title: Drosophila yw samples, rep2

city: Ames

first: Kerui

last: Huang

state: IA

address: 2437 Pammel Drive

department: Genetics and Genomics

institute: Iowa State University

description:
dros_yw_outlier_removed.xlsx
yw-200-2

data_processing:
FaastQC (v0.11.8) was first performed to check the sequencing read quality. Then sequence alignment and mapping was performed using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.7.3a). The raw reads were mapped to D. melanogaster genome (BDGP Release 6) or Genome Reference Consortium Human Build 38 (GRCh38). Reads mapped were then counted with summarizedOverlaps function using “Union” mode in R. Counts are then analyzed in DESeq2 (v1.26.0) for batch control analysis and test for differential expression.
Genome_build: D. melanogaster genome (BDGP Release 6) and Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary_files_format_and_content: Excel tables contain normalized abundance measurements from Deseq2 after outlier removal. CSV files contain raw counts for Pex5, Pex1 and Pex12 Drosophila samples.

organism: Drosophila melanogaster

source_name: oenocytes

growth_protocol: Female flies were used in all experiments. Flies were maintained at 25°C, 60% relative humidity, and 12-h light/dark cycle. Adults and larvae were reared on a standard cornmeal and yeast-based diet, unless otherwise noted. The standard cornmeal diet consists of the following materials: 0.8% cornmeal, 10% sugar, and 2.5% yeast. RU486 (mifepristone, Fisher Scientific) was dissolved in 95% ethanol, and added to standard food at a final concentration of 100 µM for all the experiments. Gene KD or overexpression was achieved by feeding flies on RU486 food for 6 days, before RNA isolation. For human cells experiments, HEK293 expressing Tet-PEX5C11A-Puro cells were cultured in Dulbecco’s Modified Eagle Medium containing 10% fetal bovine serum (FBS), with penicillin and streptomycin. HepG2 cells were cultured in Minimum Essential Medium containing 10% FBS, 1mM sodium pyruvate, 1X MEM Non-Essential Amino Acids solution (ThermoFisher, #11140050) with penicillin and streptomycin. Cells were incubated in a 37°C incubator in an atmosphere of 5% CO2 in air.

extract_protocol:
For Drosophila oenocytes, adult tissues oenocytes (20 females per replicate) were all dissected in cold 1 × PBS before RNA extraction. For oenocyte dissection, we first removed FB through liposuction and then detached oenocytes from the cuticle using a small glass needle. Tissue lysis, RNA extraction was performed using RNeasy Micro kit from QIAGEN (catalog number 74034) with the following modifications. Samples were first collected in 1.7ml centrifuge tubes. Dissected tissues were saved in 150ul of Buffer RLT (a component of RNeasy kits) with 143mM β-mercaptoethanol on ice during the dissection. Samples were then put at room temperature for 3 minutes prior to lysis and centrifuged at 7.5xg for 3minutes. Additional 150ul buffer RLT was added and pellet pestle grinder (Kimble pellet pestles, catalog number 749540-0000) was used to lyse the tissue for 1 minutes. 20ng carrier RNA was added to the cell lysates. Frozen samples was thawed in 37°C water bath for 1 minute. Total RNA was extracted using RNeasy Plus Micro columns following company manual. For human cell experiments, total RNA was extracted using TRIZOL.
Fro Drosophila oenocytes, RNA-seq libraries were constructed using 100 ng of total RNA and NEBNext Ultra II RNA Lib Prep (NEB, Ipswich, MA, USA. Catalog number: E7770L). RNA concentrations were measured using Qubit RNA BR Assay Kit (Thermo Fisher Scientific, catalog number: 10210). Poly(A) mRNA was isolated using NEBNext Oligo d(T)25 beads and fragmented into 200 nt in size. Purification of the ligation products are performed using Beckman Coulter AMPURE XP (BECKMAN COULTER, catalog number: A63880). After cDNA synthesis, each cDNA library was ligated with a NEBNext adaptor and barcoded with an adaptor-specific index (NEBNext® Multiplex Oligos for Illumina, NEB, catalog number: E7335S). Twelve libraries were pooled in equal concentration and sequenced using Illumina HiSeq 3000 platform (single end, 150bp reads format). For human cells, RNA-seq libraries were constructed using 1ug DNA-free total RNA with NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA. NEB#E7770).  Poly (A) mRNA was isolated using NEBNext Poly(A) mRNA Magnetic isolation module (New England Biolabs, Ipswich, MA, USA. NEB#E7490). After first strand and second strand and second strand cDNA synthesis, each cDNA library was ligated with a NEBNext adaptor and barcoded with an adaptor-specific index. Twelve libraries were pooled in equal concentrations and sequenced using Illumina HiSeq 3000 platform.

treatment_protocol: To prepare RNA-seq libraries, 4x10^5 HEK293 expressing Tet-PEX5C11A-Puro cells were seeded in a 12 well plate. After 1 day, 1ug/ml of doxycycline was added to the cells to induce PEX5C11A in the cells. After 72hrs, total RNA was isolated from the cells with or without doxycycline treatment. 3x10^5 HepG2 cells were seeded in a 6-well plate. Transfection of siRNA into HepG2 cells was performed with lipofectamine RNAiMAX (ThermoFisher) according to the manufacturer’s instructions. On-TARGET plus human PEX5 siRNA (Dharmacon # L-015788-00-0005) was used for knockdown of PEX5 in HepG2 cells. For negative control, On-TARGET plus non-targeting siRNA (Dharmacon # D-001810-02-05) was used. After 72hrs, total RNA was isolated from the cells. All samples were treated TURBOTM DNase (Thermofisher #AM1907) to remove all traces of DNA.

value: oenocytes

value: RU feeding

tag: genotype

value: yw


title: Drosophila yw samples, rep3

status: Public on Feb 23 2021

type: SRA

country: USA

description:
dros_yw_outlier_removed.xlsx
yw-200-3

library_source: transcriptomic

molecule: polyA RNA

tag: cell type

tag: treatment


title: CD4polarizedTh17_24h_db+IL23_rep2

type: RNA

city: Seoul

first: Jinju

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: University of Ulsan

hyb_protocol: 175 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Technologies Scanner G2505C US45102837 using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-1100 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Mus musculus

source_name: CD4 polarized Th17, 24h, db-cAMP + IL-23, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 175ng RNA using Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Beckman coulter DU730 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a Beckman coulter DU720 spectrophotometer

treatment_protocol: CD4+ T cells were cultured under the Th17-skewing conditions with IL-6 and TGF-β1 for 3 days, then incubated with db-cAMP alone, IL-23 alone or both for 24 h, and subjected to microarray analysis.

tag: tissue

value: spleen


title: HD1_memBC

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: RRBS

library_source: genomic

data_processing:
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 10).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

tag: patient id

tag: diagnosis

value: memory B cell CD5-

tag: ighv

tag: treatmentstatus


title: HD1_naiBC

description: RRBS

value: naïve B cell CD5-


title: Drosophila yw samples, rep1

description:
dros_yw_outlier_removed.xlsx
yw-200-1


title: CD4polarizedTh17_24h_db+IL23_rep1

source_name: CD4 polarized Th17, 24h, db-cAMP + IL-23, replicate1


title: +CM THP-1, rep1

city: Duesseldorf

first: Thomas

last: Schroeder

address: Moorenstr. 5

department: Department of Hematology, Oncology and Clinical Immunology

institute: University of Duesseldorf, Medical Faculty

description:
CM_THP-1_sample7
CM_healthy_CD34_HSPC_VS_CM_THP-1_output_sorted.txt
CM_healthy_CD34_HSPC_VS_CM_THP-1_output_norm-matrix.txt

data_processing:
Cropping 12 bases from 5'-end using Trimmomatic (v.0.39)
2-pass alignment using STAR (v.2.7.2a): 1st pass: identification of of new splice junctions using all input data files together and addition to reference: 2nd pass: Alignment with combined reference for each input file individually.
Identification of raw counts using featureCounts (v.1.6.5)
Identification of normalized counts and differentially expressed genes using DEseq2 (v.1.24.0)
Calculation of FPKM-values using StringTie (v.2.0.3)
Genome_build: GRCh38.97
Supplementary_files_format_and_content: *.tab: tab-delimited txt-file:Stringtie-results TPM and FPKM values per gene
Supplementary_files_format_and_content: *_norm-matrix.txt: tab-delimited txt-file: DESeq2 normalized counts matrix
Supplementary_files_format_and_content: *_sorted.txt: tab-delimited txt-file: DEseq2 sorted list of differential expressed genes

source_name: CD34+ hematopoietic stem and progenitor cells (HSPC)

growth_protocol: Mononuclear cells (MNC) were obtained from BM aspirates following density gradient separation as previously described. CD34+ HSPC were positively selected from BM-derived MNC by immunomagnetic cell separation (Miltenyi Biotec, Bergisch-Gladbach, Germany). To investigate the influence of AML-derived CM on CD34+ HSPC functionality, 2x10^5/per well healthy CD34+ HSPC were cultivated on a 6-well plate in CM derived from AML cell lines (cytokines were then added to CM of cell lines for comparability) as well as from patient-derived MNC and CD34+ HSPC (CM from primary cells already contains cytokines from generation process). After 72 hours RNA was extracted.

extract_protocol:
RNA from hematopoietic cells (CD34+) was purified using the RNeasy Mini or Micro kit (both Qiagen, Hilden, Germany) according the manufacturer’s instructions.
DNase digested total RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific Inc., Waltham, MA, USA) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ or the Bioanalyzer assay “Eukaryote Total RNA Pico” (Agilent Technologies, Inc., Santa Clara, CA, USA). The mean RNA Quality Number (RQN) of the samples in this study was 8.9. The library preparation was performed according to the manufacturer’s protocol using the ‘NuGen Universal Plus mRNA-Seq Library Prep Kit’ for Illumina®. Briefly, 10 ng total RNA were used for poly(A) RNA selection, fragmentation, cDNA generation, adapter ligation, strand selection and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA) with a read setup of 1x150 bp. The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.

