title: Cynomolgus_Macaque_SampleP2_PCR_GFP

description:
PCR_GFP_Sample_P2_S20_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

data_processing:
Sequencing data was demultiplexed into sample-level fastq files using Cell Ranger mkfastq (v3 10X Genomics).
Alignment and cell demultiplexing were run using STARsolo(14) (v2.7) with default parameters, creating raw count matrices.
GFP-barcodes were analyzed from the original scRNA-seq samples and PCR amplification of GFP from the 10x single cell prepped sample libraries. In both cases, the GFP-barcodes were identified using Salmon (Patro et al., 2017) (v0.9.1) transcript quantification. Only reads with 1 hit to a GFP barcode were kept. Using these reads, AAV variants were identified based on the GFP barcode (aav_barcode_key.txt). 10x barcodes in the reads from the PCR amplification analysis were corrected according to the 10x Cell Ranger count algorithm to mitigate any errors that may have been introduced by multiple rounds of PCR. Rarely, multiple AAV variants were found per UMI (unique molecular identifier), and in this case the AAV variant with the highest number of counts for that UMI was kept.
Genome_build: Cynomolgus macaque samples were aligned to the Macaca_fascicularis_5.0/macFas5 reference obtained from UCSC and marmoset samples were aligned to ASM275486v1 obtained from Ensembl.
Supplementary_files_format_and_content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts

organism: Macaca fascicularis

value: Retina

tag: region

value: Retina periphery region

tag: sorting strategy

value: FACS-sorted


title: MG_UKJ_9_324_brain_RNAseq

status: Public on Oct 19 2021

type: SRA

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description:
sample_counts.txt
sample_rpkms.txt

library_source: transcriptomic

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.7 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit following the manufacturer's instruction.

tag: strain

tag: tissue

value: brain, hemisphere

tag: age

value: 9 months

tag: Sex

value: male


title: MG_UKJ_9_323_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_15_234_skin_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (M. musculus sequences only)
Supplementary_files_format_and_content: The txt file includes raw counts (sample_counts.txt) of all mirBase M. musculus sequences for each sample.

source_name: skin

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.

value: skin

value: 15 months


title: MG_UKJ_2_1152_skin_smallRNAseq

value: 2 months


title: MB_FLI_MC22.1_brain_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Nothobranchius furzeri

source_name: MZM-04/10p_27 weeks_DMSO

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.

value: 27 weeks

tag: perturbation

value: DMSO

value: brain


title: Cynomolgus_Macaque_SampleP1_PCR_GFP

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

country: USA

institute: University of Pittsburgh

description:
PCR_GFP_Sample_P1_S19_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

molecule: polyA RNA

extract_protocol:
The NHP retinas were dissected and regions of interest were isolated (macula, superior and inferior periphery). For cynomolgus macaque, superior and inferior periphery were pooled. Retinal tissue was placed in Hibernate solution (Hibernate A -Ca Solution, BrainBits LLC), and cells were then dissociated using Macs Miltenyi Biotec Neural Tissue Dissociation Kit for postnatal neurons (130-094-802) according to manufacturer’s recommendations. Dissected retina pieces were incubated with agitation at 37 °C and further mechanically dissociated. The dissociated neural retina was filtered using a 70 µm MACS Smart Strainer (Miltenyi Biotec) to ensure single-cell suspension. Cells were resuspended in 0.1% BSA in D-PBS and processed immediately for scRNA-seq.
Marmoset and cynomolgus macaque samples were prepared for single cell analysis using a 10x Chromium Single Cell 3’ v3 kit. Briefly, single cells from retina samples were captured using 10X Chromium system (10X Genomics), the cells were partitioned into Gel beads-in-emulsion (GEMS), mRNAs were reverse transcribed and cDNAs with 10X Genomics Barcodes were created with unique molecular identifiers (UMIs) for different transcripts. Purified cDNA was PCR amplified and further purified with SPRIselect reagent (Beckman Coulter, B23318). Final libraries were generated after fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps according to 10x Single Cell 3’ workflow. An additional targeted sequencing analysis was run on these 10x-prepped cDNA samples, using PCR amplification with Q5 High Fidelity DNA Polymerase to target the GFP sequence and its associated AAV barcode.

treatment_protocol: Marmosets, cynomolgus macaques and rhesus macaques between 3-10 years and retinas were injected intravitreally with AAV libraries. Monkeys used for K912-scCAG-GFP fluorophore expression received daily oral doses of cyclosporine at a dose of 6 mg/kg for the duration of the study. Marmosets received oral daily doses of meloxicam (0.2 mg/kg) for one week after injection.


title: MG_UKJ_9_322_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MC21.1_brain_RNAseq


title: MG_UKJ_15_218_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JG83.1_brain_RNAseq

source_name: brain w/ physical exercise

value: GRZ

value: 10 weeks

value: swim-tunnel


title: JM_FSU_RNA1404-1_all_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: WBcel235, and respective gene annotation (WBcel235.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Caenorhabditis elegans

value: 1 day

value: hermaphrodite

value: whole worm


title: MG_UKJ_9_320_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_15_232_skin_smallRNAseq


title: MB_FLI_JG84.1_brain_RNAseq


title: Cynomolgus_Macaque_SampleC2_PCR_GFP

description:
PCR_GFP_Sample_C2_S18_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina

value: Retina center/fovea region


title: MG_UKJ_15_233_skin_smallRNAseq


title: MB_FLI_JG82.1_brain_RNAseq


title: Cynomolgus_Macaque_Sample8_PCR_GFP

description:
PCR_GFP_Sample_8_S12_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina periphery region

value: unsorted


title: Cynomolgus_Macaque_SampleC1_PCR_GFP

description:
PCR_GFP_Sample_C1_S17_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: FACS-sorted


title: Cynomolgus_Macaque_Sample12_PCR_GFP

description:
PCR_GFP_Sample_12_S14_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MB_FLI_JG78.1_brain_RNAseq

value: male


title: MB_FLI_JG80.1_brain_RNAseq


title: MG_UKJ_ 30_11_brain_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (M. musculus sequences only)
Supplementary_files_format_and_content: The text file includes raw counts (sample_counts.txt) of all mirBase M. musculus sequences for each sample.

value: brain, hemisphere

value: 30 months


title: MG_UKJ_2_984_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 2 months


title: Cynomolgus_Macaque_Sample12R_PCR_GFP

description:
PCR_GFP_Sample_12R_S16_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MB_FLI_JG81.1_brain_RNAseq


title: MG_UKJ_15_231_skin_smallRNAseq

value: skin

value: 15 months


title: MG_UKJ_ 30_9_brain_smallRNAseq


title: Cynomolgus_Macaque_Sample9_PCR_GFP

description:
PCR_GFP_Sample_9_S13_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MB_FLI_JG76.1_brain_RNAseq

value: GRZ

value: brain


title: MG_UKJ_2_983_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_2_982_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_15_230_skin_smallRNAseq


title: MG_UKJ_ 30_10_brain_smallRNAseq


title: MG_UKJ_ 30_7_brain_smallRNAseq


title: MG_UKJ_2_802_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_2_801_brain_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_30_67_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

data_processing:
Sequence information was extracted in FastQ format using CASAVA software 1.8.2 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

source_name: blood

value: blood


title: MB_FLI_JG77.1_brain_RNAseq

value: 10 weeks

value: swim-tunnel


title: Cynomolgus_Macaque_Sample7_PCR_GFP

description:
PCR_GFP_Sample_7_S11_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt


title: MG_UKJ_24_256_brain_smallRNAseq

value: 24 months


title: MG_UKJ_30_68_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_JG74.1_brain_RNAseq


title: NH_FLI_nf_12_brain_RNAseq

source_name: brain_w/o physical exercise

value: line 4010; Tg(mylz2:egfp,tfam)


title: NH_FLI_nf_11_brain_RNAseq


title: MG_UKJ_ 30_8_brain_smallRNAseq


title: MG_UKJ_30_64_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Cynomolgus_Macaque_Sample6R_PCR_GFP

description:
PCR_GFP_Sample_6R_S15_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: Retina

value: Retina center/fovea region


title: MG_UKJ_24_1054_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Cynomolgus_Macaque_Sample6_PCR_GFP

description:
PCR_GFP_Sample_6_S10_L001
PCR-amplified 10X-processed reads, targeting GFP
supplementary or processed data file:
aav_barcode_key.txt

value: unsorted


title: MG_UKJ_30_66_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_24_1053_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_JG75.1_brain_RNAseq


title: MG_UKJ_30_65_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_24_254_brain_smallRNAseq


title: MG_UKJ_24_255_brain_smallRNAseq


title: MG_UKJ_24_1051_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_15_222_brain_smallRNAseq


title: Untreated REP 2

city: Charlestown

first: Christopher

middle: J

last: Ott

state: MA

address: 149 13th Street, Rm 6614

institute: Mass Gen Hospital/Harvard Medical School

description:
Untreated REP 2
Zero-2_S12

data_processing:
Image analysis and base calling performed by HiSeq Control Software
Raw sequence files (.bcl) converted to fastq files using Illumina bcl2fastq 2.17
Transcript alignment and quantification was performed using Salmon 0.8.2 with automatic library type detection and default parameters using RefMrna sequences from hg19 as an index
Genome_build: hg19
Supplementary_files_format_and_content: Read counts .csv file derived from read alignments to the human genome

