending cell in complete RPIM-1640 media supplemented with 10% FBS, 0.5% penicillin/streptomycin mixture, 10ng/ml rmGM-CSF and 10ng/ml rmIL-4. Cells were maintained in culture at 37 °C, 5 % CO2 for 6 days before experimentation.

extract_protocol:
500ng of total RNA was subjected to library synthesis using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adaptors according to the manufacturer’s protocol (Illumina).
Total RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2. BMDCs were stimulated in FCS 10% RPMI-1640 with or without 25ug/ml c-di GMP for 18 hours.

value: No treatment for 18h


title: Irf3/7-KO NT rep2

value: Bone Marrow-derived Dendritic cells (BMDCs)


title: Irf3/7-KO CDG rep1

value: c-di-GMP (25ug/ml) for 18h


title: 4-V-16-1-13-188 [MS_294]


title: Irf3/7-KO CDG rep2


title: 5-V-16-3-2 [MS_284]


title: S353_3_WT_4

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_3_WT_4_S3

value: untreated

value: hippocampus


title: S353_1_WT_1

description:
processed data file:
3wt-vs-2mumt-genomic-counts.csv
3wt-vs-2mumt-genomic+transposable-elements-counts.csv
S353_1_WT_1_S1


title: SAM33


title: 25-X-14-2-6 [MS_293]

value: WFGB


title: Irf1-KO CDG rep2


title: SAM07


title: WB 198 [MS_283]


title: 26-IX-16-2-1-54 [MS_282]

value: transplant

value: twelve


title: Irf1-KO CDG rep1


title: SAM41

value: SUBL

value: Day 14

value: Flagellin/F1/V 6 mug


title: 27-IX-16-3-5-194 [MS_279]

value: EFGB

value: mesophotic


title: SAM27

value: peripheral blood mononuclear cells (PBMCs)


title: 25-X-14-1-7 [MS_280]

value: shallow


title: 4-V-16-4-3-179 [MS_278]

value: six


title: Tmem173-KO CDG rep1


title: SAM01

value: SUBO

value: Day 0


title: 5-V-16-4-4-124 [MS_277]


title: SAM10

value: Day 28


title: SAM39


title: Tmem173-KO NT rep2

value: Bone Marrow-derived Dendritic cells (BMDCs)

value: No treatment for 18h


title: Wild-Type CDG rep2

value: WT

value: c-di-GMP (25ug/ml) for 18h


title: SAM37

value: SUBV

value: Flagellin/F1/V 10 mug


title: Irf1-KO NT rep1


title: 26-X-14-1-9 [MS_274]


title: Tmem173-KO CDG rep2


title: SAM03


title: Wild-Type CDG rep1


title: Tmem173-KO NT rep1


title: SAM13

value: SUBL


title: Wild-Type NT rep2


title: Irf1-KO NT rep2


title: 26-X-14-2-3 [MS_281]


title: 4-V-16-4-4-178 [MS_272]

value: WFGB


title: SAM14

value: SUBA


title: SAM35


title: WB 119 [MS_271]


title: Wild-Type NT rep1


title: 26-IX-16-4-1-124 [MS_275]

value: twelve


title: EC.Vdr.KO.Co#3

source_name: EC

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X38bp reads.

value: Colon

value: EC

value: VDR KO


title: 27-IX-16-4-6-193 [MS_268]

value: EFGB

value: transplant


title: EC.Vdr.WT.Co#3

value: VDR WT


title: EB 7005 [MS_269]

value: mesophotic


title: EC.Vdr.KO.Co#2


title: 26-X-14-3-8 [MS_267]

value: shallow


title: SAM02

value: SUBH

value: Day 28

value: peripheral blood mononuclear cells (PBMCs)


title: SAM38

value: Day 14


title: 5-V-16-2-5 [MS_273]


title: SAM31

value: Day 0

value: Flagellin/F1/V 10 mug


title: EC.Vdr.KO.Co#1


title: SAM04

value: SUBB


title: 4-V-16-3-5 [MS_266]


title: 26-X-14-1-5 [MS_265]


title: EC.Vdr.WT.Co#1


title: SAM09


title: DC.Vdr.KO.Co#3

source_name: DC

value: DC


title: 25-X-14-3-1 [MS_270]

value: WFGB


title: SAM20


title: 27-IX-16-3-4 [MS_264]


title: SAM19

value: SUBA


title: SAM08


title: EC.Vdr.WT.Co#2

value: Colon

value: EC


title: DC.Vdr.WT.Co#3


title: WB 1013 [MS_263]


