title: LEUTX 4

first: Thomas

middle: Lewin

last: Lewin

state: Oxfordshire

address: 11a Mansfield Road

department: Department of Biology

institute: Thomas Lewin

data_processing:
Filtering: Reads were filtered to remove those containing adapters, those with N > 10% and those of low quality (Qscore < 5) (performed by Novogene).
QC: FastQC and MultiQC
Trimming: Trimmomatic
Pseudoalignment: Kallisto v. 0.46.1
Create count tables: Tximport v. 1.20.0
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Bovine_ARGFX_LEUTX_raw_counts.csv : Matrix containing raw counts for all genes in all 15 samples.

organism: Bos taurus

source_name: Primary foetal fibroblast cell culture

growth_protocol: Primary bovine foetal fibroblasts (BFFs) were isolated from the torso skin of a 6-month old Bos taurus foetus from an individual sacrificed at an abattoir. A 1 cm2 section of skin was excised, transported on ice and washed 3 times with sterile phosphate buffered saline (PBS) (Gibco #10010015). Subcutaneous fat was scraped off and the tissue minced with a scalpel. Five 2 mm2 pieces were placed in each well of a 0.001% poly-L-lysine-coated (Sigma-Aldrich, P4832-50ML) 6-well plate, covered with a sterile glass cover slip, and 2 mL BFF media added. BFF media is Dulbecco’s Modified Eagle Medium (Gibco #41965039) with 10% heat-inactivated Foetal Bovine Serum (Gibco #10500064), 1% penicillin-streptomycin (Gibco #15140122) and 1% amphotericin B (Gibco #15290026). Outgrowth was allowed for 18 days at 37°C with 5% CO2, with the culture media changed every 3-4 days before cells were washed three times in 2 mL PBS and detached with 2 mL TrypLE™ Express enzyme (Gibco #12604013) at 37°C with 5% CO2. TrypLE™ Express was neutralised with 5 mL BFF medium, the cover slip removed, cells and medium transferred to a 50 mL Falcon tube and centrifuged for 5 minutes at 1200 rpm. Cells were washed twice with 10 mL BFF medium and centrifuged, then seeded into 0.001% poly-L-lysine-coated T75 flasks. To maintain growth, fibroblasts were incubated at 37°C with 5% CO2 and passaged one flask to four every 3-4 days at 70-80% confluency.

extract_protocol:
After 72 h, RNA was extracted using an RNeasy Plus Micro kit using the standard protocol (Qiagen #74034).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with either the bovine ARGFX gene, LEUTX gene, mutant ARGFX gene or empty pSF-CMV-Puro-COOH vector as a control. For transfection, 1 million cells were resuspended in 98 μL Opti-MEM (Gibco #11058021), combined with 2 μL of 5 μg/μL endotoxin-free plasmid, electroporated with a 2 mm gap using a NEPA21 Super Electroporator (NEPAGENE) and seeded in 2 mL BFF medium. Medium was changed after 24 h, and puromycin (Sigma Aldrich #P8833) added at 4 μg/mL to select for transfected cells.

value: Wild-type LEUTX ectopic expression

value: Foetal dermal fibroblast

value: Passage 4


title: IL13 Treatment HBE Donor 1328 H3K27ac ChIP [D24_13_K27ac_repHBE1328]

status: Public on May 24 2022

type: SRA

city: San Francisco

first: Walter

last: Eckalbar

state: CA

address: 513 Parnassus Ave MSB-813

country: USA

institute: University of California, San Francisco

library_source: genomic

data_processing:
aligned with STAR_2.5.2b,  --readFilesCommand gzcat      --outFileNamePrefix Alignments/D28_IFN_K27ac_repHBE1243out/   --outSAMtype BAM   SortedByCoordinate      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFil  terMismatchNmax 999 --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC  --alignIntronMin 20  --alignIntronMax 1  --alignMatesGapMax 10   --alignSJDBoverhangMin 1   --quantMode GeneCounts
Coverage graphs were created with bedtools v2.29.0
Peaking calling with MACS2 (2.2.6a2)
IDR to find reproducible peaks between samples (2.0.3)
Htseq count (0.11.0) to count reads over reproducable peak regions
Genome_build: GRCh38
Supplementary_files_format_and_content: Experiment-wide Gene by sample counts tables

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Six donors of HBECs were seeded on HPC-coated Transwells and cultured at ALI for 23 d.

extract_protocol:
After removal of accumulated mucus with 10 mM DTT in PBS, cells were trypsinized with 0.25% trypsin-EDTA for 10 min at 37 °C and neutralized. . Cells were manually counted using a hemocytometer, and equal numbers of cells from each donor were pooled. Each pool included four samples (one from each donor and each representing a different cytokine stimulation).
Manufactures instructions where follow to carry out a ChIP using Diagenoid Low Cell ChIP kit, NGS libraries where created from the purified DNA using Rubicon DNA-seq kit.

treatment_protocol: Cells were cultured at ALI for 23 d without cytokine or with IFN-a (10 ng/mL for the final 1 d), IL-13 (10 ng/mL for the final 7 d), IL-17 (10 ng/mL for the final 7 d), or the combination of IFN-a and IL-13.

tag: cell type

value: ALI-cultured HBECs d 23

tag: donor id

value: Donor 1328

tag: treatment

value: IL13 Treatment

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: Pooled_input_S961

city: NEW YORK

first: Domenico

last: Accili

state: NY

address: 1150 ST NICHOLAS AVENUE, RM238

department: Medicine

institute: Columbia University

data_processing:
Reads were aligned to mouse genome mm10 using Bowtie2
The reads used in subsequent analysis passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome. Duplicate reads were removed with Picard tools. The tags were extended at their 3′-ends to 200-bp.
Peak calling was performed by MACS 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tdf files were generated using igvtools

organism: Mus musculus

source_name: liver tissue

extract_protocol:
Lysates were clarified from sonicatd nuclei and GFP- or histone-DNA complexes were isolated with antibody
ChIP-seq libraries were constructed using KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. ChIP-seq libraries were quantified by Tapestation (Agilent) and sequenced on an Illumina NEXTseq (Illumina, San Diego, CA, USA) with 75-base single-end mode.

treatment_protocol: Samples were treated by vehicle or S961 for 48hours

tag: tissue

value: liver

tag: strain

value: Combined samples 3 and 4


title: H3K27ac_Vehicle_Refeed

value: H3K27ac (Active motif, 39133)

value: 4-h-fasted / 1-h-refeed Vehicle control (Normal saline)


title: IL13 Treatment HBE Donor 1243 H3K27ac ChIP [D24_13_K27ac_repHBE1243]

value: Donor 1243


title: LEUTX 2

city: Oxford

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

tag: age


title: IL17 Treatment HBE Donor 1333 H3K27ac ChIP [D24_17_K27ac_repHBE1333]

value: Donor 1333

value: IL17 Treatment


title: IL13 Treatment HBE Donor 1605 Input [D24_13_Input_T]

source_name: IL13 Treatment HBE Donor 1605 Input

value: Donor 1605


title: IL13 Plus IFN Alpha Treatment HBE Donor 1326 H3K27ac ChIP [D24_CO_K27ac_repHBE1326]

value: Donor 1326

value: IL13 Plus IFN Alpha Treatment


title: IFN Alpha Plus IL13 Treated HBE Donor 1328 [CoT_6]

data_processing:
aligned with STAR_2.4.2a, --runThreadN 12  --readFilesCommand gzcat --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC --limitBAMsortRAM 96000000000 --outSAMtype BAM Unsorted --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Experiment-wide Gene by sample counts tables

source_name: IFN Alpha Plus IL13 Treated HBE

extract_protocol:
After removal of accumulated mucus with 10 mM DTT in PBS, cells were trypsinized with 0.25% trypsin-EDTA for 10 min at 37 °C and neutralized. . Cells were manually counted using a hemocytometer, and equal numbers of cells from each donor were pooled. Each pool included four samples (one from each donor and each representing a different cytokine stimulation).
Manufacturer's instructions for Illumina TruSeq stranded mRNA

value: IFN Alpha Plus IL13 Treated


title: IL13 Treatment HBE Donor 1605 H3K27ac ChIP [D24_13_K27ac_T]


title: IL17 Treatment HBE Donor 1243 H3K27ac ChIP [D24_17_K27ac_repHBE1243]


title: LEUTX 3

value: Wild-type LEUTX ectopic expression

value: Foetal dermal fibroblast


title: IL13 Treatment HBE Donor 1326 H3K27ac ChIP [D24_13_K27ac_repHBE1326]

value: ALI-cultured HBECs d 23


title: Mutant ARGFX 1

value: Mutant ARGFX ectopic expression

value: Passage 4


title: IFN Alpha Plus IL13 Treated HBE Donor 1324 [CoT_5]

value: Donor 1324


title: WT ARGFX 4

value: Wild-type ARGFX ectopic expression


title: IFN Alpha Plus IL13 Treated HBE Donor 1243 [CoT_1]


title: Mutant ARGFX 2


title: FoxO1_Vehicle_Fast

value: liver

value: GFP (Abcam, ab290)

value: 4-h-fasted Vehicle control (Normal saline)


title: Mutant ARGFX 3


title: 3F_apob_severe_rep1

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Genome_build: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary_files_format_and_content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Changes, logCPM,and FDR-adjusted P value.

organism: Schmidtea mediterranea

source_name: Whole animal

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in 0.5 g/L Instant Ocean salts with 0.0167 g/L sodium bicarbonate dissolved in Type I water, and fed with beef liver paste. For all experiments, planarians were starved seven days prior to fixation.

extract_protocol:
Total RNA was extracted from 5-6 uninjured planarians per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4-6 biological replicates per condition was submitted to GENEWIZ (South Plainfield, NJ) for library generation from ~ 500 ng/sample using the NEB NEXT ULTRA Library Prep Kit and RNA sequencing with standard Illumina adapters.

treatment_protocol: Planarians were fed every 3-4 days (three feedings total) with 2 µg dsRNA mixed with 1 µl blue food coloring, 8 µl water, and 40 µl 2:1 liver:water homogenate, then starved seven days prior to RNA extraction.