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were harvested with trypsinization, and RNA was purified using QIAGEN RNeasy Mini Kit.
RNA-seq library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina.
mRNA was enriched using Oligod(T) beads, followed by first and second strand cDNA synthesis. Libraries were multiplexed on two lanes of a Illumina HiSeq flowcell, 2x150 bp PE configuration.

treatment_protocol: HeLa cells were treated for 4h or 18h with vehicle or NTASO or MYCASO-3.

tag: cell line

value: HeLa

tag: cell type

value: Cervical carcinoma

tag: treatment

value: Untreated

tag: treatment duration

value: 0 hours treatment


title: Untreated REP 1

description:
Untreated REP 1
Zero-1_S1


title: Untreated REP 3

description:
Untreated REP 3
Zero-3_S2


title: NH_FLI_nf_8_brain_RNAseq

value: male


title: MYCASO3 18h REP 2

description:
MYCASO3 18h REP 2
MYCASO3-18h-2_S21

value: 18 hours treatment


title: MYCASO3 18h REP 1

description:
MYCASO3 18h REP 1
MYCASO3-18h-1_S10


title: MG_UKJ_24_253_brain_smallRNAseq

value: brain, hemisphere


title: NH_FLI_nf_6_brain_RNAseq

source_name: brain_w/ physical exercise


title: MG_UKJ_24_1050_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MYCASO3 4h REP 3

description:
MYCASO3 4h REP 3
MYCASO3-4h-3_S20

value: 4 hours treatment


title: MYCASO3 18h REP 3

description:
MYCASO3 18h REP 3
MYCASO3-18h-3_S11


title: MG_UKJ_15_220_brain_smallRNAseq

value: 15 months


title: NH_FLI_nf_5_brain_RNAseq

value: brain


title: MG_UKJ_24_1046_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: blood


title: MG_UKJ_24_252_brain_smallRNAseq


title: MG_UKJ_15_219_brain_smallRNAseq


title: NH_FLI_nf_10_brain_RNAseq

value: 10 weeks


title: MG_UKJ_15_228_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_nf_9_brain_RNAseq


title: MG_UKJ_15_221_brain_smallRNAseq


title: MG_UKJ_15_218_brain_smallRNAseq


title: MYCASO3 4h REP 2

description:
MYCASO3 4h REP 2
MYCASO3-4h-2_S9


title: MG_UKJ_15_227_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NH_FLI_nf_2_brain_RNAseq

value: swim-tunnel


title: MYCASO3 4h REP 1

description:
MYCASO3 4h REP 1
MYCASO3-4h-1_S19


title: MG_UKJ_15_229_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: NTASO 18h REP 3

description:
NTASO 18h REP 3
NT-18h-3_S8

value: NT-ASO (scrambled ASO control)


title: MG_UKJ_9_323_brain_smallRNAseq

value: 9 months


title: MB_FLI_MR34.5_skin_RNAseq

value: skin

value: 27 weeks

value: Rotenone 15 pM


title: NH_FLI_nf_3_brain_RNAseq

value: line 4010; Tg(mylz2:egfp,tfam)


title: MB_FLI_MR35.5_skin_RNAseq


title: NTASO 18h REP 2

description:
NTASO 18h REP 2
NT-18h-2_S18

value: HeLa

value: Cervical carcinoma


title: MG_UKJ_9_325_brain_smallRNAseq

value: male


title: MG_UKJ_15_223_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_MR32.5_skin_RNAseq


title: MB_FLI_MR33.5_skin_RNAseq


title: MG_UKJ_9_324_brain_smallRNAseq


title: MG_UKJ_15_226_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_15_225_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_MR31.5_skin_RNAseq


title: MG_UKJ_09_332_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: Vehicle 18h REP 3

description:
Vehicle 18h REP 3
Veh-18h-3_S5

value: Lipofectamine (vehicle control)

value: 18 hours treatment


title: MB_FLI_MC15.5_skin_RNAseq

value: DMSO


title: MG_UKJ_15_224_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: 15 months


title: NH_FLI_nf_4_brain_RNAseq

value: brain


title: MG_UKJ_9_322_brain_smallRNAseq

value: brain, hemisphere


title: MG_UKJ_09_327_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: blood


title: MB_FLI_MC13.5_skin_RNAseq


title: NTASO 18h REP 1

description:
NTASO 18h REP 1
NT-18h-1_S7


title: NTASO 4h REP 2

description:
NTASO 4h REP 2
NT-4h-2_S6

value: 4 hours treatment


title: Vehicle 4h REP 3

description:
Vehicle 4h REP 3
Veh-4h-3_S14


title: MG_UKJ_09_333_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_9_320_brain_smallRNAseq


title: Vehicle 4h REP 2

description:
Vehicle 4h REP 2
Veh-4h-2_S3


title: MG_UKJ_2_984_brain_smallRNAseq

value: 2 months


title: Vehicle 18h REP 2

description:
Vehicle 18h REP 2
Veh-18h-2_S15


title: MG_UKJ_02_1150_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_09_331_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: 9 months


title: MG_UKJ_2_982_brain_smallRNAseq


title: NTASO 4h REP 1

description:
NTASO 4h REP 1
NT-4h-1_S16

value: NT-ASO (scrambled ASO control)


title: Vehicle 4h REP 1

description:
Vehicle 4h REP 1
Veh-4h-1_S13


title: NTASO 4h REP 3

description:
NTASO 4h REP 3
NT-4h-3_S17


title: MG_UKJ_2_983_brain_smallRNAseq


title: MB_FLI_MC11.5_skin_RNAseq

value: skin

value: 27 weeks


title: MG_UKJ_OE3274_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.3 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The text files include raw counts (sample_counts.txt) and RPKM values (sample_rpkms.txt) of all genes for each sample.

value: brain, hippocampus

value: 24 months


title: MG_UKJ_2_801_brain_smallRNAseq


title: MG_UKJ_2_802_brain_smallRNAseq


title: MG_UKJ_09_326_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MG_UKJ_OE3275_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MC12.5_skin_RNAseq


title: MB_FLI_MC14.5_skin_RNAseq


title: MB_FLI_MR34.3_liver_RNAseq

source_name: liver

value: liver

value: Rotenone 15 pM


title: MG_UKJ_OE3272_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: Vehicle 18h REP 1

description:
Vehicle 18h REP 1
Veh-18h-1_S4

value: HeLa

value: Cervical carcinoma

value: Lipofectamine (vehicle control)

value: 18 hours treatment


title: MG_UKJ_02_1151_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MCF7-tet-on-shCTR9: +Dox 7D'-MTF2-Rep2

city: Madison

first: NGAI TING

last: CHAN

state: WI

address: 4849 Sheboygan Ave

department: Oncology

institute: University of Wisconsin -- Madison

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP sequencing reads that passed quality score were aligned to the human reference genome (hg38) using Bowtie2 (v2.4.1)
Only unique alignments that passed high mapping quality (MAPQ>30) were retained for downstream analysis. Duplicated reads and reads resides in hg38 blacklist regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) were eliminated by sambamba tools (v0.7.1). Sequencing reads were also aligned to the Drosophila genome (dm6) and normalization factors (Rx factor) were calculated after removing multi-mapping and duplicated reads.
Bigwig files were generated at a resolution of 20bp using the bamCoverage utility from the deepTools (v3.4.3) suits and data were subsequently visualized as ChIP-Rx normalized tracks using IGV genome browser (v2.8.9).
Peaks were called using MACS2 (v2.1.4) with FDR<0.01 for narrow beaks and FDR<0.05 for broad peaks. Peaks intersection was performed by bedtools (v2.29.2). Overlapped peaks that shorter than sequencing tag (100bp) will be discarded.
Genome_build: hg38
Supplementary_files_format_and_content: format: bigwig  content: a continous track representing the normalized ChIP-seq signal

molecule: genomic DNA

growth_protocol: Cells are maintained in Dulbecco’s modified medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (VWR) and 1% Penicillin-Streptomycin (P/S) (Gibco) and cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with corresponding antibodies.
Libraries were prepared according to manufacturer’s protocol of  the Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies).  Briefly, the DNA was end-repaired and ligated to Illumina sequencing adaptors. The ligated DNA was purified using Agencourt RNAClean XP beads (Beckman Coulter). A subsequent PCR amplification step (8-15 cycles) was performed to add linker sequence to the purified fragments for annealing to the Genome Analyzer flow-cell. Following PCR amplification, the library was separated on a 2% agarose gel (120 V, 1.5 hours) to select a narrow range of fragment sizes, and bands between 200-500 bp were excised. The library was purified from the excised agarose gel using the Qiagen MiniElute PCR Purification Kit following the manufacturer’s protocol.

treatment_protocol: Doxcycline (Clonetech,Cat# NC0424034) were directly added to cell culture medium to a final concentration of 500ng/ml. Cells were treated up to 7 days.