title: DC.Vdr.KO.Co#2

value: VDR KO


title: EB 194 [MS_262]

value: EFGB


title: 26-IX-16-1-4-177 [MS_261]

value: twelve


title: DC.Vdr.WT.Co#2

value: VDR WT


title: SAM05

value: SUBZ


title: SAM26


title: SAM34


title: DC.Vdr.KO.Co#1


title: WB 196 [MS_260]

value: shallow


title: DC.Vdr.WT.Co#1


title: SAM15

value: SUBW

value: Day 28


title: 3-V-16-1-1-71 [MS_258]

value: mesophotic


title: 4-V-16-1-5 [MS_259]


title: Tconv.Vdr.KO.Co#3

source_name: Tconv

value: Tconv


title: Tconv.Vdr.WT.Co#3


title: 26-X-14-3-3 [MS_257]


title: Tconv.Vdr.KO.Co#2


title: SAM40

value: Day 14

value: Flagellin/F1/V 10 mug

value: peripheral blood mononuclear cells (PBMCs)


title: SAM32

value: SUBX


title: 5-V-16-3-1-69 [MS_256]

value: WFGB

value: transplant

value: six


title: SAM21

value: Day 0


title: Tconv.Vdr.WT.Co#2

value: Colon


title: Tconv.Vdr.KO.Co#1

value: VDR KO


title: SAM36


title: SAM18

value: SUBE

value: Flagellin/F1/V 6 mug


title: Tconv.Vdr.WT.Co#1

value: VDR WT


title: SAM25


title: 4-V-16-3-2 [MS_253]

value: EFGB

value: shallow


title: SAM22


title: Treg.Vdr.WT.Co#3

source_name: Treg

value: Treg


title: SAM23


title: 5-V-16-1-6 [MS_251]

value: mesophotic


title: SAM12

value: SUBR

value: Day 28


title: Treg.Vdr.KO.Co#2


title: 26-X-14-2-7 [MS_254]


title: 25-X-14-1-5 [MS_255]


title: Treg.Vdr.KO.Co#3


title: 27-IX-16-4-7-189 [MS_250]

value: twelve


title: SAM11

value: Day 14

value: peripheral blood mononuclear cells (PBMCs)


title: WB 2 [MS_252]

value: WFGB


title: Treg.Vdr.WT.Co#2


title: 5-V-16-2-3-52 [MS_249]

value: transplant

value: six


title: Treg.Vdr.KO.Co#1

value: Colon


title: Treg.Vdr.WT.Co#1


title: SAM17

value: SUBD


title: 25-X-14-3-2 [MS_248]


title: SAM24

value: Day 0


title: SAM06

value: Flagellin/F1/V 6 mug


title: 4-V-16-1-12-190 [MS_246]


title: 26-X-14-2-5 [MS_247]


title: BA10_AUD_rep24

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

description:
24A
A.24

hyb_protocol: DNA was bisulfite converted (EZ DNA methylation kit, Zymo Research, Irvine, CA) then amplified, fragmented and hybridised to Illumina Infinium® MethylationEPICBeadChip  using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing:
R (v 3.4.3) and the minfi package (v 1.22.1) were used to read the idat files and compute methylated,  unmethylated, detection p-values, and normalized beta values per probe
Unmethylated and methylated signal intensities (methValues.txt)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol, taking place after hybridization

extract_protocol: DNA was extracted using QIAamp® DNA Mini Kit (Qiagen, Valencia, CA)

tag: group

value: AUD

value: brain, prefrontal cortex BA10

value: male

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year

tag: age of drinking onset


title: SAM30

tag: time


title: RNASeq_E16.5_Intestine_Replicate #1

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: RNASeq_E16.5_Intestine_Replicate #1

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method.
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing the gene expression matrix