treatment_protocol: To generate conditioned media (CM, supernatants) 2 × 10^6 cells of the AML cell lines HL-60, THP-1, and MV4-11 (all purchased from DMSZ, Braunschweig, Germany) were cultivated in T75 cm2 culture flasks for 3 days in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin/L-glutamine (PSG, all from Sigma-Aldrich Chemie GmbH, Taufkirchen Germany). For patient-derived CM 2 × 10^6/well BM-derived CD34+ AML cells and BM-derived CD34+ HSPC from healthy donors (HC) were cultivated on a 6-well plate under the same conditions. To properly maintain  CD34+ cells of patients with AML and healthy cells in culture for collection of CM, RPMI-1640 medium contained IL-3, IL-6, SCF and FLT3-ligand (all 10 ng/ml, PreproTech GmbH, Hamburg, Germany). Cells were incubated at 37°C, 5% CO2 under humidified conditions. Following incubation cell-free CM were subsequently harvested by filtration (Minisart® 0,45μm, Sartorius AG, Göttingen, Germany) and stored at -20°C for further experiments.

value: bone marrow derived CD34+ HSPC

tag: group

value: exposed to AML cell line THP-1 derived CM


title: CD4polarizedTh17_24h_IL23_rep3

source_name: CD4 polarized Th17, 24h, IL-23, replicate3


title: CD4polarizedTh17_24h_IL23_rep2

source_name: CD4 polarized Th17, 24h, IL-23, replicate2


title: +CM THP-1, rep2

description:
CM_THP-1_sample8
CM_healthy_CD34_HSPC_VS_CM_THP-1_output_sorted.txt
CM_healthy_CD34_HSPC_VS_CM_THP-1_output_norm-matrix.txt


title: Drosophila control samples for yw, rep2

description:
dros_yw_outlier_removed.xlsx
yw-0-2

value: no RU feeding

value: control for yw


title: Drosophila control samples for yw, rep3

description:
dros_yw_outlier_removed.xlsx
yw-0-3


title: +CM HL-60, rep3

description:
CM_HL-60_sample6
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_sorted.txt
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_norm-matrix.txt

value: exposed to AML cell line HL-60 derived CM


title: Drosophila control samples for yw, rep1

description:
dros_yw_outlier_removed.xlsx
yw-0-1


title: CD4polarizedTh17_24h_IL23_rep1

source_name: CD4 polarized Th17, 24h, IL-23, replicate1


title: inflammed and non inflammed IEL sample from CD donor 1818

city: Cambrdge

first: Ramya

last: Gamini

state: MA

address: 1 Portland st

institute: Pfizer Inc.,

data_processing:
Processing was performed with the 10X Chromium cellranger pipeline version 2.0.2 using default settings
Genome_build: Genome_build: GRCm38.1.2.0
Supplementary_files_format_and_content: tar.gz of  Filtered feature-barcode matrix with raw counts for each sample

extract_protocol:
T cells were sorted from processed IEL and LP as CD45+, lymphocyte gate, singlets, alive CD3+ CD19- expression.
 Using the Chromium Single Cell 3′ Reagent Kit v3 User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

tag: subject id

value: donor 1818

tag: disease status

value: Crohn's disease (CD)

tag: compartment

value: IEL

value: T cells

tag: sorting


title: CD4polarizedTh17_24h_db+IL23_rep3

source_name: CD4 polarized Th17, 24h, db-cAMP + IL-23, replicate3


title: HD1_naiBC_CD5

description: RRBS

value: naïve B cell CD5+


title: non inflammed IEL samples from CD donor 1813

source_name: non inflammed IEL samples from CD donor

value: donor 1813

value: Normal


title: CD4polarizedTh17_24h_db_rep2

source_name: CD4 polarized Th17, 24h, db-cAMP, replicate2


title: +CM HL-60, rep2

description:
CM_HL-60_sample5
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_sorted.txt
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_norm-matrix.txt


title: CD4polarizedTh17_24h_veh_rep3

source_name: CD4 polarized Th17, 24h, veh, replicate3


title: +CM HL-60, rep1

description:
CM_HL-60_sample4
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_sorted.txt
CM_healthy_CD34_HSPC_VS_CM_HL-60_output_norm-matrix.txt


title: P90p6_Eff

city: New Haven

first: Miguel

middle: F

last: Sanmamed

state: CT

address: 300 George Street 203A

institute: Yale University

data_processing:
RNA-seq reads were aligned to the human reference genome (hg38) using the HISAT2
Gene models were downloaded from the GENCODE project (v27).
read counts were extracted from StringTie outpout using the prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq)
DESeq2 was used to determine differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited read counts

source_name: Tumor-infiltrating lymphocytes

extract_protocol:
For isolation of Ebo, Em and Eff CD8 T cell subsets, 1-2 106 tumor-infiltrating leukocytes were resuspended in 200 ml staining buffer containing fluorophore-conjugated mAb cocktail against human cell surface molecules: CD45 BV510 (clone HI30), CD8 PerCP-Cy5.5 (clone RPA-T8) , CCR7 BV421 (clone G043H7), CD45RO PE (cloneUCHL1) and CD45RA PE-Cy7 (clone HI100). After 20 min incubation at 4 °C, cells were washed twice, and cell sorting was performed using a BD FACS Aria III. Approximately 1 × 104, 1.5-2× 104 and 0.5-1 × 104 of Ebo, Em and Eff cells were sorted respectively as an average across experiments. In three experiments cells were directly sorted in lysis buffer RLT (QIAGEN, RNeasy® Micro Kit) which already added b-ME and DTT, and the lysis cells were extracted total RNA follow the RNeasy® Micro Kit (QIAGEN, cat. 74004) protocol.
the total RNA samples were submit to Yale Center for Genome Analysis (YCGA) for analyzed QC  and used for RNA sequencing.

tag: condition

value: non-small cell lung cancer


title: Drosophila Pex12 knockdown samples, rep3

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-200-3

value: oenocytes

value: RU feeding

value: Pex12 knockdown


title: inflammed IEL sample from CD donor 1813

source_name: inflammed IEL sample from CD donor

value: T cells, ILCs and others

value: CD3+, CD19-, small population of Nkp44+


title: Drosophila Pex12 knockdown samples, rep2

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-200-2


title: +CM healthy CD34+ HSPC, rep3

value: bone marrow derived CD34+ HSPC

value: control


title: CD4polarizedTh17_24h_veh_rep2

source_name: CD4 polarized Th17, 24h, veh, replicate2

value: spleen


title: +CM healthy CD34+ HSPC, rep2


title: normal IEL sample from colectomy patient donor 1425

value: donor 1425


title: P90p5_Em


title: P90p4_Ebo


title: CD4polarizedTh17_24h_db_rep3

source_name: CD4 polarized Th17, 24h, db-cAMP, replicate3


title: normal IEL sample from colectomy patient donor 7420

value: donor 7420


title: +CM healthy CD34+ HSPC, rep1


title: CD4polarizedTh17_24h_db_rep1

source_name: CD4 polarized Th17, 24h, db-cAMP, replicate1


title: CD4polarizedTh17_24h_veh_rep1

source_name: CD4 polarized Th17, 24h, veh, replicate1


title: non inflammed LPL sample from CD donor 1818

source_name: non inflammed LPL sample from CD donor

value: donor 1818

value: LPL


title: Drosophila Pex12 knockdown samples, rep1

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-200-1

source_name: oenocytes


title: P81p6_Eff


title: Human cells with PEX5 C11A, rep3

description:
hm_C11A_outlier_removed.xlsx
R115-C11A-dox-3

tag: cell line

value: Doxycycline

value: PEX5 C11A


title: inflammed LPL sample from CD donor 1818

source_name: inflammed LPL sample from CD donor

value: Crohn's disease (CD)

value: T cells


title: non inflammed LPL sample from CD donor 1813

value: donor 1813

value: Normal


title: Human cells with PEX5 C11A, rep2

description:
hm_C11A_outlier_removed.xlsx
R114-C11A-dox-2


title: Human cells with PEX5 C11A, rep1

description:
hm_C11A_outlier_removed.xlsx
R113-C11A-dox-1


title: Drosophila Pex5 knockdown samples, rep3

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-200-3

value: oenocytes

value: RU feeding

value: Pex5 knockdown


title: Drosophila control samples for Pex12 knockdown, rep1

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-0-1

value: no RU feeding

value: control for Pex12 knockdown


title: inflammed LPL sample from CD donor 1813


title: Drosophila Pex5 knockdown samples, rep2

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-200-2


title: Drosophila control samples for Pex12 knockdown, rep3

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-0-3


title: Human cells control for PEX5 C11A, rep3

description:
hm_C11A_outlier_removed.xlsx
R112-C11A-ctrl-3

value: No Doxycycline

value: control for PEX5 C11A


title: P53p5_Em

value: non-small cell lung cancer


title: Drosophila control samples for Pex12 knockdown, rep2

description:
dros_pex12_outlier_removed.xlsx
dros_raw_counts_pex12.csv
Pex12-0-2


title: normal LPL sample from colectomy patient donor 1425

value: donor 1425


title: Human cells control for PEX5 C11A, rep2

description:
hm_C11A_outlier_removed.xlsx
R111-C11A-ctrl-2


title: P81p5_Em


title: MDA-MB-231 mammospheres, NC, Input DNA (control for H3K27me3)

city: London

first: Sladana

last: Zagorac

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description: IPNC

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie2
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol: MDA-MB-231 spheres were cultured in DMEM/F12 supplemented with 1-in-50 B27, 20ng/ml EGF, 20ng/ml FGF in suspension in non-adherent plates for described incubation times. MDA-MB-231 cells were reverse transfected with specific siRNAs and incubated for 48h before collection for chromatin-immunoprecipitation protocol.

extract_protocol:
Following ChIP protocol, DNA was recovered using phenol-chloroform extraction protocol.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following the manufacturer's instructions.

value: 16h MDA-MB-231 mammospheres

value: NC

tag: chip antibody


title: MDA-MB-231 mammospheres, EZH2 siRNA 2, H3K27me3_ChIPSeq

value: siRNA downregulation of EZH2

value: H3K27me3 (Cell Signaling, Catalog# 9733S)


title: Human cells control for PEX5 C11A, rep1

description:
hm_C11A_outlier_removed.xlsx
R110-C11A-ctrl-1


title: HCT116 Cell line normal control replicate 2

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Paired-end reads were filtered and trimmed using software Trimmomatic
Quality control before and after raw reads preprocessing was done using software FastQC
Count files of the aligned sequencing reads were generated by the  featurecount, using the GTF annotation file gencode.v22.gtf.file
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated matrices with read counts,

source_name: HCT116 cells

growth_protocol: HCT116 cells were routinely cultured adherently in the six hole plate in the concertration of 5*10^5 per hole with 1640 medium