value: human luminal breast cancer

tag: genotype/variation

value: Dox inducible CTR9 KD

tag: chip antibody

value: MTF2 (Thermo Fisher Scientific, Cat# PA5-77124, RRID:AB_2720851)

value: +Dox 7D (sufficient CTR9 KD)


title: MG_UKJ_OE3273_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MR35.3_liver_RNAseq


title: MB_FLI_MR32.3_liver_RNAseq


title: MG_UKJ_02_1147_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: blood

value: 2 months


title: MG_UKJ_02_1148_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_MC15.3_liver_RNAseq

value: DMSO


title: MCF7-tet-on-shCTR9: +Dox 7D'-JARID2-Rep2

value: JARID2 (Cell signaling technology, Cat# 13594, RRID:AB_2798269)


title: MG_UKJ_OE3271_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MCF7-tet-on-shCTR9: +Dox 7D'-JARID2-Rep1


title: MG_UKJ_OE3270_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months


title: Sample_46: SCO21

type: genomic

city: Berlin

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was done using the minfi package running on R version 3.6.1 (2019-07-05) -- "Action of the Toes".
Processed data: Average beta-Values after normalization using the Funnorm method and detection p values

label: Cy3, Cy5

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: histology

value: spindle cell oncocytoma (SCO)

tag: gender

value: m

tag: mutation


title: MG_UKJ_02_1146_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls

value: male


title: MCF7-tet-on-shCTR9: +Dox 7D'-MTF2-Rep1


title: MCF7-tet-on-shCTR9: +Dox 0D'-MTF2-Rep1

value: +Dox 0D (normal CTR9 expression)


title: MB_FLI_MR31.3_liver_RNAseq

value: liver

value: 27 weeks

value: Rotenone 15 pM


title: Sample_47: SCO20

value: f


title: MB_FLI_MC14.3_liver_RNAseq


title: MCF7-tet-on-shCTR9: +Dox 0D'-MTF2-Rep2

value: human luminal breast cancer

value: Dox inducible CTR9 KD


title: MG_UKJ_02_1149_blood_RNAseq

description:
sample_counts.xls
sample_rpkms.xls


title: MB_FLI_MC13.3_liver_RNAseq


title: MB_FLI_MR33.3_liver_RNAseq


title: MG_UKJ_5_84_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months

value: enriched environment


title: MG_UKJ_5_85_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_87_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: Sample_45: SCO19

value: EpiReg


title: MG_UKJ_5_86_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: IgG VitD CUT&Tag 96hr

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

data_processing: Resulting reads were processed and mapped to Hg19 (CutRunTools), with peaks called (SEACR/v1.2, stringent, all mapped fragments) and hypersequencable-regions subtracted. Known motif enrichment was determined +/−200bp from peak summits and data visualized as in CUT&RUN.

source_name: Isolated and Treated Memory CD4+ Cells (Negative Magnetic Selection)

extract_protocol: VDR, STAT3, and BACH2 CUT&Tag: VDR, STAT3, and BACH2 genome-wide binding in memory CD4+ T cells activated in the presence of 10nM VitD or carrier for 96h was detected by CUT&Tag as per the published protocol (CUT&Tag V.3, dx.doi.org/10.17504/protocols.io.bcuhiwt6) using fixed nuclei (2min fixation of isolated nuclei, RT) with 75,000 nuclei/target and antibodies targeting either VDR (D2K6W, Cell Signaling Technologies), STAT3 (D3Z2G, Cell Signaling Technologies), BACH2 (D3T3G, Cell Signaling Technologies), or non-specific IgG (31235, Thermo Fisher Scientific) diluted 1:50 accordingly and incubated with fixed-nuclei for 1h, RT. Secondary antibody (1:100) (ABIN101961, antibodies-online) was bound for 0.5h, RT. Preloaded pA-Tn5 (C01070001, Diagenode) was tethered to antibodies for 1h, RT. Libraries were sequenced paired-end by Novaseq.

treatment_protocol: Memory CD4 T Cell Isolation, Culture, and Treatment: Human PBMCs were purified from either anonymized leukodepletion cones (Blood Transfusion Service, NHS Blood and Transplantation) or healthy volunteer whole blood packs/buffy coats from the NIH Blood Bank and from fresh blood of patients. Leukodepletion cones were diluted 1 in 4 with sterile PBS and layered onto 15mL of lymphoprep (Axis-Shield). Whole blood packs/buffy coats were diluted 1 in 2 with sterile PBS onto 15mL Lymphocyte Separation Medium (25-072-CV LSM, Corning). Cells were separated by centrifugation at 20C for 20 min, with slow acceleration and no brakes and PBMC collected by harvesting interface cells. Human memory CD4+ T cells were used for RNA-seq, CUT&RUN, and CUT&Tag experiments as these cells express the VDR, while naïve T cells require pre-activation first. Human memory CD4+ T cells were isolated either from PBMCs using Miltenyi Memory CD4+ T cell Isolation Kit Human (130091893) or StemCell EasySep Human Memory CD4+ T Cell Enrichment Kit (19157) according to the manufacturer. Cells were cultured in Lonza X-VIVO-15 Serum-free Hematopoietic Cell Medium (04-418Q) supplemented with 50 IU/mL penicillin, 50µg/mL streptomycin (Invitrogen), 2mM L-glutamine (PAA Labarotories) at 37C 5% CO2. CD4+ memory T cells were cultured in a 96 well U bottom plate (Greiner) at a cell density of one million cells/mL in a total volume of 200µL. CD4+ cells were activated using Gibco Dynabeads Human T-Activator CD3/CD28 for T Cell Expansion and Activation (11131D) at a cell to bead ratio of 4:1. Cells were additionally cultured in the presence or absence of 1α,25-Dihydroxyvitamin D3 (Enzo Life Sciences), reconstituted in 99.8% ethanol (Sigma-Aldrich), used at 10nM unless indicated. 99.8% ethanol was used as a carrier control at the same concentration.

tag: sequencing method

value: PE 50bp CUT&Tag, Novaseq

value: anti-CD3 and anti-CD28 Dynabeads, Vitamin D (10nM)


title: IgG Carrier CUT&Tag 96hr

value: anti-CD3 and anti-CD28 Dynabeads, Carrier (Ethanol)


title: MB_FLI_MC12.3_liver_RNAseq

value: DMSO


title: MG_UKJ_5_82_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MCF7-tet-on-shCTR9: -Dox 0D'-SUZ12-Rep2

value: SUZ12 (Cell signaling technology, Cat# 3737, RRID:AB_2196850)

value: -Dox 0D (continous CTR9 KD)


title: MCF7-tet-on-shCTR9: +Dox 0D'-JARID2-Rep2

value: JARID2 (Cell signaling technology, Cat# 13594, RRID:AB_2798269)

value: +Dox 0D (normal CTR9 expression)


title: MG_UKJ_5_83_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: male


title: MG_UKJ_5_81_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: BACH2 VitD CUT&Tag 96hr


title: MB_FLI_MR34.1_brain_RNAseq

value: brain

value: 27 weeks

value: Rotenone 15 pM


title: MCF7-tet-on-shCTR9: +Dox 0D'-JARID2-Rep1

value: human luminal breast cancer

value: Dox inducible CTR9 KD


title: MB_FLI_MR33.1_brain_RNAseq


title: MB_FLI_MC11.3_liver_RNAseq

value: liver


title: MCF7-tet-on-shCTR9: -Dox 0D'-SUZ12-Rep1

value: -Dox 0D (continuous CTR9 KD)


title: BACH2 Carrier CUT&Tag 96hr

value: PE 50bp CUT&Tag, Novaseq


title: STAT3 VitD CUT&Tag 96hr

value: anti-CD3 and anti-CD28 Dynabeads, Vitamin D (10nM)


title: MCF7-tet-on-shCTR9: -Dox 7D'-SUZ12-Rep1

value: -Dox 7D (CTR9 restoration)


title: MB_FLI_MR32.1_brain_RNAseq


title: MB_FLI_MR35.1_brain_RNAseq


title: MG_UKJ_5_115_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months


title: STAT3 Carrier CUT&Tag 96hr

value: anti-CD3 and anti-CD28 Dynabeads, Carrier (Ethanol)


title: MCF7-tet-on-shCTR9: +Dox 7D'-SUZ12-Rep2

value: SUZ12 (Cell signaling technology, Cat# 3737, RRID:AB_2196850)

value: +Dox 7D (sufficient CTR9 KD)


title: MCF7-tet-on-shCTR9: -Dox 7D'-SUZ12-Rep2


title: VDR VitD CUT&Tag 96hr


title: MG_UKJ_5_114_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: Jurkat_shPPM1A-AS_2

city: Tianjin

first: Guoli

last: Li

address: 22 Qixiangtai Road, Heping District

country: China

institute: Tianjin Medical University

description: Jurkat_shPPM1A-AS rep 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Jurkat with knockdown of shPPM1A-AS

growth_protocol: Jurkat_control and Jurkat_shPPM1A-AS  cell line were cultred in RPMI1640 medium containg 10%FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

treatment_protocol: untreatment

value: T-ALL

tag: shRNA


title: MB_FLI_MC14.1_brain_RNAseq

value: male

value: DMSO


title: MG_UKJ_5_113_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_112_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_5_79_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: enriched environment


title: MG_UKJ_5_111_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: Jurkat_shPPM1A-AS_1

description: Jurkat_shPPM1A-AS rep 1


title: MCF7-tet-on-shCTR9: -Dox 7D'-H3K27me3-Rep2

value: H3K27me3 (Cell signaling technology, Cat# 9733, RRID:AB_916252)


title: MCF7-tet-on-shCTR9: +Dox 7D'-SUZ12-Rep1

value: human luminal breast cancer


title: Jurkat_control_1

description: Jurkat_control rep 1

source_name: Jurkat

value: control


title: MG_UKJ_5_110_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_MR31.1_brain_RNAseq

value: brain

value: 27 weeks

value: Rotenone 15 pM


title: VDR Carrier CUT&Tag 96hr

value: PE 50bp CUT&Tag, Novaseq


title: MB_FLI_MC13.1_brain_RNAseq


title: MCF7-tet-on-shCTR9: +Dox 0D'-SUZ12-Rep1

value: Dox inducible CTR9 KD

value: +Dox 0D (normal CTR9 expression)


title: FK_LGMDR9_CDI73_3

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
150 bp FastQ paired-end reads (n = 20 Million per sample) were trimmed using Trimmomatic (v 0.33). Quality control on raw sequence data was performed with FastQC. Reads were mapped using Hisat2 (v2.1.0). Raw counts were imported into iDEP9.1 (Ge et al., 2018) and raw reads were normalized using edgeR using default program values.
Genome_build: hg38
Supplementary_files_format_and_content: processed files contain tab-delimited raw expression values and normalized counts following analysis using EdgeR

source_name: differentiating hiPS cells

growth_protocol: iPAX7 myogenic progenitors were generated as previously described (Selvaraj et al., 2019). Myogenic progenitors were terminally differentiated in media containing low glucose Dulbecco’s Modified Eagle Medium (Gibco), 2% horse serum, 1% insulin-transferrin-selenium and 1% penicillin-streptomycin, supplemented with 5 µM SB-431542 and 5 µM LY-374973. After 4 days, cells were switched to terminal differentiation medium only.