source_name: Mouse E16 embryonic tissue

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
For E13.5 mouse experiments, ShhCre; R26YFP/+ embryos were used for downstream high-throughput experiments. After dissection, the stomach and intestinal organs were isolated, separated, washed in cold PBS and digested in 4ml of a 3:1 solution of Trypsin LE: 1x PBS at 37˚C. After 10 minutes, tissue was vigorously pipetted, until the organs broke down into a single cell suspension, which was confirmed using brightfield microscopy. The enzymatic reaction was then inhibited with 10% FBS. After washing cells in cold PBS, the single cells were re-suspended in 400µl of 1:5000 Sytox Blue (ThermoFisher Scientific, S34857) in cold 1x PBS, filtered through a 30µm mesh and submitted for sorting. Sorted cells were washed again and processed for ATAC-seq (50,000 cells from 3-4 YFP+ embryos) using the previously published protocol (44).    For E16.5 experiments, whole organ digestion using Trypsin was detrimental to epithelial cell viability; thus, an alternative isolation approach was employed. Given strict cell numbers are required for ATAC-seq, gut epithelium was isolated from ShhCre;R26YFP/+ embryos prior to single cell dissociation. In more detail, the E16.5 embryonic stomach, the proximal small intestine and the colon were dissected and opened longitudinally using a 0.5 cm tungsten needle. The forestomach was separated from the hindstomach along the squamous-glandular border under a dissecting microscope, and incubated in Dispase solution for 15 minutes at 37˚C. Following, the epithelial layer was manually separated from the mesenchyme and flash frozen for RNA isolation or collagenase digested for sorting. The hindstomach, proximal small intestine and colon were incubated in 10mM EDTA, 5mM EDTA and 5mM EDTA in 1x PBS, respectively, for 30-40 minutes at 4˚C on a shaker. Tissues were then moved to fresh 1x PBS and shaken vigorously for 2-3 minutes, or until epithelial glands/villi/crypts were observed in suspension. Isolated epithelial cells were immediately frozen and RNA isolation was conducted using an RNA isolation kit (Qiagen, Cat No. 74104). To prepare for sorting for ATAC-seq experiments, the fresh epithelial pellets of the forestomach, hindstomach, intestine and colon were then digested in collagenase-based solution for 20 mins at 37˚C. The resulting single cell suspension was washed in cold 1x PBS, re-suspended in 500µl of 1:5000 Sytox Blue and submitted for sorting. Sorted cells were then used for ATAC-seq using the same protocol as mentioned above.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: No treatment


title: BA10_AUD_rep20

description:
20A
A.20

tag: Sex


title: BA10_AUD_rep21

description:
21A
A.21

tag: tissue


title: WB 52 [MS_245]

tag: site

tag: depth


title: RNASeq_E16.5_Intestine_Replicate #2

description: RNASeq_E16.5_Intestine_Replicate #2

tag: age


title: F_air_3

city: Biberach

first: Karsten

last: Quast

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: ensembl70
Supplementary_files_format_and_content: tab-delimited text file contains RPKM values for each sample

source_name: Air Liquid Interface culture

growth_protocol: Human Small Airway Epithelial Cells (SAEC, CC-2547, Lonza, Basel, Switzerland) were thawed and approximately one million cells were seeded into a T175 cell culture flask with 50 ml pre-warmed PneumaCult™-Ex Plus Medium (Stemcell Technologies, Vancouver, Canada). On the following day, the medium was exchanged, to remove residuals from the cryoprotectant cocktail. On the fourth day after seeding, the cells were sufficiently confluent (max. 80 %) to be harvested for seeding onto transwell inserts. The Transwells (#3460, Corning Life Sciences B.V., Amsterdam, the Netherlands) were coated with 300 µl rat tail collagen type 1 solution (Corning Life Sciences B.V., Amsterdam, the Netherlands, 30µg/ml in phosphate buffered saline) for 45 minutes at 37 °C. Collagen solution was aspirated and transwell inserts were washed with phosphate buffered saline. The basolateral compartments of the transwells were filled with 1.5 ml PneumaCult™-Ex Plus Medium. Dissociation of SAEC was performed using the Animal Component-Free Cell Dissociation Kit (Stemcell Technologies, Vancouver, Canada) according to the manufacturer’s instructions. Subsequently, 100.000 cells per insert were seeded in 300 µl on the transwell membrane. On the following day, apical and basolateral media was exchanged using PneumaCult™-Ex Plus Medium. On day three after the transfer to transwell inserts, when the cells were fully confluent, the apical and basolateral medium was removed and 1.5 ml Pneumacult-ALI-S Medium (Stemcell Technologies, Vancouver, Canada) was added basolaterally. The apical compartment was washed with phosphate buffered saline to remove residual growth factors of the media. The cells were from then on grown in air-liquid interface (day 0). Medium exchanges were performed three times a week. The cells were fully differentiated 28 days post air-lift.   As stated by Lonza, the cells were isolated from donated human tissue after obtaining permission for their use in research applications by informed consent or legal authorization.