value: clonal line CIW4

value: live uninjured whole planarians

tag: developmental stage

value: starved 7 days


title: WT ARGFX 2


title: 3F_apob_mild_rep3


title: 3F_apob_mild_rep4


title: IFN Alpha Plus IL13 Treated HBE Donor 1326 [CoT_2]


title: Control 3

value: control


title: IFN Gamma Treated HBE Donor 1324 [IFNg_5]

source_name: IFN Gamma Treated HBE

value: IFN Gamma Treated


title: IFN Alpha Plus IL13 Treated HBE Donor 1323 [CoT_4]

value: Donor 1323


title: WT ARGFX 3


title: Control 4


title: 3F_apob_severe_rep3


title: LEUTX 1


title: 3F_apob_mild_rep2


title: IFN Alpha Plus IL13 Treated HBE Donor 1333 [CoT_3]

value: Donor 1333

value: IFN Alpha Plus IL13 Treated


title: IFN Gamma Treated HBE Donor 1323 [IFNg_4]


title: IFN Gamma Treated HBE Donor 1328 [IFNg_6]

value: Donor 1328


title: 3F_apob_severe_rep2


title: 3F_apob_severe_rep4


title: WT ARGFX 1

value: Foetal dermal fibroblast


title: IFN Gamma Treated HBE Donor 1333 [IFNg_3]

value: ALI-cultured HBECs d 23


title: Control 2

value: Passage 4


title: 3F_ctrl_rep6


title: 3F_ctrl_rep3


title: 3F_ctrl_rep1


title: IFN Gamma Treated HBE Donor 1243 [IFNg_1]

value: Donor 1243


title: IFN Alpha Treated HBE Donor 1328 [IFNa_6]

source_name: IFN Alpha Treated HBE

value: IFN Alpha Treated


title: IFN Alpha Treated HBE Donor 1324 [IFNa_5]

value: Donor 1324


title: IFN Gamma Treated HBE Donor 1326 [IFNg_2]

value: Donor 1326


title: Thy_ScaI_P_4

city: Haifa

first: Marianna

last: Yusupova

address: Technion City

country: Israel

institute: Technion- Israel Institute of Technology

description: Column S

data_processing:
RNA-seq reads were aligned using the STAR aligner
RNA-seq reads were annotated using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: primary epidermal cells

extract_protocol:
RNA was harveted using TRIzol-LS according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using Illumina Small RNA v1.5 Sample Preparation Kit and Illumina mRNA sequencing Sample Preparation Kit or SMARTer Stranded Total RNA-Seq Kit v2  (for samples sequenced with Illumina HiSeq2500) according to manufacturer's protocols.

tag: cell line

value: primary epidermal cells

value: primary Thy1+ScaI+ epidermal cells

tag: genotype

value: no treatment

tag: time

value: 23 weeks old


title: thy_ScaI_YFP_P_1

description: Column M

value: primary Thy1+YFP+ScaI- epidermal cells

value: 17 weeks old


title: thy_ScaI_YFP_P_2

description: Column N

value: 18 weeks old


title: lux_ZT14_SD_rep1

city: Großbeeren

first: Philip

last: Wigge

address: Theodor-Echtermeyer-Weg 1

country: Germany

institute: Leibniz-Institut für Gemüse- und Zierpflanzenbau (IGZ) e.V.

data_processing:
hisat2 with parameters ‘--no-mixed, --rna-strandness RF --dta --fr’ was used for aligning the raw RNA-seq reads to the rice genome assemblies (ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/oryza_sativa/dna/).
TPM values for genes were calculated by stringtie with default settings directed by gene annotation file IRGSP-1.0 (ftp://ftp.ensemblgenomes.org/pub/release-47/plants/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.47.gtf.gz).
Assembly: IRGSP-1.0

organism: Oryza sativa Japonica Group

source_name: 21-days whole plants

growth_protocol: For the measurement of flowering-time, wild-type, lux, elf3-1, elf3-2, and elf3-1 elf3-2 rice seeds were germinated in water-soaked paper at 28 ºC for 3 days. Germinated seedlings were planted in containers with soil (soil:peat:vermiculite in 2:2:1 volume ratio) and placed in controlled conditions at 28 ºC under 12h/12h light/dark photoperiod (ND conditions) at 70 % humidity.

extract_protocol:
Homogenizing samples to powder using a freeze cold mortar and pestle followed by total RNA using the RNeasy plant kit (Qiagen), followed by DNAse I treatment (Ambion)
Prepare high-throughput mRNA sequencing libraries using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Plants were grown under 14h/10h (LD conditions) and 10h/14h (SD conditions) photoperiod

tag: photoperiod

value: SD

tag: timepoint

value: OsLUX-/-


title: 3F_apob_mild_rep1

value: clonal line CIW4

value: live uninjured whole planarians

value: starved 7 days


title: lux_ZT14_SD_rep3


title: 3F_ctrl_rep4


title: IFN Alpha Treated HBE Donor 1333 [IFNa_3]

value: Donor 1333

value: ALI-cultured HBECs d 23


title: Control 1

value: control

value: Foetal dermal fibroblast

value: Passage 4


title: lux_ZT14_SD_rep2


title: WT_ZT24_SD_rep1

data_processing:
hisat2 with parameters ‘--no-mixed, --rna-strandness RF --dta --fr’ was used for aligning the raw RNA-seq reads to the rice genome assemblies (ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/oryza_sativa/dna/).
TPM values for genes were calculated by stringtie with default settings directed by gene annotation file IRGSP-1.0 (ftp://ftp.ensemblgenomes.org/pub/release-47/plants/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.47.gtf.gz).
Genome_build: IRGSP-1.0

value: WT (Rice Japonica cv. Nipponbare)


title: IFN Alpha Treated HBE Donor 1323 [IFNa_4]

value: Donor 1323

value: IFN Alpha Treated


title: WT_ZT24_LD_rep3

value: LD


title: WT_ZT24_SD_rep3


title: 3F_ctrl_rep5


title: WT_ZT24_SD_rep2


title: 3F_ctrl_rep2


title: IFN Alpha Treated HBE Donor 1326 [IFNa_2]

value: Donor 1326


title: WT_ZT18_SD_rep3


title: Thy_P_ScaI_N_2

description: Column I

value: primary epidermal cells

value: primary Thy1+ScaI- epidermal cells

value: no treatment

value: 13 weeks old


title: Thy_P_ScaI_N_3

description: Column J

value: 14 weeks old


title: Thy_P_ScaI_N_1

description: Column H

value: 12 weeks old


title: WT_ZT18_SD_rep1

value: SD


title: WT_ZT18_SD_rep2


title: WT_ZT24_LD_rep2


title: CD34_P_ScaI_N_2

description: Column E

value: primary CD34+ScaI- epidermal cells

value: 9 weeks old


title: WT_ZT18_LD_rep3


title: WT_ZT18_LD_rep2


title: IL17 Treated HBE Donor 1328 [IL17_6]

source_name: IL17 Treated HBE

value: Donor 1328

value: ALI-cultured HBECs d 23

value: IL17 Treated


title: CD34_P_ScaI_N_1

description: Column D

value: 8 weeks old


title: IL17 Treated HBE Donor 1324 [IL17_5]

value: Donor 1324


title: WT_ZT14_SD_rep3

value: WT (Rice Japonica cv. Nipponbare)


title: CD34_P_ScaI_N_3

description: Column F

value: 10 weeks old


title: IL17 Treated HBE Donor 1323 [IL17_4]

value: Donor 1323


title: IL17 Treated HBE Donor 1333 [IL17_3]

value: Donor 1333


title: WT_ZT18_LD_rep1

value: LD


title: WT_ZT14_LD_rep3


title: WT_ZT14_SD_rep1


title: IL17 Treated HBE Donor 1326 [IL17_2]

value: Donor 1326


title: WT_ZT14_LD_rep1


title: IFN Alpha Treated HBE Donor 1243 [IFNa_1]

value: Donor 1243

value: IFN Alpha Treated


title: WT_ZT14_LD_rep2


title: WT_ZT10_SD_rep3


title: WT_ZT10_SD_rep2


title: Thy_N_ScaI_P_4

description: Column W

value: primary epidermal cells

value: primary Thy1-ScaI+ epidermal cells

value: no treatment

value: 27 weeks old


title: IL17 Treated HBE Donor 1243 [IL17_1]


title: WT_ZT14_SD_rep2

value: SD


title: WT_ZT10_SD_rep1


title: WT_ZT10_LD_rep2


title: WT_ZT10_LD_rep3


title: WT_ZT10_LD_rep1


title: IL13 Treated HBE Donor 1328 [IL13_6]

source_name: IL13 Treated HBE

value: Donor 1328

value: ALI-cultured HBECs d 23

value: IL13 Treated


title: IL13 Treated HBE Donor 1324 [IL13_5]

value: Donor 1324


title: WT_ZT6_SD_rep3

value: WT (Rice Japonica cv. Nipponbare)


title: IL13 Treated HBE Donor 1333 [IL13_3]


title: WT_ZT6_SD_rep1


title: WT_ZT6_SD_rep2


title: WT_ZT6_LD_rep3


title: IL13 Treated HBE Donor 1323 [IL13_4]


title: WT_ZT6_LD_rep2


title: WT_ZT6_LD_rep1


title: SpinalCord_Control_4

type: RNA

city: Yokohama

first: Takeshi

last: Hirata

state: Kanagawa

address: 1000, Kamoshida-cho, Aoba-ku

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

description: Gene expression data from control spinal cord

hyb_protocol: Following labeling, each cDNA was hybridized for 16 hr at 45℃ at 60 rpm on GeneChip Mouse Genome 430 2.0 Array using GeneChip Hybridization, Wash and Stain Kit. The GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: CEL files were analyzed using R (ver. 4.1.1) and the affy package. MAS 5.0 was used as the normalization algorithm.

label: biotin

source_name: Control C57BL/21 mouse spinal cord

label_protocol: Biotin-labeled cDNA synthesis, fragmentation were performed using GeneChip 3’IVT PLUS Reagent Kit  (Thermo Fisher Scientific) according to the manufacturer’s recommended protocol.

growth_protocol: eight-week old female inbred C57BL/6 mice were grown up.

extract_protocol: Total RNA extraction was performed using the Maxwell® RSC simplyRNA Tissue Kit (Promega) according to the manufacturer’s protocol.

treatment_protocol: Spinal cords were sampled with a width of 4.5 mm (centered on cytokine injection site) after transcardial perfusion with ice-cold PBS, then immediately frozen with liquid nitrogen and stored at −80 °C until extraction.

tag: gender

value: Female

value: Isotype control antibody

value: Spinal cord


title: SpinalCord_Control_5

source_name: Control C57BL/22 mouse spinal cord


title: SpinalCord_Control_3

source_name: Control C57BL/20 mouse spinal cord


title: IL13 Treated HBE Donor 1326 [IL13_2]


title: WT_ZT2_SD_rep2


title: IL13 Treated HBE Donor 1243 [IL13_1]


title: SpinalCord_Control_1

source_name: Control C57BL/18 mouse spinal cord


title: SpinalCord_antiRGMa_6

description: Gene expression data from treatement spinal cord

source_name: antiRGMa C57BL/17 mouse spinal cord

value: anti-RGMa antibody


title: SpinalCord_Control_2

source_name: Control C57BL/19 mouse spinal cord


title: SpinalCord_antiRGMa_4

source_name: antiRGMa C57BL/15 mouse spinal cord


title: Untreated Control HBE Donor 1328 [UT_6]

source_name: Untreated Control HBE

value: Untreated Control


title: WT_ZT2_SD_rep1


title: WT_ZT2_LD_rep2

value: LD


title: WT_ZT2_SD_rep3


title: SpinalCord_antiRGMa_3

source_name: antiRGMa C57BL/14 mouse spinal cord


title: phyb_ZT18_SD_rep2

value: OsphyB-/-


title: Untreated Control HBE Donor 1323 [UT_4]

value: Donor 1323


title: WT_ZT2_LD_rep1


title: Untreated Control HBE Donor 1324 [UT_5]


title: phyb_ZT18_SD_rep3


title: SpinalCord_antiRGMa_5

source_name: antiRGMa C57BL/16 mouse spinal cord


title: phyb_ZT18_SD_rep1


title: SpinalCord_antiRGMa_2

source_name: antiRGMa C57BL/13 mouse spinal cord


title: Untreated Control HBE Donor 1243 [UT_1]

source_name: Untreated Control HBE

value: Donor 1243


title: phyb_ZT18_LD_rep3


title: SpinalCord_Naïve_6

description: Gene expression data from naïve spinal cord

source_name: Naïve C57BL/11 mouse spinal cord

value: Non-Treatment


title: Untreated Control HBE Donor 1333 [UT_3]

value: Donor 1333


title: phyb_ZT18_LD_rep2


title: phyb_ZT14_LD_rep2


title: phyb_ZT18_LD_rep1


title: Untreated Control HBE Donor 1326 [UT_2]

value: Donor 1326


title: Human Brochial Epithelial Cells pool 9

data_processing:
cellranger count v2.1.0 to refdata-cellranger-GRCh38-1.2.0
cell-individual demultiplexing with Demuxlet
filtering with Seurat v3.1.1 (subset(soTreatment, subset = nFeature_RNA >= 500 & nFeature_RNA < 7500 & nCount_RNA > 1200 & percent.mito < .5 & percent.ribo < .35))
Genome_build: GRCh38
Supplementary_files_format_and_content: 10x Cellranger outputs, counts tables, and demuxlet outputs for cell:sample assignment

source_name: Brochial Epithelial Cells from Lung Transplants

growth_protocol: Four donors of HBECs were seeded on HPC-coated Transwells and cultured at ALI for 23 d.