extract_protocol:
Day 5 myotubes were collected with TRIzol™ Reagent (Invitrogen), and RNA was purified using PureLinkTM RNA mini kit (Thermo Fisher Scientific) with on-column DNAse treatment as per manufacturer’s protocol.
500 ng of total RNA was used for generating pair-ended libraries using the TruSeq stranded mRNA libraries

value: skeletal muscle

tag: Stage

value: myotubes

tag: disease

tag: genotype


title: MB_FLI_MC15.1_brain_RNAseq

tag: strain

tag: tissue

tag: age


title: MG_UKJ_5_80_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 5 months

tag: Sex

tag: perturbation


title: MCF7-tet-on-shCTR9: -Dox 0D'-H3K27me3-Rep2

tag: cell line

tag: cell type

tag: treatment

value: -Dox 0D (continous CTR9 KD)


title: MG_UKJ_5_107_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: MB_JIM18_brain_RNAseq

value: 22 weeks

value: male

value: antagomiR-29a 100 pmol


title: MB_JIM16_brain_RNAseq


title: MCF7-tet-on-shCTR9: -Dox 7D'-H3K27me3-Rep1

tag: genotype/variation

tag: chip antibody

value: H3K27me3 (Cell signaling technology, Cat# 9733, RRID:AB_916252)

value: -Dox 7D (CTR9 restoration)


title: MB_FLI_MC12.1_brain_RNAseq

value: DMSO


title: Jurkat_control_2

description: Jurkat_control rep 2

value: T-ALL

value: control


title: MG_UKJ_5_106_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: FK_LGMDR9_D01_2


title: MCF7-tet-on-shCTR9: -Dox 0D'-H3K27me3-Rep1

value: human luminal breast cancer

value: -Dox 0D (continuous CTR9 KD)


title: MG_UKJ_24_1077_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months


title: FK_LGMDR9_D01_3


title: MB_JIM14_brain_RNAseq

value: brain


title: FK_LGMDR9_CDI73_1

value: skeletal muscle


title: MB_FLI_MC11.1_brain_RNAseq

value: 27 weeks


title: MCF7-tet-on-shCTR9: +Dox 0D'-SUZ12-Rep2

value: Dox inducible CTR9 KD

value: SUZ12 (Cell signaling technology, Cat# 3737, RRID:AB_2196850)

value: +Dox 0D (normal CTR9 expression)


title: FK_LGMDR9_CDI73_2

value: myotubes


title: FK_LGMDR9_D01_1


title: MG_UKJ_5_108_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 5 months

value: male


title: MCF7-tet-on-shCTR9: +Dox 7D'-H3K27me3-Rep2

value: H3K27me3 (Cell signaling technology, Cat# 9733, RRID:AB_916252)

value: +Dox 7D (sufficient CTR9 KD)


title: MG_UKJ_5_109_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_JIM15_brain_RNAseq

value: 22 weeks

value: antagomiR-29a 100 pmol


title: MCF7-tet-on-shCTR9: +Dox 7D'-H3K27me3-Rep1

value: human luminal breast cancer


title: MG_UKJ_24_1075_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_1074_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: enriched environment


title: MCF7-tet-on-shCTR9: +Dox 0D'-H3K27me3-Rep1


title: FASTKD4 sample 2

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
quality and adapter trimming performed using Trim_Galore! keeping reads longer than 20nt
alignment was performed using Bowtie2
The alignment was split by template strand (Samtools) and converted to BED files (Bedtools), before peak calling was performed with Piranha
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts for each position in the mitochondrial genome.

source_name: HeLa

growth_protocol: cells were grown in DMEM + FCS

extract_protocol:
RNA extraction after UV cross linking and enrichment of mitochondria by differential centrifugation, followed by IP with magnetic beads with antibodies against FASTKD4 or HA (control)
libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA library prep kit

value: HeLa

tag: rip antibody

value: anti-FASTKD4 (Proteintech, 16245-1-AP)

tag: rna population

value: mitochondrial enriched


title: HA control sample 3


title: MG_UKJ_24_1073_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months


title: FASTKD4 sample 1


title: MB_JIM19_brain_RNAseq

value: brain


title: FKRP_KO_1

source_name: differentiating hES cells

value: skeletal muscle

value: not applicable

value: FKRP -/-


title: MB_JIC14_brain_RNAseq

value: scrambled control


title: FK_HDR_WWS_2

description:
HDR WWS corrected
WWS_HDR_Cl40_2

value: myotubes

value: wild type


title: MB_JIC18_brain_RNAseq

value: male


title: MB_JIC16_brain_RNAseq


title: MB_FLI_JIC23_brain_RNAseq


title: FK_HDR_WWS_1

description:
HDR WWS corrected
WWS_HDR_Cl40_1


title: FK_HDR_WWS_3

description:
HDR WWS corrected
WWS_HDR_Cl40_3


title: MG_UKJ_24_1076_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus


title: Cynomolgus_Macaque_SampleP2-3

description:
Sample_P2_S12_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP2_results.csv
aav_barcode_key.txt

value: Retina

tag: region

value: Retina periphery region

tag: sorting strategy

value: FACS-sorted


title: MG_UKJ_24_1072_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: enriched environment


title: FASTKD4 sample 3

value: HeLa


title: MB_JIC15_brain_RNAseq

value: 22 weeks


title: MG_UKJ_24_1065_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MG_UKJ_24_1064_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JIC20_brain_RNAseq


title: Cynomolgus_Macaque_SampleP2-1

description:
Sample_P2_S12_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP2_results.csv
aav_barcode_key.txt


title: MG_UKJ_24_1063_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: HA control sample 2

value: mitochondrial enriched


title: FK_WWS_3

tag: Stage

value: WWS


title: MB_JIC13_brain_RNAseq

value: brain


title: MG_UKJ_24_1062_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: 24 months


title: MG_UKJ_24_1071_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt


title: MB_FLI_JIC22_brain_RNAseq


title: MB_FLI_JIM24_brain_RNAseq

value: Synthetic miR-101a  100 pmol


title: FKRP_KO_3

value: skeletal muscle

tag: disease

value: not applicable

value: FKRP -/-


title: Cynomolgus_Macaque_SampleP1-2

description:
Sample_P1_S11_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP1_results.csv
aav_barcode_key.txt


title: MCF7-tet-on-shCTR9: +Dox 0D'-H3K27me3-Rep2

value: human luminal breast cancer

value: Dox inducible CTR9 KD

value: H3K27me3 (Cell signaling technology, Cat# 9733, RRID:AB_916252)

value: +Dox 0D (normal CTR9 expression)


title: HA control sample 1


title: MB_FLI_JIC21_brain_RNAseq

value: male

value: scrambled control


title: MB_FLI_JIM23_brain_RNAseq


title: MB_FLI_JIC19_brain_RNAseq


title: Cynomolgus_Macaque_SampleP1-4

description:
Sample_P1_S11_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP1_results.csv
aav_barcode_key.txt

value: Retina

value: Retina periphery region

value: FACS-sorted


title: Cynomolgus_Macaque_SampleP2-4

description:
Sample_P2_S12_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP2_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_SampleP2-2

description:
Sample_P2_S12_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP2_results.csv
aav_barcode_key.txt


title: MG_UKJ_9_338_blood_smallRNAseq

value: blood

value: 9 months


title: Cynomolgus_Macaque_SampleP1-3

description:
Sample_P1_S11_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP1_results.csv
aav_barcode_key.txt


title: MB_FLI_JIM25_brain_RNAseq

value: brain

value: 22 weeks


title: Cynomolgus_Macaque_SampleC2-4

description:
Sample_C2_S10_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC2_results.csv
aav_barcode_key.txt

value: Retina center/fovea region


title: MG_UKJ_24_1070_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

value: brain, hippocampus

value: 24 months

value: enriched environment


title: MG_UKJ_9_337_blood_smallRNAseq


title: FKRP_KO_2

value: skeletal muscle

value: myotubes

value: not applicable

tag: genotype

value: FKRP -/-


title: FK_WWS_2

value: WWS


title: CTR_WT_2

description:
FKRP KO parental WT
H9_2

value: wild type


title: MG_UKJ_24_1056_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

tag: strain

value: male


title: Cynomolgus_Macaque_SampleC2-2

description:
Sample_C2_S10_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC2_results.csv
aav_barcode_key.txt

tag: tissue

value: Retina


title: MG_UKJ_24_1055_brain_hippocampus_RNAseq

description:
sample_counts.txt
sample_rpkms.txt

tag: age


title: CTR_WT_1

description:
FKRP KO parental WT
H9_1


title: MG_UKJ_9_335_blood_smallRNAseq

tag: Sex


title: CTR_WT3_3


title: Cynomolgus_Macaque_SampleC2-3

description:
Sample_C2_S10_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC2_results.csv
aav_barcode_key.txt

value: FACS-sorted


title: CTR_HWT_3

description:
FKRP KO parental WT
H9_3


title: Cynomolgus_Macaque_SampleP1-1

description:
Sample_P1_S11_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleP1_results.csv
aav_barcode_key.txt

value: Retina periphery region


title: FK_WWS_1


title: CTR_WT3_1


title: LoVo_fuso_2

city: Zhejiang

first: chaochao

last: xu

state: State...

