title: Input-ChIP-seq, miTSCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007275

value: miTSCs-BYKE


title: GA-11-00765

status: Public on Sep 27 2024

type: SRA

city: Ann Arbor

first: Simpa

middle: S

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
libraries were normalized using TMM method prior to downstream processing
Assembly: GRCh38.p1
Supplementary files format and content: tab delimited text file with raw counts for each sample
Supplementary files format and content: tab delimited text file with logCPM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Lymph

extract_protocol:
1ug - 6μg of total RNA was used in a reverse transcription reaction, and the obtained cDNA was taken to a second-strand DNA synthesis as described
Briefly, following second-strand synthesis, we used the Sciclone G3 NGS workstation (Perkin Elmer) with the Kappa HT library preparation kit to produce the libraries

tag: tissue

value: Lymph


title: Activated-Undivided, TCR

city: Philadelphia

first: Christoph

last: Ellebrecht

state: PA

address: 421 Curie Blvd, 1005 BRB

department: Dermatology

institute: University of Pennsylvania

description: HPG5bbz2-28-22filtered_feature_bc_matrix.h5

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation was performed with 10X genomics Cell Ranger v6.1.2
Assembly: human GENCODE v32/Ensembl 98 GRCh38 reference
Supplementary files format and content: H5
Library strategy: CITE-seq with TCR-seq

molecule: polyA RNA

source_name: T cell

extract_protocol:
Proximal, distal, activated-undivided, and resting CARTs were isolated using fluorescence-activated cell sorting. 1.5x10^5 cells of each group were separately incubated in flow cytometry staining buffer (BioLegend) with a custom TotalSeq-C antibody cocktail in 100 ul for 30 minutes at 4C prior to washing three times. 10,000 live T cells from each LIPSTIC population were loaded onto NextGem K chips (10X Genomics) and processed in a 10X chromium device according to the manufacturer's recommendations.
Library preparation for gene expression, ADT, and TCR was performed using manufacturer's instructions using 10X 5' V2 protocol.

tag: cell type

value: T cell


title: Input-ChIP-seq, mESCs, biol rep 2

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
The pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters. Duplicated reads were then removed using MarkDuplicates from the Picard toolkit. Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded. The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1). The peaks of TFs showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
genome build: mm9
processed data file: The aligned ChIP-seq reads (bam files) were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. BAM files from replicates were merged before normalized for coverage

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse ESCs were grown on 0.2% gelatine and maintained in ESC Medium (GMEM, 10% FCS, 1mM L-glutamine, 0.1mM βME, 1X Non-Essential Amino Acids, 100U/ml Leukaemia Inhibitory Factor (LIF)

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007274

tag: cell line

value: Mouse Embryonic Stem cells with Oct4-GFP reporter

tag: chip antibody

value: Input DNA control

tag: genotype

tag: treatment

value: final reprogramming


title: NF-04-40107

source_name: Bone

value: Bone


title: GU-10-34897

source_name: Adrenal

value: Adrenal


title: Activated-Undivided, ADT

library_source: other

molecule: other


title: Myc-ChIP-seq, mESCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007272


title: MyriadR 1484

source_name: Clear Cell RCC

value: Clear Cell RCC


title: Input-ChIP-seq, mESCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007273


title: Activated-Undivided, GEX


title: IF-08-24385

source_name: Lung

value: Lung


title: IF-13-23516


title: Myc-ChIP-seq, mESCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007271


title: Distal, TCR


title: Klf4-ChIP-seq, mESCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007270


title: MyriadR 260


title: Klf4-ChIP-seq, mESCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-00727-1


title: MyriadR 2159


title: MyriadR 837


title: Distal, GEX


title: Distal, ADT


title: Sox2-ChIP-seq, mESCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-00727-2


title: MyriadR 969


title: Resting, TCR


title: Proximal, GEX


title: Sox2-ChIP-seq, mESCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-00727-3


title: MyriadR 866


title: Resting, ADT


title: MyriadR 1234


title: Oct4-ChIP-seq, mESCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-00727-5

value: Oct4 (Abcam, AB19857)


title: Oct4-ChIP-seq, mESCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-00727-4


title: Resting, GEX


title: MyriadR 819


title: embryos, 96 hpf, L-glucose-3

city: nantong

first: wang

last: xiaoning

state: jiangsu

address: Qixiu Road 19

country: China

institute: Nantong University

data_processing:
Raw sequencing BCL data base-calling using bcl2fastq v2.20.0.422
Data filtering using fastp v0.23.2 (--cut_front --cut_tail --cut_mean_quality 20 --length_required 35) followed by rRNA filtering using SortMeRNA v4.3.2 with default parameters
Read alignment using STAR v2.7.10a
Quantify using Salmon v1.9.0 with default parameters
Assembly: Ensembl Danio rerio GRCz11
Supplementary files format and content: Tab-separated values files

organism: Danio rerio

source_name: whole embryo

growth_protocol: zebrafish embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.

extract_protocol:
For total mRNA extraction from  zebrafish embryos, TRIzol Reagent (Catalogue Number: C2432, Invitrogen) was used according to the manufacturer's instructions.
For library construction, NEBNext Ultra RNA Library Prep Kit for Illumina was used according to the manufacturer's instructions.

treatment_protocol: Embryos were treated with D-glucose or L-glucose at 24 hpf.

value: whole embryo

tag: developmental stage

value: 96 hpf

value: L-glucose


title: MyriadR 182


title: choroid plexus tumor, CPC, sample 5

city: Heidelberg

first: Anthony

last: Hill

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Schaller Research Group

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: transcriptomic single cell

data_processing:
Raw reads were processed and count tables were generated using the Cellranger pipeline v6.1.1
Assembly: GRCh 38
Supplementary files format and content: tab separated values and matrix files

source_name: fresh frozen ChP Tumor

extract_protocol:
Frozen tissue was thawed in ice cold wash buffer (.32 M sucrose, 5mM CaCl2, 3mM magnesium acetate, 2.0 mM EGTA, 10mM Tris-HCl pH 8.0) + .001% Triton-X and 1mM DTT. Thawed tissue fragments were transferred to a glass dounce on ice and given 10 strokes each with an A-type pestle and a B-type pestle. The resulting nuclei suspension was sequentially filtered through 100 and 40 um filters and pelleted by centrifugation for 5 minutes at 555xg and 4°C. Pellets were washed by resuspension in wash buffer and centrifugation 2-4 times. After the final wash, pellets were resuspended in sterile filtered nuclei storage buffer (0.43 M sucrose, 70mM KCl, 2mM MgCl2, 10mM Tris-HCl pH7.2, 5mM EGTA).
Single nucleus expression libraries were made from 5-10K nuclei using the Chromium Single Cell 3’ Library & Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s protocol.
snRNA-seq

value: fresh frozen ChP Tumor

tag: group

value: CPC


title: choroid plexus tumor, CPC, sample 4


title: embryos, 96 hpf, L-glucose-2


title: MyriadR 1267


title: embryos, 96 hpf, L-glucose-1


title: choroid plexus tumor, CPC, sample 3


title: choroid plexus tumor, CPC, sample 2


title: MyriadR 96


title: MyriadR 902


title: embryos, 72 hpf, L-glucose-3

value: 72 hpf


title: choroid plexus tumor, CPC, sample 1


title: choroid plexus tumor, CPP, sample 4

value: CPP


title: embryos, 72 hpf, L-glucose-1


title: MyriadR 1860


title: MyriadR 1799


title: embryos, 72 hpf, L-glucose-2


title: MyriadR 790


title: embryos, 96 hpf, D-glucose-2

value: D-glucose


title: embryos, 96 hpf, D-glucose-3


title: MyriadR 2068


title: choroid plexus tumor, CPP, sample 2


title: choroid plexus tumor, CPP, sample 1


title: choroid plexus tumor, CPP, sample 3


title: embryos, 96 hpf, D-glucose-1


title: embryos, 72 hpf, D-glucose-3


title: MyriadR 180


title: choroid plexus tumor, aCPP, sample 1

value: aCPP


title: embryos, 72 hpf, D-glucose-2


title: choroid plexus, normal, sample 4

source_name: fresh frozen ChP

value: fresh frozen ChP

value: normal


title: embryos, 72 hpf, D-glucose-1


title: hiPSC-MNs_4

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

country: Japan

institute: Niigata University

data_processing:
Sequence reads were processed using Cell Ranger software v.7.0.1 (10x Genomics)
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human motor neuron

growth_protocol: hiPSC-MNs cells were obtained and cultured form (Matsuo et al. 2021 PMID:34111668)

extract_protocol:
Differentiated human motor neurons were dissociated into a single-cell suspension using Accutase (Innovative Cell Technologies). Dissociated cells were resuspended in DMEM/F-12 medium (Thermo Fisher Scientific) containing 0.04%-BSA at a concentration of 700 cells/μL (Target cell recovery: 3,000 cells per channel). Subsequently, the suspended cells were loaded onto a Chromium Single Cell 3’ Chip (10x Genomics) and processed through the Chromium Controller to generate single-cell gel beads in emulsion (GEMs)
scRNA-seq libraries were prepared with the Chromium Single Cell 3’ Library & Gel Bead Kit v.2 (10x Genomics) according to the manufacturer’s protocol.

value: human motor neuron


title: embryos, 96 hpf, control-2

value: control


title: hiPSC-MNs_2


title: choroid plexus, normal, sample 2


title: choroid plexus, normal, sample 3


title: AUTS2-/- D75 Rep3

city: HERSHEY

first: Yen Teng

last: Tai

address: 700 HMC Cres Rd

department: Biochemistry and Molecular Biology

institute: Penn State College of Medicine

data_processing:
Gene abundances were estimated using Kallisto for raw read counts and relative gene expression (TPM).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed file is tab-separated value (tsv) files and contains TPM values generated by kallisto

growth_protocol: The hESC lines were cultured in StemFlex™ basal medium supplemented with non-essential amino acids and sodium pyruvate on Matrigel.

extract_protocol:
Total RNA was extracted using TriPure reagent
After RNA extraction, cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit

treatment_protocol: The Cerebral Organoid kit from Stem Cell Technologies was utilized to generate cerebral organoids.