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: HCT116 Cells were co-cultured with Fn .The normal control samples were treated with the bacteria medium without Fn.

value: human colorectal cancer cells

tag: passage

tag: agent


title: Drosophila control samples for Pex5 knockdown, rep2

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-0-2

tag: cell type

tag: genotype

value: control for Pex5 knockdown


title: Drosophila control samples for Pex5 knockdown, rep3

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-0-3

tag: treatment


title: normal LPL sample from colectomy patient donor 7420

value: donor 7420

value: LPL

value: T cells


title: HCT116 Cell line normal control replicate 3


title: Human cells with PEX5 knockdown, rep3

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R90-PEX5-siRNA-3

value: PEX5-targeting siRNA

value: PEX5 knockdown


title: Human cells with PEX5 knockdown, rep2

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R89-PEX5-siRNA-2


title: Drosophila Pex5 knockdown samples, rep1

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-200-1

value: oenocytes

value: RU feeding

value: Pex5 knockdown


title: HCT116 Cell line normal control replicate 1


title: P53p6_Eff


title: Drosophila control samples for Pex5 knockdown, rep1

description:
dros_pex5_outlier_removed.xlsx
dros_raw_counts_pex5.csv
Pex5-0-1

value: no RU feeding


title: Human cells with PEX5 knockdown, rep1

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R88-PEX5-siRNA-1


title: Drosophila Pex1 knockdown samples, rep3

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-200-3

value: Pex1 knockdown


title: MDA-MB-231 mammospheres, SCIRT siRNA 2, H3K27me3_ChIPSeq

value: siRNA downregulation of SCIRT


title: HCT116 Cell line treated by Fn replicate 3

value: Fusobacterium Nucleatum


title: Human cells control for PEX5 knockdown, rep3

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R86-PEX5-ctrl-3

value: non-targeting siRNA

value: control for PEX5 knockdown


title: Drosophila Pex1 knockdown samples, rep2

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-200-2


title: MDA-MB-231 mammospheres, SCIRT siRNA 1, H3K27me3_ChIPSeq

value: 16h MDA-MB-231 mammospheres

value: H3K27me3 (Cell Signaling, Catalog# 9733S)


title: HCT116 Cell line treated by Fn replicate 2

value: human colorectal cancer cells


title: P81p4_Ebo

value: non-small cell lung cancer


title: P53p4_Ebo


title: Human cells control for PEX5 knockdown, rep2

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R85-PEX5-ctrl-2


title: Drosophila Pex1 knockdown samples, rep1

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-200-1


title: MDA-MB-231 mammospheres, NC2, H3K27me3_ChIPSeq

value: NC


title: Human cells control for PEX5 knockdown, rep1

description:
hm_PEX5_siRNA_outlier_removed.xlsx
R84-PEX5-ctrl-1


title: HCT116 Cell line treated by Fn replicate 1


title: Drosophila control samples for Pex1 knockdown, rep3

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-0-3

value: control for Pex1 knockdown


title: MDA-MB-231 mammospheres, NC1, H3K27me3_ChIPSeq


title: MDA-MB-231 mammospheres, EZH2 siRNA 1, H3K27me3_ChIPSeq

value: siRNA downregulation of EZH2


title: C3H10T1-2_H3K36M_CpG

city: New York

first: Chao

last: Lu

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For ATAC-seq, ChIP-seq and RNA-seq samples, Reads were aligned to the mm10 genome assembly using HISAT2 version 2.1.0 using default parameters
For ChIP-seq samples, ChIP-Rx normalization was performed according to Weinberg et al., Nature, 2019
For RNA-seq samples, 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.
For WGBS samples, Reads were aligned to the mm10 genome assembly using BWA version 0.6.1 after converting the reference  genome to bisulfite mode
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools
Supplementary_files_format_and_content: tdf files were generated using IGVtools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Cell line

extract_protocol:
Genomic DNA  was extracted from cells and spiked with 0.1% (w/w) unmethylated λ DNA (Roche Diagnostics)
Libraries were prepared using KAPA High Throughput Library Preparation Kit (KAPA Biosystems). Samples were then bisulfite-converted using the EZ-DNA Methylation Gold Kit (Zymo Research) according to the manufacturer’s protocol. DNA was amplified by nine cycles of PCR using the Kapa Hifi Uracil+ DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol. The amplified libraries were purified using Ampure XP Beads (Beckman Coulter).

tag: tissue

value: embryo

value: fibroblast

tag: genotype/variation


title: 48hrAPF_Male

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Raw reads were processed using the CellRanger software pipeline (v.2.1.1) “cellranger count” command to align reads to the Drosophila melanogaster (BDGP6.92) STAR reference genome, customized to contain the sequence for the mCD8-GFP cDNA and generate a multidimensional feature-barcode matrix.
Genome_build: Drosophila melanogaster (BDGP6.92)

source_name: Central nervous system

growth_protocol: Pupae were sex-sorted at white pre-pupal stage and aged to 48hr after Puparium formation (APF) on Bromophenol blue agar plates at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
The tissue was dissected in cold Schneider 2 Drosophila culture medium (S2 medium, Gibco) and transferred to a LoBind tube (Eppendorf), containing 200μl of S2 medium. The tissue was centrifuged at 500g for 5 minutes, and then was washed with 300μl of EBSS (Earle’s Balanced Salt Solution), and centrifuged again at 500g for 5 minutes. After centrifugation, the supernatant was replaced with 100μL of papain for disassociation (50 units/ml, Worthington) diluted in EBSS. Brains were dissociated at 25°C in a LoBind tube for 30 min., with pipette mixing to reinforce dissociation every 3 min with a P200 tip during the first 15 minutes, and a P10 tip for the final 15 min. Cells were washed twice with 700μl cold S2 medium containing 10% FBS (Gibco) and centrifuged at 700g for 10 minutes to quench the papain. Cell suspensions were passed through a 30μM pre-separation filter (MiltenyiBiotech). Cell viability and concentration were assessed by hemocytometer using Trypan blue.
Single-cell libraries were generated using Single Cell 3’ Library & Gel Bead Kit v2, Chip Kit, and the GemCode 10X Chromium instrument (10X Genomics, CA), according to the manufacturer’s protocol (Zheng et al. 2017). In brief, single cells were suspended in S2 medium with 10% FBS and the maximum volume of cells, 34μl, was added to a single chip channel. After the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), the mRNA in GEMs underwent reverse transcription. Next, GEMs were broken, and the single-stranded cDNA was isolated, cleaned with Cleanup Mix containing DynaBeads MyOne Silane beads (Thermo Fisher Scientific). cDNA was then amplified with the following PCR machine settings: 98°C for 3 min, 9 cycles of (98°C for 15s, 67°C for 20s), 72°C for 1 min, held at 4°C. Subsequently, the amplified cDNA was cleaned up with SPRIslect Reagent kit (Beckman Coulter), fragmented, end-repaired, A-tailed, adaptor ligated, and cleaned with SPRIselect magnetic beads between steps. This product was PCR amplified with the following PCR machine settings: 98°C for 45s, 12 cycles of (98°C for 20s, 54°C for 30s, 72°C for 20s), 72°C for 1 min, and hold at 4°C. The library was cleaned and size-selected with SPRIselect beads, followed by Pippin size selection for a 350-450bp library size range. Single cell libraries were sequenced on the Illumina NovaSeq with 150bp paired-end reads on an S2 flowcell. This produced 1,870,220,065 reads.

treatment_protocol: Twenty freshly dissected male brains and ventral nerve cords, from 48 hour after puparium formation (APF) stage, were used. The flies had expression of membrane-bound GFP in fru P1-expressing neurons and were the following genotype: w[*]; P{y[+t7.7] w[+mC]=10XUAS-IVS-mCD8::GFP}attP40/UAS-Gal4,fru P1-Gal4/+.

tag: Sex

value: Male


title: C3H10T1-2_Setd2KO_CpG


title: Drosophila control samples for Pex1 knockdown, rep1

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-0-1

value: oenocytes


title: 60_ROi15-12-15-16_d415_37

status: Public on Feb 22 2021

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.4.0g1.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.

treatment_protocol: rhesus macaques (RM) were intravenously infected with SIVmac239 and at day (d) 35 post-infection (p.i.) initiated triple formulation ART17. 8 RM were administered rhesus rIL-21-IgFc (IL-21) at d42 and d189 p.i. in two cycles of four doses given once per week followed by weekly rhesus IFNaplha-IgFc (rIFNalpha) starting at d323 (3 doses) and d383 p.i. (2 doses; i.e. ART + IL-21 + rIFNalpha). Following ART analytical treatment interruption (ATI) treated animals transitioned to human PEGylated-IFNalpha (PEG-IFNalpha; 7 doses, once every 6-8 days, s.c., 7 ug/kg) starting at day 5 post-ATI. 5 RM served as cytokine treatment-naïve, ART-only controls. Blood was taken 24 hr following the first (d6 post-ATI) and the fifth PEG-IFNα dose (d37 post-ATI). Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density gradient centrifugation

value: PBMC

tag: animalid

value: Treated

tag: days post art


title: 59_ROi15-11-17-16_d385_6


title: 62_RUo13-11-17-16_d385_6


title: 56_RZn14-11-17-16_d385_6


title: 57_RZn14-12-15-16_d415_37


title: 51_269_10-12-15-16_d415_37


title: 54_RBe13-12-15-16_d415_37


title: 53_RBe13-11-17-16_d385_6


title: 50_269_10-11-17-16_d385_6


title: 48_RQb13-12-15-16_d440_37


title: 47_RQb13-11-17-16_d411_6


title: Rat spleen No Stimulation

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima

department: Forensic medicine

country: Japan

institute: Tokyo Medical and Dental University

description: RNA expression value

hyb_protocol: Hybridization was performed according to the manufacturer's instruction.

scan_protocol: Array scanning was performed according to the manufacturer's instruction.