extract_protocol:
Total RNAs were individually extracted using the Ambion Magmax™-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, 5 mg of tissue was placed in the lysis solution and homogenised in Qiagen Tissuelyzer™ for a period of 30 sec. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. RNA quality and concentration was measured using an RNA Pico chip on an Agilent Bioanalyzer.
The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp fragment including adapters in average size. Libraries have  been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3 - cBot - HS(GD-401-3001, Illumina Inc, San Diego, CA)  sequencing was then performed on an Illumina HiSeq3000 instrument

treatment_protocol: SAECs were exposed to whole cigarette smoke of K3R4F reference cigarettes (University of Kentucky, Lexington, KY, USA) using an automated cigarette smoking machine (In-Expose smoking robot, Scireq Montreal, QC, Canada) and the P.R.I.T. (Professional In-Vitro Technologies) ExpoCube in the experimental setup developed by Fraunhofer Institute for Toxicology and Experimental Medicine. Four cigarettes were smoked in parallel in compliance to ISO 3308, drawing every 15 seconds a puff from the sequentially smoked cigarettes (9 puffs per cigarette). The smoke was diluted with ambient air (dilution rate: 0.5 l/min). The cells were exposed to CS three times a week during the differentiation phase (28 days) beginning on day 0 (= day of air-lift). Readouts were performed 24 hours post last exposure.

tag: donor

tag: lonza id

tag: disease state

value: COPD

value: F

tag: ethnicity

value: Black

tag: smoker

value: Y

tag: treatment

value: air

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week

value: Small Airway Epithelial Cells (SAECs)


title: BA10_AUD_rep18

description:
18A
A.18

tag: group

tag: postmortem interval (h)

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year


title: 4-V-16-2-2 [MS_244]

tag: site

value: EFGB

tag: depth

value: shallow


title: BA10_AUD_rep17

description:
17A
A.17

tag: tissue

tag: Sex

tag: age of drinking onset


title: F_air_2

tag: donor

tag: lonza id

tag: disease state

tag: age

tag: ethnicity

tag: cell type


title: BA10_AUD_rep25

description:
25A
A.25

tag: group


title: BA10_AUD_rep19

description:
19A
A.19

tag: postmortem interval (h)


title: RNASeq_E16.5_Hindstomach_Replicate #1

description: RNASeq_E16.5_Hindstomach_Replicate #1


title: F_air_1

tag: smoker

tag: treatment

tag: cigarettes per treatment

tag: dilution rate (l/min)

tag: number of treatments a week


title: RNASeq_E16.5_Hindstomach_Replicate #2

description: RNASeq_E16.5_Hindstomach_Replicate #2


title: BA10_AUD_rep12

description:
12A
A.12

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year


title: WB 1015 [MS_242]

tag: site

value: WFGB

tag: depth

value: mesophotic


title: RNASeq_E16.5_Forestomach_Replicate #2

description: RNASeq_E16.5_Forestomach_Replicate #2


title: 3-V-16-1-3 [MS_243]


title: F_CS_3

tag: donor

tag: lonza id

tag: disease state

tag: Sex

value: CS


title: EB 7006 [MS_241]


title: BA10_AUD_rep7

description:
7A
A.7

tag: group

tag: tissue

tag: age of drinking onset


title: BA10_AUD_rep13

description:
13A
A.13

tag: postmortem interval (h)


title: F_CS_2

tag: age

tag: ethnicity

tag: smoker

tag: treatment

tag: cigarettes per treatment

tag: cell type


title: RNASeq_E16.5_Forestomach_Replicate #1

description: RNASeq_E16.5_Forestomach_Replicate #1


title: RNASeq_E16.5_Colon_Replicate #2

description: RNASeq_E16.5_Colon_Replicate #2


title: 4-V-16-2-5-187 [MS_240]

tag: time

value: six


title: BA10_AUD_rep6

description:
6A
A.6

tag: total drinking years

tag: etoh daily use (g)

tag: drinks per week

tag: cigarette packs per year


title: BA10_AUD_rep9

description:
9A
A.9


title: BA10_AUD_rep23

description:
23A
A.23


title: 26-X-14-2-4 [MS_239]

tag: site

tag: depth


title: RNASeq_E16.5_Colon_Replicate #1

description: RNASeq_E16.5_Colon_Replicate #1


title: BA10_AUD_rep22

description:
22A
A.22

tag: group

tag: Sex


title: BA10_AUD_rep16

description:
16A
A.16

tag: tissue

tag: age of drinking onset


title: E_air_3

tag: donor

tag: lonza id

tag: disease state

tag: age

value: Caucasian

tag: dilution rate (l/min)

tag: number of treatments a week