value: Embryonic stem cells

value: Cerebral organoids differentiation


title: embryos, 72 hpf, control-3


title: MyriadR 850

value: Clear Cell RCC


title: choroid plexus tumor, aCPP, sample 2


title: choroid plexus, normal, sample 1


title: Low Quality Blastocyst 14

city: Detroit

first: Grace

middle: Michelle

last: Swanson

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

data_processing:
adapters were trimmed with Trimmomatic
sequences aligned in Hisat2 to the Telomere to telomere (T2T) genome and hg38 Gencode version 41.
transcript integrity was assessed using the Transcript Integrity Index (TII) algorithm
RNA Element (RE, exon sized sequences) discovery was done using the RNA Element Discovery algorithm (REDa)
Assembly: Telomere-to-telomere, hg38 Gencode version 41
Supplementary files format and content: total_RPKMgenomic_gencode.txt
Supplementary files format and content: total_RPKMgenomic_T2T.txt
Supplementary files format and content: sample_annotations.txt

source_name: spermatozoa

extract_protocol:
QIAzol phenol/guanidine-based Rneasy Kit
SeqPlex RNA Amplification Kit (Sigma Aldrich) to generate cDNA.  cDNA was cleaned using Zymo DNA Clean & Concentrator-5 (Zymo Research), and the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) was used to prepare libraries.

value: spermatozoa


title: AUTS2-/- D75 Rep2


title: AUTS2-/- D75 Rep1


title: Low Quality Blastocyst 12


title: hiPSC-MNs_1


title: MyriadR 1161

extract_protocol:
1ug - 6μg of total RNA was used in a reverse transcription reaction, and the obtained cDNA was taken to a second-strand DNA synthesis as described
Briefly, following second-strand synthesis, we used the Sciclone G3 NGS workstation (Perkin Elmer) with the Kappa HT library preparation kit to produce the libraries


title: embryos, 72 hpf, control-1

value: whole embryo


title: Low Quality Blastocyst 13


title: AUTS2+/- D75 Rep3


title: Low Quality Blastocyst 10


title: embryos, 96 hpf, control-3

value: 96 hpf


title: Low Quality Blastocyst 9


title: AUTS2+/- D75 Rep1


title: embryos, 96 hpf, control-1


title: Low Quality Blastocyst 8


title: hiPSC-MNs_3


title: eat-2 dve1_2

city: Gainesville

first: Yi

last: Sheng

state: FL

address: 1600 SW Archer Road

department: Department of Physiology & Aging

institute: UNIVERSITY OF FLORIDA

data_processing:
sequencing reads and accounts are analysed follow the standard protocol by the UF ICBR core service.
Assembly: WS289
Supplementary files format and content: normalized counting numbers for each genes and samples are included in the excel files

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: worms grow under the specific RNAi bacteria RNAi NGM plates from egg till Day1 adulthood stage under 20 degree.

extract_protocol:
Total RNA were extracted with Tri-Reagent, and then using Zymo Rneasy mini-plus kit follow the manufacturer's protocol.
amount total RNA were used for the library construction follow the standard protocol by the UF ICBR SERVICE.

treatment_protocol: Worms were collected with M9 buffer, and washed 3-4 times to get rid of bacteria. And using Liquid Nitrigen frsh frozen, and store in -80 freezer.

value: whole worms

value: dve-1 RNAi


title: eat-2 atfs1_3

value: atfs=1 RNAi


title: eat-2 dve1_1


title: Low Quality Blastocyst 7


title: AUTS2+/+ D75 Rep3

value: WT


title: embryos, 72 hpf, control-2

value: 72 hpf


title: AUTS2+/+ D75 Rep2


title: eat-2 atfs1_2


title: Low Quality Blastocyst 6


title: Low Quality Blastocyst 5


title: AUTS2+/+ D75 Rep1


title: Low Quality Blastocyst 11


title: eat-2 atfs1_1


title: eat-2 dve1_3


title: Low Quality Blastocyst 3


title: eat-2 EV_3

value: EV RNAi


title: AUTS2+/- D75 Rep2


title: eat-2 EV_2


title: Low Quality Blastocyst 4


title: DMSO.M.29863R

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Quality check and reference mapping were performed with Kallisto using the Rattus norvegicus assembly and gene annotation from Ensembl. Alignments were processed using tximport and further analyzed with the edgeR and limma voom pipelines for differential expression analyses for various comparisons of WT, P23H and reserpine-treated samples. When specified, female and male samples were analyzed separately to characterize sex-bias disease mechanism as well as drug response.
Lowly expressing genes were filtered out by only retaining genes that had greater than 5 CPM expression in two or more replicates. Sample outliers were identified from PCA and removed from downstream analysis.
Differential expression analysis was performed with the edgeR and limma-voom pipeline, and thresholds of 0.05 FDR and 2-fold change (abs(log2FC) > 1) were used to determine significantly differential genes.
Assembly: Rnor_6.0 (Ensembl release 104)
Supplementary files format and content: Tab-delimited text files containing transcript level counts, gene level counts, or normalized gene level counts-per-million results.

organism: Rattus norvegicus

source_name: 29863R DMSO treated P23H rats

growth_protocol: Hemizygous P23H-1 rats were produced by crossing homozygous transgenic P23H line 1 rats, obtained from Matthew LaVail (University of California, San Francisco School of Medicine) (43), with wild-type Long Evans rats purchased from Charles River. For control animals, wild-type Sprague-Dawley rats were crossed with Long-Evans rats, also from Charles River. Seven to eight animals per were used per experimental group, and each was assigned a 5-digit ID number via an ear tag for tracking purposes. Rats were housed in groups of 3 to 5 in spacious cages situated on ventilated shelves, following a 12-hour dark/light cycle. Each cage was equipped with refuges, gnawing, and nesting material. Daily monitoring was conducted to detect gross behavioral changes such as lack of activity, lack of grooming, and intolerance, which could be considered humane end points. All procedures were carried out in accordance with guidelines approved by the Institutional Animal Care and Use Committee of EyeCRO (2021-10-16-001).

extract_protocol:
Total RNA was purified from homogenized rat retinas (WT, DMSO controls, and reserpine-treated samples) using TriPure isolation reagent (Roche, Indianapolis, IN) according to the manufacturer’s protocol. The quality and quantity of RNA were both assessed using the RNA ScreenTape assay on the Agilent TapeStation system.
Samples (with RNA integrity number >8) were used for library generation using the TrueSeq RNA sample Prep Kit v2 (Illumina).

treatment_protocol: Prior to each procedure, pupils were dilated, and a combination of ketamine (85 mg/kg) and xylazine (4 mg/kg) was administered via intraperitoneal injection, following light sedation using isoflurane. A total volume of 5 µL of either 0.4% DMSO or 40 µM reserpine (diluted from 10 mM stock solution) was injected into the vitreous at the pars plana using a Hamilton syringe with a 33-gauge needle. Upon completion of the procedures, Yohimbine was administered via intraperitoneal injection at a concentration of 1 µL per gram of body weight as a reversing agent for ketamine-xylazine anesthesia. Male and female rats from two litters were randomly allocated to two groups, and information about the injected materials was blinded to the researchers who conducted the animal experiments and performed the initial analysis for each experiment.

value: Retina

tag: Sex

value: Male

tag: replicate

value: DMSO treated P23H


title: DMSO.M.29862R

source_name: 29862R DMSO treated P23H rats


title: eat-2 EV_1


title: Low Quality Blastocyst 2


title: Low Quality Blastocyst 1


title: RES.M.29840R

source_name: 29840R Reserpine treated P23H rats

value: Reserpine treated P23H


title: High Quality Blastocyst 17


title: daf-10 dve1_2


title: daf-10 dve1_3


title: daf-10 dve1_1


title: High Quality Blastocyst 16


title: DMSO.M.29861R

source_name: 29861R DMSO treated P23H rats


title: daf-10 atfs1_3


title: RES.M.29839R

source_name: 29839R Reserpine treated P23H rats


title: WT.M.32006R

source_name: 32006R WT untreated rats

value: WT untreated


title: DMSO.M.29864R

source_name: 29864R DMSO treated P23H rats


title: High Quality Blastocyst 15


title: daf-10 atfs1_2


title: DMSO.F.29843R

source_name: 29843R DMSO treated P23H rats

value: Female


title: High Quality Blastocyst 12


title: WT.M.32004R

source_name: 32004R WT untreated rats


title: WT.M.32005R

source_name: 32005R WT untreated rats


title: High Quality Blastocyst 14


title: DMSO.F.29844R

source_name: 29844R DMSO treated P23H rats


title: High Quality Blastocyst 13


title: daf-10 EV_2


title: daf-10 EV_3


title: High Quality Blastocyst 11


title: daf-10 EV_1


title: RIL treated-replicate 2

city: Columbus

first: Jing

middle: Jenny

last: Wang

state: OH

address: 460 W. 12th Street

department: Cancer Biology and Genetics

institute: Ohio State University

description: Sample C15

data_processing:
hisat2
featureCounts version 1.5.0-p3
DESeq2
edgeR
Assembly: mm39
Supplementary files format and content: riluzolevscontrol_deg_down original.xslx, excel file of downregulated genes following rizuole treatment
Supplementary files format and content: riluzolevscontrol_deg_up-original.xslx, excel file of upregulated genes following rizuole treatment

growth_protocol: CT26 cells were cultured in DMEM supplemented with 10% FBS at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Trizol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis

treatment_protocol: 24hr treatment with DMSO or 25uM Riluzole

value: Riluzole


title: DMSO.F.29842R

source_name: 29842R DMSO treated P23H rats


title: High Quality Blastocyst 9


title: RES.F.29858R

source_name: 29858R Reserpine treated P23H rats


title: ATAC-seq_P1_NGO_DcKO_rep2

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
Raw paired-end ATAC-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with default arguments.
The aligned reads were filtered to remove alignments mapped to multiple locations by calling grep with the -v option before being subjected to downstream analyses.
PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Biological replicates were pooled for visualization and other analyses after validation of reproducibility.
Peak calling for ATAC-seq data was performed using MACS3 (version 3.0.0a7) with default arguments.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: ovary