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization.

label: biotin

organism: Rattus norvegicus

source_name: Spleen

label_protocol: Labeling was performed according to the manufacturer's instruction.

extract_protocol: RNA was isolated from rat spleen with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 50 mg/kg cocaine was injected i.p. to rats daily for 7 days.

value: male


title: 44_185_11-11-17-16_d411_6

value: Untreated


title: 42_RSp14-12-15-16_d440_37


title: 41_RSp14-11-17-16_d411_6


title: 38_143_10-11-17-16_d411_6


title: Drosophila control samples for Pex1 knockdown, rep2

description:
dros_pex1_outlier_removed.xlsx
dros_raw_counts_pex1.csv
Pex1-0-2

value: no RU feeding


title: 36_RQm14-12-15-16_d440_37


title: 63_RUo13-12-15-16_d415_37


title: Rat spleen Cocaine

description: RNA expression value


title: 21_RYb12-10-21-16_d411_37


title: 20_RYb12-9-20-16_d376_6


title: 15_RHr12-10-21-16_d439_37


title: 14_RHr12-9-20-16_d408_6


title: 11_RNa12_7-19-16

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.5.2b.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Transcript abundance was estimated using htseq-count v0.6.1p1
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

treatment_protocol: rhesus macaques (RM) were intravenously infected with SIVmac239 and at day (d) 35 post-infection (p.i.) initiated triple formulation ART17. 6 RM were administered rhesus rIL-21-IgFc (IL-21) at d42 and d189 p.i. in two cycles of four doses given once per week followed by weekly rhesus IFNaplha-IgFc (rIFNalpha) starting at d323 (3 doses). 5 RM served as cytokine treatment-naïve, ART-only controls. Blood was drawn after the third rIFNalpha dose. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density gradient centrifugation.


title: 5_219_03-9-20-16_d408_6


title: 6_219_03-10-21-16_d439_37


title: 8_248_09_7-19-16


title: 9_RPk11_7-19-16


title: 4_RKd9_7-19-16


title: 10_RIl11_7-19-16


title: 7_RYb12_7-19-16


title: 5_RHr12_7-19-16


title: 6_138_10_7-19-16


title: 45_185_11-12-15-16_d440_37


title: 39_143_10-12-15-16_d440_37


title: 35_RQm14-11-17-16_d411_6


title: 2_219_03_7-19-16


title: 1_RWm11_7-19-16


title: Chip 3

first: Chen

middle: Chen

last: Xu

address: No.646, Songtao Road

institute: Shanghai Institute of Materia Medica Chinese Academy Sciences

data_processing:
Basecalls
Data were filtered using BBduk (Q<20)
ChIP-seq reads were aligned to the PAO1 genome assembly using BBMap
Peaks were identified using MACS14 (version 1.4.2)
Annotation of the peaks was performed using the SnpEff (4.3s)
Genome_build: PAO1
Supplementary_files_format_and_content: peak text files

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Wild type P. aeruginosa PAO1 containing mini-gltR-flag-lacZ was cultured in M8 minimal medium supplemented with 10 mM glucose overnight at 37°C with shaking (250 rpm), diluted 10-fold in fresh M8 minimal medium supplemented with 10 mM glucose. The diluted cultures were grown in a 1 L Erlenmeyer flask with a flask volume-to-medium ratio of 5:1 at 37 °C with shaking (250 rpm) for 6 h .

extract_protocol:
DNA was sonicated to shear DNA to an average size of 200–500 bp.Insoluble cellular debris was removed by centrifugation and the supernatant was saved. Immunoprecipitation samples were incubated overnight at 4°C on a rotating wheel with protein A beads (Cat#: SA015), which was incubated with 100 μl agarose-conjugated anti-flag antibodies (Cat#: AGM12165, Aogma) in IP buffer. Input samples without antibody were set up as negative control. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols with minor changes. Briefly, the beads were then collected and washed once with 1 ml of IP buffer, once with 1 ml of IP buffer plus 500 mM NaCl, once with 1 ml of IP buffer plus 250 mM LiCl, and once with 1 ml of Tris-EDTA buffer (pH 7.5). Immunoprecipitated complexes were eluted from the beads by treatment with 100 μl elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) at 65°C for 20 min. Samples were then treated with Protease K (TIANGEN) and cross-links were reversed by incubation overnight at 65°C. Overnight samples were then treated with 50 μg RNase A at 37°C for 1 h. DNA was extracted twice with phenol-chloroform, precipitated with ethanol at -80°C for 4 h, and then resuspended in 20 μl of deionized water.
DNA fragments (200 to 500 bp) were selected for library construction, and sequencing libraries prepared using the NEBNext Ultra II DNA Library Prep kit. The final DNA libraries were validated with Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit, then the libraries were sequenced using the HiSeq PE150 system (Illumina).

treatment_protocol: untreated

tag: strain

value: Anti-flag(Cat#:AGM12165, Aogma)

value: untreated


title: Input


title: Chip 2


title: Chip 4


title: 7Lb_9Lc_1D_2_rep3 [RNA-seq_mRNA-selection]

city: Columbia

first: James

last: Birchler

state: MO

address: 310 Tucker Hall

institute: University of Missouri-Columbia

description:
7Lb_9Lc_1D_2_H72
TB-7Lb_disomy_comparison_mRNA-selection
TB-9Lc_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt
TB-9Lc_gene_exp_mRNA-selection.txt

data_processing:
RNA-seq (rRNA removal): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Non-ERCC and non-organelle reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
RNA-seq (mRNA selection): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts from the gene regions or 1Mb genome region. The counts from the gene region were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses and tables reporting RPKM normalized counts in DNA-seq.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
RNA extracted by mirVana™ miRNA Isolation Kit; DNA extracted by DNeasy Plant Mini Kit (QIAGEN)
TruSeq library construction

tag: age

tag: rna/dna-seq approaches

value: polyA selection


title: 7Lb_9Lc_1D_2_rep2 [RNA-seq_mRNA-selection]

description:
7Lb_9Lc_1D_2_H71
TB-7Lb_disomy_comparison_mRNA-selection
TB-9Lc_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt
TB-9Lc_gene_exp_mRNA-selection.txt


title: 7Lb_9Lc_1D_2_rep4 [RNA-seq_mRNA-selection]

description:
7Lb_9Lc_1D_2_H73
TB-7Lb_disomy_comparison_mRNA-selection
TB-9Lc_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt
TB-9Lc_gene_exp_mRNA-selection.txt


title: 3Sb_6Lc_1D_2_rep2 [RNA-seq_mRNA-selection]

description:
3Sb_6Lc_1D_2_H68
TB-3Sb_disomy_comparison_mRNA-selection
TB-6Lc_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt
TB-6Lc_gene_exp_mRNA-selection.txt


title: 3Sb_6Lc_1D_2_rep3 [RNA-seq_mRNA-selection]

description:
3Sb_6Lc_1D_2_H69
TB-3Sb_disomy_comparison_mRNA-selection
TB-6Lc_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt
TB-6Lc_gene_exp_mRNA-selection.txt


title: 3Sb_6Lc_1D_2_rep1 [RNA-seq_mRNA-selection]

description:
3Sb_6Lc_1D_2_H66
TB-3Sb_disomy_comparison_mRNA-selection
TB-6Lc_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt
TB-6Lc_gene_exp_mRNA-selection.txt


title: 1La_1D_2_rep4 [RNA-seq_mRNA-selection]

description:
1La_1D_2_H27
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 1La_1D_2_rep2 [RNA-seq_mRNA-selection]

description:
1La_1D_2_H24
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 1La_1D_2_rep1 [RNA-seq_mRNA-selection]

description:
1La_1D_2_H23
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 1La_1D_2_rep3 [RNA-seq_mRNA-selection]

description:
1La_1D_2_H26
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 4Sa_1D_2_rep4 [RNA-seq_mRNA-selection]

description:
4Sa_1D_2_H20
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 3_RWc11_7-19-16


title: 4Sa_1D_2_rep3 [RNA-seq_mRNA-selection]

description:
4Sa_1D_2_H19
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 4Sa_1D_2_rep2 [RNA-seq_mRNA-selection]

description:
4Sa_1D_2_H18
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 4Sa_1D_2_rep1 [RNA-seq_mRNA-selection]

description:
4Sa_1D_2_H17
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 4_2018_P_M1

city: Durham

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

data_processing:
General read quality was evaluated using FastQC v0.11.5 and multiqc, version 1.9
Genome and GTF files were downloaded from Ensembl Fungi (release 39) and indexed using STAR_2.5.4b
FASTQs were filtered and trimmed using fastq-mcf v1.04.807 using paramteres “-q 20 -x 0.5” and the following adapter sequences, which were supplied by NEB, and their reverse complements: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Filtered and trimmed reads were mapped and counted using STAR_2.5.4b with these parameters: –runMode alignReads –outSAMtype None –quantMode GeneCounts –genomeLoad NoSharedMemory –twopassMode None –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMatchNmin 0 –outFilterMismatchNmax 2
An Rmarkdown notebook containing the counting pipeline is available at https://github.com/granek-pubs/rna_enrichment/tree/master/geo_submission
Genome_build: GCA_000149245.3
Supplementary_files_format_and_content: Tab-delimited text files containing raw read counts per gene in STAR format. The appropriate counts are in column 4 (counts for the 2nd read strand aligned with RNA), because the directional reads were generated using the dUTP method

organism: Cryptococcus neoformans

source_name: yeast liquid culture

growth_protocol: Samples were prepared by growing each biological replicate of the WT and mar1d strain to mid-logarithmic growth phase in separate flasks of liquid YPD medium, with 150 rpm shaking.

extract_protocol:
Cells were then pelleted, flash frozen on dry ice, and lyophilized for ~18 hours. Total RNA was isolated using the Qiagen RNeasy Plant Mini Kit (Qiagen, Valencia, CA); on-column DNase digestion was performed to eliminate contaminating genomic DNA. Total RNA quantity and quality were assessed using the Agilent 2100 Bioanalyzer. Purified RNA was subsequently stored at -80°C.
Purified total RNA was processed unenriched or was rRNA was depleted using either Ribo-Zero Yeast kit (Illumina), the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA), or the RNase H method with custom oligos. Ribo-Zero and RNase H treated RNA were then cleaned up with the RNA Clean & Concentrator-5 (Zymo Research) before library preparation.  RNA-Seq libraries were prepared from these enriched samples and from unenriched control samples (i.e. “Unenriched”) using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (NEB #E7765) (New England Biolabs, Ipswich, MA).

treatment_protocol: Approximately 1 × 109 cells from each sample were pelleted, resuspended in fresh YPD medium or tissue culture media, and incubated at 30°C for 90 min with 150 rpm shaking.