extract_protocol:
After removal of accumulated mucus with 10 mM DTT in PBS, cells were trypsinized with 0.25% trypsin-EDTA for 10 min at 37 °C and neutralized. . Cells were manually counted using a hemocytometer, and equal numbers of cells from each donor were pooled. Each pool included four samples (one from each donor and each representing a different cytokine stimulation).
Manufacturer's instructions for 10x Genomics 3' v1 GEX

value: ALI-cultured HBECs


title: phyb_ZT14_SD_rep3

source_name: 21-days whole plants

value: SD


title: phyb_ZT14_SD_rep2


title: phyb_ZT6_SD_rep3


title: phyb_ZT14_LD_rep1


title: Rice Salt_F_6h_R2

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

description:
Salt_F_6h_R2
FAIRE-seq on salt treated  for 6 hour, replicate 2

data_processing:
FASTQC for quality control
Bowtie2/Tophat2 for mapping to TAIR 10
Samtools for pre-processing
MACS2 for peak calling
3D-RNA-seq for RNA-seq
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: broad peak containing coordinates of the open chromatin region with tag density

organism: Oryza sativa

source_name: seedlings

growth_protocol: Oryza sativa L. Japonica nipponbare was grown in a plant growth chamber (Conviron®) at 28°C under a photoperiod of 16 h/8 h.

extract_protocol:
For RNA-seq, total RNA was extracted with Qiagen plant RNA extraction kit.   For FAIRE-seq, seedlings were fixed with formaldehyde before extracting nuclei and chromatin was extracted as described by Giresi et al 2007 and Raxwal et al 2020.
DNA library were prepared with NEB kit whereas RNA-seq was prepared as per protocol of Illumina TruSeq RNA sample preparation kit.
50 bp single end on Illumina HiSeq 2000

treatment_protocol: 14-day old seedlings were subjected to heat (42°C for 30 min and 3 h), cold (4°C for 12 h and 24 h), and salt (250 mM NaCl for 2 h and 6 h) stress. The 14-day old seedlings grown at 28°C were taken as the control sample.

tag: genetic accession

value: Japonica nipponbare

tag: abiotic stress

value: Salt

value: 14 day old


title: phyb_ZT6_SD_rep1


title: phyb_ZT14_SD_rep1


title: phyb_ZT14_LD_rep3


title: SpinalCord_Naïve_1

source_name: Naïve C57BL/6 mouse spinal cord

value: Female


title: Human Brochial Epithelial Cells pool 10


title: SpinalCord_Naïve_4

source_name: Naïve C57BL/9 mouse spinal cord


title: SpinalCord_Naïve_3

source_name: Naïve C57BL/8 mouse spinal cord


title: phyb_ZT6_LD_rep1


title: Rice Salt_F_2h_R2

description:
Salt_F_2h_R2
FAIRE-seq on salt treated  for 2 hour, replicate 2


title: phyb_ZT6_SD_rep2


title: Human Brochial Epithelial Cells pool 8


title: Human Brochial Epithelial Cells pool 7


title: phyb_ZT6_LD_rep3


title: Rice Salt_F_2h_R1

description:
Salt_F_2h_R1
FAIRE-seq on salt treated  for 2 hour, replicate 1


title: Human Brochial Epithelial Cells pool 6


title: WT_ZT24_LD_rep1

value: WT (Rice Japonica cv. Nipponbare)


title: SpinalCord_Naïve_5

source_name: Naïve C57BL/10 mouse spinal cord

value: Spinal cord


title: Human Brochial Epithelial Cells pool 5


title: Rice Salt_F_6h_R1

description:
Salt_F_6h_R1
FAIRE-seq on salt treated  for 6 hour, replicate 1


title: SpinalCord_Naïve_2

source_name: Naïve C57BL/7 mouse spinal cord


title: Rice Heat_F_3h_R2

description:
Heat_F_3h_R2
FAIRE-seq on heat treated  for 3 hour, replicate 2

value: Heat


title: Human Brochial Epithelial Cells pool 4


title: elf3_ZT18_LD_rep2


title: elf3_ZT18_SD_rep1


title: elf3_ZT18_SD_rep2


title: elf3_ZT18_LD_rep1


title: SpinalCord_antiRGMa_1

source_name: antiRGMa C57BL/12 mouse spinal cord

value: anti-RGMa antibody


title: Rice Heat_F_3h_R1

description:
Heat_F_3h_R1
FAIRE-seq on heat treated  for 3 hour, replicate 1


title: Rice Heat_F_30m_R2

description:
Heat_F_30m_R2
FAIRE-seq on heat treated  for 30 min, replicate 2


title: elf3_ZT14_SD_rep3


title: phyb_ZT6_LD_rep2

value: LD


title: elf3_ZT18_SD_rep3


title: Rice Heat_F_30m_R1

description:
Heat_F_30m_R1
FAIRE-seq on heat treated  for 30 min, replicate 1


title: Human Brochial Epithelial Cells pool 2


title: elf3_ZT14_SD_rep1


title: elf3_ZT14_LD_rep3


title: elf3_ZT14_SD_rep2


title: Rice Cold_F_24h_R2

description:
Cold_F_24h_R2
FAIRE-seq on cold treated  for 24 hour, replicate 2

value: Cold


title: Human Brochial Epithelial Cells pool 1


title: elf3_ZT6_SD_rep3


title: elf3_ZT14_LD_rep2


title: elf3_ZT18_LD_rep3


title: Rice Cold_F_12h_R2

description:
Cold_F_12h_R2
FAIRE-seq on cold treated  for 12 hour, replicate 2


title: elf3_ZT6_LD_rep2


title: elf3_ZT6_SD_rep1


title: Rice Cold_F_24h_R1

description:
Cold_F_24h_R1
FAIRE-seq on cold treated  for 24 hour, replicate 1


title: Human Brochial Epithelial Cells pool 3


title: elf3_ZT6_LD_rep1


title: elf3_ZT6_LD_rep3


title: Rice Cold_F_12h_R1

description:
Cold_F_12h_R1
FAIRE-seq on cold treated  for 12 hour, replicate 1


title: ELF3_ZT14_SD_ChIP-seq

data_processing:
For processing ChIP-seq fastq files, bwa was used to map raw reads to rice genome IRGSP-1.0. Unmapped reads, mate unmapped reads, non-primary alignment and duplicate reads were removed.
Peaks were identified using MACS2 and filtered by q-value < 0.01.
Bigwig files for IGV tracks were generated using deeptools function bamCoverage and normalized using RPKM.
Genome_build: IRGSP-1.0

source_name: 14-days whole plants

growth_protocol: rice WT cv. Nipponbare seeds were surface sterilized and germinated in sterile water in the dark. Germinated seedlings were then transferred to tubes containing sterile ½ MS solid medium and placed in a growth chamber at 28 ºC under SD for 2 weeks. A pool of 20 plants was collected from each genotype at ZT14 using liquid nitrogen and stored at -80 ºC.

extract_protocol:
3 g seedlings for each set were fixed under vacuum for 20 min in 1xPBS containing 1% Formaldehyde (F8775 SIGMA). The  reaction was quenched by adding glycine to a final concentration of 62 mM. The ChIP was performed according to Jaeger et al., 2013 https://doi.org/10.1105/tpc.113.109355
Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina  IP-202-1024)

treatment_protocol: Plants were grown under 10h/14h (SD conditions) photoperiod

value: Custome made (Agrisera, AS184168, lot# 1808)


title: Input_ZT14_SD_ChIP-seq


title: WTCHG_836238_212_1

first: Ashwin

last: Jainarayanan

address: Roosevelt Dr, Headington, Oxford OX3 7FY

department: KIR, NDORMS

institute: University of Oxford

data_processing:
Batch corrections were performed using miRNAQC
Reads were aligned to the human genome reference (Human37) using sRNAtoolboxDB
Reads are mapped to microRNA reference libraries miRBase and MirGeneDB.
QC was done using miRNAQC
Expression matrix (Reads Per Millions) was also obtained using mirnaQC
Genome_build: Human37
Supplementary_files_format_and_content: Expression matrix (Reads Per Millions) of the identified miR per species, source file (raw) is listed on the heading row

source_name: CD8 EV

growth_protocol: T cells were activated with anti-CD3/CD28 beads for 72h, then expanded using IL-2 100 U/mL in the absence of beads

extract_protocol:
FACS sorted BSLB were lysed and RNA was purified using miRNA advance kit
microRNA libraries were prepared following NEBNext Small RNA kit (NEB) and the low yield protocol
Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers and size selection was performed using Pippin Prep instrument (Sage Science) using the 3% Agarose, dye free gel with internal standards (size selection: 120 to 230bp).

treatment_protocol: Cells were splt. One half was cultured in OptiMEM-I for isolation of EVs for no longer than 48h and the other half was cocultured with BSLBs to capture and isolate tSV

value: PBMC

value: CD8 T cells


title: WTCHG_836236_212_1


title: WTCHG_836237_212_1


title: Rice Control_T_R2

description:
Control_T_R2
RNA-seq on control sample, replicate 2

value: Control


title: WTCHG_834294_212_1


title: LUX_ZT14_SD_ChIP-seq

value: Anti-MYC (Sigma, C3956, Lot# 059M4801V)


title: Rice Control_T_R1

description:
Control_T_R1
RNA-seq on control sample, replicate 1


title: Bat7_PreM_rna

city: Pittsburgh

first: Morgan

last: Wirthlin

state: Pennsylvania

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
ATAC-seq alignment Bat reads were mapped to the mRouAeg1 assembly with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) with default parameters except for "atac.multimapping" : 0 (read filtering), "atac.cap_num_peak" : 300000 (peak calling), "atac.smooth_win" : 150 (peak calling), "atac.enable_idr" : true (peak calling), and "atac.idr_thresh" : 0.1 (peak calling).
ATAC-seq filtering Duplicate reads, mitochondrial reads, and multi-mapping reads were filtered out as a part of the ENCODE ATAC-seq pipeline. The pipeline also created signal tracks using MACS2.
ATAC-seq peak calling Within the ENCODE ATAC-seq pipeline workflow, peaks were called on each sample individually, on the pool of biological replicates, on pooled pseudo-replicates, and on self pseudo-replicates using MACS2 and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
RNA-seq read quantification Bat RNA-seq samples were quantified with Salmon 1.5.2 using default parameters, which mapped reads to a transcriptome derived from the mRouAeg1 assembly.
Other More information on all data processing and conclusions can be found in the publication.
Genome_build: mRouAeg1
Supplementary_files_format_and_content: Open chromatin peaks called in each ATAC-seq sample in narrowPeak format
Supplementary_files_format_and_content: MACS2 pval signal tracks for each ATAC-seq sample in bigwig format
Supplementary_files_format_and_content: Transcript read quantifications for each RNA-seq sample in Salmon quantification output file (.sf) format

molecule: polyA RNA

organism: Rousettus aegyptiacus

source_name: adult male Egyptian fruit bat premotor cortical area (PreM)

extract_protocol:
For ATAC-seq, nuclei were extracted from cryopreserved tissue with Dounce homogenization in lysis buffer. The nuclei were pelleted by centrifugation and filtered through 70µm and 40µm strainers. For RNA-seq, total RNA was purified from flash-frozen tissue using the Qiagen RNeasy Mini Kit.
ATAC-seq libraries were constructed with standard amplification and size selection methods. RNA-seq libraries were prepared using NEBNext RNA Library Prep Kit with Poly(A) Selection, selecting for 300bp fragments. See publication for more details.

value: premotor cortical area (PreM)

tag: celltype

value: bulk tissue

tag: Sex

value: M


title: Bat7_Putamen_rna

source_name: adult male Egyptian fruit bat putamen of the striatum

value: putamen of the striatum


title: Bat7_wM1_rna

source_name: adult male Egyptian fruit bat primary motor cortex, wing region (wM1)

value: primary motor cortex, wing region (wM1)


title: elf3_ZT6_SD_rep2

value: SD


title: Bat7_Caudate_rna

source_name: adult male Egyptian fruit bat caudate nucleus of the basal ganglia

value: caudate nucleus of the basal ganglia


title: Rice Control_F_R2

description:
Control_F_R2
FAIRE-seq on control sample, replicate 2

value: Japonica nipponbare

value: 14 day old


title: Rice Control_F_R1

description:
Control_F_R1
FAIRE-seq on control sample, replicate 1


title: Bat7_ofM1_rna

source_name: adult male Egyptian fruit bat primary motor cortex, orofacial region (ofM1)


title: WTCHG_834291_212_1

tag: cell type


title: WTCHG_834292_212_1


title: WTCHG_836235_212_1


title: WTCHG_836238_210_1


title: Bat6_wM1_rna

source_name: adult female Egyptian fruit bat primary motor cortex, wing region (wM1)

value: F


title: PF+3%PEGDA EPCaT, 5:1, Day 15

city: Auburn University

first: Elizabeth

middle: A

last: Lipke

state: AL

address: 212 Ross Hall

institute: Auburn University

description: PF+3%PEGDA EPCaT

data_processing:
Partek flow data analysis software was used to normalize RNAseq data.
The FastQC tool was employed in a quality control check on RNAseq raw reads.
RNAseq reads were mapped to the human genome using the STAR aligner tool.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing normalized gene counts.

source_name: 3D in vitro Engineered Prostate Cancer Tissue

growth_protocol:
3%PEGDA
PC-3 cells were cultured in F-12K culture media supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) Pen-Strep. BJ-5ta normal human fibroblasts were cultured in 4 parts of DMEM containing 4 mM L-glutamine, 4.5 g/L glucose and 1.5 g/L sodium bicarbonate, and 1 part of Medium 199, supplemented with 0.01 mg/mL hygromycin B, and 10% (v/v) FBS. All cells were maintained in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly. EPCaTs were formed by encapsulating PC-3 and BJ-5ta cells within a poly(ethylene glycol)-fibrinogen matrix at a concentration of 20 x 10^6 cells/mL and a cell ratio of 5:1 PC-3 cancer cells to BJ-5ta fibroblasts; the PF matrix was modulated with excess PEGDA at volumetric ratios of 96:4 (1% w/v), 92:8 (2% w/v), and 88:12 (3% w/v) to tune EPCaT mechanical properties to mimic prostate cancer xenograft tumors. EPCaTs were maintained in PC-3 culture media in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly.

extract_protocol:
Total RNA was extracted using QIAshredder and an Rneasy kit, according to manufacturer protocols.
Libraries were constructed using a TruSeq RNA Sample Preparation kit v2, according to manufacturer protocols.

value: PC-3 and BJ-5ta

value: Prostate cancer, fibroblast

tag: treatment


title: PC-3 and BJ-5ta 2D Coculture

description: PC-3 and BJ-5ta 2D coculture

source_name: 2D in vitro coculture

growth_protocol: PC-3 cells were cultured in F-12K culture media supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) Pen-Strep. BJ-5ta normal human fibroblasts were cultured in 4 parts of DMEM containing 4 mM L-glutamine, 4.5 g/L glucose and 1.5 g/L sodium bicarbonate, and 1 part of Medium 199, supplemented with 0.01 mg/mL hygromycin B, and 10% (v/v) FBS. All cells were maintained in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly. EPCaTs were formed by encapsulating PC-3 and BJ-5ta cells within a poly(ethylene glycol)-fibrinogen matrix at a concentration of 20 x 10^6 cells/mL and a cell ratio of 5:1 PC-3 cancer cells to BJ-5ta fibroblasts; the PF matrix was modulated with excess PEGDA at volumetric ratios of 96:4 (1% w/v), 92:8 (2% w/v), and 88:12 (3% w/v) to tune EPCaT mechanical properties to mimic prostate cancer xenograft tumors. EPCaTs were maintained in PC-3 culture media in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly.

value: 2D in vitro coculture


title: Bat7_2A_rna

source_name: adult male Egyptian fruit bat secondary auditory cortex (2A)

value: secondary auditory cortex (2A)


title: WTCHG_836237_210_1

value: PBMC

value: CD8 T cells


title: Bat6_Putamen_rna

source_name: adult female Egyptian fruit bat putamen of the striatum


title: PF+2%PEGDA EPCaT, 5:1, Day 15

description: PF+2%PEGDA EPCaT

growth_protocol:
2%PEGDA
PC-3 cells were cultured in F-12K culture media supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) Pen-Strep. BJ-5ta normal human fibroblasts were cultured in 4 parts of DMEM containing 4 mM L-glutamine, 4.5 g/L glucose and 1.5 g/L sodium bicarbonate, and 1 part of Medium 199, supplemented with 0.01 mg/mL hygromycin B, and 10% (v/v) FBS. All cells were maintained in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly. EPCaTs were formed by encapsulating PC-3 and BJ-5ta cells within a poly(ethylene glycol)-fibrinogen matrix at a concentration of 20 x 10^6 cells/mL and a cell ratio of 5:1 PC-3 cancer cells to BJ-5ta fibroblasts; the PF matrix was modulated with excess PEGDA at volumetric ratios of 96:4 (1% w/v), 92:8 (2% w/v), and 88:12 (3% w/v) to tune EPCaT mechanical properties to mimic prostate cancer xenograft tumors. EPCaTs were maintained in PC-3 culture media in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly.

value: 3D in vitro Engineered Prostate Cancer Tissue


title: PF EPCaT, 5:1, Day 15

description: PF EPCaT

growth_protocol:
control
PC-3 cells were cultured in F-12K culture media supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) Pen-Strep. BJ-5ta normal human fibroblasts were cultured in 4 parts of DMEM containing 4 mM L-glutamine, 4.5 g/L glucose and 1.5 g/L sodium bicarbonate, and 1 part of Medium 199, supplemented with 0.01 mg/mL hygromycin B, and 10% (v/v) FBS. All cells were maintained in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly. EPCaTs were formed by encapsulating PC-3 and BJ-5ta cells within a poly(ethylene glycol)-fibrinogen matrix at a concentration of 20 x 10^6 cells/mL and a cell ratio of 5:1 PC-3 cancer cells to BJ-5ta fibroblasts; the PF matrix was modulated with excess PEGDA at volumetric ratios of 96:4 (1% w/v), 92:8 (2% w/v), and 88:12 (3% w/v) to tune EPCaT mechanical properties to mimic prostate cancer xenograft tumors. EPCaTs were maintained in PC-3 culture media in a humidified atmosphere with 5% CO2 and a constant temperature of 37 C; culture media was renewed twice weekly.


title: WTCHG_834293_212_1


title: Bat6_PreM_rna

source_name: adult female Egyptian fruit bat premotor cortical area (PreM)

value: premotor cortical area (PreM)


title: Leaves, PepMV inoculated 10dpi

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
Raw reads were filtered into clean reads and aligned to the Tomato genome (GCF_000188115.3_SL2.50_ncbi_20180905)
RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters ‘‘-l 15 -q 0.4 -n 0.1’’ and the HISAT2 pipeline (version 2.0.4) with parameters ‘‘--phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000’’
Clean reads were mapped to reference with Bowtie2 (version v2.2.5).
Gene expression level was calculated with RSEM with default parameters.
Analysis of differential gene expression was performed with Poisson Distribution with parameters ‘‘Fold Change ≥ 2.00 and Adjusted Pvalue ≤ 0.001’’
Assembly: Tomato genome reference (GCF_000188115.3_SL2.50_ncbi_20180905)
Supplementary files format and content: Excel files with gene expression values and log2FoldChange between samples as generated by Poisson Distribution

organism: Solanum lycopersicum

source_name: Solanum lycopersicum leaves

growth_protocol: Tomato (Solanum lycopersicum) Belladonna F1 hybrid seeds (Nirit seeds Ltd., Moshav Hadar Am, Israel),  were planted in plastic pots containing a natural turf mixture (Potgrond P, Agrohoum SA, Greece), and grown at 22°C in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long day photoperiod with 16 h of light and 8 h of darkness per day and 100 μmol m-2 s-1 light intensity.

extract_protocol:
Exactly 10 days post inoculation (dpi), approximately 0.1 g of tissue was cut from the upper two or three leaves of each plant. The material was immediately frozen in liquid nitrogen and stored at -80°C until processing. Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).
Sequencing was performed on BGISEQ-500 platform instrument at BGI (Beijing Genomics Institute).

treatment_protocol: Mechanical inoculations of tomato plants were performed by applying a suspension culture of PepMV prepared by grinding 0.5g of TomCr3 infected leaves in 5mL of Infection Buffer (0.1M Na2HPO4, 0,2% w/v Na2SO3) onto young leaves at the fourth leaf stage. Mock infected tomato leaves were used as a control.

value: tomato leaf

tag: accession

value: Belladonna F1 hybrid

tag: infection

value: PepMV infected


title: Leaves, mock treated 10dpi

tag: tissue

value: mock treated


title: WTCHG_836236_210_1


title: WTCHG_836235_210_1


title: WTCHG_834292_210_1


title: WTCHG_834294_210_1


title: Bat6_2A_rna

source_name: adult female Egyptian fruit bat secondary auditory cortex (2A)

value: bulk tissue


title: WTCHG_834293_210_1


title: SUDHL1 HES1-depleted

city: Philadelphia

first: Wasik

last: Mariusz

address: 422 Curie Blvd

institute: University of Pennsylvania

description: RNA Highthrough sequence

data_processing:
Sequencing on a HiSeq 2500
Image analysis by HiSeq Control software (Illumina)
Base calling by Real Time Analysis software (Illumina)
Demultiplexing by bcl2fastq
Quality checks Sequencing Analysis Viewer FASTQC
Contaminant screening by FastQ screen using Bowtie2 v2.2.9
Counting HTSeq-count (version 0.9.0)
Normalization DESeq2 v1.14.1 and R version 3.4.0
Differential Analysis DESeq2
Genome_build: GRCh37

source_name: T-lyphocyte

growth_protocol: Cells were cultured at 37 °C and 5% CO2 in RPMI medium 1640, supplemented with 2-mM L-glutamine, 10% heat-inactivated FBS (FBS), 1% penicillin/streptomycin mixture and, where applicable, 200 units of IL-2 (Bender MedSystems)

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen (Germantown, MD) RNeasy mini kit and column DNase treatment.  RNAseq libraries were prepared using Illumina (San Diego, CA) TruSeq stranded mRNA sample preparation kit following manufacturer’s recommended procedure with minor modifications.
RNAseq libraries were prepared using Illumina (San Diego, CA) TruSeq stranded mRNA sample preparation kit following manufacturer’s recommended procedure with minor modifications.

treatment_protocol: Cells were treated by siHES1 RNA

value: ALK positive TCL cells

tag: genotype/variation


title: SUP-M2 control

description: RNA Highthrough sequence

value: control


title: Bat3_wM1_atac

value: primary motor cortex, wing region (wM1)

value: M


title: Thy_N_ScaI_P_3

description: Column V

source_name: primary epidermal cells

value: primary epidermal cells

value: primary Thy1-ScaI+ epidermal cells

value: no treatment

value: 26 weeks old


title: WTCHG_834291_210_1

value: PBMC


title: SUDHL1 control

description: RNA Highthrough sequence


title: WTCHG_836237_209_1

value: CD8 T cells


title: Bat3_Testis_atac

source_name: adult male Egyptian fruit bat testis

value: testis


title: Bat3_Putamen_atac

value: putamen of the striatum


title: SUP-M2 HES1-depleted

description: RNA Highthrough sequence


title: WTCHG_836238_209_1

source_name: CD8 EV


title: Thy_ScaI_P_3

description: Column R

value: primary Thy1+ScaI+ epidermal cells

value: 22 weeks old


title: Thy_N_ScaI_P_1

description: Column T

value: 24 weeks old


title: Bat3_PreM_atac

source_name: adult male Egyptian fruit bat premotor cortical area (PreM)

value: premotor cortical area (PreM)


title: Thy_ScaI_P_2

description: Column Q

value: 21 weeks old


title: WTCHG_836235_209_1


title: WTCHG_836236_209_1


title: Bat3_Caudate_atac

value: caudate nucleus of the basal ganglia

value: bulk tissue


title: WTCHG_834294_209_1


title: Bat3_ofM1_atac

value: primary motor cortex, orofacial region (ofM1)


title: Thy_N_ScaI_P_2

description: Column U

value: 25 weeks old


title: Thy_ScaI_P_1

description: Column P

value: primary epidermal cells

value: 20 weeks old


title: Bat3_Muscle_atac

source_name: adult male Egyptian fruit bat pectoralis muscle

value: pectoralis muscle

value: M


title: WTCHG_834293_209_1

value: PBMC


title: WT_ZT2_LD_rep3

source_name: 21-days whole plants

value: LD

value: WT (Rice Japonica cv. Nipponbare)


title: Bat3_Cerebellum_atac

source_name: adult male Egyptian fruit bat cerebellum

value: cerebellum


title: HT-29, rep1, PLE-extract

city: Madrid

first: Alberto

last: Valdés

state: Madrid

address: C\Nicolás Cabrera, 9

department: Bioactividad y Análisis de Alimentos

country: Spain

institute: Instituto de Investigación en Ciencias de la Alimentación

description: Biological replicate 1 of 3. Banana passion fruit seeds PLE-extract treated vs untreated control HT-29 cells

hyb_protocol: Cy3 and Cy5 samples were mixed, placed on ice, and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes. Slides were SurePrint G3 Human Gene Expression, 8x60K (G4858A-028004).

scan_protocol: Slides were scanned on an Agilent G2505C scanner, and images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Background signal correction using the normexp method with an offset of 50, within array normalization using the LOESS method, and between array scaling using the quantile method were applied using the BioConductor package LIMMA.

source_name: HT-29 (ATCC® HTB-38™), treated

label_protocol: 300 ng of total RNA were labeled. For each hybridization 600 ng of Cy3 or Cy5 probes were added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

growth_protocol: HT-29 colon cancer cells were cultured in a growth medium (RPMI 1640 medium supplemented with Hepes 25 mM, L-glutamine 2.05 mM, fetal bovine serum 10% and gentamicin 50 μg/mL) and were maintained in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions.

treatment_protocol: HT-29 cells were seeded at a density of 1.0 ×104 cells/cm2 in T25 cm2 culture flasks and incubated for 24 h at 37 °C with 5% CO2 for cell attachment. Thereafter, cell cultures were treated for 48 h with the seeds PLE-extract at IC50 concentration according to the results of the anti-proliferative activity assay (three replicates). In parallel, cell cultures were treated with extract vehicle (DMSO 0.1% in RPMI 1640) regarded as untreated controls (three replicates).

value: banana passion fruit seeds PLE-extract, 48h

source_name: HT-29 (ATCC® HTB-38™), untreated

value: vehicle, control, 48h


title: Thy_P_ScaI_N_5

description: Column L

value: primary Thy1+ScaI- epidermal cells

value: no treatment

value: 16 weeks old


title: Thy_ScaI_YFP_P_3

description: Column O

value: primary Thy1+YFP+ScaI- epidermal cells

value: 19 weeks old


title: Bat3_2A_atac

value: secondary auditory cortex (2A)

value: bulk tissue


title: Thy_P_ScaI_N_4

description: Column K

value: primary epidermal cells

value: 15 weeks old


title: WTCHG_834292_209_1

value: CD8 T cells


title: WTCHG_834291_209_1


title: HT-29, rep3, PLE-extract

description: Biological replicate 3 of 3. Banana passion fruit seeds PLE-extract treated vs untreated control HT-29 cells


title: HT-29, rep1

description: Biological replicate 1 of 3. Goldenberry calyx PLE-extract treated vs untreated control HT-29 cells

hyb_protocol: Cy3 and Cy5 samples were mixed, placed on ice, and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes. Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005).

source_name: HT-29 (ATCC® HTB-38™)

label_protocol: For each hybridization 600 ng of Cy3 or Cy5 probes were added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

treatment_protocol: HT-29 cells were seeded at a density of 1.0 ×104 cells/cm2 in T25 cm2 culture flasks and incubated for 24 h at 37 °C with 5% CO2 for cell attachment. Thereafter, cell cultures were treated for 48 h with the calyx PLE-extract at IC50 concentration according to the results of the anti-proliferative activity assay (three replicates). In parallel, cell cultures were treated with extract vehicle (DMSO 0.1% in RPMI 1640) regarded as untreated controls (three replicates).

value: treatment, goldenberry calyx PLE-extract

value: vehicle, control


title: CD34_P_ScaI_N_4

description: Column G

value: primary CD34+ScaI- epidermal cells

value: 11 weeks old


title: HT-29, rep2, PLE-extract

description: Biological replicate 2 of 3. Banana passion fruit seeds PLE-extract treated vs untreated control HT-29 cells


title: Bat6_Caudate_rna

source_name: adult female Egyptian fruit bat caudate nucleus of the basal ganglia

value: caudate nucleus of the basal ganglia

value: F


title: HT-29, rep2

description: Biological replicate 2 of 3. Goldenberry calyx PLE-extract treated vs untreated control HT-29 cells


title: WTCHG_836237_213_1

source_name: CD4 EV

value: PBMC

value: CD4 T cells


title: WTCHG_836238_213_1


title: Bat1_Testis_atac

value: testis

value: M


title: WTCHG_836236_213_1


title: Sorted CCK+ Cells rep3

first: Zachary

last: Knight

address: 1550 Fourth St

institute: UCSF

data_processing:
Illumina HiSeq 4000 was used for sequencing of sample 1; Illumina HiSeq 2500 was used for sequencing of sample 2.
For sample 1: De-multiplexing alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using Cell Ranger version 2.0.1, available from 10X Genomics with default parameters. A gene-barcode matrix was generated. 0.3 billion reads over 7701 cells were captured, with 39.5 thousand mean reads per cell and 1.8 thousand median genes per cell.
For samples 2-5: Raw fastq reads were trimmed by trim_galore (v0.6.7) to remove residual sequencing adapter sequences and low-quality reads. Next, reads were mapped to the Mus musculus reference transcriptome (GRCm39.cdna.all.release-105) and quantified by Salmon (v1.6.0). The Bioconductor package `tximeta`(1.12.4) was then used to convert transcript-level abundance to gene-level counts and package `DESeq2`(v1.34.0) was used to perform count normalization and differential expression analysis. Note that only the most minimal filtering rule was applied: genes that have no counts or only a single count across all samples were removed. before running `DESeq2`. Normalized counts for all genes were then combined with the metadata file to generate the csv file for GEO deposition.
Assembly: mm10
Supplementary files format and content: For sample 1: matrix.mtx file generated by Cell Ranger v2.0.1, including all cells in Sample 1
Supplementary files format and content: For samples 2-5:  CCK_normalized_counts_long_GEO . A csv file containing normalized counts for all genes identified in experiments in Samples 2-5

source_name: Intestinal epithelial cells

extract_protocol:
Sample 1 was extracted using the GemCode Single Cell Platform (10X Genomics, Pleasanton) ; Samples 2-5 were extracted using Ovation RNA-Seq System V2
Sample 1 was prepared using the GemCode Library Kits (10X Genomics, Pleasanton) ; Samples 2-5 were prepared using the Ovation Ultralow DR Multiplex system

tag: strain

value: Small intestine epithelium

value: CCK- intestinal epithelial cells

value: Fasted overnight

value: Cck-Cre; R26-LSL-tdTomato


title: Bat3_Liver_atac

source_name: adult male Egyptian fruit bat liver

value: liver

value: bulk tissue


title: Sorted CCK+ Cells rep4

value: Fasted then refed Ensure


title: Bat1_Putamen_atac

source_name: adult male Egyptian fruit bat putamen of the striatum

value: putamen of the striatum


title: WTCHG_834294_213_1


title: Sorted CCK+ Cells rep2

value: CCK+ intestinal epithelial cells


title: WTCHG_834293_213_1


title: WTCHG_836235_213_1


title: Sorted CCK+ Cells rep1


title: Bat1_ofM1_atac

source_name: adult male Egyptian fruit bat primary motor cortex, orofacial region (ofM1)


title: Bat1_PreM_atac

value: premotor cortical area (PreM)


title: HT-29, rep3

description: Biological replicate 3 of 3. Goldenberry calyx PLE-extract treated vs untreated control HT-29 cells

value: treatment, goldenberry calyx PLE-extract

value: vehicle, control


title: WTCHG_834291_213_1


title: Human ESC ZRSR2 CLIP-seq IgG control 2

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

description:
Sequences from indepentent ZRSR2 CLIP IgG control libraries were combined to obtain sequence coverage.
ZRSR2 IgG control 2

data_processing:
Reads were demuliplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie verions 1.12.7  with the following configurations -q –m 70 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 11 --sam --norc for noncoding RNAs. The remaining reads were aligned with the hg19 human genome  with the configuration -q –m 1 -n 0 -l 70 -5 1 -3 5 -a --best --strata -p 11 --sam  unique genomic sequences to generate bedGraph files.
Assembly: UCSC reference human genome hg19
Supplementary files format and content: bedGraph. Scores stand for CLIP-seq read coverage

source_name: Human embryonic stem cell H1

growth_protocol: The H1 hESC cells were maintained on a mitotically inactivated mouse feeder (MEF) layer as follows. As a culture medium, DMEM/F12 supplemented with 20% Knockout Serum Replacement, 1% MEM non-essential amino acids, 1mM L-glutamine, 0.1mM β-mercaptoethanol and 4ng/ml basic FGF (Invitrogen) was used. Before analyses, hESCs were passaged three times without the feeder cells. For feeder-free culture, hESCs were dissociated with collagenase IV and plated on a Geltrex-coated plate with MEF-conditioned media supplemented with 50ng/ml basic FGF.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 10 U/μl or 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with anti-U2AF1 (Bethyl), anit-HA or IgG antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C. Beads were washed twice with PNK buffer again and labeled with [γ- 32P] ATP for visualization. The labeled RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Protein-associated RNAs purified by IP or CLIP were ligated to a pre-adenylylated 3’ adaptor that contains a 2-nt adapter code for de-multiplexing and a 3-nt random sequence to minimize the loss of information after collapsing identical sequences. The RNA-adapter hybrids were converted into cDNAs with RT primer and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, in which one of them contained a 6-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.

treatment_protocol: For CLIP experiments H1 cells were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

tag: cell line

value: Human embryonic stem cell H1

value: Replace ZRSR2 with HA3-tagged ZRSR2 at its native locus


title: WTCHG_834292_213_1

value: PBMC

value: CD4 T cells


title: Bat1_wM1_atac

source_name: adult male Egyptian fruit bat primary motor cortex, wing region (wM1)

value: primary motor cortex, wing region (wM1)

value: M


title: Bat1_Cerebellum_atac

value: cerebellum


title: Human ESC ZRSR2 CLIP-seq IgG control 1

description:
Sequences from indepentent ZRSR2 CLIP IgG control libraries were combined to obtain sequence coverage.
ZRSR2 IgG control 1

tag: genotype


title: Human ESC ZRSR2 CLIP-seq replicate 4

description:
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.
ZRSR2 CLIP-seq replicate 4


title: Bat1_Muscle_atac

value: pectoralis muscle


title: Human ESC ZRSR2 CLIP-seq replicate 2

description:
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.
ZRSR2 CLIP-seq replicate 2


title: WTCHG_836238_211_1


title: WTCHG_836236_211_1


title: Bat1_Caudate_atac

source_name: adult male Egyptian fruit bat caudate nucleus of the basal ganglia

value: caudate nucleus of the basal ganglia


title: Bat1_2A_atac

source_name: adult male Egyptian fruit bat secondary auditory cortex (2A)

value: secondary auditory cortex (2A)


title: Human ESC U2AF1 CLIP-seq IgG control

description:
Sequences from a U2AF1 IgG control CLIP library were combined to obtain sequence coverage.
U2AF1 IgG control

value: Wild type


title: WTCHG_834294_211_1


title: Human ESC ZRSR2 CLIP-seq replicate 1

description:
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.
ZRSR2 CLIP-seq replicate 1


title: Bat1_Liver_atac

value: liver

value: bulk tissue


title: ZWCH34

city: Beijing

first: jiawen

last: wang

address: Beijing

country: China

institute: NIBS

description: Mouse tamoxifen-induced at 2 months of age

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned mm10 whole genome, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 5.0.1 (10XGenomics)
Assembly: mm10
Supplementary files format and content: The processed files are combined digital expression matrix divided in three files. The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and features.tsv contains the list of genes detected.

source_name: Myc

growth_protocol: C57BL/6 mice were used in this study. All mice were housed at the UCSC vivarium in a Specific Pathogen Free (SPF) facility within individually ventilated cages as well as the controlled temperature, humidity and light-dark cycle, and a regular rodent chow diet.

extract_protocol:
Prostate samples were dissected and minced to small clumps, followed by enzymatic dissociation with 0.2% Collagenase/Hyaluronidase in DMEM/F12 media with 5% FBS for 3 h at 37°C. Tissues were digested with 0.25% Trypsin-EDTA for 1 h at 4°C, and filtered through a 40-mm cell strainer to obtain single-cell suspensions.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice of 2 months of age were tamoxifen-induced by oral gavaging for 4 consecutive days.

value: prostate

value: Myh11-CreERT2; R26R-CAG-EYFP/+; Hi-Myc

tag: age

value: 14 months


title: 786-O cells, siZDHHC2, 3

city: Changsha

first: Jin

last: xin

state: Hunan

address: 139 Renmin Zhong Lu, Changsha, Hunan, China

department: Department of Urology

institute: The Second Xiangya Hospital, Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: 786-O cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: 786-O cells

value: renal cancer cells

value: ZDHHC2 knockdown


title: Human ESC ZRSR2 CLIP-seq replicate 3

description:
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.
ZRSR2 CLIP-seq replicate 3

value: Human embryonic stem cell H1

value: Replace ZRSR2 with HA3-tagged ZRSR2 at its native locus


title: WTCHG_836235_211_1

value: PBMC

value: CD4 T cells


title: Human ESC U2AF1 CLIP-seq replicate low RNase 2

description:
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.
U2AF1 CLIP-seq replicate 4


title: ZWCH35

source_name: strAR- Myc

value: Myh11-CreERT2; AR flox/Y;  R26R-CAG-EYFP/+; Hi-Myc


title: 786-O cells, siZDHHC2, 2


title: a1A-CD8-Runx3-No

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned tomm10 using bowtie2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. Bigwig peaks were computed using UCSC tools on the SPMR treated bdg files from MACS2
Downstream analyses of chromatin accessibility counts were performed with chromVAR, including motif accessibility deviations and footprinting analyses.
Consensus counts tables for a consensus bed file were computed using R / chromVAR
Assembly: mm10
Supplementary files format and content: bigiwig, bed, tsv

source_name: Hematopoietic cells

extract_protocol: OMNI-ATAC Lysis

treatment_protocol: CD4 or CD8 T cells were treated with TGFB or no stimulation as well as Runx3 or no overexpressed vector

value: CD8 T cell

value: Runx3 Overexpression

tag: stimulation


title: a1A-CD8-Empty-TG

value: Empty Vector

value: TGFB


title: a1A-CD8-Runx3-TG


title: 786-O cells, siZDHHC2, 1


title: WTCHG_834292_211_1


title: WTCHG_834293_211_1


title: WTCHG_836238_208_1


title: WTCHG_834291_211_1


title: 786-O cells, control, 2

value: WT


title: a1A-CD4-Runx3-TG

value: CD4 T cell


title: 786-O cells, control, 3


title: WTCHG_836237_211_1


title: WTCHG_836237_208_1


title: Human ESC U2AF1 CLIP-seq replicate high RNase 1

description:
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.
U2AF1 CLIP-seq replicate 1

value: Wild type


title: 786-O cells, control, 1


title: a1A-CD8-Empty-No


title: Human ESC U2AF1 CLIP-seq replicate high RNase 2

description:
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.
U2AF1 CLIP-seq replicate 3


title: WBC.Cluster1

city: Atlanta

first: A. Fatih

last: Sarioglu

state: GA

address: 315 Ferst Dr. NW

department: Electrical and Computer Engineering

institute: Georgia Institute of Technology

data_processing:
Raw fastq files were analyzed for quality using FASTQC and trimmed using TrimGalore (ref: https://github.com/FelixKrueger/TrimGalore) to remove adapter sequences and low quality reads (minimum Phred score >24).
Trimmed reads were mapped to the hg38 build of the human genome using STAR mapper (PMID: 23104886)
Transcripts were quantified by mapping to the GenCODE.v24 annotation version of the human transcriptome.
Assembly: hg38 build of the human genome
Supplementary files format and content: ".csv" and ".tab" files include raw counts
Supplementary files format and content: ".txt" files include FPKM values

extract_protocol:
The cells were lysed using RLT+BME buffer. RNA was extracted from the lysed samples using the Macherey-Nagel Nucleospin RNA XS kit. Double stranded cDNA was generated using the Takara Bio SMART-Seq v4 ultra low input RNA kit for sequencing.
Barcoded Illumina compatible sequencing libraries were generated using the Illumina Nextera XT DNA library preparation kit with a reduced tagmentation time of 3 minutes and the samples were cleaned using a 1:1 bead ratio to eliminate the presence of primer dimers.

value: white blood cell

value: male

tag: disease status


title: WBC.Cluster2


title: Patient.2.Cluster4

value: circulating tumor cell cluster

value: Castration-resistant

value: ADT, enzalutamide, taxotere


title: Human ESC U2AF1 CLIP-seq replicate low RNase 1

description:
Sequences from indepentent U2AF1 CLIP libraried were combines to obtain sequence coverage.
U2AF1 CLIP-seq replicate 2

value: Human embryonic stem cell H1


title: Patient.2.Cluster3


title: a1A-CD4-Runx3-No


title: WTCHG_836235_208_1


title: WTCHG_836236_208_1


title: a1A-CD4-Empty-TG


title: LNCaP.Cluster2

source_name: LNCaP

value: cell line

value: LNCaP


title: WTCHG_834294_208_1

value: PBMC

value: CD4 T cells


title: PC3.Cluster1


title: a1A-CD4-Empty-No


title: KO.36h.Rep4

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

data_processing:
The adapters and low quality bases were removed by using cutadapt (v3.2).
The Fastq files were aligned to the reference genome (mm10) using Hisat2 (v2.2.1).
Reads mapped to tRNA and rRNA are removed and each sample obtained ~ 30 million useful reads for the following analysis.
Stringtie (v2.1.4) was used to calculate the TPM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Peritoneal neutrophils

extract_protocol:
Total RNA was isolated from peritoneal neutrophils with TRIzol reagent (Invitrogen) and subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit ( Invitrogen) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal neutrophils

value: cecal ligation and puncture for 36h


title: Patient.2.Cluster2


title: Patient.2.Cluster1


title: WTCHG_834292_208_1


title: WTCHG_834293_208_1


title: KO.36h.Rep3


title: KO.36h.Rep2


title: LNCaP.Cluster1


title: Patient.1.Cluster1

value: ADT, taxotere, abiraterone, cabazitaxel


title: Patient.1.Cluster2


title: KO.36h.Rep1


title: PC3.Cluster2


title: HL60.m6A.Rep2.IP

data_processing:
The adapters and low quality bases were removed
The Fastq files were aligned to the reference genome (hg38) using Hisat2 (v2.1.0)
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Assembly: hg38
Supplementary files format and content: txt

source_name: human neutrophils

extract_protocol:
Total RNA was isolated from neutrophils with TRIzol reagent (Invitrogen) then subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit (61006, Invitrogen) following the manufacturer’s instructions. For m6A-immunoprecipitation (IP) samples, RNA fragmentation and immunoprecipitated of m6A-containing RNA fragments via anti-m6A antibody (202003, Synaptic System) were performed.
The input mRNA sample (Input) and purified mRNA sample (m6A-IP) were prepared for library construction and sequencing using standard Illumina protocols
m6A-seq

value: HL-60 neutrophil-like cells

value: Wild-type

value: Infection with Escherichia coli

tag: merip antibody


title: HL60.m6A.Rep1.IP

value: anti-m6A antibody (202003, Synaptic System)


title: WT.36h.Rep4


title: WTCHG_836238_237_1

source_name: CD8 S0

value: CD8 T cells


title: input

first: Jiwei

last: Ding

address: Nanwei Rd 2#

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Low quality bases were trimmed by using trim Galore(version: 0.5.0)
Clean reads were mapped to human reference genome (hg38) using Bowtie2  (version:2.3.4.3) with default parameters.
Peak calling representing enriched binding sites was performed using MACS2 (version: 2.1.2) software from filtered alignment file.
Genome_build: hg38

growth_protocol: SupT1 cells were cultured in RPMI1640 medium with 10% FBS.

extract_protocol:
RNA were isolated from SupT1 cells using Trizol reagents.
Libraries were prepared according to Illumina's instructions.

tag: antibody

value: input


title: SLFN5_IP


title: WT.36h.Rep3


title: Bat6_ofM1_rna

source_name: adult female Egyptian fruit bat primary motor cortex, orofacial region (ofM1)

value: bulk tissue

value: F


title: HKMe2_IP


title: X126_4_Day3

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Reads were converted from the native Illumina BCL format to fastq format, which were processed with a standard RNA-Seq pipeline, available through the open-source ‘bcbio-nextgen’ project (https://github.com/chapmanb/bcbio-nextgen).
The bcbio-nextgen pipeline runs qualimap, a computational tool that examines SAM/BAM alignment files and provides an overview of the data to detect common QC problems. Reads were aligned against the hg38 reference genomes using the ultra-rapid STAR aligner and concurrently pseudo-align reads to the transcriptome using the Salmon aligner.
Following alignment, expression values were summarized at the gene and transcript level. FeatureCounts was used for STAR-aligned data while Salmon performed its own internal quantitation, yielding estimated counts and values in length-normalized TPM (transcripts per million).
Raw counts at the gene and transcript level were used for differential gene expression (DEG) analysis using DESeq2. The sets of DEGs were imported into iPathwayGuide commercial software (https://advaitabio.com/ipathwayguide). The sets of differentially expressed genes (DEGs) between PCB126-treated and DMSO-treated cells were converted to Microsoft Excel format.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: raw count, DEG output

source_name: subcutateous adipose tissue

growth_protocol: Immortal human subcutaneous preadipocytes were cultured in PGM2 media

extract_protocol:
RNA was extracted using Trizol followed by DNase treatment and column purification using Qiagen RNeasy columns
500 ng of Dnase treated total RNA was used to enrich for polyA containing transcripts using beads coated with oligo(dT) primers. The enriched RNA pool was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample prep kit. The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into pools for sequencing.  The concentration of the pools were measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced on the Illumina HiSeq 6000 genome sequencer using 50 bp paired-end SBS chemistry with a minimum of 25 million reads per sample.

treatment_protocol: Cells were treated over a timecourse with 10 micromolar PCB126 or vehicle (DMSO)

value: preadipocytes

value: immortalized

value: NPAD

tag: time of treatment

value: 3 days


title: WTCHG_836236_237_1

city: Oxford

value: PBMC


title: WTCHG_836235_237_1


title: WT.36h.Rep2


title: X126_3_Day3


title: HKMe3_IP


title: WT.36h.Rep1


title: HL60.m6A.Rep1.Input


title: KO.12h.Rep4

value: cecal ligation and puncture for 12h


title: X126_2_Day3


title: HEK293T C9ORF72 reporter, negative for repeat expansion hrt

city: Worcester

first: Heleen

last: van 't Spijker

state: Massachusetts

address: 55 Lake Avenue North

institute: University of Massachusetts Medical School

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with hrt and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_neg_ltm

data_processing:
Library strategy: Ribo-Seq
Individual samples were first separated based on the 5nt barcode sequences and then adaptor sequences were removed using cutadapt.
Trimmed reads were quality filtered and mapped to human rRNA and tRNA references using Bowtie2.
Tophat2 was used to then map the remaining unmapped reads to a modified hg19 human genome containing the C9orf72 reporter sequence.
Due to our modified genome containing both endogenous C9orf72 and reporter C9orf72 reporter gene sequences, multimapped reads were included to retain reads mapping to sequences shared between these two genes (e.g., exon 1a, exon 2 and intronic sequences 5’ to the G4C2 repeat).
Genome_build: hg19 human transcriptome

growth_protocol: iPSC lines from three C9ORF72 carriers and three healthy individuals were cultured on Matrigel and mTeSR1. Cortical neuron differentiation was performed as described (Almeida et al. 2013). HEK293T cells cultured in DMEM with 20%FBS and antibiotic-antimyotic were transfected with reporter plasmids using lipofectamine 2000.

extract_protocol:
RNA was extracted using TRIZol LS following the manufacturer’s protocol
Ribosome profiling libraries were prepared following published protocols (Heyer et al. 2015; Liu et al. 2018, 2019).

treatment_protocol: For harringtonine treatment, harringtonine was added to the medium for a final concentration of 2ug/mL and incubated at 37˚ for 5min. Cycloheximide was subsequently added to the media (100ug/mL) and the cells were then washed twice with ice-cold PBS containing cycloheximide (100ug/mL).For cycloheximide treatment alone, cycloheximide was added to the medium for a final concentration of 100ug/mL for a 1min incubation.

value: hrt and RNAse1


title: HL60.m6A.Rep2.Input


title: WTCHG_836237_237_1

data_processing:
Batch corrections were performed using miRNAQC
Reads were aligned to the human genome reference (Human37) using sRNAtoolboxDB
Reads are mapped to microRNA reference libraries miRBase and MirGeneDB.
QC was done using miRNAQC
Expression matrix (Reads Per Millions) was also obtained using mirnaQC
Genome_build: Human37
Supplementary_files_format_and_content: Expression matrix (Reads Per Millions) of the identified miR per species, source file (raw) is listed on the heading row

extract_protocol:
FACS sorted BSLB were lysed and RNA was purified using miRNA advance kit
microRNA libraries were prepared following NEBNext Small RNA kit (NEB) and the low yield protocol
Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers and size selection was performed using Pippin Prep instrument (Sage Science) using the 3% Agarose, dye free gel with internal standards (size selection: 120 to 230bp).


title: KO.12h.Rep3

value: peritoneal neutrophils


title: Veh_4_Day3

value: Vehicle


title: X126_1_Day3


title: WTCHG_834293_237_1


title: HEK293T C9ORF72 reporter, negative for repeat expansion chx

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with chx and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_neg_chx

value: chx and RNAse1


title: WTCHG_834294_237_1


title: HEK293T C9ORF72 reporter hrt

description:
HEK293T cells expressing the C9ORF72 reporter were treated with hrt and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_c9_ltm


title: HEK293T C9ORF72 reporter, negative for repeat expansion 4egi

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with 4egi and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_neg_ltm

value: 4egi and RNAse1


title: Veh_3_Day3


title: WTCHG_834291_237_1


title: KO.12h.Rep1


title: Veh_2_Day3


title: HEK293T C9ORF72 reporter chx

description:
HEK293T cells expressing the C9ORF72 reporter were treated with chx and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_c9_chx


title: HEK293T C9ORF72 reporter 4egi

description:
HEK293T cells expressing the C9ORF72 reporter were treated with 4egi and RNAse1
Processed data files:
c9.rnase.rsem.gene.summary.counts.txt
c9.rnase.rsem.gene.summary.tpm.txt
Name of column in processed data file: rnase1_c9_ltm


title: WTCHG_836238_238_1

source_name: CD8 S1


title: WTCHG_836237_238_1


title: WT.12h.Rep4

value: Wild-type


title: WT.12h.Rep3


title: Veh_1_Day3


title: X126_4_Day1

value: 1 day


title: WTCHG_834292_237_1

value: CD8 T cells


title: WT.12h.Rep2


title: WTCHG_836236_238_1


title: X126_3_Day1


title: WTCHG_836235_238_1


title: HEK293T C9ORF72 reporter, negative for repeat expansion hrt, RNASe 1

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with hrt and RNAse1
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: ctrl_ltm


title: WT.12h.Rep1


title: KO.12h.Rep2


title: WTCHG_834294_238_1


title: WTCHG_834293_238_1


title: X126_2_Day1


title: HEK293T C9ORF72 reporter, negative for repeat expansion chx, RNASe AT

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with chx and RNAse2
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: ctrl_chx

value: chx and RNAse2


title: BMDMs, DC Apo rep3

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

data_processing:
Illumina software used for base calling
Samples were aligned to mouse mm10 genome using STAR alignment in Partek flow software
Reads were quantified to mm10 annotation model using Partek E/M tool
Differentially expressed features were determined by running normalized reads through the Partek GSA tool
The read counts for each sample were used for differential expression analysis with the DESeq2 (version 3.13) package
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample with annotation intergrated by Partek flow

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow cells were collected from femur and tibia of mice from 7-12 weeks of age. Cells were grown in petri dishes in complete RPMI with 20% L929 cell supernatant containing M-CSF. Media changes were performed every 2 days until cells were differentiated into macrophages by day 7. Differentiated macorphages were removed from petri dishes and plated 300,000 cells per well in 24 well plates.

extract_protocol:
RNA was collected using a Qiagen Rneasy kit. Contaminating DNA was removed. RNA concentration and quality was verified and samples were frozen at -80C until use
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were untreated, or treated with 1uM CpG for 6 hours, or treated with1:5 apoptotic cells for 2 hours followed by 3 hour incubation after removal of apoptotic cells by washing. Treatments were perfomed in complete RPMI with heat inactivated FBS and 5% L929 cell supernatant

value: Bone marrow derived macrophage

tag: disease state

value: Sjögren's syndrome model

value: Apoptotic cells 2 hours


title: HEK293T C9ORF72 reporter, negative for repeat expansion chx, RNASe 1

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with chx and RNAse A+T
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: ctrl_chx

value: chx and RNAse A+T


title: Mixed_multiplexed [Mouse Tamoxifen and control]