extract_protocol:
FACS-sorted cells were isolated from P1 ovaries or P3 testis and pooled as one replicate. Samples were lysed in 50 μl of lysis buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) on ice for 10 min. Immediately after lysis, nuclei were spun at 500 × g for 10 min at 4 °C to remove the supernatant.
Nuclei were then incubated 10 μl of transposition mix (0.5 µl homemade Tn5 transposase, 5 µl 2× TD buffer (10 mM Tris–HCl (pH 7.6), 10 mM MgCl2, and 20% Dimethyl Formamide), 3.3 µl PBS, 0.1 μl 1% digitonin, 0.1 μl 10% Tween-20, and 1 μl water) at 37 °C for 30 min in a thermomixer with shaking at 500 rpm.
the transposed DNA was purified with a MinElute kit (Qiagen). DNA libraries were prepared through the omni-ATAC method (PMID: 28846090)

tag: strain

value: C57BL/6 X 129S1/Sv X FVB/NJ

value: ovary

value: Non-growing oocytes

value: Chd4 f/-; Ddx4-Cre Tg/+

tag: age

value: postnatal day 1


title: ATAC-seq_P1_NGO_Dctrl_rep2

value: Chd4 f/+; Ddx4-Cre Tg/+


title: RES.F.29857R

source_name: 29857R Reserpine treated P23H rats


title: High Quality Blastocyst 10

source_name: spermatozoa

value: spermatozoa


title: daf-10 atfs1_1

source_name: whole worms

value: whole worms

value: atfs=1 RNAi


title: Control treated-replicate 2

description: Sample C13

value: WT

value: DMSO


title: ATAC-seq_P1_NGO_DcKO_rep1


title: High Quality Blastocyst 8


title: RES.F.29859R

source_name: 29859R Reserpine treated P23H rats

value: Retina


title: High Quality Blastocyst 6


title: RIL treated-replicate 1

description: Sample C3


title: WT.F.32011R

source_name: 32011R WT untreated rats


title: ATAC-seq_P1_NGO_Dctrl_rep1


title: RNA-seq_P3_male_DcKO_rep2

data_processing:
Raw paired-end RNA-seq reads after trimming by trimmomatic (version 0.39) were aligned to the mouse (GRCm38/mm10) genome using by STAR (version STAR_2.5.4b) with default arguments.
All unmapped and non-uniquely mapped reads were filtered out by samtools (version 1.9) before being subjected to downstream analyses.
To quantify aligned reads in RNA-seq, aligned read counts for each gene were generated using featureCounts (v2.0.1), which is part of the Subread package based on annotated genes (GENCODE vM25).
The TPM values of each gene were for comparative expression analyses.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample from RNA-seq analyses.

source_name: testis

extract_protocol:
Total RNA was extracted using the RNeasy plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions.
Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instruction. Prepared RNA-seq libraries were sequenced on the HiSeq X system (Illumina) with paired-ended 150-bp reads.

value: testis

value: Undifferentiated Spermatogonia

value: postnatal day 3


title: thymocytes, CD24-TCRb-, Bcl11b D/N440K, rep.1

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

description:
Bcl11b-N440K_count_table.csv
Bcl11b-N440K_norm_count_table.csv

data_processing:
Sequence reads were trimmed to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Low-quality parts and adapter sequences were trimmed by fastp (v0.20.0)
Trimmed short reads were mapped to the mm10 genome using STAR (v2.7.3a) with a GTF file from EMBL-EBI (GRCm38.99)
Unmapped reads and reads mapped with low-quality scores (MAPQ < 5) were removed by SAMtools (v1.9)
Duplicated reads were filtered out using Picard Tools (v2.21.1)
Mapped reads on each gene were counted using htseq-count (v0.11.2) with --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Raw counts were normalized using edgeR in R programming language (v3.38.2, Robinson et al.,  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010)
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts of each transcript for all samples
Supplementary files format and content: comma-separated values file includes edgeR normalized abundances of each transcript for all samples

source_name: Thymus

extract_protocol:
RNA was isolated using RNAClean XP beads (x2.2 vol., Beckman Coulter) directly from the lysis buffer, and was eluted into 10 uL of water containing RNase inhibitor (4u/uL RNasinPlus RNase Inhibitor, Promega).
RNA-seq libraries were prepared by applying a RamDA-seq method for single-cell RNA-seq (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018) with some modifications. The RNA was denatured by incubating at 65C for 5min, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 15min. Then cDNA was synthesized in 30uL of 1xRT Buffer containing RT Enzyme Mix (1.5uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (3.3uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 5uL of 10x NEB buffer2 (NEB), 1.25uL of dNTP mix (10mM each nt, NEB), 1.5uL of Klenow Fragment (3'→5' exo-, NEB), 5uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 7.25uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (x2 vol., Beckman Coulter) and quantified using Qubit (Qubit dsDNA HS Assay Kit, Invitrogen). Then ds-cDNA less than 1ng was applied for Tn5 tagmentation in a 25uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). DNA was purified using AMPure XP beads (x1.7 vol.) and amplified by 10~15 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.2 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: Thymus

value: CD24-TCRb- thymocytes

value: Bcl11b D/N440K

value: FACS purified


title: thymocytes, CD24-TCRb-, Bcl11b D/N440K, rep.2


title: WT.F.32010R

source_name: 32010R WT untreated rats

value: Female

value: WT untreated


title: Control treated-replicate 1

description: Sample C1


title: High Quality Blastocyst 7


title: High Quality Blastocyst 5


title: RNA-seq_P3_male_DcKO_rep1

value: C57BL/6 X 129S1/Sv X FVB/NJ

value: Chd4 f/-; Ddx4-Cre Tg/+


title: thymocytes, CD24-TCRb-, Bcl11b +/N440K, rep.2


title: RNA-seq_P3_male_Dctrl_rep1

value: Chd4 f/+; Ddx4-Cre Tg/+


title: thymocytes, CD24-TCRb-, Bcl11b +/N440K, rep.1


title: WT.F.32009R

source_name: 32009R WT untreated rats


title: thymocytes, CD24-TCRb-, Bcl11b +/+, rep.2


title: High Quality Blastocyst 2

value: spermatozoa


title: RNA-seq_P3_male_Dctrl_rep2


title: High Quality Blastocyst 4


title: WT.F.32008R

source_name: 32008R WT untreated rats


title: Thymocytes, TCF1-ChIP, Bcl11b +/N440K, rep.3

data_processing:
Low-quality parts and adapter sequences were trimmed from the short reads by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using bowtie2 (v2.3.5, Langmead & Salzberg, Fast gapped-read alignment with Bowtie 2, 2012)
Removing reads with low mapping quality (MAPQ<30), and duplicated reads using SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Piling up fragments using MACS2 with options -g mm -B --SPMR (v2.1.4, Zhang et al., Model-based analysis of ChIP-Seq (MACS), 2008)
Converting bedgraph into bigwig files using bdg2bw (https://gist.github.com/taoliu/2469050)
bam files from WT and N440K were merged respectively and peaks were called using MACS2 with options -g mm -q 0.05 --call-summits and input samples as control
Regions were extended 100bp for both directions from summits while keeping the most significant summit when nearby regions were overlapped and assigned as peaks
Counting the number of reads overlapping the peak using bedtools for each sample (v2.29.0, Quinlan et al., BEDTools: a flexible suite of utilities for comparing genomic features, 2010), which were normalized using edgeR (v3.38.2, Robinson et al.,  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010)
Assembly: mm10
Supplementary files format and content: tabular file including normalized counts of each transcript for all samples

extract_protocol:
Freshly isolated thymocytes cross-linked with 1% formaldehyde. Nuclei were isolated from the cells and lysed in Lysis Buffer by sonication. The lysate was incubated with rabbit anti-TCF1 antibody (CST, C46C7) pre-bound to Dynabeads® M-280 Sheep anti-Rabbit IgG overnight at 4 oC. Chromatin DNA was reverse-crosslinked and eluted. Samples were treated with RNase A and Proteinase K, and precipitated chromatin DNA was purified by use of ChIP DNA Clean & ConcentratorTM (ZYMO Research, CA).
Purified DNA was subjected to the re-sonication with a Covaris S220 to produce DNA fragments with an average size of 200 bp, and was used for library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed by Immugen with NovaSeq X.

value: Thymocytes

value: C46C7 (CST)


title: RNA-seq_P10_GO_GcKO_rep1

value: ovary

value: Growing oocytes

value: Chd4 f/f; Gdf9-iCre Tg/+

value: postnatal day 10


title: thymocytes, Bcl11b-ChIP, Bcl11b +/N440K, rep.2

description:
Bcl11b-ChIP_norm_count_in_peak.csv
Bcl11b-ChIP_raw_count_in_peak.csv

data_processing:
Low-quality parts and adapter sequences were trimmed from the short reads by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using bowtie2 (v2.3.5, Langmead & Salzberg, Fast gapped-read alignment with Bowtie 2, 2012)
Removing reads with low mapping quality (MAPQ<30), and duplicated reads using SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Piling up fragments using MACS2 with options -g mm -B --SPMR (v2.1.4, Zhang et al., Model-based analysis of ChIP-Seq (MACS), 2008)
Converting bedgraph into bigwig files using bdg2bw (https://gist.github.com/taoliu/2469050)
bam files from WT and N440K were merged respectively and peaks were called using MACS2 with options -g mm -q 0.05 --call-summits and input samples as control
Regions were extended 100bp for both directions from summits while keeping the most significant summit when nearby regions were overlapped and assigned as peaks
Counting the number of reads overlapping the peak using bedtools for each sample (v2.29.0, Quinlan et al., BEDTools: a flexible suite of utilities for comparing genomic features, 2010), which were normalized using edgeR (v3.38.2, Robinson et al.,  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, 2010)
Assembly: mm10
Supplementary files format and content: bigWig files: read coverage across the whole genome (fragment pileup per million reads)
Supplementary files format and content: comma-separated values file includes raw read counts in peaks for all samples
Supplementary files format and content: comma-separated values file includes normalized read counts in peaks for all samples

extract_protocol:
Freshly isolated thymocytes cross-linked with 1% formaldehyde. Nuclei were isolated from the cells and lysed in Lysis Buffer by sonication. The lysate was incubated with rabbit anti-mouse Bcl11b antibody (Bethyl, A300-385A) pre-bound to Dynabeads® M-280 Sheep anti-Rabbit IgG overnight at 4 oC. Chromatin DNA was reverse-crosslinked and eluted. Samples were treated with RNase A and Proteinase K, and precipitated chromatin DNA was purified by use of ChIP DNA Clean & ConcentratorTM (ZYMO Research, CA).
Purified DNA was subjected to the re-sonication with a Covaris S220 to produce DNA fragments with an average size of 200 bp, and was used for library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed by genomics facility at RIKEN IMS with Illumina HiSeq 2500.