address: Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, China

institute: zhejiang University

description: Gene expression after treated with Fusobacterium nucleatum

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: LoVo cells treated with Fusobacterium nucleatum

growth_protocol: LoVo colorectal cancer cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in F-12K (Genom, China) with 10 % fetal bovine serum.

extract_protocol:
Total RNAs were extracted from each cell samples using the TRIZOL reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LoVo cells were treated with or without Fusobacterium nucleatum.

value: LoVo

value: colorectal cancer cell line

value: Fusobacterium nucleatum


title: MB_FLI_JIM21_brain_RNAseq

source_name: brain

value: brain

value: 22 weeks

tag: perturbation

value: Synthetic miR-101a  100 pmol


title: CTR_WT3_2


title: MG_UKJ_9_334_blood_smallRNAseq

value: blood

value: 9 months


title: LoVo_fuso_3

tag: cell line


title: LoVo_fuso_1

tag: cell type


title: MB_FLI_JIM22_brain_RNAseq


title: Cynomolgus_Macaque_SampleC2-1

description:
Sample_C2_S10_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC2_results.csv
aav_barcode_key.txt

value: Retina center/fovea region


title: 190856B_C17

type: RNA

city: Quanzhou

first: Guorong

last: Lyu

state: Fujian

address: No.950, Donghai street

department: Department of Ultrasound

institute: The Second Affiliated Hospital of Fujian Medical University

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Fluid-Derived Exosomal

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: disease state

value: TOF

tag: tissue preparation

value: frozen tissue

value: Amniotic Fluid-Derived Exosomes


title: Cynomolgus_Macaque_SampleC1-3

description:
Sample_C1_S9_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC1_results.csv
aav_barcode_key.txt

data_processing:
Sequencing data was demultiplexed into sample-level fastq files using Cell Ranger mkfastq (v3 10X Genomics).
Alignment and cell demultiplexing were run using STARsolo(14) (v2.7) with default parameters, creating raw count matrices.
GFP-barcodes were analyzed from the original scRNA-seq samples and PCR amplification of GFP from the 10x single cell prepped sample libraries. In both cases, the GFP-barcodes were identified using Salmon (Patro et al., 2017) (v0.9.1) transcript quantification. Only reads with 1 hit to a GFP barcode were kept. Using these reads, AAV variants were identified based on the GFP barcode (aav_barcode_key.txt). 10x barcodes in the reads from the PCR amplification analysis were corrected according to the 10x Cell Ranger count algorithm to mitigate any errors that may have been introduced by multiple rounds of PCR. Rarely, multiple AAV variants were found per UMI (unique molecular identifier), and in this case the AAV variant with the highest number of counts for that UMI was kept.
Genome_build: Cynomolgus macaque samples were aligned to the Macaca_fascicularis_5.0/macFas5 reference obtained from UCSC and marmoset samples were aligned to ASM275486v1 obtained from Ensembl.
Supplementary_files_format_and_content: Matrix tables with raw gene expression counts for every cell; Cell-by-GFP tables with raw GFP-barcode expression counts


title: MG_UKJ_9_336_blood_smallRNAseq


title: LoVo_control_3

description: Gene expression after treated with PBS control

source_name: LoVo cells treated with PBS control

tag: treatment

value: PBS control


title: 190856B_C22


title: Cynomolgus_Macaque_SampleC1-4

description:
Sample_C1_S9_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC1_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_SampleC1-2

description:
Sample_C1_S9_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC1_results.csv
aav_barcode_key.txt


title: 190856B_C23


title: MG_UKJ_30_71_blood_smallRNAseq

value: 30 months

value: male


title: LoVo_control_2


title: 190856B_C12


title: 190856B_C18


title: MG_UKJ_30_73_blood_smallRNAseq


title: MCF-7mammo _ OGP_treated_rep3

city: Guangzhou

first: shubin

last: Yu

address: YANJIANG XILU

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM. estimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKMs and counts for each Sample

source_name: breast cancer cells

growth_protocol: MCF-7 cells were grown in low-attachment and serum-free condition, and prolonged culture for 5 weeks

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The prolonged mammosphere culture of MCF-7 cells were treated without or with 5 nM OGP for 10 days

value: MCF-7 cells

value: MCF-7 cells after prolonged mammosphere culture for 5 weeks

value: treated with OGP for 10 days


title: MG_UKJ_30_70_blood_smallRNAseq

source_name: blood


title: LoVo_control_1

value: LoVo

value: colorectal cancer cell line


title: MCF-7mammo _ OGP_treated_rep2


title: Cynomolgus_Macaque_SampleC1-1

description:
Sample_C1_S9_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sampleC1_results.csv
aav_barcode_key.txt

value: Retina

value: FACS-sorted


title: 190856B_N19

value: healthy


title: Cynomolgus_Macaque_Sample12R-3

description:
Sample_12R_S8_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12R_results.csv
aav_barcode_key.txt

value: Retina periphery region

value: unsorted


title: 190856B_N18


title: MCF-7mammo _ OGP_treated_rep1


title: Cynomolgus_Macaque_Sample12R-2

description:
Sample_12R_S8_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12R_results.csv
aav_barcode_key.txt


title: MG_UKJ_30_72_blood_smallRNAseq

value: blood


title: MG_UKJ_24_1059_blood_smallRNAseq

value: 24 months


title: 190856B_N13

value: frozen tissue


title: 190856B_N20

value: Amniotic Fluid-Derived Exosomes


title: Cynomolgus_Macaque_Sample12R-4

description:
Sample_12R_S8_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12R_results.csv
aav_barcode_key.txt


title: 190856B_N12


title: Purified cilia_Fmr-i1-Exp.2

city: Boston

first: Jiehui

last: Chen

address: 320 Longwood Ave

institute: Boston Children’s Hospital

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS)+OLB+GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Reference genome sequences and gene annotation files were downloaded from Ensemble (GRCm38/mm10). Hisat2 (v2.1.0)  was used to index reference genome sequence. Raw data were pre-processed by Fastp (v0.12.1) with default parameters. Cleaned data were then aligned to the reference genome via software Hisat2 (v2.1.0). FeatureCounts (v1.5.3) was used to count the reads numbers mapped to each gene.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: xlsx file include FPKM values for each Sample.

source_name: Purified cilia

growth_protocol: Dissociated telencephalon from postnatal day 0 to 1 mouse pups of either sex were digested with freshly prepared 10 U/ml Papain for 30 min at 37°C, and plated at a density of 25 × 105 cells/cm2 on 10μg/ml laminin-coated 75-cm2 flask. After inoculation for one day, oligodendrocytes and neurons were shaken off and removed (weakly attached cells). The ependymal progenitors proliferated until confluence before established the serum-starvation (culture medium without serum) to trigger differentiation until 10 days to harvest cilia.

extract_protocol:
Total RNA was isolated from purified multicilia using TRIzol Reagent (ThermoFisher Scientific, 15596-018). 10 mg linear acrylamide (Yeasen, 10408ES03) and 15 mg GlycoBlue (ThermoFisher Scientific, AM9515) were added to facilitate RNA precipitation and recovery.
Total mRNAs were captured by Poly(A) Magnetic Isolation Module (NEB, E7490) for generation of cDNA libraries using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760)

treatment_protocol: mEPCs attached on 75-cm2 flask were transfected with 40pmol siRNA every three days from the day before serum-starvation to the day cilia harvested.