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

data_processing:
Raw sequencing reads were mapped to the GRCm38, assembly version 93 (version STAR-2.7.1a).
Demultiplexing of hashtag-oligos was performed to assign individual cells to respective hashtag barcodes by implementing HTODemux function of Seurat 3.0 (Satija Lab).
Quality control was applied by imposing a threshold of <10% reads mapped to mitochondrial genes and removing non-T-cell clusters (mainly hepatocytes expressing Alb, Apoe and Ttr).
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix.mtx.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: barcodes.tsv.gz

source_name: murine hepatic CD4+ T-cells

growth_protocol: Eight Cdh5:Cre-ERT2;Rela fl / fl mice were used.

extract_protocol:
Livers were harvested and digested using the Miltenyi Biotec Mouse Liver Dissociation kit; 1 million purified CD4+ T-cells from each liver were flow-sorted and individually-labelled with hashtag-oligos according to manufacturer’s protocol (Biolegend, TotalSeqTM-B, v3.1 single index).
A total of 50k cells were loaded per lane on a 10x Chromium Genomics platform, with the expectancy rate of capture at 60%. Standard 10x Genomics parameters were used; read1: 28bp, index1: 8bp, index2: 0bp, read2: 91bp. Downstream single-cell sequencing library preparation followed the manufacturer’s instructions (10x Genomics Chromium Single Cell 3’ GEM v3 workflow).
The library was then sequenced on 2 lanes of an SP flowcell on an Illumina NovaSeq6000, providing 979 million reads in total.

treatment_protocol: On day 0, all mice were subjected to HDTV injection of NRAS^G12V-containing transposons, as previously described. The mice received 100ul tamoxifen (20mg/ml) or corn oil solution via intraperitoneal injection once every 24 h for a total of 5 consecutive days (day 0-4). On day 9 post-HDTV, all mice were sacrificed and livers were harvested.

value: Liver

value: CDH5+ Rela fl/fl

tag: hashtag

tag: hashtag sequence

value: vehicle or tamoxifen


title: HEK293T C9ORF72 reporter hrt, RNAse AT

description:
HEK293T cells expressing the C9ORF72 reporter were treated with hrt and RNAseA+T
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_ltm

tag: treatment

value: hrt and RNAseA+T


title: Veh_4_Day1

tag: cell type

value: preadipocytes

value: immortalized

value: NPAD


title: HEK293T C9ORF72 reporter, negative for repeat expansion hrt, RNASe AT

description:
HEK293T cells expressing the C9ORF72 reporter without repeat expansion were treated with hrt and RNAseA+T
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: ctrl_ltm


title: BMDMs, DC Apo rep2


title: HEK293T C9ORF72 reporter hrt, RNAse 1

description:
HEK293T cells expressing the C9ORF72 reporter were treated with hrt and RNAse1
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_ltm

value: hrt and RNAse1


title: BMDMs, DC Apo rep1


title: Veh_3_Day1

value: Vehicle


title: BMDMs, B6 Apo rep3

value: control


title: WTCHG_836238_228_1

first: Ashwin

last: Jainarayanan

address: Roosevelt Dr, Headington, Oxford OX3 7FY

institute: University of Oxford

value: PBMC


title: HEK293T C9ORF72 reporter chx, RNAseAT

description:
HEK293T cells expressing the C9ORF72 reporter were treated with chx and RNAseA+T
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_chx

value: chx and RNAseA+T


title: WTCHG_836237_228_1

value: CD8 T cells


title: WTCHG_834291_238_1


title: Veh_1_Day1

value: 1 day


title: X126_1_Day1


title: Veh_2_Day1


title: HEK293T C9ORF72 reporter chx, RNAse1

description:
HEK293T cells expressing the C9ORF72 reporter were treated with chx and RNAse1
Processed data files:
c9.all.rsem.gene.summary.counts.txt
c9.all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_chx

value: chx and RNAse1


title: BMDMs, B6 Apo rep2

value: Bone marrow derived macrophage

value: Apoptotic cells 2 hours


title: WTCHG_834292_238_1


title: BMDMs, B6 Apo rep1


title: X126_4_9h

value: 9 hours


title: WTCHG_836236_228_1


title: WTCHG_836235_228_1


title: control female 37#20, hht combined

description:
iPSCs induced neurons were treated with harr, samples were merged to increase read count
Processed data files:
c9.ipsc.neurons.combined.gene.summary.counts.txt
c9.ipsc.neurons.combined.gene.summary.tpm.txt
Name of column in processed data file: ctrl_ipsc_neuron_harr_merged.sorted.wodup.uniq.fq

source_name: iPSCs

tag: individual

value: control female 37#20

value: iPSCs, induced neurons

value: harr


title: WTCHG_834294_228_1

tag: tissue


title: X126_3_9h

value: preadipocytes


title: control male 35#11, hht combined

value: control male 35#11


title: BMDMs, DC CpG rep3

value: Sjögren's syndrome model

value: 1uM CpG 6 hours


title: X126_2_9h

value: immortalized

value: NPAD


title: WTCHG_834293_228_1

value: PBMC


title: BMDMs, DC CpG rep2


title: BMDMs, DC CpG rep1


title: X126_1_9h


title: C9ORF72 mutation carrier male 28ALS, hht combined

description:
iPSCs induced neurons were treated with harr, samples were merged to increase read count
Processed data files:
c9.ipsc.neurons.combined.gene.summary.counts.txt
c9.ipsc.neurons.combined.gene.summary.tpm.txt
Name of column in processed data file: c9_ipsc_neuron_harr_merged.sorted.2.wodup.uniq.fq

value: C9ORF72 mutation carrier male 28ALS


title: control male 2#20, hht combined

value: control male 2#20


title: BMDMs, B6 CpG rep3

value: control


title: C9ORF72 mutation carrier male 27#11, hht combined

value: C9ORF72 mutation carrier male 27#11


title: WTCHG_834292_228_1

value: CD8 T cells


title: WTCHG_834291_228_1


title: Veh_3_9h

value: Vehicle


title: C9ORF72 mutation carrier female 26#6, hht combined

value: C9ORF72 mutation carrier female 26#6


title: WTCHG_836238_225_1


title: control female 37#20, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (control line #37)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_37_chx

value: control female 37#20

value: iPSCs

value: hht and RNAse A+T


title: control female 37#20, chx treated

description:
iPSCs were treated with chx and with RNAse A+T (control line #37)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_37_chx

value: chx and RNAse A+T


title: Veh_1_9h

value: preadipocytes

value: 9 hours


title: WTCHG_836237_225_1


title: control male 35#11, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (control line #35)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_35_chx

value: control male 35#11


title: WTCHG_834294_225_1


title: WTCHG_836236_225_1


title: BMDMs, DC Con rep2

value: Bone marrow derived macrophage

value: Sjögren's syndrome model

value: Untreated


title: BMDMs, DC Con rep1


title: BMDMs, B6 Con rep3


title: Veh_4_9h

value: immortalized

value: NPAD


title: BMDMs, B6 CpG rep2

value: control

value: 1uM CpG 6 hours


title: Veh_2_9h


title: WTCHG_834292_225_1

value: PBMC

value: CD8 T cells


title: WTCHG_834293_225_1


title: BMDMs, B6 CpG rep1


title: control male 2#20, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (control line #2)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_2_chx

value: control male 2#20


title: control male 35#11, chx treated

description:
iPSCs were treated with chx and with RNAse A+T (control line #35)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_35_chx


title: C9ORF72 mutation carrier male 28ALS, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (C9 line #28)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_29_chx

value: C9ORF72 mutation carrier male 28ALS


title: WTCHG_834291_225_1


title: WTCHG_834291_208_1

source_name: CD4 EV

value: CD4 T cells


title: BMDMs, B6 Con rep1


title: control male 2#20, chx treated

description:
iPSCs were treated with chx and with RNAse A+T (control line #2)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_2_chx

value: iPSCs


title: 3_WTA

city: Guangzhou

first: li

middle: hao

last: yuan

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

description: one sample from  TG tissue of male Mus musculus

data_processing:
use single-cell RNA sequencing ; trim_data use fastp
The cwlref-runner software pipeline provided by BD
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: tirgeminal ganglion

extract_protocol:
TG tissue was extracted and placed in the pre-cooling papain solution. Then, slightly minced or cut into small pieces, tissue was incubated in the solution at 37 ℃ with constant agitation for 30 to 90 min. The digestive system was centrifuged at 300 g for 5 min at room temperature and the cell pellet was resuspended in DNase dilute albumin-inhibitor solution. Then, the cells isolated by density gradient centrifugation were resuspended in complete medium to obtain single-cell suspensions.
Libraries were sequenced utilizing the Illumina NovaSeq platform

treatment_protocol: Orofacial inflammation in mice was induced by injections of 20 μL CFA (Sigma-Aldrich, Saint Louis, MI, USA; 1:1 in 0.9% sterile saline) into the right vibrissal pad

tag: Sex

value: male

value: treated with CFA injection


title: WTCHG_836235_225_1


title: C9ORF72 mutation carrier male 27#11, chx treated

description:
iPSCs were treated with chx and with RNAse A+T (C9 line #27)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_27_chx

value: C9ORF72 mutation carrier male 27#11

value: chx and RNAse A+T


title: 1_WTA

value: untreated


title: ZWA5423

description: Mouse inplanted with T+E2 tubes at 2-months of age and then tamoxifen-induced

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned mm10 whole genome, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 5.0.1 (10XGenomics)
Genome_build: mm10
Supplementary_files_format_and_content: The processed files are combined digital expression matrix divided in three files. The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and features.tsv contains the list of genes detected.

source_name: strAR- T+E

treatment_protocol: Mice of 2-months of age were subcutaneously implanted with silastic tubes filled with testosterone and 17beta-estradiol and treated for 8 months. Mice were tamoxifen-induced for 4 consecutive days after tube implantation.

tag: strain

value: prostate

value: Myh11-CreERT2; AR flox/Y;  R26R-CAG-EYFP

value: 10 months


title: WTCHG_836237_233_1

source_name: CD4 S1


title: WTCHG_836238_233_1


title: BMDMs, DC Con rep3

value: Bone marrow derived macrophage

value: Sjögren's syndrome model

value: Untreated


title: C9ORF72 mutation carrier male 27#11, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (C9 line #27)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_27_chx

value: hht and RNAse A+T


title: BMDMs, B6 Con rep2

value: control


title: C9ORF72 mutation carrier female 26#6, hht treated

description:
iPSCs were treated with hht and with RNAse A+T (C9 line #26)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_26_chx

value: C9ORF72 mutation carrier female 26#6


title: ZWA5436

source_name: T+E

value: Myh11-CreERT2; R26R-CAG-EYFP


title: C9ORF72 mutation carrier male 28ALS, chx treated

description:
iPSCs were treated with chx and with RNAse A+T (C9 line #28)
Processed data files:
all.rsem.gene.summary.counts.txt
all.rsem.gene.summary.tpm.txt
Name of column in processed data file: c9_29_chx

value: C9ORF72 mutation carrier male 28ALS