value: var. grubii H99

tag: media

tag: rna sample number

tag: enrichment method

value: Poly(A)

tag: library prep person

value: J


title: 3_2018_P_M1


title: 9Lc_2D_2_rep4 [RNA-seq_mRNA-selection]

description:
9Lc_2D_2_9Lc43
TB-9Lc_disomy_comparison_mRNA-selection
TB-9Lc_gene_exp_mRNA-selection.txt


title: 9Lc_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
9Lc_2D_2_9Lc38
TB-9Lc_disomy_comparison_mRNA-selection
TB-9Lc_gene_exp_mRNA-selection.txt


title: 2_2018_P_M1


title: 4_2018_P_T1

value: Unenriched


title: 9Lc_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
9Lc_2D_2_9Lc35
TB-9Lc_disomy_comparison_mRNA-selection
TB-9Lc_gene_exp_mRNA-selection.txt


title: 3_2018_P_T1


title: 9Lc_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
9Lc_2D_2_9Lc34
TB-9Lc_disomy_comparison_mRNA-selection
TB-9Lc_gene_exp_mRNA-selection.txt


title: 7Lb_9Lc_1D_2_rep1 [RNA-seq_mRNA-selection]

description:
7Lb_9Lc_1D_2_H70
TB-7Lb_disomy_comparison_mRNA-selection
TB-9Lc_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt
TB-9Lc_gene_exp_mRNA-selection.txt


title: 2_2018_P_T1


title: 7Lb_2D_2_rep4 [RNA-seq_mRNA-selection]

description:
7Lb_2D_2_7Lb47
TB-7Lb_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt


title: 7Lb_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
7Lb_2D_2_7Lb41
TB-7Lb_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt


title: 7Lb_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
7Lb_2D_2_7Lb42
TB-7Lb_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt


title: 2_2018_P_H2

value: RNase H


title: 7Lb_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
7Lb_2D_2_7Lb23
TB-7Lb_disomy_comparison_mRNA-selection
TB-7Lb_gene_exp_mRNA-selection.txt


title: 3_2018_P_H2


title: 4_2018_P_H1


title: 6Lc_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
6Lc_2D_2_6Lc9
TB-6Lc_disomy_comparison_mRNA-selection
TB-6Lc_gene_exp_mRNA-selection.txt


title: 3_2018_P_H1


title: 6Lc_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
6Lc_2D_2_6Lc18
TB-6Lc_disomy_comparison_mRNA-selection
TB-6Lc_gene_exp_mRNA-selection.txt


title: 4Sa_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
4Sa_2D_2_4Sa8
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 4_TOT_P

value: P


title: 47_RZ_P

value: Ribo-Zero


title: 6Lc_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
6Lc_2D_2_6Lc29
TB-6Lc_disomy_comparison_mRNA-selection
TB-6Lc_gene_exp_mRNA-selection.txt


title: 4Sa_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
4Sa_2D_2_4Sa5
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 38_RZ_P


title: 27_RZ_P


title: 35_RZ_P


title: 4Sa_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
4Sa_2D_2_4Sa3
TB-4Sa_disomy_comparison_mRNA-selection
TB-4Sa_gene_exp_mRNA-selection.txt


title: 4_2018_P_H2


title: 3Sb_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
3Sb_2D_2_3Sb25
TB-3Sb_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt


title: 3Sb_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
3Sb_2D_2_3Sb20
TB-3Sb_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt


title: 3Sb_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
3Sb_2D_2_3Sb24
TB-3Sb_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt


title: 12_RZ_P


title: 4_RZ_P


title: 1La_2D_2_rep4 [RNA-seq_mRNA-selection]

description:
1La_2D_2_1La5
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 47_MA_P


title: 1La_2D_2_rep3 [RNA-seq_mRNA-selection]

description:
1La_2D_2_1La19
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 1La_2D_2_rep2 [RNA-seq_mRNA-selection]

description:
1La_2D_2_1La11
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 1La_2D_2_rep1 [RNA-seq_mRNA-selection]

description:
1La_2D_2_1La10
TB-1La_disomy_comparison_mRNA-selection
TB-1La_gene_exp_mRNA-selection.txt


title: 48_O12_GSK173_Pax_12_1-4

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.4.0g1.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Transcript abundance was estimated using htseq-count v0.6.1p1
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
Total RNA was prepared using QIAGEN Paxgene RNA kits. Globin transcripts were depleted using Ambion GlobinClear solution.
500-1000 ng of Globin depleted RNA was used for library preparation. Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq™ mRNA stranded kit as per manufacturer’s instructions.

treatment_protocol: rhesus macaques were infected with SIVmac251, then treated with ART, and followed while on ART treatment. Blood samples were collected in paxgene tubes 1 week prior to infection, 8 weeks later immediately prior to ART initiation, and at 9 weeks and 18 weeks post ART treatment.

tag: week post infection


title: 35_MA_P


title: 45_MA_P


title: 38_MA_P


title: 2_2018_P_H1


title: 45_RZ_P


title: 45_O9_GSK170_Pax_12_1-4


title: 44_O8_GSK169_Pax_11-17


title: 16_MA_P


title: 12_MA_P


title: 42_O6_GSK167_Pax_12_1-4


title: 4_MA_P


title: 27_MA_P


title: 16_RZ_P


title: 38_O2_GSK163_Pax_12_1-4


title: 37_O1_GSK162_Pax_12_1-4


title: 3Sb_2D_2_rep4 [RNA-seq_mRNA-selection]

description:
3Sb_2D_2_3Sb26
TB-3Sb_disomy_comparison_mRNA-selection
TB-3Sb_gene_exp_mRNA-selection.txt


title: 36_N12_GSK161_Pax_9-30


title: 32_N8_GSK157_Pax_9-30


title: 3_TOT_J


title: 40_RZ_J


title: 36_RZ_J


title: 30_N6_GSK155_Pax_9-30


title: 24_RZ_J


title: 13_RZ_J


title: 33_N9_GSK158_Pax_9-30


title: 23_RZ_J


title: 26_N2_GSK151_Pax_9-30


title: 24_M12_GSK149_Pax_7-28


title: 25_N1_GSK150_Pax_9-30


title: 3_RZ_J


title: 11_RZ_J


title: 21_M9_GSK146_Pax_7-28


title: 1_RZ_J


title: 20_M8_GSK145_Pax_7-28


title: 36_MA_J


title: 40_MA_J


title: 13_M1_GSK138_Pax_7-28


title: 24_MA_J


title: 23_MA_J


title: 13_MA_J


title: 11_MA_J


title: 12_L12_GSK137_Pax_5-28


title: 9_L9_GSK134_Pax_5-28


title: 3_MA_J


title: 8_L8_GSK133_Pax_5-28


title: 6_L6_GSK131_Pax_5-28


title: 1_L1_GSK126_Pax_5-28


title: 1_MA_J


title: 2_TOT_C

value: C


title: 22_RZ_C


title: 2_L2_GSK127_Pax_5-28


title: 21_RZ_C


title: 15_RZ_C


title: 18_M6_GSK143_Pax_7-28


title: 14_RZ_C


title: 14_M2_GSK139_Pax_7-28


title: 9_RZ_C


title: 2_RZ_C


title: 26_MA_C


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, Input, 2. Replicate

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
Reads were aligned to a pre-compiled index of the mouse mm9 genome using Bowtie2 (default options) 2.2.9
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization bigwig files with coverage information were generated using deeptools bamCoverage functio
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigwig files (of coverage) at 25 bp resolution

source_name: HeLa Kyoto cells

growth_protocol: HeLa Kyoto cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin/streptomycin (Thermo Fisher Scientific) in a humidified atmosphere at +37 °C and 5% CO2.

extract_protocol:
Cells were harvested, fixed and lysed followed by Chromatin shearing. Lysates were used for ChIP experiments and precipitated DNA reverse crosslinked, purified and subsequently used for Library preparation.
Libraries were generated with MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions.

treatment_protocol: HeLa Kyoto cells were transfected with control or JAZF1 siRNA pools using oligofectamine (Invitrogen) according to the manufacturer’s instructions and harvested after two days incubation.

value: Cervix carcinoma cells

value: control siRNA pool

tag: antibody


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, Input, 2. Replicate

tag: cell type

value: JAZF1 siRNA pool


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, Input, 1. Replicate


title: 22_MA_C

tag: genotype


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, Input, 1. Replicate

tag: treatment


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, ChIP H2A.Zac, 2. Replicate

value: alpha-H2A.Zac (Merck Millipore, ABE1363)


title: 26_RZ_C


title: 15_MA_C


title: 21_MA_C


title: 14_MA_C


title: 10_MA_C


title: 9_MA_C


title: NT-3N 3 hr_2

city: Ota-ku

first: Takashi

last: Nishina

state: Tokyo

address: 5-21-16 Omori-nishi

department: Biochemistry

institute: Toho University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to SurePrint G3 Mouse Gene Expression 8x60K according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
Probe quality check and filtering by FlagRaw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array.  Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: NT-3N 3hr

label_protocol: labeled cRNA were prepared from 1.65 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNAs were extracted using TRI-reagent according to the manufacturer’s instructions (Molecular Research Center, Inc.).

tag: tissue

value: Colon tissue


title: Control 1

source_name: Control


title: 2_MA_C


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, ChIP H2A.Zac, 2. Replicate


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, ChIP H2A.Z, 2. Replicate

value: alpha-H2A.Z (Active motif, 39944)


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, ChIP H2A.Zac, 1. Replicate


title: 10_RZ_C


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, ChIP H2A.Z, 2. Replicate


title: NT-3N 3 hr_1


title: ChIP-Seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, ChIP H2A.Z, 1. Replicate