value: Motile cilia from cultured ependymal cell


title: MCF-7mammo _ Ctrl_rep2

value: untreated


title: Cynomolgus_Macaque_Sample12-4

description:
Sample_12_S6_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12_results.csv
aav_barcode_key.txt


title: MG_UKJ_24_1058_blood_smallRNAseq

value: male


title: Cynomolgus_Macaque_Sample12-3

description:
Sample_12_S6_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12_results.csv
aav_barcode_key.txt


title: MCF-7mammo _ Ctrl_rep1

value: MCF-7 cells


title: MG_UKJ_2_1156_blood_smallRNAseq

value: 2 months


title: Cynomolgus_Macaque_Sample12-1

description:
Sample_12_S6_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12_results.csv
aav_barcode_key.txt


title: MG_UKJ_24_1056_blood_smallRNAseq


title: Purified cilia_Ctrl-i_Exp.1


title: MG_UKJ_24_1057_blood_smallRNAseq


title: Cynomolgus_Macaque_Sample12R-1

description:
Sample_12R_S8_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12R_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_Sample9-4

description:
Sample_9_S5_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample9_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_Sample9-3

description:
Sample_9_S5_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample9_results.csv
aav_barcode_key.txt


title: VitD Treated Healthy Donor IgG CUT&RUN 48hr

description: Mem_CD4_VitD.Treated.Healthy.Donor.IgG.CUTnRUN.48hr

data_processing: H3K27Ac reads aligned to the human reference genome (GRCh37; hg19) using Bowtie2 with parameters ‘--local --maxins 250’ with sorting and indexing of aligned reads by samtools/1.10, reads with mapping quality <30 removed. H3K27Ac peaks were called by MACS2 with parameter ‘-f BAMPE --nomodel’. JUN reads were mapped without ‘--local’ parameter. <120 bp fragments were further sorted and indexed by samtools. JUN induced peaks called by MACS2 parameters ‘--nomodel -g hs -f BAMPE -q 0.01 --SPMR --keep-dup all’. IgG BAM files were included as controls for MACS2. Peaks for H3K27Ac and JUN experiments were screened against previously characterized hypersequencable-regions (Hg19 Blacklist, CutRunTools). H3K27ac and JUN mean binding intensities in peak regions calculated by UCSC bigWigAverageOverBed. Peaks, combined from two conditions, with mean binding intensity greater than 0.2 in at least one condition and fold change of signal>1.5 were differential. Known motifs +/−100bp from differential peak summits were identified (HOMER, findMotifsGenome.pl, parameter ‘-size given’). De novo motif footprinting for c-JUN was performed (CutRunTools). Average cuts per bp proximal to JUN peaks was plotted as a histogram relative to IgG. CUT&RUN tracks and heatmaps were visualized using IGV (Broad Institute) and deepTools, respectively.

source_name: VitD Treated Healthy Donor IgG CUT&RUN

extract_protocol: H3K27Ac and c-JUN CUT&RUN: CUT&RUN sequencing was performed on memory CD4+ T cells activated as above in the presence of carrier or VitD for 0.75h, 48h and 72h using the published protocol of Skene et al (Nature Protocols 2018). Antibodies against H3K27Ac (ab4729, Abcam), c-JUN (60AB, Cell Signaling Technologies), and non-specific IgG (31235, Thermo Fisher Scientific) were used with pAG-MNase (123461, Addgene) on 50,000 cells per target. CUT&RUN (and CUT&Tag below) buffer components were purchased from Sigma-Aldrich and Thermo Fisher Scientific. Post-CUT&RUN, short DNA fragments were prepared for paired-end sequencing (NEB Ultra II, New England Biolabs) with NovaSeq (Illumina). Amplified libraries were quantified by high sensitivity fluorometry (DeNovix) and sized via the 4200 TapeStation (Agilent Technologies).

tag: bach2 genotype

value: Wildtype (Healthy Donor)

value: Isolated and Treated Memory CD4+ Cells (Negative Magnetic Selection)

value: anti-CD3 and anti-CD28 Dynabeads, Vitamin D (10nM)

tag: sequencing method

value: PE 50bp CUT&RUN, Novaseq

tag: molecule subtype

value: CUT&RUN Fragment gDNA


title: MG_UKJ_2_1153_blood_smallRNAseq


title: MG_UKJ_30_69_blood_smallRNAseq

value: 30 months


title: Cynomolgus_Macaque_Sample12-2

description:
Sample_12_S6_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample12_results.csv
aav_barcode_key.txt

value: Retina

tag: region

value: Retina periphery region

tag: sorting strategy


title: Cynomolgus_Macaque_Sample9-2

description:
Sample_9_S5_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample9_results.csv
aav_barcode_key.txt

value: unsorted


title: MG_UKJ_24_1055_blood_smallRNAseq

value: blood

value: 24 months


title: MG_UKJ_2_1154_blood_smallRNAseq


title: VitD Treated Healthy Donor IgG CUT&RUN 72hr

description: Mem_CD4_VitD.Treated.Healthy.Donor.IgG.CUTnRUN.72hr


title: MG_UKJ_2_1155_blood_smallRNAseq


title: Purified cilia_Fmr-i1-Exp.1


title: Cynomolgus_Macaque_Sample9-1

description:
Sample_9_S5_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample9_results.csv
aav_barcode_key.txt


title: VitD Treated Healthy Donor IgG CUT&RUN .75hr

description: Mem_CD4_VitD.Treated.Healthy.Donor.IgG.CUTnRUN.0.75hr


title: MCF-7mammo _ Ctrl_rep3

value: MCF-7 cells after prolonged mammosphere culture for 5 weeks


title: MG_UKJ_2_1152_blood_smallRNAseq


title: Carrier Treated Healthy Donor IgG CUT&RUN 48hr

description: Mem_CD4_Carrier.Treated.Healthy.Donor.IgG.CUTnRUN.48hr

value: anti-CD3 and anti-CD28 Dynabeads, Carrier (Ethanol)


title: 6_1132_O_RNA_C_S6

city: Atlanta

first: Philip

middle: N

last: Rather

state: Georgia

address: 1510 Clifton Rd.

department: Department of Microbiology and Immunology

institute: Emory University

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Acinetobacter baumannii AB5075 genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done with htseq-count.
Normalized abundance calculation and differential expression analysis was performed with DESeq2.
Genome_build: Genome_build: ASM96381v1 Strain: AB5075-UW GenBank assembly accession: GCA_000963815.1
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files with raw or DESeq2 normailzed read count values for each Sample

organism: Acinetobacter baumannii

source_name: LB media

growth_protocol: Samples were grown at 37 degrees with shaking to an OD of 0.5.

extract_protocol:
RNA was prepared from 1 ml of pelleted culture using the MasterPure RNA Purification kit (Epicentre, Madison, WI)
Libraries were prepared from 2ug of bacterial RNA using the ScriptSeq v2 Complete (Bacteria) kit. After pooling at equimolar ratios, the libraries were sequenced on a HiSeq3000 using a SR100 configuration

tag: population

value: VIR-O delta1132


title: Purified cilia_Ctrl-i_Exp.2

value: Motile cilia from cultured ependymal cell


title: 4_1132_O_RNA_B_S4


title: 2_1132_O_RNA_A_S2


title: 3_WT_O_RNA_B_S3

value: VIR-O


title: 5_WT_O_RNA_C_S5


title: MG_UKJ_15_234_blood_smallRNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were trimmed und filtered using trimmomatic (0.36) [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20].
Reads per gene were counted using samtools (1.3.1-9-ge5dfb0a).
Genome_build: mirBase Release 21 (M. musculus sequences only)
Supplementary_files_format_and_content: The text file includes raw counts (sample_counts.txt) of all mirBase M. musculus sequences for each sample.

value: 15 months

value: male


title: VitD Treated Healthy Donor c-JUN CUT&RUN 72hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.c-JUN.CUTnRUN.72hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx

value: Wildtype (Healthy Donor)

value: Isolated and Treated Memory CD4+ Cells (Negative Magnetic Selection)


title: MG_UKJ_15_233_blood_smallRNAseq


title: 1_WT_O_RNA_A_S1


title: Cynomolgus_Macaque_Sample8-3

description:
Sample_8_S4_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample8_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_Sample8-4

description:
Sample_8_S4_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample8_results.csv
aav_barcode_key.txt


title: Carrier Treated Healthy Donor IgG CUT&RUN .75hr

description: Mem_CD4_Carrier.Treated.Healthy.Donor.IgG.CUTnRUN.0.75hr

value: PE 50bp CUT&RUN, Novaseq


title: MG_UKJ_15_232_blood_smallRNAseq


title: VitD Treated Healthy Donor c-JUN CUT&RUN 48hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.c-JUN.CUTnRUN.48hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx

value: anti-CD3 and anti-CD28 Dynabeads, Vitamin D (10nM)

value: CUT&RUN Fragment gDNA


title: Carrier Treated Healthy Donor IgG CUT&RUN 72hr

description: Mem_CD4_Carrier.Treated.Healthy.Donor.IgG.CUTnRUN.72hr


title: MG_UKJ_15_231_blood_smallRNAseq


title: Carrier treated Healthy Donor 3 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD3.RNAseq.72h

data_processing: RNA-seq Data Processing and Analysis: The expression level of all genes in all RNA-seq libraries was quantified by ‘rsem-calculate-expression’ in RSEM v1.3.1 with parameters ‘--bowtie-n 1 --bowtie-m 100 --seed-length 28 --bowtie-chunkmbs 1000’. The bowtie index for RSEM alignment was generated by ‘rsem-prepare-reference’ on all RefSeq genes, downloaded from UCSC table browser in April 2017. EdgeR/v3.26.8 was used to normalize gene expression among all libraries and identify differentially expressed genes among samples. Analysis of microarray data sourced from GSE119416 was carried out using Partek Genomics Suite (Partek, Inc.). Differentially expressed gene thresholds were defined using the following criteria: at least 1.5-fold change in either direction at p-value<0.05 for microarray analysis; at least 1.75-fold change in either direction at FDR<0.05 for RNA-seq analysis. Genome_build: GRCh37; hg19. Supplementary_files_format_and_content: RNA-seq data presented as RPKMs in tablature format.

source_name: Carrier treated Healthy donor

extract_protocol: Isolation of mRNA and RNA-seq: Memory CD4+ T cells, including from BACH2 WT and L24P patient samples, were isolated and activated with or without VitD treatment as described.  600,000 unactivated cells, or cells activated for 48 or 72 hrs, were pelleted at 300g for 5 min. RNA was stabilized by lysing cells in 100µL of RNAqueous lysis buffer, snap-freezing on dry-ice, followed by storage at -80C and isolation of total RNA by the RNAqueous-Micro kit (AM1931, Thermo Fisher Scientific) as per manufacturers guidelines. 1µg total RNA for each sample was subjected to NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490). Resulting mRNA was prepared for RNA-seq using a NEB Ultra II RNA Sequencing Library Prep Kit (New England Biolabs) as per the manufacturer's guidelines.