title: thymocytes, CD24-TCRb-, Bcl11b +/+, rep.1


title: Average Quality Blastocyst 13


title: thymocytes, Bcl11b-ChIP, Bcl11b +/N440K, rep.1


title: RNA-seq_P10_GO_Gctrl_rep1

value: Chd4 f/f


title: High Quality Blastocyst 1


title: Thymocytes, TCF1-ChIP, Bcl11b +/N440K, rep.2

value: Thymus


title: Thymocytes, TCF1-ChIP, Bcl11b +/N440K, rep.1


title: thymocytes, Bcl11b-ChIP, Bcl11b +/N440K, rep.3


title: High Quality Blastocyst 3


title: Thymocytes, TCF1-ChIP, Bcl11b +/+, rep.3


title: Average Quality Blastocyst 11


title: RNA-seq_P10_NGO_GcKO_rep2

value: Non-growing oocytes


title: RNA-seq_P10_GO_GcKO_rep2


title: RNA-seq_P10_GO_Gctrl_rep2


title: Thymocytes, TCF1-ChIP, Bcl11b +/+, rep.2


title: Average Quality Blastocyst 10


title: RNA-seq_P10_NGO_GcKO_rep1


title: thymocytes, Bcl11b-ChIP, Bcl11b +/+, rep.3


title: Average Quality Blastocyst 9


title: thymocytes, Bcl11b-ChIP, Bcl11b +/+, rep.1


title: RNA-seq_P10_NGO_Gctrl_rep1


title: thymocytes, Bcl11b-ChIP, Bcl11b +/+, rep.2


title: Old CR 28 months old_17

city: Liverpool

first: Gulam

last: Altab

address: 6 West Derby Street

institute: University of Liverpool

data_processing:
The raw Fastq files were trimmed for the presence of Illumina adapter sequences using Cutadapt version 1.2.1.
The reads were further trimmed using Sickle version 1.200 with a minimum window quality score of 20
The filtered reads were mapped to the rat reference genome (ftp.ensembl.org/pub/release-100/fasta/rattus_norvegicus/dna/) using STAR 2.3.0e. MultiQC showed the alignment score was above 80% for all the samples.
To count the number of reads that mapped to each gene, featureCount was used to obtain the read count. Ensembl Rattus_norvegicus.Rnor_6.0.96.gtf were chosen as annotation references for the analyses.
Assembly: Ensembl Rattus_norvegicus.Rnor_6.0.96.gtf
Supplementary files format and content: rawcounts_protein_coding.txt

source_name: gastrocnemius muscle

extract_protocol:
Total RNA from gastrocnemius muscle tissues was isolated using RNeasy Plus Universal Mini Kit (Qiagen, UK) according to manufacturer instructions.
Strand-specific RNA-seq library preparation was done using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina, according to manufacturer protocol.

treatment_protocol: Between 21–28 days of age, rats were kept in barrier conditions on a 12-h light:12-h dark cycle (08:00–20:00). Regular health monitoring occurred through sentinel animal screening. Until 2 months old, rats were group-caged and fed the non-supplemented CRM diet ad libitum. At 2 months, rats were individually housed and randomly assigned to either caloric restriction (CR) or ad libitum (AL) groups. AL and CR rats were sacrificed at 6, 12, and 28 months. CR rats were fed the CRM diet at 55% of the daily intake of control rats to maintain body weight at ~55% of age-matched AL-fed animals. CR rats received pre-weighed rations daily between 10:30 and 11:00 h.

value: gastrocnemius muscle

value: 28 months

value: Caloric Restriction


title: Average Quality Blastocyst 8


title: Old CR 28 months old_16


title: RNA-seq_P10_NGO_Gctrl_rep2


title: thymocytes, total input, Bcl11b +/+, rep.1


title: Average Quality Blastocyst 6


title: Old CR 28 months old_14


title: JQ1_biol-rep2

city: Sevilla

first: Elena

last: Gómez Marín

address: Av. Américo Vespucio, 24

country: Spain

institute: CSIC

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using the subjunc function from the Rsubread package, and reads were mapped to the hg19 human reference genome.
The downstream analysis was performed on .bam files with duplicates removed using the samtools (v0.1.19) rmdup command.
The FeatureCounts() function from the Rsubread package was used to assign reads to the UCSC hg19 KnownGenes using GTF.featureType = “exon”, GTF.attrType = “gene_id” and strandSpecific = 2 parameters with the duplicate-removed .bam files.
Differential gene expression analysis and statistics were performed using the DESeq2 Bioconductor. Differentially expressed genes with adjusted p value < 0.05 and Log2FC ≥ 0.5 (upregulated genes) or Log2FC < - 0.5 (downregulated genes) were selected for further analysis.
Assembly: hg19
Supplementary files format and content: Raw counts per UCSC knownGenes for every gene and every sample in a .tsv file

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 150 μg of total RNA was used for the construction of sequencing libraries.
The libraries were prepared with the Stranded mRNA Prep kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NextSeq 500 MID Output y 2x75 pb length parameters

treatment_protocol: Cell were transfected with the indicated plasmids for 24 hours, using lipofectamine as transfection agent. For JQ1 drug treatment, a concentration of 1 μM was used for 16 hours.

value: epithelial

value: WT

value: JQ1 1 μM treatment


title: JQ1_biol-rep1


title: Thymocytes, TCF1-ChIP, Bcl11b +/+, rep.1


title: E+SEED_biol-rep2

value: Plasmid transfection for overexpression of E and SEED proteins


title: RNA-seq_P5_NGO_DcKO_rep1

value: C57BL/6 X 129S1/Sv X FVB/NJ

value: Chd4 f/-; Ddx4-Cre Tg/+

value: postnatal day 5


title: Old CR 28 months old_15


title: Average Quality Blastocyst 12

value: spermatozoa


title: RNA-seq_P5_NGO_Dctrl_rep1

value: ovary

value: Chd4 f/+; Ddx4-Cre Tg/+


title: Average Quality Blastocyst 5


title: Average Quality Blastocyst 7


title: Old 28 months old_11

value: Ad Libitum


title: Old 28 months old_12


title: Average Quality Blastocyst 4


title: RNA-seq_P5_NGO_DcKO_rep2


title: RNA-seq_P1_NGO_DcKO_rep1

value: postnatal day 1


title: E+SEED_biol-rep1


title: Average Quality Blastocyst 3


title: Old CR 28 months old_13


title: Average Quality Blastocyst 2


title: Old 28 months old_10


title: E-protein_biol-rep2

value: Plasmid transfection for overexpression of E protein


title: RNA-seq_P1_NGO_DcKO_rep2

value: Non-growing oocytes


title: RNA-seq_P5_NGO_Dctrl_rep2


title: Average Quality Blastocyst 1


title: Old CR 28 months old_18

value: gastrocnemius muscle


title: thymocytes, total input, Bcl11b +/+, rep.2

value: Thymus

value: Thymocytes


title: E-protein_biol-rep1

value: epithelial


title: RNA-seq_P1_NGO_Dctrl_rep1


title: heart, COX8-AGO2, 1

city: Wuhan

first: zhan

last: jiabing

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Low quality reads were filtered by fastp. Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed. Reads with length between 20-40bp were retained for subsequent analysis. Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed.
Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2-pass setting enabled. The reads mapped to classical noncoding RNAs (including long noncoding RNAs, microRNA precursors) were abandoned. Then remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment.
Three-nucleotide periodicity was plotted using the riboWaltz R package[6] as described. For RFs with specific length (e.g. RFs with length of 30nt), reads were assigned to frame 1,2,or 3 according to their position of 5’end in transcripts of protein coding gene, then proportion of total RFs in fame 1, 2 and 3 were calculated among all protein coding genes. Because the translocation of ribosomes occurs along the mRNA one codon at a time, the potential of single-codon resolution pauses were investigated. Using PausePred（https://pausepred.ucc.ie/）, which infers the locations of ribosome pauses, global single codon pauses were analyzed.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. Reads counts in the open reading frame of coding genes was calculated by software RSEM,and the gene expression level was normalized by using FPKM (fragment per kilobase of transcript per million mapped reads) method
Assembly: Ensembl_release 109
Supplementary files format and content: Mus musculus (Ensembl_release109)
Library strategy: Ribo-seq

source_name: Heart

extract_protocol:
Cells pellet were immediately frozen in liquid nitrogen and ground to power in liquid nitrogen with a mortar and pestle, then dissolved in 400μL of lysis buffer. The resuspended extracts in lysis buffer were transferred to new microtubes, pipetted several times and incubated on ice for 10 min. Then cells were triturated ten times through a 26-G needle. The lysate was centrifuged at 20000g for 10min at 4℃, and the supernatant was collected. To prepare RFs , 10μL of RNase I (NEB, Ipswich, MA, USA) and 6μL of DNase I (NEB, Ipswich, MA, USA) were added to 400μL of lysate，which was then incubated for 45 min at room temperature with gentle mixing on a Nutator mixer. Nuclease digestion was stopped by adding 10μL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27- 5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and centrifuged at 600g for 4 min at room temperature. 100μL of digested RFs were added to the column and centrifuged at 600g for 2 min. Next, 10μL 10% (wt/vol) SDS was added to the elution, and RFs with a size greater than 17nt was isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research;R1017). short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China).
After obtaining ribosome footprints above, Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). Briefly, adapters were added to both ends of RFs, followed by reverse transcription and PCR amplification. The 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM X10 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Heart


title: Old 28 months old_7

value: 28 months


title: AUTS2-/- D75

data_processing:
For aligning the sequence data to the reference genome (GRCh38/hg38), Bowtie was employed, while HTseq was used to compile the gene abundance matrix for each cell.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data is tab-separated values (tsv) file and contains the unfiltered raw counts for each cells, whose row names are gene symbol and column names are sample ID.

extract_protocol:
The cerebral organoids were treated with Papain to dissociate them into single cells and were loaded onto a Fluidigm C1™ Single-Cell Autoprep System (C1).
Individual cells were loaded onto a Fluidigm C1™ Single-Cell Autoprep System (C1) for automated capture and subsequent sequencing-ready library preparation.