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, ChIP H2A.Zac, 1. Replicate


title: ChIP-Seq of HeLa Kyoto cells treated with control siRNA pool, ChIP H2A.Z, 1. Replicate


title: NC8HSC

city: Tianjin

first: Coral

last: Tong

address: 288 Nanjing Rd, Heping

institute: Institute of Hematology & Blood Disease Hospital

data_processing:
remove low-quality reads and adapters by trimmomatic
aligning by hisat2
mark and remove duplicates by Picard
quantification by stringtie
Genome_build: hg38(gencode v27)
Supplementary_files_format_and_content: csv

source_name: hematopoietic stem cells (HSCs)

growth_protocol: patient samples

extract_protocol:
BMMNCs were stained with a lineage-marker cocktail (biotinylated anti-CD2, -CD3, -CD11b, -CD14, -CD15, -CD16, -CD19, -CD56, -CD123, and -CD235a) and subsequently magnetically labeled with Anti-Biotin MicroBeads (Miltenyi Biotec). Lineage-negative stem and progenitor cells (Lin- cells) were obtained by depleting the magnetically-labeled cells after passing through LS columns (Miltenyi Biotec). Lin- cells were stained with antibodies of PE-cy7-conjugated anti-CD38 (BD Biosciences), APC-conjugated anti-CD34 (BD Biosciences), Percp-cy5-conjugated anti-CD45RA (BD Biosciences) and APC-cy7-conjugated anti-CD123 (BD Biosciences). HSCs (CD34+CD38-CD45RA-CD123-) and MEPs (CD34+CD38+CD45RA-CD123-) were sorted with an Aria III instrument (BD Biosciences)
Briefly, cells were lysed in lysis buffer (Novogene), and the direct first-strand cDNA was synthesized from polyA-selected RNA with a SMARTer® Ultra Low RNA Kit for Illumina® Sequencing (Clontech) (Cat. #. 634888). cDNAs were purified using AMPure XP beads, followed by LD-PCR, to yield the full-length first-strand cDNA. Double-stranded cDNA was synthesized and amplified with an Advantage® 2 PCR kit. After generating the sequencing libraries using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: no treatment

tag: sample type

value: healthy donor


title: NC9HSC


title: NC11HSC


title: NC7HSC


title: NC2HSC


title: NC10HSC


title: NC1HSC


title: ET10HSC

value: essential thrombocythemia patient


title: ET12HSC


title: Control 2


title: ET7HSC


title: RO_whole_replicate_4

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

institute: Massachusetts Institute of Technology

description:
all neurons in whole brain
RO_whole_4

data_processing:
FASTQ files of 50-bp single-end sequencing reads were aligned to the Mus musculus genome using STAR v2.7.2b.
Read counts were generated by STAR using the --quantMode GeneCounts option, using the default options.
Genome_build: The Ensembl Genome build GRCm38 and annotation build 96
Supplementary_files_format_and_content: TXT file containing raw count

source_name: Whole brain

extract_protocol:
Whole brain or COApm were homogenized with a glass/Teflon power-driven Potter-Elvehjem homogenizer in an ice-cold lysis buffer (150 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5mM dithiothreitol, 100 μg/mL cycloheximide, 20 U/µL SUPERaseIn RNase Inhibitor, 40 U/µL RNasin Plus Rnase Inhibitor, and EDTA-free protease inhibitors).  Following homogenization, samples were centrifuged at 2,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  NP-40 (final concentration 1%) and 1,2-Diheptanoyl-sn-glycero-3-phosphocholine (DHPC, final concentration 15 mM) were subsequently added and samples were incubated on ice for 5 min.  Samples were centrifuged at 13,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  Streptavidin Dynabeads (ThermoFisher Scientific, Waltham MA) coated with biotin-linked mouse anti-GFP antibodies were then added to this supernatant and the samples were incubated overnight at 4°C with end-over-end rotation.  Beads were collected on a magnetic rack and washed three times with wash buffer (350 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/mL cycloheximide, 1% NP-40).  RNA was subsequently purified using the Absolutely RNA Isolation Nanoprep kit (Agilent Technologies, Santa Clara CA).
Libraries were constructed using the Takara Bio SMART-Seq v4 kit (Takara Bio USA, Inc.).
The SMART-Seq v4 for low input whole transcriptome RNA-Seq.

treatment_protocol: Retro-orbital injection of AAV-Syn-L10a-EGFP or microinjection of RVdG-L10a-EGFP into medial amygdala.

value: brain

tag: virus type


title: RO_whole_replicate_1

description:
all neurons in whole brain
RO_whole_1


title: RV_CoA_replicate_1

description:
COApm cells projecting to MEA
RV_CoA_1

source_name: Posteromedial cortical amygdala (COApm)


title: RV_CoA_replicate_2

description:
COApm cells projecting to MEA
RV_CoA_2


title: RO_CoA_replicate_4

description:
neurons in COApm
RO_CoA_4


title: RO_whole_replicate_2

description:
all neurons in whole brain
RO_whole_2


title: RO_CoA_replicate_1

description:
neurons in COApm
RO_CoA_1


title: RV_CoA_replicate_4

description:
COApm cells projecting to MEA
RV_CoA_4


title: RV_CoA_replicate_3

description:
COApm cells projecting to MEA
RV_CoA_3


title: RO_CoA_replicate_2

description:
neurons in COApm
RO_CoA_2


title: RO_CoA_replicate_3

description:
neurons in COApm
RO_CoA_3


title: ET9HSC


title: ET2HSC


title: ET3HSC


title: ET5HSC


title: ET4HSC


title: RO_whole_replicate_3

description:
all neurons in whole brain
RO_whole_3


title: ET6HSC


title: PV9HSC

value: polycythemia vera patient


title: PV6HSC


title: PV1HSC


title: PV7HSC


title: HFD-Vehicle-4

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

data_processing:
FastQC Snakemake Wrapper v0.36.0
Trimmomatic SE Snakemake Wrapper v0.36.0 ILLUMINACLIP:adapters/TruSeq3-SE-2.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:10:20 MINLEN:50
hisat2 v0.17.4 -p 6 --remove-chrname --dta --summary-file {output.log} -x INDEXES/{ASSEMBLY_VERSION} -1 {input.r1} -2 {input.r2} -S {output.sam}
htseq-count v0.11.1 -s no {input.sam} {input.gff} > {output}
Genome_build: Mus_musculus.GRCm38.94.gtf.gz
Supplementary_files_format_and_content: Collated count matrix derived from raw data files

source_name: liver

extract_protocol:
Liver tissue was removed, wshed in ice-cold PBS, and  flash frozen using a liquid nitrogen-cooled biosqueezer. RNA was harvested using Trizol reagent. KAPA Stranded mRNA Sequencing Kit (Roche) 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: At 2 weeks of age, mice were randomized to receive vehicle or DEN injections; at 6-weeks of age, mice were further randomized to remain on control diet or switched to 60% high fat diet for the duration of the experiment

value: liver

value: wild type

value: Vehicle-high fat diet


title: HFD-DEN-4

value: DEN-high fat diet


title: HFD-Vehicle-3


title: HFD-DEN-1


title: PV2HSC


title: NT-3N 3 hr_3


title: HFD-DEN-2


title: HFD-DEN-3


title: ET1HSC


title: CD-DEN-4

value: DEN-control diet


title: CD-DEN-3


title: CD-DEN-2


title: MB04

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

country: Canada

institute: University Health Network

description: Gene Expression Data from Isolated Male mouse liver tissue treated with PPT

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA

label_protocol: Affymetrix

extract_protocol: RNA was isolated from mouse livers (male and female) using RNeasy mini kit (Qiagen). Integrity of DNA and RNA was assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). 500 nanograms of RNA was used for analysis with Affymetrix Mouse Gene 2.0 ST platform

treatment_protocol: HCC was generated through hydrodynamic tail vein injection of proto-oncogene-coding plasmids in 8-10-week-old FVB/N mice; 2 weeks post-injection  mice where given a 5-week treatment of the following: 1) ESR1 agonist Propyl pyrazole triol (PTT) subcutaneously at 1mg/kg (Sigma-Aldrich H6036) N=6; 2) ESR1 antagonist methyl-piperidino-pyrazole (MPP) given subcutaneously at 200ug/kg

value: FVB/N

tag: Sex

value: Male

value: PPT


title: MB10

description: Gene Expression Data from Isolated Male mouse liver tissue no treatment

value: Control


title: MB12

description: Gene Expression Data from Isolated Female mouse liver tissue no treatment

value: Female


title: MB05

description: Gene Expression Data from Isolated Female mouse liver tissue treated with MPP

value: MPP


title: MB08

description: Gene Expression Data from Isolated Male mouse liver tissue treated with MPP


title: CD-DEN-1


title: MB03

source_name: Isolated Male mouse liver tissue treated with PPT


title: MB01

description: Gene Expression Data from Isolated Female mouse liver tissue treated with PPT


title: MB06

source_name: Isolated Female mouse liver tissue treated with MPP


title: CD-Vehicle-4

value: Vehicle-control diet


title: MB11

source_name: Isolated Female mouse liver tissue no treatment


title: MB09

source_name: Isolated Male mouse liver tissue no treatment


title: MB07

source_name: Isolated Male mouse liver tissue treated with MPP


title: MB02

source_name: Isolated Female mouse liver tissue treated with PPT


title: CD-Vehicle-2


title: HFD-Vehicle-2


title: CD-Vehicle-1


title: SM_30_cntr_244

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16 h, the staining and washing, processed in the Fluidics Station 450.

scan_protocol: GeneChipScanner 3000 G7 system (as recommended by Affymetrix (Affymetrix Inc., Santa Clara, CA, USA)).

data_processing: Data were processed using Partek Genomics Suite 6.4 software and normalization according to RMA method.

source_name: daily injection of solvent cremophore for 7 days

label_protocol: RNA integrity was checked by analyzing on the 2100 Bioanalyzer (Agilent technologies, PA, USA). For the first and subsequent second strand cDNA synthesis 200 ng of total RNA was used and, also, poly-A Spike Controls (containing several B. subtilis genes, that are absent in eukaryotic samples) are added in the recommended dilution to achieve the final concentrations corresponding to the given RNA amount of 200 ng. During the following in vitro transcription reaction cRNA was obtained and used as starting material for the second cycle cDNA synthesis. The second cycle random-primed single strand DNA synthesis resulted in a product containing incorporated deoxyuridine at predefined ratios relative to thymidine, according to the manufacturers recommendation: WT Expression Plus Kit (Affymetrix Inc., Santa Clara, CA, USA). Subsequently, 5.5 μg of this generated single-strand DNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled. The biotinylated DNA was added to a hybridization cocktail for hybridization to the Mouse Gene st 2.0 Array, also containing 50 pM control oligonucleotide B2, eukaryotic hybridization controls (bioB, bioC, bioD, 1,5, 5; 25 pM respectively), accordingly to the manufacturer’s protocol (Hybridization Wash and Stain Kit, Affymetrix).

growth_protocol: Studies were carried out in 10- to 12-week-old mice having a C57BL/6 background  (obtained from Robert Koesters, Heidelberg, Germany) in which Pax8-rtTAdependent Vhl-KO was inducible (Mathia et al. 2013; doi: 10.1111/apha.12058) by means of a single SC injection of doxycycline (3 mg; Hexal, Holzkirchen, Germany). Animals had free access to both tap water and standard rodent chow with 0.2% sodium content, or to distilled water and low sodium chow (0.05% sodium content from Altromin, Lage, Germany [#TD94268].

extract_protocol: Animals were euthanized by cervical dislocation under isoflurane narcosis, and kidneys were rapidly removed, halved, and snap frozen in liquid nitrogen. Halved mouse kidneys were ground into fine powder in liquid nitrogen. RNA was isolated using RNA-Bee (AMS Biotechnology (Europe) Ltd - Germany) according to the manufacturer’s instructions.

treatment_protocol: Mice fed at low sodium diet received either SC CsA (Novartis, Nuremberg, Germany) or a similar SC volume of the CsA solvent cremophore (controls). A single CsA dose (60 mg/kg) without further intervention was applied daily. Changes in the renal transcriptome were assessed after seven daily CsA injections.

value: kidney


title: SM_29_cntr_243


title: SM_27_cntr_241


title: SM_25_treat_237

source_name: daily injection of CsA for 7 days


title: CD-Vehicle-3


title: SM_26_cntr_240


title: RNA-seq_D14_F_injury_rep2

city: Beijing

first: Cong

last: LIU

address: 北京市朝阳区北辰西路1号院5号

institute: Chinese Academy Science

description:
D14_injury_sham-Diff.xls, Female_D14_injury_sham-Diff.xls
D14_F_injury_rep2

data_processing:
Alignment-based quantification methods were applied on mappings processed with Salmon (v1.0.0, SAF Pattern). To minimize the effect of libraries construction bias and sequencing depth, we performed pseudo-replicates of FASTQ files according to uniform processing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/src/encode_task_spr.py). Briefly, the two biology repetitions were combined together, and then were randomly divided into two equal parts that calling pseudo-replicates (Fu et al., 2018; Yan et al., 2020). Differential gene expression was performed with DESeq2 (v1.26.0).
Supplementary_files_format_and_content: Diff
Genome_build: gencode.vM24 for mouse
Supplementary_files_format_and_content: NormalizedCount
Supplementary_files_format_and_content: ReadCount
Supplementary_files_format_and_content: TPM

source_name: FACS-sorted microglia

growth_protocol: Eight- to ten-week-old heterozygous Cx3cr1CreER mice to inject intraperitoneally with tamoxifen (180 mg/kg body weight, 30 mg/ml in corn oil) daily for five consecutive days to induce the expression of EYFP in microglia before receiving cortical stab wound injury.

extract_protocol:
RNA was extracted from the FACS-sorted microglia using Qiagen RNeasy Plus Micro kit (Qiagen, 74034)
RNA-Seq libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096)
RNA was extracted from the FACS-sorted microglia using Qiagen RNeasy Plus Micro kit (Qiagen, 74034) in a final volume of 15μl.
For construction of RNA-Seq libraries, total RNA performed first strand cDNA synthesis using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, 634889) and second strand cDNA synthesis using KAPA HiFi HotStart DNA Polymerase (KK2502). After purification with beads (Agencourt AMPure XP, Beckman coulter, A63881) and libraries validation (Agilent 2100 bioanalyzer), RNA-Seq libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096).

treatment_protocol: Fluorescence-activated cell sorting (FACS) sorted EYFP+ microglia were collected from freshly dissociated cortex at the site of cortical stab wound injury or from the equivalent site at the contralateral non-injured hemisphere of adult Cx3cr1CreER mice on days 1, 4, 7 and 14 following stab wound injury.

tag: Stage

value: adult

value: cerebral cortex

value: injured hemisphere

tag: time point

value: female


title: SM_23_treat_233


title: SM_24_treat_235


title: SM_22_treat_230


title: RNA-seq_D14_F_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Female_D14_injury_sham-Diff.xls
D14_F_sham_rep2

tag: strain

value: non-injured hemisphere


title: RNA-seq_D14_F_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Female_D14_injury_sham-Diff.xls
D14_F_injury_rep1


title: RNA-seq_D14_M_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Male_D14_injury_sham-Diff.xls
D14_M_injury_rep2

value: male


title: RNA-seq_D14_F_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Female_D14_injury_sham-Diff.xls
D14_F_sham_rep1


title: PDGF_KO_MEDIA

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

description: single-cell total RNA

data_processing:
Basecalls performed using CASAVA
Reads were aligned against mouse genome mm10 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R using Seurat v342. Cells were filtered for 200-5000 reads per UMI, 10% or less mitochondrial and less than 5% hemoglobin gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test with 10000 repetitions, and clusters were calculated with 19 PCs
Differential expression analysis was done using MAST
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene-barcode matrices

source_name: Atherosclerosis plaques

extract_protocol:
Individual atherosclerotic plaques from the brachiocephalic artery were removed from underlying media with forceps and deposited into FACS buffer (1% BSA in PBS) plus 1 ug/mL Actinomycin D,(Gibco, #11805017). Samples were then minced and digested with 1mL Liberase (Roche, #355374) plus 1ug/mL ActinomycinD for 1 hour at 37 degrees, then resuspended in PBS plus 0.04% UltraPure non-Acetylated BSA (ThermoFisher #AM2616) and filtered through 30um filters on ice. Samples were then either counted and submitted directly for scRNAseq or sorted by flow cytometry. Samples for flow were stained with Sytox Blue viability dye and sorted with a BD FACSAria Fusion cell sorter with gating on live, single cells that were eYFP+. Cells were collected into LoBind tubes containing 0.04% non-acetylated BSA.
2,000 cells in each group were targeted in Chromium 10X genomics libraries, which after barcoding, were pooled and sequenced on the Illumina NextSeqTM, 150 cycle high-output.
single-cell RNA-seq

treatment_protocol: Animals were maintened in a Western Diet for 18 weeks

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

tag: diet

value: Western Diet


title: SM_28_cntr_242


title: PDGF_KO_YFP_POS_MEDIA

description: single-cell total RNA

value: Sorted eYFP+ SMC cells


title: PDGF_WT_LESION

description: single-cell total RNA


title: RNA-seq_D14_M_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Male_D14_injury_sham-Diff.xls
D14_M_injury_rep1


title: RNA-seq_D14_M_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Male_D14_injury_sham-Diff.xls
D14_M_sham_rep1


title: PDGF_KO_LESION

description: single-cell total RNA


title: RNA-seq_D14_M_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D14_injury_sham-Diff.xls, Male_D14_injury_sham-Diff.xls
D14_M_sham_rep2


title: SM_21_treat_229


title: RNA-seq_D7_F_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Female_D7_injury_sham-Diff.xls
D7_F_injury_rep2


title: PDGF_WT_YFP_POS_MEDIA

description: single-cell total RNA


title: PDGF_WT_MEDIA

description: single-cell total RNA


title: RNA-seq_D7_F_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Female_D7_injury_sham-Diff.xls
D7_F_injury_rep1


title: RNA-seq_D7_F_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Female_D7_injury_sham-Diff.xls
D7_F_sham_rep1


title: RNA-seq_D7_F_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Female_D7_injury_sham-Diff.xls
D7_F_sham_rep2


title: RNA-seq_D7_M_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Male_D7_injury_sham-Diff.xls
D7_M_injury_rep2


title: RNA-seq_D7_M_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Male_D7_injury_sham-Diff.xls
D7_M_injury_rep1


title: RNA-seq_D7_M_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Male_D7_injury_sham-Diff.xls
D7_M_sham_rep1


title: RNA-seq_D7_M_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D7_injury_sham-Diff.xls, Male_D7_injury_sham-Diff.xls
D7_M_sham_rep2


title: RNA-seq_D4_F_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Female_D4_injury_sham-Diff.xls
D4_F_injury_rep1


title: RNA-seq_D4_F_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Female_D4_injury_sham-Diff.xls
D4_F_sham_rep1


title: RNA-seq_D4_M_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Male_D4_injury_sham-Diff.xls
D4_M_injury_rep2


title: RNA-seq_D4_F_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Female_D4_injury_sham-Diff.xls
D4_F_sham_rep2


title: RNA-seq_D4_M_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Male_D4_injury_sham-Diff.xls
D4_M_injury_rep1


title: bladder tumour 2498

city: Leeds

first: Margaret

middle: A

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

institute: University of Leeds

description: bladder tumour

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 7G microarray scanner.

data_processing:
Data QC was analysed using Affymetrix Expression Console Software and samples were normalised using RMA.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

source_name: fresh frozen bladder tumour tissue

label_protocol: Total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to manufacturer's instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45 degrees C.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from fresh frozen tissue samples comprising at least 70% tumour using an RNeasy  Plus Micro Kit (Qiagen). The protocol for fibrous tissue was followed with the inclusion of an on-column DNase digestion step

treatment_protocol: not applicable

tag: tumour stage

value: tumour stageTa


title: RNA-seq_D4_M_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Male_D4_injury_sham-Diff.xls
D4_M_sham_rep2


title: bladder tumour 2483

description: bladder tumour


title: bladder tumour 2350

description: bladder tumour


title: bladder tumour 2356

description: bladder tumour

value: tumour stageT1


title: bladder tumour 2338

description: bladder tumour


title: bladder tumour 2390

description: bladder tumour


title: RNA-seq_D4_F_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Female_D4_injury_sham-Diff.xls
D4_F_injury_rep2


title: bladder tumour 2429

description: bladder tumour


title: bladder tumour 2452

description: bladder tumour


title: bladder tumour 2492

description: bladder tumour


title: bladder tumour 2357

description: bladder tumour


title: bladder tumour 2425

description: bladder tumour


title: bladder tumour 2437

description: bladder tumour


title: bladder tumour 2334

description: bladder tumour


title: RNA-seq_D1_F_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Female_D1_injury_sham-Diff.xls
D1_F_injury_rep2


title: bladder tumour 2472

description: bladder tumour


title: bladder tumour 2423

description: bladder tumour


title: bladder tumour 2291

description: bladder tumour


title: RNA-seq_D1_F_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Female_D1_injury_sham-Diff.xls
D1_F_sham_rep2


title: RNA-seq_D1_F_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Female_D1_injury_sham-Diff.xls
D1_F_sham_rep1


title: RNA-seq_D4_M_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D4_injury_sham-Diff.xls, Male_D4_injury_sham-Diff.xls
D4_M_sham_rep1


title: RNA-seq_D1_M_injury_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Male_D1_injury_sham-Diff.xls
D1_M_injury_rep2


title: bladder tumour 2272

description: bladder tumour


title: RNA-seq_D1_F_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Female_D1_injury_sham-Diff.xls
D1_F_injury_rep1


title: RNA-seq_D1_M_injury_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Male_D1_injury_sham-Diff.xls
D1_M_injury_rep1


title: RNA-seq_D1_M_sham_rep2

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Male_D1_injury_sham-Diff.xls
D1_M_sham_rep2


title: bladder tumour 2282

description: bladder tumour


title: H36D_control_rep1 [DNA-seq]

description:
H36D
TB2Sa_disomy_comparison_DNA-seq
TB2Sa_deletion_disomy_comparison_DNA-seq
TB-2Sa_DNA_count_combine_raw_genecount_RPKM.txt
TB-2Sa_DNA_count_combine_raw_res1MB.txt
TB-2Sa_deletion_DNA_count_combine_raw_genecount_RPKM.txt
TB-2Sa_deletion_DNA_count_combine_raw_res1MB.txt

data_processing:
Library strategy: DNA-seq
RNA-seq (rRNA removal): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Non-ERCC and non-organelle reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
RNA-seq (mRNA selection): Adaptors at the 3' end of the reads were trimmed using cutadapt. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). The remaining reads were aligned to ERCC sequences using TopHat2 with default parameters. Non-ERCC reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts from the gene regions or 1Mb genome region. The counts from the gene region were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses and tables reporting RPKM normalized counts in DNA-seq.

source_name: Leaf tissue

tag: age

tag: rna/dna-seq approaches

value: Whole genome sequencing


title: TB-2Sa_deletion_disomy_rep1 [DNA-seq]

description:
2S5D
TB2Sa_deletion_disomy_comparison_DNA-seq
TB-2Sa_deletion_DNA_count_combine_raw_genecount_RPKM.txt
TB-2Sa_deletion_DNA_count_combine_raw_res1MB.txt


title: RNA-seq_D1_M_sham_rep1

address: 北京市朝阳区北辰西路1号院5号

description:
D1_injury_sham-Diff.xls, Male_D1_injury_sham-Diff.xls
D1_M_sham_rep1


title: H_2B_rep3 [RNA-seq_rRNA removal]

description:
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_2B_HB60
2B_0B_comparison_rRNA_depletion
2B_0B_gene_exp_rRNA_depletion.txt

value: ribosomal RNAs depletion


title: TB-2Sa_disomy_rep1 [DNA-seq]

description:
2S16D
TB2Sa_disomy_comparison_DNA-seq
TB-2Sa_DNA_count_combine_raw_genecount_RPKM.txt
TB-2Sa_DNA_count_combine_raw_res1MB.txt


title: H_2B_rep4 [RNA-seq_rRNA removal]

description:
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_2B_HB61
2B_0B_comparison_rRNA_depletion
2B_0B_gene_exp_rRNA_depletion.txt


title: bladder tumour 2267

description: bladder tumour


title: H_2B_rep1 [RNA-seq_rRNA removal]

description:
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_2B_HB57
2B_0B_comparison_rRNA_depletion
2B_0B_gene_exp_rRNA_depletion.txt


title: bladder tumour 2224

description: bladder tumour


title: H_2B_rep2 [RNA-seq_rRNA removal]

description:
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_2B_HB59
2B_0B_comparison_rRNA_depletion
2B_0B_gene_exp_rRNA_depletion.txt


title: H_1B_rep2 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_1B_HB67
1B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt


title: H_1B_rep4 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_1B_HB83
1B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt


title: H_1B_rep1 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_1B_HB64
1B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt


title: bladder tumour 2223

description: bladder tumour


title: H_0B_rep2 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_0B_HB40
1B_0B_comparison_rRNA_depletion
2B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt
2B_0B_gene_exp_rRNA_depletion.txt


title: HFD-Vehicle-1

value: liver

value: wild type

value: Vehicle-high fat diet


title: bladder tumour 2220

description: bladder tumour


title: bladder tumour 2214

description: bladder tumour


title: bladder tumour 2222

description: bladder tumour


title: H_0B_rep3 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_0B_HB63
1B_0B_comparison_rRNA_depletion
2B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt
2B_0B_gene_exp_rRNA_depletion.txt


title: bladder tumour 2169

description: bladder tumour


title: bladder tumour 2175

description: bladder tumour


title: bladder tumour 2178

description: bladder tumour


title: H_1B_rep3 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_1B_HB81
1B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt


title: H_0B_rep1 [RNA-seq_rRNA removal]

description:
1B_0B_gene_exp_rRNA_depletion_bioreps.txt
2B_0B_gene_exp_rRNA_depletion_bioreps.txt
H_0B_HB27
1B_0B_comparison_rRNA_depletion
2B_0B_comparison_rRNA_depletion
1B_0B_gene_exp_rRNA_depletion.txt
2B_0B_gene_exp_rRNA_depletion.txt


title: 7Lb_9Lc_10L19_1D_rep5 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
7Lb_9Lc_10L19_1D_H74
TB-7Lb_disomy_comparison_rRNA_depletion
TB-9Lc_disomy_comparison_rRNA_depletion
TB-10L19_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt
TB-9Lc_gene_exp_rRNA_depletion.txt
TB-10L19_gene_exp_rRNA_depletion.txt


title: 7Lb_9Lc_10L19_1D_rep4 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
7Lb_9Lc_10L19_1D_H73
TB-7Lb_disomy_comparison_rRNA_depletion
TB-9Lc_disomy_comparison_rRNA_depletion
TB-10L19_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt
TB-9Lc_gene_exp_rRNA_depletion.txt
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 2167

description: bladder tumour


title: bladder tumour 2161

description: bladder tumour


title: 7Lb_9Lc_10L19_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
7Lb_9Lc_10L19_1D_H72
TB-7Lb_disomy_comparison_rRNA_depletion
TB-9Lc_disomy_comparison_rRNA_depletion
TB-10L19_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt
TB-9Lc_gene_exp_rRNA_depletion.txt
TB-10L19_gene_exp_rRNA_depletion.txt


title: 7Lb_9Lc_10L19_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
7Lb_9Lc_10L19_1D_H71
TB-7Lb_disomy_comparison_rRNA_depletion
TB-9Lc_disomy_comparison_rRNA_depletion
TB-10L19_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt
TB-9Lc_gene_exp_rRNA_depletion.txt
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 2155

description: bladder tumour


title: bladder tumour 2164

description: bladder tumour


title: 3Sb_4Lb_6Lc_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
3Sb_4Lb_6Lc_1D_H69
TB-3Sb_disomy_comparison_rRNA_depletion
TB-4Lb_disomy_comparison_rRNA_depletion
TB-6Lc_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt
TB-4Lb_gene_exp_rRNA_depletion.txt
TB-6Lc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2165

description: bladder tumour


title: 7Lb_9Lc_10L19_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-10L19_gene_exp_rRNA_depletion_bioreps.txt
TB-7Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-9Lc_gene_exp_rRNA_depletion_bioreps.txt
7Lb_9Lc_10L19_1D_H70
TB-7Lb_disomy_comparison_rRNA_depletion
TB-9Lc_disomy_comparison_rRNA_depletion
TB-10L19_disomy_comparison_rRNA_depletion
TB-7Lb_gene_exp_rRNA_depletion.txt
TB-9Lc_gene_exp_rRNA_depletion.txt
TB-10L19_gene_exp_rRNA_depletion.txt


title: bladder tumour 2132

description: bladder tumour


title: bladder tumour 2138

description: bladder tumour


title: bladder tumour 2148

description: bladder tumour


title: bladder tumour 2139

description: bladder tumour


title: bladder tumour 2208

description: bladder tumour


title: bladder tumour 2118

description: bladder tumour


title: 3La_7Sc_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
3La_7Sc_1D_H58
TB-3La_disomy_comparison_rRNA_depletion
TB-7Sc_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt
TB-7Sc_gene_exp_rRNA_depletion.txt


title: 3La_7Sc_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
3La_7Sc_1D_H60
TB-3La_disomy_comparison_rRNA_depletion
TB-7Sc_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt
TB-7Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2104

description: bladder tumour


title: 3Sb_4Lb_6Lc_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
3Sb_4Lb_6Lc_1D_H66
TB-3Sb_disomy_comparison_rRNA_depletion
TB-4Lb_disomy_comparison_rRNA_depletion
TB-6Lc_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt
TB-4Lb_gene_exp_rRNA_depletion.txt
TB-6Lc_gene_exp_rRNA_depletion.txt


title: 3La_7Sc_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-3La_gene_exp_rRNA_depletion_bioreps.txt
TB-7Sc_gene_exp_rRNA_depletion_bioreps.txt
3La_7Sc_1D_H57
TB-3La_disomy_comparison_rRNA_depletion
TB-7Sc_disomy_comparison_rRNA_depletion
TB-3La_gene_exp_rRNA_depletion.txt
TB-7Sc_gene_exp_rRNA_depletion.txt


title: bladder tumour 2111

description: bladder tumour


title: 3Sb_4Lb_6Lc_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-3Sb_gene_exp_rRNA_depletion_bioreps.txt
TB-4Lb_gene_exp_rRNA_depletion_bioreps.txt
TB-6Lc_gene_exp_rRNA_depletion_bioreps.txt
3Sb_4Lb_6Lc_1D_H68
TB-3Sb_disomy_comparison_rRNA_depletion
TB-4Lb_disomy_comparison_rRNA_depletion
TB-6Lc_disomy_comparison_rRNA_depletion
TB-3Sb_gene_exp_rRNA_depletion.txt
TB-4Lb_gene_exp_rRNA_depletion.txt
TB-6Lc_gene_exp_rRNA_depletion.txt


title: 1Sb_1D_rep4 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_1D_H50
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: bladder tumour 2108

description: bladder tumour


title: 1Sb_1D_rep2 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_1D_H47
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: 1Sb_1D_rep1 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_1D_H46
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt


title: 1Sb_1D_rep3 [RNA-seq_rRNA removal]

description:
TB-1Sb_gene_exp_rRNA_depletion_bioreps.txt
1Sb_1D_H48
TB-1Sb_disomy_comparison_rRNA_depletion
TB-1Sb_gene_exp_rRNA_depletion.txt