value: SE 50bp RNA-seq, HiSeq


title: VitD Treated Healthy Donor c-JUN CUT&RUN .75hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.c-JUN.CUTnRUN.0.75hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx


title: MG_UKJ_15_230_blood_smallRNAseq

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.


title: Carrier Treated Healthy Donor c-JUN CUT&RUN 72hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.c-JUN.CUTnRUN.72hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx


title: Cynomolgus_Macaque_Sample7-3

description:
Sample_7_S3_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample7_results.csv
aav_barcode_key.txt

value: Retina

value: Retina center/fovea region


title: Carrier Treated Healthy Donor c-JUN CUT&RUN .75hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.c-JUN.CUTnRUN.0.75hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx


title: Unstimulated Healthy Donor 3

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
NoStim.HD3.RNAseq

source_name: Unstimulated Healthy donor


title: Carrier treated Healthy Donor 3 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD3.RNAseq.48h


title: VitD treated Healthy Donor 3 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD3.RNAseq.72h

source_name: VitD treated Healthy donor


title: VitD Treated Healthy Donor H3K27Ac CUT&RUN 72hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.72hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx


title: VitD treated Healthy Donor 2 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD2.RNAseq.72h


title: Cynomolgus_Macaque_Sample7-1

description:
Sample_7_S3_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample7_results.csv
aav_barcode_key.txt

value: unsorted


title: TM_FSU_WTsed3_muscle_RNAseq

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: GRCm38, and respective gene annotation (GRCm38.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

source_name: wild type_w/o exercise_muscle

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.

tag: strain background

tag: genotype/variation

value: wild type

value: 5 months

value: muscle


title: TM_FSU_WTTr1_muscle_RNAseq

source_name: wild type_Treadmill_muscle

value: Treadmill

tag: tissue


title: Cynomolgus_Macaque_Sample7-2

description:
Sample_7_S3_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample7_results.csv
aav_barcode_key.txt

extract_protocol:
The NHP retinas were dissected and regions of interest were isolated (macula, superior and inferior periphery). For cynomolgus macaque, superior and inferior periphery were pooled. Retinal tissue was placed in Hibernate solution (Hibernate A -Ca Solution, BrainBits LLC), and cells were then dissociated using Macs Miltenyi Biotec Neural Tissue Dissociation Kit for postnatal neurons (130-094-802) according to manufacturer’s recommendations. Dissected retina pieces were incubated with agitation at 37 °C and further mechanically dissociated. The dissociated neural retina was filtered using a 70 µm MACS Smart Strainer (Miltenyi Biotec) to ensure single-cell suspension. Cells were resuspended in 0.1% BSA in D-PBS and processed immediately for scRNA-seq.
Marmoset and cynomolgus macaque samples were prepared for single cell analysis using a 10x Chromium Single Cell 3’ v3 kit. Briefly, single cells from retina samples were captured using 10X Chromium system (10X Genomics), the cells were partitioned into Gel beads-in-emulsion (GEMS), mRNAs were reverse transcribed and cDNAs with 10X Genomics Barcodes were created with unique molecular identifiers (UMIs) for different transcripts. Purified cDNA was PCR amplified and further purified with SPRIselect reagent (Beckman Coulter, B23318). Final libraries were generated after fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR steps according to 10x Single Cell 3’ workflow. An additional targeted sequencing analysis was run on these 10x-prepped cDNA samples, using PCR amplification with Q5 High Fidelity DNA Polymerase to target the GFP sequence and its associated AAV barcode.


title: Cynomolgus_Macaque_Sample8-2

description:
Sample_8_S4_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample8_results.csv
aav_barcode_key.txt

value: Retina periphery region


title: Carrier Treated Healthy Donor c-JUN CUT&RUN 48hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.c-JUN.CUTnRUN.48hr
processed data file: c-JUN_CUTnRUN_Differential_Peak_Analysis.xlsx

value: anti-CD3 and anti-CD28 Dynabeads, Carrier (Ethanol)


title: Cynomolgus_Macaque_Sample8-1

description:
Sample_8_S4_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample8_results.csv
aav_barcode_key.txt


title: TM_FSU_WTTr2_muscle_RNAseq

tag: age


title: Cynomolgus_Macaque_Sample6R-3

description:
Sample_6R_S7_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6R_results.csv
aav_barcode_key.txt


title: TM_FSU_WTsed2_muscle_RNAseq

tag: Sex


title: Cynomolgus_Macaque_Sample6R-4

description:
Sample_6R_S7_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6R_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_Sample6R-2

description:
Sample_6R_S7_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6R_results.csv
aav_barcode_key.txt


title: TM_FSU_WTTr3_muscle_RNAseq

tag: perturbation


title: Cynomolgus_Macaque_Sample7-4

description:
Sample_7_S3_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample7_results.csv
aav_barcode_key.txt


title: TM_FSU_KOTr2_muscle_RNAseq


title: VitD treated Healthy Donor 2 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD2.RNAseq.48h


title: VitD Treated Healthy Donor H3K27Ac CUT&RUN 48hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.48hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx


title: VitD treated Healthy Donor 3 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD3.RNAseq.48h


title: VitD Treated BACH2 L24P Patient

description:
processed data file: Mem_CD4.BACH2lof_VitD_RNAseq.RPKMs.txt
VitD.BACH2lof.RNAseq.72h

source_name: VitD Treated BACH2 L24P Patient


title: VitD Treated Healthy Donor H3K27Ac CUT&RUN .75hr

description:
Mem_CD4_VitD.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.0.75hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx


title: Carrier Treated Healthy Donor H3K27Ac CUT&RUN .75hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.0.75hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx


title: VitD treated Healthy Donor1 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD1.RNAseq.72h


title: TM_FSU_KOTr3_muscle_RNAseq


title: Carrier treated Healthy Donor 2 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD2.RNAseq.48h


title: Cynomolgus_Macaque_Sample6-3

description:
Sample_6_S2_L003
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6_results.csv
aav_barcode_key.txt


title: Carrier Treated BACH2 L24P Patient

description:
processed data file: Mem_CD4.BACH2lof_VitD_RNAseq.RPKMs.txt
Carrier.BACH2lof.RNAseq.72h

source_name: Carrier Treated BACH2 L24P Patient


title: VitD treated Healthy Donor1 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
VitD.HD1.RNAseq.48h


title: VitD treated Healthy Donor 4 at 48h (control for BACH2 L24P patient)

description:
processed data file: Mem_CD4.BACH2lof_VitD_RNAseq.RPKMs.txt
VitD.HD4.BACH2.control.RNAseq.48h


title: Cynomolgus_Macaque_Sample6-4

description:
Sample_6_S2_L004
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6_results.csv
aav_barcode_key.txt


title: TM_FSU_WTsed1_muscle_RNAseq


title: TM_FSU_KOSed2_muscle_RNAseq

source_name: NRF2-KO_w/o exercise_muscle


title: Cynomolgus_Macaque_Sample6-1

description:
Sample_6_S2_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6_results.csv
aav_barcode_key.txt


title: Cynomolgus_Macaque_Sample6-2

description:
Sample_6_S2_L002
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6_results.csv
aav_barcode_key.txt


title: Unstimulated Healthy Donor 1

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
NoStim.HD1.RNAseq


title: TM_FSU_KOSed1_muscle_RNAseq


title: Unstimulated Healthy Donor 2

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
NoStim.HD2.RNAseq


title: miR-34a-transfected H1299

status: Public on Oct 18 2021

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy- N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http:// ) directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Genome_build: GRCh38

source_name: Non-small cell lung cancer

growth_protocol: Human non-small cell lung cancer cell line NCI-H1299 (CRL-5803) was purchased from American Type Culture Collection (ATCC) and cultured at 37℃ in the supplier's recommended media supplemented with 10% fetal calf serum.

extract_protocol:
Total RNA was prepared from cell lines using miRNeasy RNA isolation kit (Qiagen, Inc.). Firstly, ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation.
Subsequently, sequencing libraries were generated using the TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Transfection experiment were performed using the lipofectamine RNAiMAX transfection reagent with a final RNA concentration of 25 nmol/l and harvested after 48 hours.

tag: cell line

value: mimic miR-34a-transfected


title: Non-treated H1299

value: Non-treated


title: Cynomolgus_Macaque_Sample6R-1

description:
Sample_6R_S7_L001
supplementary or processed data file:
barcodes.tsv
cynomolgus_macaque_genes.tsv
cell_by_aav_cyno_macaque_sample6R_results.csv
aav_barcode_key.txt


title: Carrier Treated Healthy Donor H3K27Ac CUT&RUN 72hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.72hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx

value: Wildtype (Healthy Donor)

tag: cell type


title: Carrier treated Healthy Donor 1 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD1.RNAseq.72h

value: Isolated and Treated Memory CD4+ Cells (Negative Magnetic Selection)


title: Carrier treated Healthy Donor 1 at 48h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD1.RNAseq.48h


title: Carrier Treated Healthy Donor H3K27Ac CUT&RUN 48hr

description:
Mem_CD4_Carrier.Treated.Healthy.Donor.H3K27Ac.CUTnRUN.48hr
processed data file: H3K27Ac_CUTnRUN_Differential_Peak_Analysis.xlsx

value: PE 50bp CUT&RUN, Novaseq


title: 231-control

city: Jinan City

first: Wenjie

last: Zhu

state: Shangdong Province

address: Wen Hua Xi Road 44

department: Department of Pathology

institute: School of Basic Medical Sciences, Shandong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
The exomePeak（Version 3.8）software was used for peak calling. Peaks were annotated using bedtools（Version 2.25.0）. The deepTools（version 2.4.1）was used for peak distribution analysis.
The differentially binding peaks were identified by a python script，using fisher test. Sequence motifs enriched in peak regions were identified using Homer（version 4.10）. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Supplementary_files_format_and_content: tab-delimited xlsx file include FPKM values for each Sample.