value: Embryonic stem cells

value: Cerebral organoids differentiation


title: RNA-seq_P1_NGO_Dctrl_rep2

value: C57BL/6 X 129S1/Sv X FVB/NJ


title: Old 28 months old_9


title: Control_biol-rep1

value: WT

value: Empty plasmid vector transfection


title: AC16 cells, AGO2-KO, 2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Homo sapiens (Ensembl_release109)
Supplementary files format and content: AGO2-KO AC16-mRNA-expression.txt (tpm and count)

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

value: AGO2 knock out


title: hiPSC-MNs_siQKI3

data_processing:
alignment with OLego
to have BAM and Bed file
transcript level and alternative splicing events with Quantas
Assembly: hg19
Supplementary files format and content: .txt gene_id gene_symbol, Tag_Number, RPKM, start and end position, strand and isoform tag_number

source_name: hiPSC-MNs

extract_protocol:
Total RNA was obtained from each three biological replicates of hiPSC-MNs  treatment with control siRNA and three different siRNA for QKI gene. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using Illumina TruSeq protocols, fragmentation, and adaptor ligation according to the manufacturer’s instructions.
TruSeq RNA Sample Prep Kit

value: siRNA for QKI gene


title: Young 6 months old_5

value: 6 months

value: Ad Libitum


title: AC16 cells, AGO2-KO, 1


title: hiPSC-MNs_siQKI1


title: Old 28 months old_8


title: AC16 cells, AGO2-KO, 3


title: Control_biol-rep2


title: thymocytes, CD24-TCRb-, Tcf7 F/F : Vav1-Cre, rep.3

description:
Tcf7-KO_count_table.csv
Tcf7-KO_norm_count_table.csv

value: CD24-TCRb- thymocytes

value: Tcf7 F/F :Vav1-Cre

value: FACS purified


title: Young 6 months old_6

value: gastrocnemius muscle


title: Young 6 months old_3


title: AUTS2+/- D75


title: heart, GFP, 1

value: GFP


title: thymocytes, CD24-TCRb-, Tcf7 F/F : Vav1-Cre, rep.1

value: Thymus


title: AC16 cells, WT, 2

value: wild type


title: hiPSC-MNs_siQKI2


title: thymocytes, CD24-TCRb-, Tcf7 F/F : Vav1-Cre, rep.2


title: hiPSC-MNs_NC3

value: control siRNA


title: Young 6 months old_2


title: AC16 cells, WT, 3


title: Young 6 months old_4


title: AC16 cells, WT, 1


title: hiPSC-MNs_NC2


title: thymocytes, CD24-TCRb-, Tcf7 +/+, rep.1


title: Young 6 months _1


title: hiPSC-MNs_NC1


title: thymocytes, CD24-TCRb-, Tcf7 +/+, rep.2


title: uphill treadmill running group-U

status: Public on Sep 26 2024

type: RNA

city: Ji’nan ,China

first: jie

middle: -yong

last: yang

address: 山东省济南市世纪大道10600号

institute: Human Movement Science

description: Gene expression data from PBMCs

hyb_protocol: Hybridization Cocktail for Single Probe Array with fragmented cRNA (49/64 Format Array ,100 Format(Midi) Array and 169/400 Format Array) used Eukaryotic Hybridization Control Kit(Affymetrix ) for Pre-Hybridization. Hybridization solution was incubated at 99 ° C for 5 min and then incubated at 45 ° C for 5 min. chips were took out from  Pre-Hybridization Mix and put into  Hybridization Cocktail for  Hybridizatio in Hybridization Oven 640  (Affymetrix) ,then wash and stain using Hybridization, Wash, and Stain Kit (Affymetrix) with 45℃，60 rpm for16 hr . Chips were stained and washed in 600 µL Stain Cocktail ,1600 µL Stain Cocktail 2  and 800 µL Array Holding Buffer in turn acording  to the number of chips  AGCC  software (Affymetrix® GeneChip® Command Console® Software) for 90 min.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000

data_processing: The fluorescence scan image of the chip is saved as a .DAT file. Use AGCC software (Affymetrix® GeneChip® Command Console® Software) to convert the .DAT file from the image signal to a digital signal, that is, a .CEL file. The .CEL file records the fluorescence signal intensity at the probe level. Use .CEL files as source files for data preprocessing: including background correction, integrating probe signals into probeset signals, and normalizing between slices to remove inter-sample variation caused by non-biological factors. Data preprocessing uses RMA algorithm

label: biotin

source_name: the peripheral blood mononuclear cells (PBMCs)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: PBMCs was extracted from 2ml of the mixture and total RNA extracted with RNeasy Fibrous Tissue (US, OMEGA).

value: two-month-old

value: male

value: Sprague–Dawley

value: uphill treadmill running group-U


title: controlgroup-C

address: 山东省济南市世纪大道10600号

description: Gene expression data from PBMCs

value: peripheral blood mononuclear cells (PBMCs)

value: control group-C


title: downhill treadmill running group-D

address: 山东省济南市世纪大道10600号

description: Gene expression data from PBMCs

value: downhill treadmill running group-D


title: CJ

type: genomic

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

description: MethylatinEPIC array of TNBC tumor sample

hyb_protocol: Hybridization was performed according to Illumina DNA methylation experimental guide

scan_protocol: MethylationEPIC arrays were scanned according to the manufacturer's instructions and recommendation at the Dartmouth Genomics Shared Resources

data_processing: Raw intensities were preprocessed using the minfi R/Bioconductor framework. Technical probes and probes failed to be consistently detected in the samples were excluded.

label: Cy3, Cy5

label_protocol: standard Illumina protocol

extract_protocol: DNA were extracted with the QIAamp (Qiagen) kit and measured on the MethylationEPIC kit according to manufacturer's instructions

tag: idatbasename

tag: macrodissected

value: TRUE

tag: ageatdx

tag: brcamutation

value: FALSE

value: Yes


title: F


title: J

value: No


title: CP


title: S


title: CH


title: K


title: P


title: N


title: BS


title: CG


title: C

value: wild-type


title: CK


title: BP


title: G


title: BQ


title: L


title: E


title: I


title: U


title: D


title: H


title: B


title: A


title: CL


title: X


title: AP


title: AF


title: AD


title: AL


title: AI


title: O


title: Z


title: AR


title: AJ


title: Q


title: AE


title: BI


title: AG


title: CA


title: CO


title: AQ


title: CN


title: BC


title: AK


title: W


title: AN


title: AS


title: AY


title: AT


title: AW


title: AX


title: V


title: BZ


title: AZ


title: BD


title: T60

value: Not applicable (fresh frozen)


title: R


title: T59


title: AM


title: T58


title: T42


title: T54


title: T55


title: T53


title: hiPSC-EP, growth factor, rep 2

city: Austin

first: Brett

last: Stern

state: Texas

address: 2515 Speedway

institute: The University of Texas at Austin

data_processing:
Deduplication as well as Tag, adapter, and polyA tail removal were contucted by the UT Austin Bioinformatics Consulting Group
FASTQ files were processed using nf-core/rnaseq (v3.14.0)
Triming was conducted using fastp
Trimed reads were mapped to the CRCh38.p14 using STAR
Reads were quantified using SALMON
Assembly: GRCh38.p14
Supplementary files format and content: tab delimited text file containing the raw counts for each sample

growth_protocol: hiPSCs were maintained in Essential 8 Media (ThermoFisher Scientific) in a humidified incubator at 37°C and 5% CO2. Cells were passaged at 70-80% confluency.

extract_protocol:
A total of 500,000 CD34+-hiPSC-EPs from both differentiation protocols were centrifuged twice and messenger RNA (mRNA) was isolated using an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. Each sample was diluted in nuclease-free water to a total volume of 25 µL at 25 ng/µL and submitted to the University of Texas at Austin Genomic Sequencing and Analysis Facility for 3'-Tag RNAseq (TagSeq) preparation.
Library preparation was created by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin.

treatment_protocol: hiPSCs were differentiated using a protocol that utilizes either small molecules or growth factors. In brief, the small molecule protocol induces mesoderm formation through CHIR99021 (LC Laboratories) followed by endothelial specification using ascorbic acid (Sigma-Aldrich). The growth factor induces mesoderm formation through a combination of Activin A (R&D Systems), BMP4 (R&D Systems) and BIO (Selleckchem) followed by endothelial specification using VEGF (R&D Systems) and SB431542 (Tocris). hiPSC-derived endothelial progenitors were lifted using Accutase (StemCell Technologies) and stained using a CD34-PE antibody (Miltenyi Biotec). CD34+-hiPSC-EPs were isolated using fluorescence activated cell sorting.

value: induced pluripotent stem cell

value: WT

value: Endotheial progenitor differentiation, growth factor


title: hiPSC-EP, growth factor, rep 1


title: hiPSC-EP, growth factor, rep 3


title: T48


title: T41


title: T45


title: hiPSC-EP, growth factor, rep 4


title: T37


title: hiPSC-EP, small molecule, rep 4

value: Endotheial progenitor differentiation, small molecule


title: hiPSC-EP, small molecule, rep 3


title: T43


title: T21


title: T28


title: hiPSC-EP, small molecule, rep 1


title: T23


title: T35


title: T11


title: T30


title: T27


title: T12


title: T14


title: Peripheral blood CD8+ T cells, MS Twin cohort, scRNAseq

city: Planegg

first: Vladyslav

last: Kavaka

address: Großhaderner Str. 9

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

data_processing:
Cell Ranger software (10x Genomics, v.6.1.0) was used to demultiplex samples, process raw data, align reads to the GRCh38 human reference genome, and summarize unique molecular identifier (UMI) counts. Subsequently, the filtered UMI count matrices were processed with Seurat R Package (v.4.1.0) by discarding the cells expressing fewer than 500 and more than 5000 features and/or >15% mitochondrial reads. In the next step, the samples were split and integrated via the rPCA method with the 5000 variable features per sample (vst method) selected. After the integration, the corresponding TCR information was added to the meta.data slot of the Seurat object, and cells lacking TCR data were discarded. T cells with TCRs presented in more than two cells per clonotype were considered as expanded. Cells containing either no TCR-β chain information or more than one TCR-β chain were removed to exclude the possibility of contamination by doublets/multiplets. After quality control steps, the variable features were newly identified using the FindVariableFeatures function of the Seurat package (vst method, n = 2000). The expression data were scaled with regression of the number of counts and percentage of mitochondrial genes per cell and subsequent PCA calculation. In the next step, unbiased k-nearest neighbors and cluster identification were achieved with the FindNeighbors and FindClusters functions of the Seurat R package. Next, the two-dimensional uniform manifold approximation and projection (UMAP) was generated to visualize the cell embedding. The differential gene expression (DGE) comparison of each cell cluster against the rest of the cells was performed with the FindAllMarkers function by filtering the genes according to the p-adjusted threshold of 0.05. Based on the output, clusters containing genes associated with the myeloid cell compartment, and those with low-quality cells, were discarded. The steps described above were repeated to achieve final embedding using the first 20 PCA dimensions for UMAP calculation under 0.8 resolution for cluster estimation. The clusters were annotated using one of the differentially expressed genes from the output of the FindAllMarkers function. T cell subsets were sorted from 1 to 10 by the fraction of expanded cells per cluster. The pseudotime analysis was performed by using the R package monocle3. The visualization plots were computed with ggplot2 (v.3.4.0) and Seurat R packages.
Assembly: GRCh38
Supplementary files format and content: Seurat objects, meta.data tables with single-cell TCR information

source_name: Peripheral blood

extract_protocol:
After blood collection into EDTA-containing tubes (Sarstedt), we performed a 1:1 dilution with PBS and transferred the cell suspension to a SepMate tube containing human Pancoll (Pan Biotech). Subsequently, PBMCs were isolated by density gradient centrifugation at 1200g for 10 mins at 4°C. The isolated cells were concentrated by centrifugation at 300g for 10 min at 4°C before resuspension at 1 × 107 cells per ml in serum-free cryopreservation medium (CTL-Cryo™ ABC Media Kit, Immunospot), and storage over liquid nitrogen. Cryopreserved PBMCs were quick-defrosted, diluted in a 1% BSA (Sigma-Aldrich) in PBS solution, and washed twice by centrifugation at 300g for 10 minutes at 4°C. Subsequently, the cells were resuspended in 100 µl of antibody cocktail containing: anti-human CD45RO-FITC (ThermoFisher, #11-0457-42, dilution 1:40), CCR7-APC (ThermoFisher, #17-1979-42, 1:40), CD3-AF700 (ThermoFisher, #56-0037-42, 1:50), Fixable Viability Dye eFluor™ 780 (ThermoFisher, #65-0865-14, 1:1000), CD4-Pacific Blue (ThermoFisher, #MHCD0428, 1:25), CD8-PerCP (BioLegend, #344708, 1:50), Fc-block (Miltenyi, #130-059-901, 1:50), and 1% BSA in PBS (85.9 µl). After 30 minutes of incubation at 4°C, the cells were resuspended in 700 µl of 1% BSA in PBS solution and subjected to fluorescence-activated cell sorting.
The collected antigen-experienced CD8+ T cells (all single CD3+CD8+CD4- lymphocyte events falling outside the CD45RO-CCR7+ population/gate) were subsequently washed by centrifugation in 0.04% BSA (Invitrogen) in PBS solution at 300 g for 10 mins at 4°C, resuspended according to the 10x Genomics manufacturer’s protocol (Chromium NextGEM Single Cell V(D)J Reagent kits v1.1) and approximately 25,000 cells per sample were loaded onto the Chromium Next GEM Chip G (10x Genomics). Once on the chip, the loaded T cells were processed according to the 10x Genomics manufacturer’s protocol (Chromium NextGEM Single Cell V(D)J Reagent kits v1.1). The generated gene expression and TCR libraries were sequenced with NovaSeq S4 Flowcells using 150 bp paired-end reads and 8bp for the i7 index, aiming for 50,000 reads-per-cell for gene expression and 5,000 reads-per-cell for the TCR data.

value: Peripheral blood

value: CD8+ T cells


title: T20


title: Peripheral blood CD8+ T cells, validation cohort, scRNAseq


title: patient 21

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

data_processing:
RNA was aligned to the HG38 genome using HISAT2. Gene counts were determined using Subread featurecounts. Counts were normalized using DESeq2 and DEGs called using Deseq2.
Assembly: HG38
Supplementary files format and content: CSV file containing raw counts from each sample

source_name: ffpe-tumor

extract_protocol:
Consecutive 10 μm sections were prepared from formalin-fixed paraffin embedded (FFPE) blocks and areas of relevant pathology were circled on one slide which had been stained with H&E. The identified areas were macrodissected from the slides and placed into AutoLys M Tubes (ThermoFisher) for deparaffinization. Sequential DNA and RNA isolation from the recovered tissue was performed on a KingFisher Flex using the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit (ThermoFisher).
RNA quality was assessed using a TapeStation 4200 (Agilent) and 50 nanograms of total RNA was used as input for library preparation using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio) according to the manufacturer’s instructions. RNA-Seq Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~50 million reads per sample on average.

value: ffpe-tumor

value: clear cell RCC

value: cabozantinib


title: patient 20


title: patient 22


title: patient 17


title: patient 16


title: patient 15


title: T34


title: T32


title: patient 14


title: T15


title: patient 10


title: patient 11


title: patient 7


title: patient 8


title: T19


title: CAF rep 3

city: Bengaluru

first: Prathibha

last: Ranganathan

state: Karnataka

address: Electronic City Phase I

country: India

institute: Centre for Human Genetics

data_processing:
Paired-end raw sequence reads quality report is generated by using FastQC to estimate base quality and contamination by sequencing artefacts.
Trim Galore is used to perform trimming of adapters and poor-quality sequences.
Trimmed sequence reads was mapped to reference with splice aware alignment tool STAR.
Feature specific expression counts were estimated by using the Rsubread R package; Detection and removal of low count features across samples was performed NOISeq R package.
Expression counts normalization was performed with TMM method from NOISeq R package;  Estimation of significant differential features was performed with NOISeq R package which simulates technical replicates for data without biological replicates
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
Supplementary files format and content: >txt fle containing the raw read counts for all samples (counts_raw.txt)

source_name: Prostate cancer

extract_protocol:
Total RNA was isolated using Rneasy mini kit (Qiagen). 200ng of total RNA was used for making the libraries.
KAPA Riboerase kit was used to deplete rRNA. KAPA RNA Hyper prep kit was used to construct the libraries.

value: Prostate cancer


title: patient 5


title: A549 cells, shD3#4, biol_rep_3

city: Cambridge

first: Tony

last: Kouzarides

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
Adapter sequences were trimmed from paired-end reads using Trimmomatic (v0.40-rc1)
Reads were aligned to the human reference genome (GRCh38.p14) using STAR (v2.7.10a), with –quantMode GeneCounts to quantify gene counts with the annotation source NCBI RefSeq reference transcriptome GTF file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: A549 cells were grown in DMEM supplemented with 1 x penicillin-streptomycin (pen-strep) antibiotics and 10% [v/v] foetal bovine serum (FBS).

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104) was used for RNA extraction. An additional step of DNase digestion was incorporated after the first wash following the RNase-Free DNase Set protocol (QIAGEN, 79254). 13 µl of rRNA depleted RNA sample were used for the preparation of the RNA-seq library.
The NEXTFLEX® Rapid Directional RNA- Seq Kit 2.0 protocol was followed to perform all the remaining steps for library construction steps.

value: lung carcinoma epithelial cells

value: THUMPD3 knockdown


title: patient 4


title: patient 3


title: A549 cells, shD3#4, biol_rep_2


title: CAF rep 1


title: A549 cells, shD3#4, biol_rep_1


title: patient 1


title: HE-hema, normoxia, GEX

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
CellRangerARC 2.0.2 used for demultiplexing + read mapping + barcode assignment + UMI counting + fragment calling
Assembly: GRCh38.p13
Supplementary files format and content: CellRanger ARC output files: Filtered tab-delimited feature and cell-barcode files; matrix market files
Supplementary files format and content: CellRAngerARC output files: CellRanger-called peaks file in BED format, tab-delimited fragments files

source_name: human iPS cell line RB11

growth_protocol: CD34+ hemogenic endothelial cells were subcultured on rhLaminin-521-coated flat bottom 48-well plates (100,000-130,000 cells per well), in a humidified incubator at 37°C in normoxia (5% CO2, 20% O2) or hypoxia (5% CO2, 4% O2).

extract_protocol:
On day 3 of subculture, nuclei were isolated following the low nuclei input protocol by 10x Genomics (with 10-minute centrifugations). The diluted nuclei buffer, the wash buffer and the lysis buffer were freshly prepared according to manufacturer’s instructions. The lysis buffer used at 0.5x for 2 minutes for all conditions. In all conditions, we confirmed 100% lysis by microscopy.
The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) was used to prepare the samples according to manufacturer’s instructions. A Chromium iX was used to do the droplet encapsulation. An Agilent TapeStation and a QubitFlex were used to generate cDNA and library traces and to measure concentrations. Libraries were sequenced on a NovaSeq 6000 according to the recommendations by 10x Genomics with the aim to reach 50.000 reads/nucleus.

value: human iPS cell line RB11

value: HE-derived cells


title: BPH fibroblasts rep 3

source_name: Prostate (BPH)

value: Prostate (BPH)


title: CAF rep 2


title: A549 cells, sh4Control, biol_rep_3


title: T02

value: FALSE

value: Yes


title: HE-hema, hypoxia, ATAC

source_name: human iPS cell line RB10

value: human iPS cell line RB10


title: hiPSC-EP, small molecule, rep 2

value: induced pluripotent stem cell

value: WT


title: patient 13


title: 22Rv1, siMED12, rep3

city: Innsbruck

first: Florian

last: Handle

address: Müllerstrasse 44

department: Institute of Pathology, Neuropathology and Molecular Pathology

country: Austria

institute: Medical University of Innsbruck

data_processing:
The multiplexed fastq file was split into individual per sample fastq files with STARsolo using the cellular barcodes and PCR duplicates were removed using the UMIs. Read alignment and counting of the individual fastq files were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13)
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID, gene symbol and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID, gene symbol and log2 transformed CPM gene expression values for each sample

growth_protocol: All cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.

extract_protocol:
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Library prep was performed with the high throughput 3’ tag BRB-seq kit from Alithea genomics using early barcoding RT primers.

treatment_protocol: Cells were seeded in 6-well plates and incubated for 24 h. Cells were transfected with 25pmol ON-TARGETplus SMARTpools (siCtrl: non-targeting pool, #D-001810-10-05; siMED12: human MED12 siRNA, #L-009092-00-0005) or siAR (5'GCACUGCUACUCUUCAGCA dTdT 3' ) using Lipofectamine RNAiMAX. The medium was changed after 6 h and the cells were harvested at 3 days after transfection.


title: BPH fibroblasts_rep 2


title: T08

value: Not applicable (fresh frozen)

value: No


title: HE-hema, normoxia, ATAC

source_name: human iPS cell line RB12

value: human iPS cell line RB12


title: T01


title: BPH fibroblasts_rep 1


title: 22Rv1, siMED12, rep1


title: A549 cells, sh4Control, biol_rep_1


title: 22Rv1, siCtrl, rep3

value: siCtrl


title: T06

value: wild-type


title: 22Rv1, siCtrl, rep1


title: 22Rv1, siCtrl, rep2


title: HE-hema, hypoxia, GEX

source_name: human iPS cell line RB9

value: human iPS cell line RB9


title: T17


title: A549 cells, shD3#1, biol_rep_2


title: ATAC-Ino80KO_TGFb_Rep2

city: New York

first: Jun Ho

last: Lee

address: 417 E 68th St

institute: MSKCC

data_processing:
Sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to mouse assembly mm10 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain regions of chromatin accessibility, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/ mm10-mouse/mm10.blacklist.bed.gz) then merging all peaks within 500 bp for ChIP and CUT&RUN or taking 500 bp windows around peak summits for ATAC and counting reads with featureCounts (v1.6.1). DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts. Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site. Peak intersections were calculated using bedtools and intersectBed with 1 bp overlap. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu).
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
samples containing 5x104 cells were washed twice with cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) and resuspended with ice-cold ATAC-lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P-40, 0.1% Tween-20, 0.01% digitonin), followed by incubation on ice for 3 min. After washing the cells with cold ATAC-wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20), cells were resuspended with 50 μL of transposition mix (10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 10% dimethyl formamide, 100 nM Nextera TDE1 (Illumina, Cat #: FC-121–1030), 0.01% Digitonin, 0.1% Tween-20) and incubated at 37ºC for 30 min in a thermomixer with 1000 rpm mixing. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2× PCR Master Mix (NEB, Cat #: M0541). Libraries were purified by double-sided size selection with AMPure XP beads (Beckman Coulter) and assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent, Cat #: 5067-4626).

value: Lung adenocarcinoma cells

value: TGF-Beta for 1.5 h


title: 22Rv1, siMED12, rep2


title: PC3, siMED12, rep3


title: A549 cells, shD3#1, biol_rep_3

value: lung carcinoma epithelial cells

value: THUMPD3 knockdown


title: ATAC-Ino80KO_SB_Rep2


title: ATAC-Ino80KO_TGFb_Rep1


title: T10


title: PC3, siMED12, rep2


title: A549 cells, shD3#1, biol_rep_1


title: PC3, siMED12, rep1


title: ATAC-Ino80KO_SB_Rep1


title: A549 cells, sh1Control, biol_rep_3


title: PC3, siCtrl, rep1


title: A549 cells, sh1Control, biol_rep_2


title: LNCaP, siAR, rep3

source_name: LNCaP

value: LNCaP

value: siAR


title: LNCaP, siAR, rep2


title: A549 cells, sh1Control, biol_rep_1


title: LNCaP, siAR, rep1


title: ATAC-Rreb1KO_SB_Rep2


title: LNCaP, siMED12, rep3


title: A549 cells, siTHUMPD3, biol_rep_3


title: Placenta, PBS treat, rep5

city: Guangzhou

first: Shanshui

last: Zeng

address: Bsogao Road

institute: Southern medical university

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome (Ensembl_release104) using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release104
Supplementary files format and content: raw counts, FPKM for each Sample

source_name: Placenta

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)  beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB  #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The  ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were  subjected to size selection by agarose gel electrophoresis and polymerase chain reaction  (PCR) amplified.

value: Placenta

value: wild type

value: PBS treat


title: Placenta, PBS treat, rep4


title: LNCaP, siMED12, rep2


title: A549 cells, siTHUMPD3, biol_rep_2


title: A549 cells, siTHUMPD3, biol_rep_1


title: PC3, siCtrl, rep3


title: LNCaP, siCtrl, rep3


title: ATAC-Rreb1KO_SB_Rep1


title: ATAC-WT_TGFb_Rep1


title: PC3, siCtrl, rep2


title: Placenta, PBS treat, rep2


title: A549 cells, siControl, biol_rep_2


title: LNCaP, siCtrl, rep2


title: ATAC-Rreb1KO_TGFb_Rep2


title: ATAC-WT_SB_Rep2


title: LNCaP, siMED12, rep1


title: Placenta, PBS treat, rep1


title: A549 cells, siControl, biol_rep_1


title: LNCaP, siCtrl, rep1


title: 22Rv1, siMED12, rep3 (FT)

data_processing:
Read alignment and counting were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13) genome assembly.
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID and log2 transformed CPM gene expression values for each sample

growth_protocol: 22Rv1 cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.

extract_protocol:
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
polyA capture and strand specific library prep were performed by Novogene

treatment_protocol: Cells were seeded in 6-well plates and incubated for 24 h. Cells were transfected with 25pmol ON-TARGETplus SMARTpools (siCtrl: non-targeting pool, #D-001810-10-05; siMED12: human MED12 siRNA, #L-009092-00-0005) using Lipofectamine RNAiMAX. The medium was changed after 6 h and the cells were harvested at 3 days after transfection.


title: Placenta, Fn treat, rep4

value: Fn treat


title: ATAC-Rreb1KO_TGFb_Rep1


title: Placenta, PBS treat, rep3


title: ROL sample 3 [C6]

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

data_processing:
Raw reads were cleaned (adpater trimming, quality-trimming, removal of reads less than 50bp) was performed using Fastp toolkit.
Quality trimmed reads were mapped against the indexed C. auris B11221 reference genome using STAR3 aligner (v2.7.10a).
STAR derived mapping results and annotation (GTF) file were fed into the FeatureCounts package (version 2.1).
Differential expression analysis was performed with R-package edgeR (v3.16.5).
Assembly: C. auris NCBI reference genome version B11221
Supplementary files format and content: Excel file includes raw counts for each sample

organism: Candidozyma auris

growth_protocol: C. auris was grown on YPD broth

extract_protocol:
RNA extraction was performed following standard protocol from Ambion RiboPure yeast kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Candida cells were treated with the tested drugs in RPMI media

value: Candida cells

value: ROL 4 µg/mL

tag: ng/µl

tag: total volume

value: 40 µl


title: Placenta, Fn treat, rep5

tag: tissue


title: BxPC3 cells, PK9328, #2

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

data_processing:
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Homo sapien sapien hg38.
Assembly: Human hg38
Supplementary files format and content: SALMON - format - .sf - TMM and read counts

source_name: pancreas

growth_protocol: BxPC3 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% Penicilin-Streptomycin. Cell line was cultured in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed with ice-cold PBS and pelleted. The flash frozen samples were sent to Azenta Life Sciences where RNA was harvested.
RNA-seq libraries were constructed from the PolyA selected mRNA (prepared by Azenta Life Sciences)

treatment_protocol: Vehicle or 5µM of PK9328 or MS78 treated for 6h

value: pancreas

tag: cell line

tag: cell type

value: pancreatic adenocarcinoma cell


title: BxPC3 cells, PK9328, #3

tag: genotype


title: 22Rv1, siMED12, rep2 (FT)

tag: treatment


title: 22Rv1, siMED12, rep1 (FT)


title: ATAC-WT_TGFb_Rep2


title: Placenta, Fn treat, rep3


title: BxPC3 cells, PK9328, #1


title: Placenta, Fn treat, rep2


title: ROL sample 2 [C5]


title: 22Rv1, siCtrl, rep2 (FT)

value: siCtrl


title: Placenta, Fn treat, rep1


title: BxPC3 cells, DMSO, #3

value: DMSO


title: ROL sample 1 [C4]


title: ATAC-WT_SB_Rep1

value: Lung adenocarcinoma cells


title: BxPC3 cells, DMSO, #1


title: ChIP-H4K20ac_SB

data_processing:
Sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to mouse assembly mm10 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain regions of chromatin accessibility, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001. ChIP and CUT&RUN target enrichment also used MACS2 with the same parameters and scored against matched input or IgG as the control, respectively. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/ mm10-mouse/mm10.blacklist.bed.gz) then merging all peaks within 500 bp for ChIP and CUT&RUN or taking 500 bp windows around peak summits for ATAC and counting reads with featureCounts (v1.6.1). DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts. Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site. Peak intersections were calculated using bedtools and intersectBed with 1 bp overlap. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was performed with the pre-ranked option and default parameters, where each gene was assigned the single peak with the largest (in magnitude) log2 fold change associated with it. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu). Profile and tornado plots were created using deepTools v3.3.0 by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 3 kb.
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
For ChIP, 1x107 cells were crosslinked at room temperature for 10 min by swirling with 1% formaldehyde (Sigma Aldrich) followed by addition of 125 mM glycine to quench the reaction. After washing the cells three times with PBS, cells were resuspended with ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 150 mM NaCl, 0.1% Na-deoxycholate, 1% Triton X-100, 1 mM EDTA, 0.1% SDS) supplemented with protease inhibitors (Roche, cOmplete, mini, EDTA-free protease inhibitor tablets, Cat #: 11836170001) and phosphatase inhibitors (Thermo Scientific, Halt Phosphatase Inhibitor Cocktail, Cat #: 78427, 1:1000). Cell lysates in 1 mL of ChIP lysis buffer were sonicated for sheared chromatin to be 200-500 bp. Supernatants cleared by centrifugation were incubated with the designated antibody at 4ºC overnight on a rotator. Dynabeads™ Protein G were blocked with 2.5 mg/mL UltraPure™ BSA (Thermo Scientific, Cat #: AM2616) at 4ºC overnight. The beads were then washed three times with ChIP buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100) and incubated with the chromatin-antibody samples at 4ºC for 1-2 h. These samples were washed 6 times with high salt ChIP buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% of Triton X-100, 0.1% of SDS) followed by two washings with Tris-EDTA (TE) buffer. Chromatin complexes were eluted twice in TE with 1% ultrapure SDS (Thermo Fisher Scientific) at 65ºC for 15 min, and reverse-crosslinked with RNAse A (Thermo Fisher Scientific, Cat #: EN0531) for 4 h or overnight, followed by incubation with Proteinase K solution (Thermo Fisher Scientific, Cat #: EO0491) for 1 h at 45ºC. DNA was purified using QIAquick PCR Purification Kit (Qiagen). For CUT&RUN, samples were prepared with CUTANA™ ChIC/CUT&RUN Kit (Epicypher, Cat #: 14-1048). For each CUT&RUN reaction, cell pellets (5x105 cells) were washed twice with wash buffer (20 mM HEPES–KOH, pH 8.0; 150 mM NaCl; 0.5mM spermidine; and protease inhibitor (Roche), followed by resuspension with wash buffer. Cells in wash buffer were incubated with activated Concanavalin-A beads for 10 min at room temperature. Beads were resuspended with immunoprecipitation buffer (Wash buffer; 0.01% digitonin; 2 mM EDTA) and incubated with 0.5 µg of designated antibody at 4ºC overnight on a nutator. The following day, beads were washed twice with digitonin buffer (wash buffer including 0.01% digitonin) and incubated with CUTANA pAG-MNase for 10 min at room temperature, followed by wash twice with digitonin buffer. pAG-MNase was activated by incubation with 1 µL of 100 mM CaCl2 for 2 h at 4ºC on nutator. The reaction was terminated by incubation with stop buffer for 10 min at 37 ºC in thermocycler. CUT&RUN enriched DNA was purified using CUTANA DNA purification kit (Epicypher, Cat #: 14-0050).
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems, Cat #: KK8234) according to the manufacturer’s instructions with 0.02-5 ng input DNA and 8-14 cycles of PCR.
Barcoded libraries were run on the NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 Reagent Kit (200 or 300 Cycles) (Illumina).


title: RNAseq-Dhx9KO_TGFb_Rep2

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), and then aligned to mouse assembly mm10 with STAR v2.7.10b using default parameters. Data quality and transcript coverage were assessed using the tool CollectRNASeqMetrics from Picard (http://broadinstitute.github.io/picard/). Read count tables were generated with HTSeq v0.9.1. Normalization and expression dynamics were evaluated with DESeq2 using the default parameters and outliers were assessed by sample grouping in principal component analysis. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was run against MSigDB v6 using the pre-ranked option and log2 fold change for pairwise comparisons.
Assembly: mm10
Supplementary files format and content: Excel

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, Cat #: 74106).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by TruSeq Stranded mRNA LT Kit (Illumina, Cat #: RS-122-2102), with 8 cycles of PCR.

value: TGF-Beta for 1.5 h


title: 22Rv1, siCtrl, rep1 (FT)


title: BxPC3 cells, MS172, #3


title: antiYY1_dTAG_3

city: Farmington

first: Jinhong

last: Dong

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

data_processing:
Adapter trimming: cutadapt
Alignment: bowtie2
File manipulation: samtools v1.16.1
File manipulation: https://github.com/guertinlab/seqOutBias v1.4.0
Peak calling: macs3
File manipulation: bedtools
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: peak summit counts files

growth_protocol: HEK293T-ZNF143-dTAG cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (R&D Systems), 1% L-glutamine (Gibco), 1% sodium pyruvate (Gibco), and 1% penicillin-streptomycin (Gibco).

extract_protocol:
After treatment, cells were fixed with 1% formaldehyde for 10 minutes at 37°C and quenched with 125mM Glycine (Fisher) for 10 minutes at 37°C. Plates were moved to ice, and cells were washed and scraped into ice cold PBS containing Complete EDTA-free Protease Inhibitor Cocktail (Roche). Cells were pelleted in aliquots of 2*10^7 cells, snap frozen in liquid nitrogen, and stored at -80°C. Pellets were thawed, and cells were lysed in 1mL ChIP Lysis Buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCL pH 8.0), with protease inhibitor cocktail added fresh, for 10 minutes with rotation at 4°C. Lysates were sonicated at 70% amplitude for 15 seconds on and 45 seconds off for 4 sets of 20-minute cycles. Sonicated lysates were moved to 1.5ml tubes and clarified by centrifugation at 14,000rpm for 10 min in 4°C. 50μL of the supernatant was diluted into 760μL ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl, 16.6mM Tris-HCl pH 8.0), with protease inhibitor cocktail added fresh (1*10^6 cells in 200μL). 1ml (4*106 cells) was aliquoted into each of 3 tubes with antibody (7.32μg anti-NRF1 Invitrogen MA5-35366 or 3μg anti-YY1 Invitrogen 703054), and incubated with end-over-end rotation at 4°C overnight. 80μL Protein A/G Magnetic Beads (New England Biolabs) per sample were washed with bead washing buffer (PBS with 0.1% BSA and 2mM EDTA) and then incubated with samples for 90 minutes with rotation at 4°C. The samples were washed once each with low salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 150mM NaCl, 20mM Tris HCl pH8.0), high salt immune complex buffer (0.1% SDS, 1% Triton x-100, 2mM EDTA, 500mM NaCl, 20mM Tris Hcl pH 8.0), LiCl immune complex buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.0), and 1xTE (10mM Tris-HCl, 1mM EDTA pH8.0). Immune complexes were eluted in elution solution, (1% SDS, 0.1M sodium bicarbonate). 1μl RNase A was added to each sample for 10 min at 37°C. Proteins were digested with the addition of 5μl Proteinase K and incubated in a 65°C water bath overnight.
DNA was purified with a MinElute PCR purification kit (Qiagen), and libraries were prepared with a NEBNext Ultra II Library Prep Kit (New England Biolabs).

treatment_protocol: HEK-293T cells were harvested after either no treatment or after 30 minutes of 50nm dTAGV-1 treatment


title: antiYY1_dTAG_2


title: RNAseq-Dhx9KO_TGFb_Rep1


title: antiYY1_dTAG_1


title: BxPC3 cells, MS172, #2


title: RNAseq-Dhx9KO_SB_Rep2


title: 22Rv1, siCtrl, rep3 (FT)


title: antiYY1_control_3

description: antiYY1-control_merged_normalized.bigWig


title: 11039_MN_Diff3

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Raw, paried reads were processed via CHURP pipelien (https://github.com/msi-ris/CHURP) using default setting.
The cleaned gene count table per sample was analyzed with R (v4.1.0) package edgeR to identify differentially expressed genes.
R package clusterProfiler was used for pathway enrichment. Various R packages, including pheatmap and ggplto2, were used to generate visualization plots.
Assembly: GRCh38
Supplementary files format and content: Txt file of Tab separated values

source_name: human MN derived from iPSCs

extract_protocol:
RNA was extracted using TRIZOL extraction protocol, 3nl of total RNA used fr construction of libraries
Library construction and sequencing were done by University of Minnesota Genomic Center according to the manufacter’s instructions (Illumina TruSeq Stranded).

value: human MN derived from iPSCs

value: WT


title: antiYY1_dTAG_4


title: LNCaP_72h_rep2_STARTseq

city: Vancouver

first: Nathan

last: Lack

state: BC

address: 2660 Oak S

country: Canada

institute: Vancouver Prostate Centre

description: nascent RNA

data_processing:
Adaptor sequences and low-quality 3′ ends were removed from paired-end reads of all samples using cutadapt (v1.2.1).
Reads shorter than 20 nucleotides were discarded (-m 20 -q 10), and a single nucleotide was trimmed from the 3′ end of all remaining reads to enable successful alignment with bowtie (v1.1.1).
The first in pair flagged reads were filtered to generate signal (bigwig) files for each strand using bedtools genomecov (-bg -5 -strand +/-,respectively).
Assembly: hg19
Supplementary files format and content: BigWig
Library strategy: Start-seq

growth_protocol: LNCaP cells were grown in RPMI with 10% FBS and antiboitics.

extract_protocol:
RNA was extracted using TRIzol.
Libraries were prepared using the TruSeq Small RNA Kit (Illumina)

treatment_protocol: LNCaP cells were grown in phenol red free RPMI (#11835030, GIBCO) with 10% charcoal stripped FBS (#100-119, GemBio) for 3 days and then were stimulated with 10 nM dihydrotestosterone (DHT) (5α-Androstan-17β-ol-3-one, A8380, Sigma) for 30 min, 4 hr, 16 hr or 72 hr.

value: LNCaP

value: 72h 10nM DHT


title: 11038_MN_Diff3


title: BxPC3 cells, DMSO, #2


title: antiYY1_control_4


title: RNAseq-Dhx9KO_SB_Rep1


title: 11037_pMN_S113

source_name: human pre-MN derived from iPSCs

value: human pre-MN derived from iPSCs


title: RNAseq-Ino80KO_TGFb_Rep2


title: LNCaP_72h_rep1_STARTseq

description: nascent RNA


title: antiYY1_control_1


title: RNAseq-Ino80KO_TGFb_Rep1


title: 11037_MN_Diff3


title: LNCaP_16h_rep2_STARTseq

description: nascent RNA

value: 16h 10nM DHT


title: 11038_pMN_S202


title: BxPC3 cells, MS172, #1


title: RNAseq-Ino80KO_SB_Rep1


title: LNCaP_4h_rep2_STARTseq

description: nascent RNA

value: 4h 10nM DHT


title: LNCaP_16h_rep1_STARTseq

description: nascent RNA


title: 11036_pMN_S201


title: antiNrf1_dTAG_2


title: LNCaP_4h_rep1_STARTseq

description: nascent RNA


title: RNAseq-WT_TGFb_Rep2


title: antiYY1_control_2


title: antiNrf1_dTAG_1


title: 11034_pMN_S200


title: RNAseq-WT_TGFb_Rep1


title: RNAseq-WT_SB_Rep2


title: 11034_MN_Diff3


title: LNCaP_30m_rep2_STARTseq

description: nascent RNA

value: 30m 10nM  DHT


title: 11039_pMN_S203


title: 11034_MN_Diff1


title: RNAseq-Ino80KO_SB_Rep2


title: antiNrf1_control_3

description: antiNrf1-control_merged_normalized.bigWig


title: antiNrf1_dTAG_4


title: LNCaP_0m_rep2_STARTseq

description: nascent RNA

value: EtOH


title: antiNrf1_control_4


title: RNAseq-WT_SB_Rep1


title: LNCaP_30m_rep1_STARTseq

description: nascent RNA


title: antiNrf1_dTAG_3


title: antiNrf1_control_2


title: 11036_MN_Diff3