source_name: Brest cancer celline 231

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

value: Brest cancer cell line

value: PCDNA3.1 overexpression


title: Carrier treated Healthy Donor 2 at 72h

description:
processed data file: Mem_CD4.HealthyDonor_VitD_RNAseq.RPKMs.txt
Carrier.HD2.RNAseq.72h

value: SE 50bp RNA-seq, HiSeq


title: SIRT6

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The exomePeak（Version 3.8）software was used for peak calling. Peaks were annotated using bedtools（Version 2.25.0）. The deepTools（version 2.4.1）was used for peak distribution analysis.
The differentially binding peaks were identified by a python script，using fisher test. Sequence motifs enriched in peak regions were identified using Homer（version 4.10）. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Supplementary_files_format_and_content: RPKM values

extract_protocol:
RIP assay was conducted with antibodies against Ago2 or IgG according to the protocols provided in the Magna RIP™ RNA-Binding Protein Immunoprecipitation kit (Millipore). RNAs were extracted from the immunoprecipitation product, and RT-qPCR was utilized to quantitatively determine the level of HOXC-AS3 pulled down by Ago2 or IgG.
The RNA of input and IP was extracted using TRIzol reagent(Invitrogen, Invitrogen, cat. NO 15596026). The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

tag: rip antibody


title: Cyt49_GT.ChIP-Seq.GATA6.replicate.1

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: Transcription factor

data_processing:
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

source_name: Cyt49 Control

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019). iAEC2 cells were maintained and differentiatied as previously described (Hurley et al 2020)

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit

value: differentiated hESCs

tag: developmental stage

value: Gut tube

tag: chip antibody


title: miR-34a-transfected DDx21 KO

tag: treatment


title: TM_FSU_KOSed3_muscle_RNAseq

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

value: male


title: Cyt49_PP2_shPDX1.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker

data_processing:
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were generated.

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019). iAEC2 cells were maintained and differentiated as previously described (Hurley et al. 2020).

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit.

value: Late pancreatic progenitor


title: Cyt49_GT.ChIP-Seq.GATA4.replicate.1

description: Transcription factor


title: input.dedup


title: SIRT6.dedup


title: Carrier treated Healthy Donor 4 at 48h (control for BACH2 L24P patient)

description:
processed data file: Mem_CD4.BACH2lof_VitD_RNAseq.RPKMs.txt
Carrier.HD4.BACH2.control.RNAseq.48h

tag: bach2 genotype

tag: sequencing method


title: TM_FSU_KOTr1_muscle_RNAseq

value: 5 months


title: Cyt49_PP2_shSCRAM.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: 231-HOXC-AS3


title: input.filtlowGC


title: H1_FOXA1_2_Exon_Deletion_PP2.ATAC-Seq.replicate.1

description: Genomic DNA

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

source_name: H1 FOXA1/2 Exon Deletion

extract_protocol:
Genomic DNA was extracted using Dneasy Blood and Tissue Kit from Qiagen.
Cells were collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for tapestation analysis.
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)


title: H1_FOXA1_2_Exon_Deletion_GT.ATAC-Seq.replicate.1

description: Genomic DNA


title: Non-treated DDX21 KO


title: Cyt49_PP2_shSCRAM.ATAC-Seq.replicate.1

description: Genomic DNA

source_name: Cyt49 shSCRAM


title: Cyt49_PP2_shPDX1.ATAC-Seq.replicate.1

description: Genomic DNA

source_name: Cyt49 shPDX1


title: Cyt49_PP2_shPDX1.ATAC-Seq.replicate.2

description: Genomic DNA


title: Cyt49_GT.ChIP-Seq.GATA4.replicate.2

description: Transcription factor


title: Cyt49_HP.ATAC-Seq.replicate.2

description: Genomic DNA

value: Hepatic progenitor


title: SIRT6.filtlowGC


title: H1_WT_PP2.RNA-Seq.replicate.4

description: RNA

source_name: H1 Control

extract_protocol:
RNA was isolated from cell samples using the RNeasy® Micro Kit (Qiagen) according to the manufacturer instructions.
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)


title: H1_WT_PP2.ATAC-Seq.replicate.1

description: Genomic DNA


title: H1_WT_PP2.RNA-Seq.replicate.1

description: RNA


title: Cyt49_GT.ChIP-Seq.GATA6.replicate.2

description: Transcription factor


title: H1_WT_PP1.RNA-Seq.replicate.2

description: RNA

value: Early pancreatic progenitor


title: H1_FOXA1_2_Exon_Deletion_PP2.ATAC-Seq.replicate.2

description: Genomic DNA


title: H1_WT_PP1.RNA-Seq.replicate.1

description: RNA


title: input


title: H1_WT_PP1.RNA-Seq.replicate.4

description: RNA


title: Cyt49_HP.ATAC-Seq.replicate.1

description: Genomic DNA


title: Cyt49_PP2_shSCRAM.ATAC-Seq.replicate.2

description: Genomic DNA


title: H1_FOXA1_2_Exon_Deletion_GT.ATAC-Seq.replicate.2

description: Genomic DNA


title: H1_WT_PP2.ATAC-Seq.replicate.2

description: Genomic DNA


title: H1_WT_GT.ATAC-Seq.replicate.1

description: Genomic DNA


title: H1_WT_GT.ATAC-Seq.replicate.2

description: Genomic DNA


title: H1_WT_PP2.RNA-Seq.replicate.3

description: RNA


title: H1_WT_GT.RNA-Seq.replicate.3

description: RNA


title: H1_WT_GT.RNA-Seq.replicate.2

description: RNA


title: H1_WT_GT.RNA-Seq.replicate.1

description: RNA


title: H1_WT_PP1.RNA-Seq.replicate.3

description: RNA


title: H1_WT_GT.RNA-Seq.replicate.4

description: RNA


title: H1_WT_DE.RNA-Seq.replicate.3

description: RNA

value: Definitive endoderm


title: H1_WT_DE.RNA-Seq.replicate.4

description: RNA


title: H1_FOXA1_2_Frameshift_PP2.RNA-Seq.replicate.1

description: RNA

source_name: H1 FOXA1/2 Frameshift Mutation


title: H1_WT_DE.RNA-Seq.replicate.1

description: RNA


title: H1_FOXA1_2_Frameshift_PP2.RNA-Seq.replicate.2

description: RNA


title: H1_WT_PP2.RNA-Seq.replicate.2

description: RNA


title: H1_WT_DE.RNA-Seq.replicate.2

description: RNA


title: H1_FOXA1_2_Frameshift_DE.RNA-Seq.replicate.1

description: RNA


title: H1_FOXA1_2_Frameshift_DE.RNA-Seq.replicate.2

description: RNA


title: H1_FOXA1_2_Frameshift_GT.RNA-Seq.replicate.2

description: RNA


title: H1_FOXA1_2_Frameshift_GT.RNA-Seq.replicate.1

description: RNA


title: H1_FOXA1_2_Exon_Deletion_PP2.RNA-Seq.replicate.2

description: RNA


title: H1_FOXA1_2_Exon_Deletion_DE.RNA-Seq.replicate.2

description: RNA


title: iAEC2_DE.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

source_name: iAEC2 Control

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

value: Rabbit anti-H3K27ac

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog number


title: iAEC2_DE.ChIP-Seq.Input.replicate.1

description: Input


title: iAEC2_DE.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_GT.RNA-Seq.replicate.1

description: RNA


title: iAEC2_ALV.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor

value: Alveolosphere

value: Goat anti-FOXA1

value: Abcam


title: iAEC2_ALV.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: iAEC2_AFG.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

value: Anterior foregut


title: iAEC2_ALV.ChIP-Seq.Input.replicate.1

description: Input


title: Cyt49_HP.RNA-Seq.replicate.1

description: RNA


title: H1_WT_PP2.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker

value: Rabbit anti-H3K4me1


title: H1_WT_PP2.ChIP-Seq.Input.replicate.1

description: Input


title: H1_WT_PP2.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: H1_WT_PP2.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_DE.RNA-Seq.replicate.1

description: RNA


title: iAEC2_AFG.ChIP-Seq.Input.replicate.1

description: Input


title: H1_WT_GT.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_PP2.ChIP-Seq.Input.replicate.1

description: Input


title: iAEC2_AFG.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: iAEC2_AFG.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor


title: H1_WT_GT.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: H1_WT_GT.ChIP-Seq.Input.replicate.1

description: Input


title: iAEC2_ALV.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: H1_FOXA1_2_Exon_Deletion_PP2.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_GT.RNA-Seq.replicate.2

description: RNA


title: iAEC2_ALV.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker


title: H1_WT_GT.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_PP2.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker