title: in situ Hi-C on CyT49 differentiated to endoderm of foregut with MboI - 4DNEXCVNMNQ1

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXCVNMNQ1
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXCVNMNQ1/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a7e64eb4-1728-4dc1-a03e-774230c156b4/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFICH9C5H8.bam, 4DNFIL39SMHI.bam, 4DNFIK2DRLGB.bam, 4DNFIWLKRTQ3.bam, 4DNFIP3USCB1.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIZUV87TW.pairs.gz


title: ovary_OA_rep2

status: Public on Dec 12 2024

type: SRA

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

description: NEL0067581_exp1a_ovary_all_expressed_genes.csv

library_source: transcriptomic

data_processing:
Sequencing reads were pseudoaligned to the Bombus terrestris transcriptome using Kallisto v0.46.1 with parameters --single -l 200 -s 20
Estimated transcript counts were summarised per gene for brain, fat body and ovary samples in R v4.1.3 using the tximport package v1.22.0 with parameter type="kallisto". For egg samples, the parameter countsFromAbundance = "scaledTPM" was used.
Differential expression analysis was conducted on brain, fat body and ovary samples in R v4.1.3 using the DESeq2 package v1.34.0, with technical replicates (sequencing the same library on different lanes of the sequencing machine) collapsed using the collapseReplicates() function.
Assembly: Bombus_terrestris.Bter_1.0.cdna.all.fa
Supplementary files format and content: CSV file with scaled TPM counts from tximport for all genes expressed in eggs
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in brain
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body
Supplementary files format and content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

molecule: total RNA

organism: Bombus terrestris

source_name: ovary

extract_protocol:
B. terrestris workers were quickly dissected on ice to minimize RNA degradation, with the brains and ovary being stored in RNAlater (Sigma-Aldrich) and the fat body being stored in AllProtect (Qiagen). Tissue from seven individuals were pooled together to make a sample. Samples were ground in liquid nitrogen using a 2 ml pestle (Eppendorf) and the powder resuspended in Tri-Reagent (Ambion). The RNA was then extracted using a Direct-zolTM RNA extraction kit (Zymo Research), including an on-column DNase treatment. The eluted RNA was further treated with TurboTM DNase (Ambion). The same protocol was used for preparation of RNA from eggs.
Standard mRNA-seq was conducted for the brain, fat body and ovary samples by Edinburgh Genomics (The University of Edinburgh, Edinburgh, UK) on an Illumina HiSeq 2500 sequences using Illumina TruSeq adapters. The two egg mRNA-seq libraries were constructed and sequenced by Baseclear (Leiden, The Netherlands) using an Illumina HiSeq 2500 sequences with Illumina TruSeq adapters.

treatment_protocol: Bombus terrestris audax colonies were reared in wooden boxes (300 x 200 x 170 mm) in constant darkness at 28oC and 60% humidity, and were supplied with sugar solution and pollen ad libitum.

tag: tissue

value: ovary

tag: phenotype

value: active ovaries


title: Male24_UT_3

city: Chicago

first: Kun Woo

last: Shin

state: IL

address: 5841 S Maryland Ave

department: Medicine

country: USA

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using Kallisto v.0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 45 (GRCh38.14) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: est_counts      tpm

organism: Homo sapiens

source_name: Lung

growth_protocol: Primary normal human lung fibroblasts (HLFs) were grown in DMEM containing 0.1% bovine serum albumin, 5.5mM glucose, 2 mM glutamine, and 1mM pyruvate for 24 hours. Primary normal, control male, and IPF patient's HLFs were gorwn in HPLM containing 0.1% bovine serum albumin for 24 hours.

extract_protocol:
Total RNA was isolated from fibroblasts using, GenElute™ Mammalian Total RNA Miniprep Kit
Oligo-dT mRNA directional

treatment_protocol: HLFs were treated with TGF-beta (Peprotech) or left untreated.

value: Lung

tag: cell line

value: Primary Fibroblast

tag: cell type

value: Fibroblast

tag: treatment

value: HPLM

tag: clone

value: Control

tag: Sex

value: Male


title: VEH-5-Day-3

city: Portland

first: Pengtao

last: Dang

address: 2720 S Moody Ave

institute: Oregon Health & Science University

description:
Library name: Sample 19
Merged_counts_ILMN1656.txt
17_VEH-5-Day-3_S55_L002

data_processing:
Data is mapping to genome UCSC mm10 or GRCH38 using STAR software
Assembly: UCSC mm10; GRCH38
Supplementary files format and content: txt; counts

organism: Mus musculus

source_name: MPNST Tumor Tissue

growth_protocol: Growth protocol - In vitro studies: Cells were cultured in serum-free medium supplemented with B27 and N2, plus EGF and FGF (10 ng/ml each) in 5% oxygen at 37C. Every culture was passaged for no longer than 4 weeks. In vivo studies: were performed with NP and NI mutant GEMMs and PDX models. For GEMM experiments, NI and NP mutant MPNST cells (5000 cells) were injected into nu/nu mice. For PDX experiments, tumor chunks of equal size were implanted adjacent to the sciatic nerve of nude mice. Mice were divided into 4 groups once tumors reached a volume of 250-500 mm3.

extract_protocol:
Extract protocol - Primary tumors were dissected and minced into small tissue blocks, and then were dissociated by using a gentleMACS Octo Dissociator (Miltenyi Biotec) and 1g/ml collagenase (Sigma-Aldrich, Cat# C8051), following the preset protocol. The dissociated cells were washed in PBS 3 times and treated with blood cell lysate buffer (Sigma-Aldrich, Cat# R7757).
RNA was extracted from mice with NP mutant MPNST tumors treated with SHP2i for 5 or 20-28 days (n=3 animals each). RNA was extracted from a 20-30 mg portion of  flash-frozen NP mutant MPNST tumor tissue using the Qiagen RNeasy Plus kit following the manufacturer’s protocol. Tissue homogenization/disruption was by mortar and pestle and Buffer RLT Plus supplemented with beta-mercaptoethanol followed by passing homogenized samples over Qiagen QIAshredder columns. Qiagen RNase-Free DNase Set was used for on-column DNA digestion. Total RNA was submitted to the IU Center for Medical Genomics (CMG) for library preparation and sequencing. Total RNA was first evaluated for its quantity and quality using an Agilent Bioanalyzer 2100. A RIN number of above 8 was achieved for all samples. One hundred nanograms of total RNA was used. cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified, its quality was accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled at equal molarity. Pooled libraries were then denatured and neutralized before loading onto a NovaSeq 6000 sequencer at 300pM final concentration for 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. was used to measure the quality of sequencing. More than 90% of the sequencing reads reached a Phred quality score Q30 of (99.9% base call accuracy)

treatment_protocol: Treatment protocol - Vehicle and drugs were administered by oral gavage at the following doses and schedules. SHP099 and Trametinib combination studies: SHP099 50 mg/kg daily, trametinib 0.25 mg/kg daily, or the combination (SHP099 50 mg/kg every other day and trametinib 0.25 mg/kg daily). SHP099 and HQ combination studies: Hydroxychloroquine (50 mg/kg daily), SHP099 (50mg/kg daily), or the combination of SHP099 (50 mg/kg daily) plus HQ (50 mg/kg daily).

value: MPNST Tumor Tissue

tag: genotype

value: WT

value: Vehicle Control

tag: batch

value: 5 days


title: ovary_OA_rep1


title: ovary_OI_rep3

value: inactive ovaries


title: Shp-21-Day-1

description:
Library name: Sample 18
Merged_counts_ILMN1656.txt
19_Shp-21-Day-1_S57_L002

value: SHP099 treated

value: 21 days


title: ovary_OI_rep1


title: V1

description:
Library name: Sample 9
Merged_counts_ILMN833.txt
1_V1_S1


title: in situ Hi-C on CyT49 differentiated to pancreatic endoderm with MboI - 4DNEXJH3AAC8

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Bing Ren, UCSD
award: 1U54DK107977-01
4DN accession: 4DNEXJH3AAC8
pcr_cycles: 11
submitted_by: Bin Li
ligation_time: 240
biotin_removed: Yes
digestion_time: 920
tagging_method: biotin-14-dATP
experiment_type: in situ Hi-C
ligation_volume: 0.95
digestion_enzyme: MboI
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 1% Formaldehyde
fragment_size_range: 150-500
fragmentation_method: sonication
ligation_temperature: 20
average_fragment_size: 300
digestion_temperature: 37
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXJH3AAC8/

library_source: genomic

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/816f5223-6d54-48bd-955f-0e18558450f1/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIBSH7NJ5.bam, 4DNFIAXS27KE.bam, 4DNFIFBW4EKD.bam, 4DNFI9QGLIK4.bam, 4DNFIAHLZSJS.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFITKCX2DO.pairs.gz

molecule: genomic DNA

source_name: biosource_summary: CyT49 differentiated to pancreatic endoderm

growth_protocol:
url: https://www.ncbi.nlm.nih.gov/pubmed/18288110
description: Kroon et al. 2008 describes differentiation of human embryonic stem cells to pancreatic endoderm

extract_protocol:
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf

value: pancreatic endoderm

value: male

value: in vitro differentiated cells

tag: url

value: embryonic


title: fatbody_OA_rep3

description: NEL0067581_exp1a_fatbody_all_expressed_genes.csv

source_name: fat body

value: fat body

value: active ovaries


title: Male24_UT_1

value: Lung

value: Primary Fibroblast

value: Fibroblast


title: Shp-21-Day-4

description:
Library name: Sample 20
Merged_counts_ILMN1656.txt
22_Shp-21-Day-4_S60_L002


title: S1

description:
Library name: Sample 8
Merged_counts_ILMN833.txt
7_S1_S7


title: fatbody_OA_rep2


title: DMEM_TGFb_4

value: wt

value: DMEM + TGFb

value: NHLF


title: fatbody_OA_rep1


title: fatbody_OI_rep1


title: fatbody_OI_rep3


title: S6

description:
Library name: Sample 6
Merged_counts_ILMN833.txt
12_S6_S12

value: MPNST Tumor Tissue

value: WT


title: S2

description:
Library name: Sample 5
Merged_counts_ILMN833.txt
8_S2_S8

value: 5 days


title: fatbody_OI_rep2

value: inactive ovaries


title: DMEM_TGFb_2


title: brain_OA_rep2

description: NEL0067581_exp1a_brain_all_expressed_genes.csv

source_name: brain

value: brain


title: brain_OI_rep3


title: DMEM_TGFb_1


title: ovary_OI_rep2

value: ovary


title: Male24_UT_2

value: HPLM

value: Control

value: Male


title: brain_OA_rep1


title: brain_OI_rep1


title: brain_OI_rep2


title: DMEM_UT_4

value: DMEM


title: V2

description:
Library name: Sample 3
Merged_counts_ILMN833.txt
2_V2_S2

value: Vehicle Control


title: NE 72h WT replicate 2

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: RNAseq_NE72h_rep2
NE_72h_R2

data_processing:
Alignment using STAR STAR_2.5.1b
Quantification using RSEM v1.2.23
Assembly: hg38
Supplementary files format and content: Gene quantification text file

molecule: polyA RNA

growth_protocol: Human ESCs were maintained in Essential 8 medium on tissue culture-treated polystyrene plates coated with 5 μg/mL vitronectin

extract_protocol:
Total RNA was isolated from cell pellets using Quick-RNA Miniprep kits (ZYMO Research, R1055) per the manufacturer’s instructions, including the digestion and removal of DNA.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 100-500 ng of total RNA with RIN values of 9.4-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit; RS-122-2102). Samples were amplified by 8 cycles of PCR, barcoded, and run on a NovaSeq 6000 platform in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).


title: DMEM_UT_3

value: Lung


title: S3

description:
Library name: Sample 2
Merged_counts_ILMN833.txt
9_S3_S9

value: SHP099 treated


title: DMEM_UT_2

value: Primary Fibroblast

value: Fibroblast


title: brain_OA_rep3

value: active ovaries


title: DMEM_TGFb_3

value: wt

value: DMEM + TGFb

value: NHLF


title: S5

description:
Library name: Sample 1
Merged_counts_ILMN833.txt
11_S5_S11

value: MPNST Tumor Tissue

value: WT

value: 21 days


title: S4

description:
Library name: Sample 7
Merged_counts_ILMN833.txt
10_S4_S10


title: V3

description:
Library name: Sample 4
Merged_counts_ILMN833.txt
3_V3_S3


title: ET0310BPhha62630523

type: genomic

city: College Park

first: Gerald

last: Wilkinson

state: MD

address: Biology-Psychology Building

department: Department of Biology

institute: University of Maryland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Phyllostomus hastatus

label_protocol: Standard Illumina protocol

extract_protocol: DNA extracted using Zymo DNA miniprep

treatment_protocol: Standard Illumina protocol

value: Skin

value: M


title: DMEM_UT_1


title: ET0310BPhha62210523

value: F


title: HPLM_TGFb_4

value: HPLM + TGFb


title: 21d Nkapl-KO_RS rep1

city: Nanjing

first: Chen

last: Xu

address: 101 Longmian Avenue, Jiangning District

country: China

institute: Nanjing Medical University

data_processing:
Clean data were obtained by trimming the adaptor sequence and removing sequences with low quality.
Clean reads were mapped to the mouse genome (mm10) with HISAT2 (v.2.1.0; Johns Hopkins University, Baltimore, MD, USA) with a GTF file download from the UCSC database (University of California, Santa Cruz).
The aligned reads of genes were counted using HTSeq followed by DESeq2 normalization to evaluate gene expression as normalized counts per million.
Assembly: mouse genome (mm10)
Supplementary files format and content: gene reads count

source_name: Testis

extract_protocol:
Testes were collected from wild-type, Nkapl-KO, Sox30-KO, and Nkapl TGdel/TGdel mice, and RNA was harvested using Trizol reagent.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina).

value: Testis

value: round spermatids(RS)

value: NKAPL KO


title: 21d Nkapl-KO_PS rep2

value: pachytene spermatocytes(PS)


title: HPLM_TGFb_2

value: Lung

value: Primary Fibroblast


title: HPLM_TGFb_1

value: Fibroblast


title: ET0310BPhha62470523


title: 21d Nkapl-KO_RS rep2


title: 21d Nkapl-KO_PS rep1


title: Spatial transcriptomics of mouse liver

city: Palo Alto

first: Xun

last: Ding

state: CA

address: 2500 Faber Pl

institute: Centrillion Technologies

description:
Library name: M187-9
Male C57BL/6 mice, 8 weeks postnatal (PN), liver

data_processing:
Raw sequencing data were processed using a custom bioinformatics pipeline developed by Centrillion Technologies.
Reads were decoded to spatial barcodes and UMIs using PostMaster software and trimmed with Cutadapt.
Sequences were aligned to the mouse genome (GRCm39) using the STAR aligner and annotated with FeatureCounts.
Deduplication was performed to remove redundant reads using in-house scripts, and data were converted to h5ad format for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: 2100G_3end_matrix.h5ad.gz: Gzipped AnnData file (h5ad format) containing the processed spatial transcriptomics data from all sequencing batches combined, including the count of each detected gene at each physical location with provided row and column coordinates.
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Fresh frozen tissue was OCT embedded, and 10 µm frozen sections were used.
Spatial transcriptome sequencing libraries were prepared using high-resolution DNA chips with 2 µm × 2 µm features and spatial barcoding following standard methods.

value: Liver

tag: strain

tag: age

value: Adult

value: Male


title: 21d Nkapl-WT_RS rep2

value: Wild-type


title: ET0310BPhha61500523


title: ET0310BPhha62170523


title: ET0310BPhha62250523


title: ET0310BPhha60400123


title: ET0310BPhha62450523


title: ET0310BPhha61990523


title: 21d Nkapl-WT_RS rep1


title: ET0310BPhha61040123


title: ET0310BPhha62600523


title: ET0310BPhha62000523


title: ET0310BPhha60350123


title: 21d Nkapl-WT_PS rep2


title: HPLM_UT_4

value: wt

value: HPLM

value: NHLF


title: ET0310BPhha62590523

value: Skin


title: ET0310BPhha61490523

value: F


title: 21d Nkapl-WT_PS rep1


title: ET0310BPhha61030123


title: HPLM_UT_3


title: HPLM_TGFb_3

value: HPLM + TGFb


title: HPLM_UT_2


title: HPLM_UT_1


title: ET0310BPhha61920523

value: M


title: KO_RS_Pol ll_rep2

data_processing:
Reads were aligned to the mouse reference genome mm10 with BOWTIE software (bowtie2 version 2.3.4.3), followed by the removal of those reads that with low mapping quality and duplicated through sample amplification or sequencing.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Fresh testes were collected from wild-type and Nkapl KO mice at postnatal day 21, ground into powder in liquid N2, and crosslinked by 1% formaldehyde, followed by quenching with glycine solution. Chromatin was fragmented by sonication in ChIP SDS lysis buffer (50 mM Tris-HCl, pH=8; 10 mM EDTA, pH=8; 1% SDS) using the Covaris-S220 sonicator. Crosslinked chromatin was incubated with indicated antibodies in ChIP dilution buffer (50 mM HEPES, pH7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxycholate) with protease inhibitors overnight. Crosslinking was reversed overnight at 65°C, and DNA was extracted by using phenol/chloroform/isoamyl alcohol.
Precipitated DNA was amplified for deep-sequencing. For ChIP-seq, equal DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers.

value: Testis

value: round spermatids(RS)


title: HEK293, UBFD1mock, clone6

city: Paris

first: Yago

middle: A

last: Arribas

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Raw RNA-seq files were aligned using STAR (v2.5.3a) two-pass modes. Bam files were processed by featureCounts to quantify gene expression84. Gene read counts were uploaded to R and converted to Transcript per million (TPM) using tpm function from drfun R package. Only raw gene counts from genes with TPM >0.5 were submitted to differential expression analysis using DESeq2 R package85.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include featureCounts output

extract_protocol:
For RNA extraction, 1M cells were collected with 750 µL of RLT lysis buffer supplemented with 1% β-mercaptoethanol. Total RNA was extracted from cell lines using RNeasy Mini Kit (Qiagen) following manufacturer instructions. For sequencing purposes, RNA interrogation number (RIN) was measured using a Bioanalyzer RNA 6000 nano assay (Agilent) to verify a RIN >7.
Libraries were generated from 500 ng or 1000 ng of total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit. PolyA enrichment was done using magnetic beads and then, RNA was fragmented. cDNA was synthetized from the resulting fragments, and after dA-tailing, they were ligated to TruSeq indexed adapters, and amplified by PCR (12-15 cycles). Sequencing was performed (paired-end reads, 100 nucleotide length) on a Novaseq 6000 system with a demanded depth of 200 million reads.

value: Embrionic kidney

value: WT

value: Untreated


title: HEK293, UBFD1mock, clone3


title: WT_NKAPL

value: germ cell


title: ET0310BPhha61590523


title: HEK293, UBFD1mock, clone2


title: KO_RS_Pol ll_rep1

value: NKAPL KO


title: KO_PS_Pol ll_rep2

value: pachytene spermatocytes(PS)


title: ET0310BPhha62150523


title: ET0310BPhha62160523


title: ET0310BPhha60990123


title: ET0310BPhha61270123


title: ET0310BPhha62430523


title: ET0310BPhha62140523


title: ET0310BPhha60340123


title: ET0310BPhha62440523


title: HEK293, UBFD1KO, clone26

value: UBFD1-JET KO


title: HEK293, UBFD1mock, clone4


title: ET0310BPhha62580523


title: ET0310BPhha60970123


title: HEK293, UBFD1KO, clone21


title: HEK293, UBFD1mock, clone1


title: ET0310BPhha63100623


title: WT_RS_Pol ll_rep2

value: Wild-type


title: ET0310BPhha61080123


title: HEK293, UBFD1KO, clone14


title: HEK293, UBFD1KO, clone7


title: ET0310BPhha61910523


title: WT_PS_Pol ll_rep2


title: ET0310BPhha62130523


title: WT_PS_Pol ll_rep1


title: KO_PS_Pol ll_rep1


title: ET0310BPhha61650523


title: HEK293, UBFD1KO, clone6


title: WT_RS_Pol ll_rep1


title: HEK293, HTTmock, clone4


title: ET0310BPhha61260123


title: ET0310BPhha62290523


title: ET0310BPhha60330123


title: ET0310BPhha61230123


title: HEK293, HTTmock, clone2


title: HEK293, HTTmock, clone3


title: ET0310BPhha62560523


title: ET0310BPhha63070623


title: ET0310BPhha60310123


title: ET0310BPhha61640523


title: ET0310BPhha60940123


title: ET0310BPhha62080523


title: HEK293, HTTKO, clone52

value: HTT-JET KO


title: ET0310BPhha61180123


title: HEK293, HTTKO, clone5


title: ET0310BPhha60820123


title: H1650, UT, rep5

value: Lung


title: H1650, UT, rep4


title: HEK293, HTTmock, clone1


title: ET0310BPhha62280523


title: ET0310BPhha62540523


title: ET0310BPhha63060623


title: ET0310BPhha62070523


title: H1650, UT, rep3


title: ET0310BPhha60710123


title: ET0310BPhha62060523


title: ET0310BPhha62260523


title: ET0310BPhha63050623


title: H1650, UT, rep2


title: ET0310BPhha62270523


title: ET0310BPhha62520523


title: ET0310BPhha47950123


title: ET0310BPhha60300123


title: HEK293, HTTKO, clone27


title: ET0310BPhha61630523


title: H1650, PTEN-CAN+, rep5

value: PTEN-CAN+


title: ET0310BPhha61150523

value: Skin


title: H1650, PTEN-CAN+, rep4


title: ET0310BPhha62980623

value: F


title: H1650, UT, rep1


title: H1650, PTEN-CAN+, rep3


title: H1650, PTEN-CAN+, rep2


title: ET0310BPhha62040523


title: H1650, PTEN-JET+, rep5

value: PTEN-JET+


title: ET0310BPhha62510523


title: H1650, PTEN-CAN+, rep1


title: H1650, PTEN-JET+, rep4


title: ET0310BPhha61120123


title: ET0310BPhha61610523

value: M


title: H1650, PTEN-JET+, rep3


title: ET0310BPhha47910123


title: H1650, PTEN-JET+, rep2


title: ET0310BPhha62030523


title: ET0310BPhha62710523


title: ET0310BPhha62500523


title: ET0310BPhha47900123


title: ET0310BPhha60640123


title: ET0310BPhha61100123


title: ET0310BPhha62720523


title: ET0310BPhha62200523


title: H1650, PTEN-JET+, rep1


title: ET0310BPhha61070123


title: ET0310BPhha47930123


title: ET0310BPhha60660123


title: ET0310BPhha60670123


title: ET0310BPhha62490523


title: H1650, Scramble, rep4

value: Scramble SSO


title: H1650, Scramble, rep3


title: ET0310BPhha61600523


title: ET0310BPhha61580523


title: ET0310BPhha61060123


title: ET0310BPhha62700523


title: ET0310BPhha62190523


title: ET0310BPhha62020523


title: H1650, Scramble, rep2


title: ET0310BPhha62480523


title: ET0310BPhha60600123


title: H1650, Scramble, rep1


title: ET0310BPhha62180523


title: H1650, SSO56, rep5


title: H1650, SSO56, rep3


title: H1650, SSO56, rep2


title: H1650, SSO56, rep4


title: H1650, SSO56, rep1


title: H1650, SSO13, rep5


title: H1650, SSO13, rep4


title: ET0310BPhha62010523


title: ET0310BPhha62570523


title: ET0310BPhha61050123


title: ET0310BPhha60550123


title: ET0310Phha47970123


title: ET0310BPhha39400123


title: H1650, SSO13, rep3


title: Phha_6091_012023


title: H1650, SSO13, rep2


title: Phha_6083_012023


title: Phha_6087_012023


title: ET0310BPhha39330123


title: ET0310Phha3933011523


title: Phha_2417_012023


title: Phha_6049_012023


title: Phha_4735_012023


title: ET0310BPhha62240523


title: Phha_6088_012023


title: Phha_4730_012023


title: Phha_3845_012023


title: HHF1 cells, Mock, DUX4, rep2 [R]

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

data_processing:
Sequence reads were mapped to the T2T genome + HSV1 genome (KOSstrain KT899744.1) with MACS2
bigwig files were generated with bamcoverage and normalized to the Drosophila Spikein DNA
Assembly: T2T+ HSV1 genome (KOSstrain)
Supplementary files format and content: bigwig files were generated with bamcoverage, spike in DNA normalized
Library strategy: CUT&RUN

growth_protocol: DMEM, 10% fetal bovine serum,  1mM HEPES and 1x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2

extract_protocol:
CUT&RUN was performed according to the CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers V.3 protocol.
Library was constructed using the NEBNext Ultra II DNA library Prep Kit for Illumina

treatment_protocol: Infection in PBS MOI1, 0.1% Glucose, 1% fetal bovine serum for 1h. Washing of remaining virus with low pH Wash buffer (40mM Citic acid, 10mM KCl, 135 NaCl, ph3)

tag: antibody

value: wildtype

value: mock


title: HHF1 cells, 12h HSV1 GFP (KOSstrain), H3K27me3, rep2

value: 12h HSV1 GFP (KOSstrain)


title: Phha_3966_012023


title: Phha_4068_012023


title: Phha_4949_012023


title: Phha_4776_012023


title: HHF1 cells, Mock, DUX4, rep1 [R]


title: Phha_6001_012023


title: Phha_6076_012023


title: Phha_4940_012023


title: H1650, SSO13, rep1

value: WT


title: Phha_4764_012023


title: ET0310BPhha61570523


title: HHF1 cells, 12h HSV1 GFP (KOSstrain), DUX4, rep2


title: Phha_6072_012023


title: Phha_6036_012023


title: Phha_4731_012023


title: Phha_6125_012023


title: Phha_4787_012023


title: Phha_4395_012023


title: Phha_6038_012023


title: Phha_6085_012023


title: HHF1 cells, 12h HSV1 GFP (Fstrain), IgG, rep2

data_processing:
Sequence reads were mapped to the T2T genome + HSV1 genome (Fstrain GU734771.1) with MACS2
bigwig files were generated with bamcoverage and normalized to the Drosophila Spikein DNA
Assembly: T2T+ HSV1 genome (Fstrain)
Supplementary files format and content: bigwig files were generated with bamcoverage, spike in DNA normalized
Library strategy: CUT&RUN

value: IgG

value: 12h HSV1 GFP (Fstrain)


title: HHF1 cells, 12h HSV1 GFP (KOSstrain), IgG, rep1


title: HHF1 cells, 12h HSV1 GFP (Fstrain), IgG, rep1


title: Phha_6089_012023


title: ET0310BPhha61620523


title: Phha_4593_012023


title: Phha_6026_012023


title: Phha_4951_012023


title: HHF1 cells, 12h HSV1 GFP (KOSstrain), DUX4, rep1


title: HHF1 cells, 12h HSV1 GFP (KOSstrain), IgG, rep2


title: HHF1 cells, 12h HSV1 GFP (Fstrain), DUX4, rep2


title: Phha_3976_012023


title: HHF1 cells, 12h HSV1 GFP (Fstrain), DUX4, rep1


title: Phha_4741_012023


title: F. nucleatum delta-eutV Rep 3

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

data_processing:
Base calling with Illumina CASAVA
quality trimming with trimmomatic v0.36 from both ends with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
reverse complementing of R1 reads
mapping with bowtie2 2.2.7, --ff read orientation, default parameters
converting SAM to BAM with samtools 1.2
visualization and read counting with readXplorer 2.2.3
Analysis of differentially transcribed genes with DESeq2 in default parameters
Assembly: ASM17889v1
Supplementary files format and content: Supplementary Table S1.xlsx is a Excel file containing differential expression data for each gene including log2foldchange and adjusted p-values

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

source_name: bacterial culture

extract_protocol:
F. nucleatum RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacture’s protocol. Fusobacterial cell pellets from 3 ml log-phase culture (OD600 ~ 0.6) were harvested and resuspended into 200 μl of chilled 10 mM RNA-free TE (10 mM Tris-HCl, pH 8; 1 mM EDTA). Each suspension was transferred to a fast-protein tube (Q BIOgene), which contained 700 μl RLT buffer (RNeasy Mini Kit, Qiagen) and 7 μL β-mercaptoethanol (BME) (ThermoFischer Scientific. Cells were lysed by using Ribolyser (Hybaid), and supernatants were obtained by centrifugation at 13000 x g for 5 min at 4°C. RNA was then purified from the supernatant accordingly, and purified RNA was treated with DNAse (Qiagen) and cleaned by using an RNeasy clean up kit (Qiagen). Quality of RNA samples was determined RNA Integrity Number (RIN) values greater than 8 using an Agilent 2100 Bioanalyzer (Agilent Technologies).
2 µg total RNA from F.nucleatum parent and mutant strains were used. Stable RNAs were depleted with the RiboZero Kit according to manufacturer's instructions (Epicentre). Afterwards the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality with the Bioanalyzer (Agilent). Fragmentation of mRNA, reverse transcription to cDNA, adenylation of 3' ends, adapter ligation and PCR amplification were performed according to TrueSeq Stranded mRNA library instructions (Illumina). Prior to paired-end sequencing of the whole transcriptome cDNA libraries on an Illumina MiSeq, the quality and concentration of the libraries were checked using the Bioanalyzer (Agilent).

value: bacterial culture

value: {delta}galK {delta}eutV

value: gene galK and eutV deleted


title: Phha_6080_012023


title: HHF1 cells, Mock, DUX4, rep1


title: F. nucleatum Parent Strain Rep 3

value: {delta}galK

value: gene galK deleted


title: Phha_4748_012023


title: Phha_6050_012023


title: F. nucleatum delta-eutV Rep 2


title: HHF1 cells, Mock, DUX4, rep2


title: Phha_4738_012023


title: Phha_6084_012023


title: Phha_4716_012023


title: Phha_4736_012023

source_name: AllBat clock age 3.201196880537


title: H1395, RiboSeq, rep 3

description: Ribosome profiling

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore software (RNAseq samples) or Cutadapt (ribosome profiling samples)
STAR-2.5.3a single-pass mode was used to alignment the reads (all samples)
STAR-2.5.3a with two-pass mode was used to alignment the reads (only samples for StringTie/transcriptome assembly)
Assembly: hg19 (Ensembl)
Supplementary files format and content: stringtie output transcriptome assembly gtf file
Supplementary files format and content: tab-delimited text files include featureCounts output (PTEN-WWOX differential expression)
Supplementary files format and content: gtf of ORF quantification (RiboSeq samples)
Library strategy: Ribosome profiling

extract_protocol:
kit from Qiagen “allprep DNA/RNA/miRNA Universal kit” (ref. 80224) was used. Before extraction, samples were cut with cryostat to obtain around 200µm of thickness of tissue.  The homogenization step with lysis buffer were done with tissue lyzer system
Stranded mRNA prep Ligation-Illumina

value: lung

value: untreated


title: F. nucleatum Parent Strain Rep 2


title: F. nucleatum delta-eutV Rep 1


title: H1395, RiboSeq, rep 2

description: Ribosome profiling


title: F. nucleatum Parent Strain Rep 1


title: lib2_DNA_biol rep2

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

description: Library name: lib2_DNA_r2

library_source: other

data_processing:
The UMI was extracted and added to the read name using custom python scripts.
Libraries were aligned to the reference sequences using BWA-MEM.
Alignments were filtered using a custom python script.
UMIs were deduplicated using UMI-tools with unique matching.
Alignments for each reference were counted using a custom python script. Fold-change values were calculated from the count data of the two replicates using PyDESeq2.
Assembly: Not applicable.
Supplementary files format and content: CSV files contain count data and the DESeq2 output for each cell line.
Supplementary files format and content: CSV files contain count data normalized stability data for each cell line.

molecule: other

organism: synthetic construct

source_name: plasmid

growth_protocol: HEK293T, HeLa, MCF7, A549, HUH7, and HaCaT cells were cultured in DMEM supplemented with 10% FBS and 100 U/ml Penicillin/Streptomycin (ThermoFisher 15140122). SKNSH and JEG3 cells were cultured in EMEM supplemented with 10% FBS and 100 U/ml Penicillin-Streptomycin. K562 and PC3 cells were cultured in RPMI supplemented with 10% FBS and 100 U/ml Penicillin-Streptomycin. Tera1 cells were cultured in McCoy's 5A medium supplemented with 15% FBS and 100 U/ml Penicillin-Streptomycin.

extract_protocol:
We detached cells with TrypLE, added media, then spun down for 5 min at 210 g. We resuspended the cells in 1 ml of cold PBS and placed them on ice. We took 25 µl of each sample, added 175 µl of PBS, and measured the GFP fluorescence on the Attune NxT flow cytometer to determine cell numbers and transfection efficiencies. We used the Monarch Total RNA Miniprep Kit (NEB, T2010S) to purify total RNA. We eluted in 100 µl of nuclease-free water and determined concentrations using a NanoDrop 2000c (Thermo Fisher). mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L). We eluted in 18 µl of nuclease-free water.
mRNA was reverse transcribed and amplified using custom primers.

treatment_protocol: Transient transfection with plasmid libraries using Lipofectamine 3000.

value: plasmid


title: H1395, RiboSeq, rep 1

description: Ribosome profiling


title: Phha_6045_012023

value: Skin


title: Phha_4743_012023

value: M


title: H1650, RiboSeq, rep 3

description: Ribosome profiling


title: Phha_6052_012023


title: ES medium L5M_2

city: Viborg

first: Maibritt

last: Mardahl

address: Blichers Alle 20

department: Department of Animal and Veterinary Research

country: Denmark

institute: Aarhus University

data_processing:
The data submitted are processed data files. The associated articles generated these fasta files as briefly described below.
1) umi_extract
2) cutadapt with arguments: -j 8 --minimum-length=18 —maximum-length=30 -a AACTGTAGGCACCATCAAT
3) bowtie with arguments: -v 2 -a --norc --best --strata --threads 16 AND reference was to S. vulgaris miRNA precursor complement identified for this study and build to a bowtie index using bowtie_build before alignment.
4) samtools view -h -F 4 filename.sam > filename.bam”
5) samtools sort filename.bam
6) samtools index filename.bam
7) umicollapse with parameters: bam -k 1
8) samtools fastq with parameter: -0
9) fastx_collapser
10) Rename each entry with gsed -i "s/>/>$name\_/g; s/-/_x/g" filename.fasta”
Assembly: Bowtie build of svulgarisPrecursormiRNAComplement.fa
Supplementary files format and content: Fasta of processed raw fasta files with the data processing steps given.

organism: Strongylus vulgaris

source_name: ES-medium

extract_protocol:
miRNeasy Serum/Plasma Kit and miRNeasy mini kit (Qiagen, MD, USA).
QIAseq miRNA Library Kit

treatment_protocol: Live L4 and L5 S. vulgaris larvae were collected from the cranial mestenteric artery of naturally infected foals. A subset of the live larvae (still separated into L4s, L5Ms and L5Fs) were transferred in groups of 2-5 larvae, to T25 culture cell flasks (Thermo Fisher Scientific, Waltham, MA, USA), containing 37˚C Roswell Park Memorial Institute 1640 medium (RPMI 1640 medium) with Antibiotic-Antimycotic Solution, containing 10.000 U/mL penicillin, 10 mg/mL streptomycin and 25 µg/ml Amphotericin B (Sigma-Aldrich, Merck-group, St. Louis, MO, USA). Four ml of RPMI medium were added per flask, regardless of the number of larvae. The larvae were then incubated at 37˚C, and after 30 min., the media was discarded, replaced, and the larvae incubated for another 30 min. This step was performed three times to promote clear-out of the larvae’s intestinal tracts. After the initial three consecutive 30 min. incubation cycles, both the T25 flask and media were replaced, and the larvae were incubated for six hours at 37˚C. Hereafter, the media were collected, and the larvae were incubated with new media for another 6 hours.

value: ES-medium

tag: developmental stage

value: Stage 5 Male


title: H1650, RiboSeq, rep 1

description: Ribosome profiling


title: H1650, RiboSeq, rep 2

description: Ribosome profiling


title: HeLa mNG1-10+, rep 5

description: Differential expression analysis

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore software (RNAseq samples) or Cutadapt (ribosome profiling samples)
STAR-2.5.3a single-pass mode was used to alignment the reads (all samples)
STAR-2.5.3a with two-pass mode was used to alignment the reads (only samples for StringTie/transcriptome assembly)
Assembly: hg19 (Ensembl)
Supplementary files format and content: stringtie output transcriptome assembly gtf file
Supplementary files format and content: tab-delimited text files include featureCounts output (PTEN-WWOX differential expression)
Supplementary files format and content: gtf of ORF quantification (RiboSeq samples)

source_name: HeLa

value: HeLa

value: cervix

value: mNeonGreen+


title: ES medium L5M_1


title: lib2_DNA_biol rep1

description: Library name: lib2_DNA_r1


title: HeLa mNG1-10+, rep 4

description: Differential expression analysis


title: ES medium L5F_3

value: Stage 5 Female


title: HeLa mNG1-10+, rep 3

description: Differential expression analysis


title: Phha_3952_012023

value: F


title: Phha_6124_012023


title: Phha_4777_012023


title: ES medium L5F_2


title: ES medium L5F_1


title: HeLa mNG1-10+, rep 2

description: Differential expression analysis


title: Phha_6079_012023


title: HeLa mNG1-10+, WWOX-CAN+, rep 5

description: Differential expression analysis

value: WWOX-CAN+


title: Phha_4762_012023


title: HeLa mNG1-10+, rep 1

description: Differential expression analysis


title: Phha_4739_012023


title: HeLa mNG1-10+, WWOX-CAN+, rep 4

description: Differential expression analysis


title: Phha_3991_012023


title: Phha_2312_012023


title: HeLa mNG1-10+, WWOX-CAN+, rep 3

description: Differential expression analysis


title: ES medium L4_1

value: Stage 4


title: L5M larvae_3

source_name: Larvae

value: Larvae


title: Phha_6053_012023


title: HeLa mNG1-10+, WWOX-CAN+, rep 2

description: Differential expression analysis


title: Phha_6081_012023


title: Phha_6054_012023


title: Phha_3937_012023


title: HeLa mNG1-10+, WWOX-CAN+, rep 1

description: Differential expression analysis


title: ES medium L4_3


title: HeLa mNG1-10+, WWOX-JET+, rep 5

description: Differential expression analysis

value: WWOX-JET+


title: ES medium L4_2


title: L5F larvae_3


title: L5M larvae_1


title: HeLa mNG1-10+, WWOX-JET+, rep 4

description: Differential expression analysis


title: HeLa mNG1-10+, WWOX-JET+, rep 3

description: Differential expression analysis


title: L5F larvae_1


title: H1650, Scramble, rep5

value: Lung

value: WT

value: Scramble SSO


title: HeLa mNG1-10+, WWOX-JET+, rep 2

description: Differential expression analysis

value: untreated


title: ES medium L5M_3


title: L5F larvae_2


title: L4 larvae_3


title: HeLa mNG1-10+, WWOX-JET+, rep 1

description: Differential expression analysis


title: L4 larvae_2


title: Phha_3938_012023

value: Skin


title: Phha_6090_012023

value: M


title: Phha_4060_012023


title: Phha_4967_012023


title: Phha_4733_012023


title: Phha_3990_012023


title: L4 larvae_1


title: HeLa mNG1-10+, PTEN-CAN+, rep 5

description: Differential expression analysis

value: PTEN-CAN+


title: Phha_4765_012023


title: HeLa mNG1-10+, PTEN-CAN+, rep 4

description: Differential expression analysis


title: Phha_4780_012023


title: HeLa mNG1-10+, PTEN-CAN+, rep 2

description: Differential expression analysis


title: ATACseq_7d_rep2

city: Rehovot

first: Efrat

last: Shema

state: Israel

address: 234 Hertzel

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
ATAC-seq analysis was preformed using the UTAP transcriptome analysis pipeline. Reads were trimmed using cutadapt (parameters: -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT –times 2 -q 25 -m 30), and mapped to the human genome hg19 or hg38 using bowtie2. Uniquely mapped reads were extracted using samtools (-F 4, -f 0x2, -q 39). Following alignment, mitochondrial genes were removed from the analysis, and duplicated reads were removed using picard-tools. Nucleosome-free fragments at the length <120bp were selected from the remaining unique reads.
Assembly: hg19
Supplementary files format and content: Broad peaks were called using MACS2 (with the parameters –bw 120 -B -f BAMPE –SPMR –B –shift -50 –extsize 100 -keep-dup all -q 0.05). The resulting peaks underwent filtering to exclude peaks from the blacklist.
Supplementary files format and content: Coverage files (bigwig) were generated using DeepTools2, using bamCoverage (--normalizeUsing RPKM --binSize 10).

source_name: immortalized human astrocytes (IHA)

growth_protocol: Immortalized Human Astrocytes (IHA), fetal - SV40 (abm) were cultures in PriCoat flasks (abm), with Prigrow IV medium (abm) supplemented with 10% FBS, 1% L-glutamine, 1% P/S and 10ng/ml EGF.

extract_protocol:
Sample preparation was conducted according to omni-ATAC protocol previously described by Grandi et al.  Briefly, 50,000 cells per samples culture were used, and for each condition three replicates were analyzed. Cell lysis was performed using ATAC-seq Lysis Buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin). Following washes (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20) nuclei were incubated with 2.5ul of Nextera Tn5 enzyme (TDE1, Illumina) for 0.5h at 37°C. Transposition was terminated by adding 5 volumes of DNA Binding Buffer from the DNA Clean and Concentrator-5 Kit (Zymo Research, D4014) and tagmentated DNA was isolated using the same kit.
Libraries were prepared using NEBNext Ultra II Q5 2× Master Mix (New England Biolabs, M0544S), followed by library quantification using NEBNext Library Quant Kit (New England Biolabs, E7630) and additional amplification. DNA concentration was measured with a Qubit fluorometer (Life Technologies) and library sizes were determined using TapeStation (Agilent Technologies).

treatment_protocol: Expression of mutant-IDH1 was induced using 1 ug/ml doxycycline.

value: immortalized human astrocytes (IHA)

value: Astrocytes


title: ATACseq_7d_rep1


title: HeLa mNG1-10+, PTEN-CAN+, rep 1

description: Differential expression analysis

value: HeLa

value: cervix


title: ATACseq_48h_rep3


title: L5M larvae_2

value: Stage 5 Male


title: HeLa mNG1-10+, PTEN-CAN+, rep 3

description: Differential expression analysis


title: HeLa mNG1-10+, PTEN-JET+, rep 4

description: Differential expression analysis

value: PTEN-JET+


title: Phha_4727_012023

value: F


title: Phha_4737_012023


title: Phha_3934_012023


title: Phha_3863_012023


title: Phha_6116_012023


title: HeLa mNG1-10+, PTEN-JET+, rep 5

description: Differential expression analysis


title: ATACseq_7d_rep3


title: HeLa mNG1-10+, PTEN-JET+, rep 2

description: Differential expression analysis


title: ATACseq_noDOX_rep3

value: WT IDH1

value: noDOX


title: ATACseq_noDOX_rep1


title: H1395, puromycin, 200ug/ul, rep 3

description: Input transcriptome assembly

value: lung

value: puromycin, 200ug/ul


title: Phha_6115_012023


title: ATACseq_48h_rep2


title: Phha_4954_012023


title: Phha_6075_012023


title: Phha_4775_012023


title: ATACseq_48h_rep1


title: fpECs term control 7

city: Graz

first: Hanna

middle: Helene

last: Allerkamp

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

data_processing:
The trimmomatic tool on Galaxy was used to generate clean reads by removing the adapter-containing and low-quality reads
The clean reads were mapped using the RNA STAR tool against the built-in human reference genome GRCh38
The aligned reads were counted using the htseq-count tool with the human GRCh38 data set retrieved from Ensemble (https://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/, accessed 08 Nov 2023)
Assembly: GRCh38 data set retrieved from Ensemble (https://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/, accessed 08 Nov 2023)
Supplementary files format and content: tabstop-delimeted text file containing a matrix with raw counts of all samples

source_name: fpEC

growth_protocol: Cells were grown in endothelial cell growth medium (C-22220, Promocell, Heidelberg, Germany) supplemented with endothelial cell growth factor, hydrocortisone, epidermal growth factor (C-39220, Promocell), 0.05 mg/ml gentamicin, and 10% defined FCS at 37°C in 12% O2 and 5% CO2.

extract_protocol:
1x10^6 fpECs per sample were harvested using TrypLE and stored in QIAzol Lysis Reagent. RNA was isolated using the miRNeasy Micro Kit (Qiagen) and quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, USA).
A NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) was used to extract mRNA from total RNA followed by library preparation with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: fpEC

tag: group

value: term control


title: H1395, puromycin, 200ug/ul, rep 2

description: Input transcriptome assembly

value: WT


title: HeLa mNG1-10+, PTEN-JET+, rep 3

description: Differential expression analysis

value: untreated


title: fpECs term control 3


title: H1395, untreated, rep 2

description: Input transcriptome assembly


title: H1395, untreated, rep 3

description: Input transcriptome assembly


title: H1395, puromycin, 200ug/ul, rep 1

description: Input transcriptome assembly


title: H1395, untreated, rep 1

description: Input transcriptome assembly


title: Phha_4701_012023

value: Skin

value: M


title: Phha_4745_012023


title: HeLa mNG1-10+, PTEN-JET+, rep 1

description: Differential expression analysis


title: Phha_3953_012023


title: HeLa, puromycin, 200ug/ul, rep 3

description: Input transcriptome assembly


title: ATACseq_noDOX_rep2

value: immortalized human astrocytes (IHA)


title: Phha_3980_012023


title: fpECs term control 4


title: fpECs term control 1


title: Phha_2311_012023


title: HeLa, puromycin, 200ug/ul, rep 2

description: Input transcriptome assembly


title: Phha_4734_012023


title: fpECs term control 5


title: fpECSs preterm control 4

value: preterm control


title: fpECSs preterm control 5


title: HeLa, untreated, rep 3

description: Input transcriptome assembly

value: HeLa


title: HeLa, puromycin, 200ug/ul, rep 1

description: Input transcriptome assembly

value: cervix


title: Phha_6078_012023


title: fpECSs preterm control 2


title: fpECSs preterm control 3


title: fpECs term control 2


title: HeLa, untreated, rep 2

description: Input transcriptome assembly


title: HeLa, untreated, rep 1

description: Input transcriptome assembly


title: HEK293, puromycin, 200ug/ul, rep 3

description: Input transcriptome assembly

value: kidney


title: fpECs early-onset preeclampsia 5

value: early-onset preeclampsia


title: fpECSs preterm control 1


title: Phha_4786_012023


title: Phha_2314_012023

value: F


title: HEK293, puromycin, 200ug/ul, rep 2

description: Input transcriptome assembly


title: fpECs early-onset preeclampsia 4


title: HEK293, puromycin, 200ug/ul, rep 1

description: Input transcriptome assembly


title: HEK293, untreated, rep 3

description: Input transcriptome assembly


title: fpECs early-onset preeclampsia 2


title: fpECs term control 6


title: fpECs early-onset preeclampsia 3


title: Phha_4672_012023


title: Phha_4594_012023


title: Phha_4788_012023


title: HEK293, untreated, rep 1

description: Input transcriptome assembly


title: HEK293, untreated, rep 2

description: Input transcriptome assembly


title: Phha_4778_012023


title: Phha_6086_012023


title: lib1_SKNSH_biol rep2

description: Library name: lib1_SKNSH_r2

source_name: SKNSH

value: SKNSH


title: Phha_4610_012023


title: Phha_4742_012023


title: Phha_4779_012023


title: H1650, puromycin, 200ug/ul, rep 3

description: Input transcriptome assembly


title: lib1_SKNSH_biol rep1

description: Library name: lib1_SKNSH_r1


title: MO3

city: Pullman

first: Min

last: Du

address: 1815 Ferdinand's Ln

department: Animal Science

institute: Washington State University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using Cell Ranger from 10xgenomics
Cell transcriptomes were integrated in R using the Seurat package (v5). Dataset was normalized with a global-scaling normalization method (“LogNormalize”) with default parameters.
Assembly: mouse mm10
Supplementary files format and content: Compressed tab-separated value files and matrix files

source_name: Embryo

growth_protocol: Female mice were fed with either a control or high-fat diet for 10 weeks before breeding with male mice on a regulat chow.

extract_protocol:
After mincing, embryo samples were incubated with TryLE Express dissociation reagent (Life Technology) at 37 °C for 15 min, swirled every two minutes, and the reaction was quenched with heat inactivated serum. After washing, the dissociated single-cell suspensions were re-suspended in PBS with 0.04% BSA and filtered through a 40 μm cell strainer.
After checking the viability and counting, single-cell suspensions of each group were loaded onto the Chromium Controller and cDNA libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 following the manufacturer’s protocol (10X Genomics, Inc.).

treatment_protocol: Mouse embryos were dissected and collected on embryonic 9.5, 11.5 and 13.5 day.After removing the portion of head and first 7 somite pairs, the portion starting from the 8th somite pair till the tail end was collected.For each sample, a total of 15 embryos from three litters of maternal obese (MO) or lean (CON) mice respectively were pooled together for the preparation of cell suspension.  One sample for the CON or MO was collected on the same day and repeated on a second day.

value: Embryo

value: embryonic 13.5 day

value: High Fat diet (45% energy)


title: Phha_3959_012023


title: Phha_4732_012023


title: MO4

description: 10X Genomics


title: H1650, puromycin, 200ug/ul, rep 2

description: Input transcriptome assembly

value: lung

value: puromycin, 200ug/ul


title: MO2

description: 10X Genomics

value: embryonic 11.5 day


title: lib1_MCF7_biol rep2

description: Library name: lib1_MCF7_r2


title: MO1

description: 10X Genomics


title: H1650, puromycin, 200ug/ul, rep 1

description: Input transcriptome assembly

value: WT


title: H1650, untreated, rep 3

description: Input transcriptome assembly

value: untreated


title: lib1_HeLa_biol rep2

description: Library name: lib1_HeLa_r2


title: fpECs early-onset preeclampsia 1

value: fpEC


title: Phha_4714_012023

value: Skin


title: CON4

description: 10X Genomics

value: Control Diet


title: Phha_6051_012023

value: M


title: H1650, untreated, rep 2

description: Input transcriptome assembly


title: lib1_HeLa_biol rep1

description: Library name: lib1_HeLa_r1

value: HeLa


title: Phha_4744_012023


title: lib1_HEK293T_biol rep2

description: Library name: lib1_HEK293T_r2


title: Phha_6037_012023


title: H1650, untreated, rep 1

description: Input transcriptome assembly


title: H1395, untreated, rep 0

description: Input transcriptome assembly


title: CON3

description: 10X Genomics


title: Phha_4800_012023


title: Phha_4740_012023


title: MDA-MB-231, untreated, rep 0

description: Input transcriptome assembly

value: breast


title: lib1_MCF7_biol rep1

description: Library name: lib1_MCF7_r1


title: CON1

description: 10X Genomics


title: lib1_HEK293T_biol rep1

description: Library name: lib1_HEK293T_r1


title: 3d-Dox_b2-12

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline. Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to hg38 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 1.5-fold change.
Assembly: hg38
Supplementary files format and content: DESeq2 analysis

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel)
A bulk adaptation of the MARS-Seq protocol was used to generate RNA-Seq libraries for expression profiling. 30 ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.

value: immortalized human astrocytes (IHA)

value: Astrocytes

value: WT IDH1

value: Dox


title: Mosaic Tumor Replicate 3 ZipSeq

city: Houston

first: Kenneth

middle: H

last: Hu

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

description: 10X Genomics

data_processing:
We demultiplexed bca files into fastq using mkfastq from CellRanger v4.0. Processed feature barcode count matrices were generated using the CellRanger count functon in v4.0 using alignment to mm10.
Assembly: mm10
Supplementary files format and content: feature/barcode matrix in sparse mtx format  and accompanying tab seperated feature and barcode files

source_name: Squamous Cell Carcinoma Subcutaneous tumors

growth_protocol: To generate cell lines, carcinomas were resected at a size of >1 cm in longest diameter, finely chopped, digested in DMEM containing Collagenase I and IV and DNase I for 45 minutes at 37 °C, washed with PBS, plated in supplemented DMEM (high-glucose DMEM (Gibco, catalog# 11995065) plus 10% heat-inactivated FBS (Gibco), 2mM L-glutamine, with 100 units/ml penicillin, 100 µg/ml streptomycin, and 2.5 µg/ml amphotericin B (Gibco)), and passaged until cells stably grow in culture. The established cell lines were cultured in the supplemented DMEM for all experiments.

extract_protocol:
Tumor sections wwere digested in a Collagenase I (100U/mL) and IV (400U/mL) blend in RPMI 1640 for 30 minutes at room temperature. CD45+ cells were sorted using a FACSAria for encapsulation
For gene expression (GEX) libraries, we followed the manufacturer's instructions for 10x 3' v3 library construction.

value: CD45+ cells

value: FVB


title: Phha_6077_012023

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201


title: MCF7, untreated, rep 0

description: Input transcriptome assembly


title: 3d-Dox_b2-10


title: 3d-Dox_b2-11


title: Mosaic Tumor Replicate 1 ZipSeq

description: 10X Genomics

value: Squamous Cell Carcinoma Subcutaneous tumors


title: 21d Nkapl KO2 DRIP input

data_processing:
Adapters and low mapping quality bases of raw reads were removed by Cutadapt (v3.6) after quality control.
Clean reads were aligned to the mouse reference genome mm10 with BOWTIE software (Bowtie2 version 2.4.5), then the duplicate reads marked by Picard Mark Duplicates tools (v2.27.4) were dropped.
After splitting signals on forward and reverse strands, peak calling was carried out by using MACS2 (version 2.2.7.1) only on ssDRIP samples firstly, these peaks were merge by Deseq2 to find significant peaks throughs samples in replicates against the input.
BigWig fomat files were created by bamCoverage tool in deepTools (version 3.5.1) with library size normalized. Motifs were searched by MEME (v5.0.5) with custom parameters. Peaks annotation referred to GTF file(vM23) from Gencode.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: ssDRIP-seq

extract_protocol:
Nuclei was isolated from testis tissues before SDS/proteinase K treatment at 37°C for 4-6 hours, followed by genomic DNA extraction with the phenol:chloroform:isoamyl alcohol method. The precipitated DNA pellet was washed, air dried, resuspended in TE buffer, and quantified by the Qubit dsDNA HS Assay kit (Invitrogen, Q32854). 10 μg gDNA was digested with a combination of restriction enzymes of MseI, DdeI, AluI, and MboI at 37°C overnight, and the negative control was treated with RNase H (New England Biolabs, M0297S). For DNA:RNA hybrids immunoprecipitation (DRIP), 5 μg gDNA was resuspended in 500 μl TE buffer. 450 μl gDNA mixture was incubated with 10 µg S9.6 antibody for DNA:RNA immunoprecipitation, and the remaining 50 μl was used as input DNA. Protein G dynabeads were pre-washed for three times with 1×DRIP binding buffer (100 mM sodium phosphate, pH 7.0; 1.4 M NaCl; 0.5% Triton X-100) and then added to the DNA-antibody mixtures with gentle shaking at 4 °C for 3~4 hours. DNA was eluted with DRIP elution buffer, and then sheared to 250 bp in size by sonication using the Covaris-S220. These DNA samples was denatured at 95°C for 2 mins and then incubated on ice for 2 mins to obtain ssDNA fragments.
ssDRIP-seq libraries were constructed by using the VAHTS ssDNA Library Prep Kit for Illumina (Vazyme, ND620-02), following instructions from the manufacturer.

value: Testis

tag: time

value: postnatal day 21

value: Knockout


title: H1650, untreated, rep 0

description: Input transcriptome assembly

value: lung

value: WT

value: untreated


title: Phha_2430_12013

value: Skin


title: 3d-Dox_b2-9


title: Phha_4548_12015

value: M


title: CON2

description: 10X Genomics

value: Embryo

value: embryonic 11.5 day

value: Control Diet


title: XenoCFPACPlusDox5

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

data_processing:
TrimGalore to trim low quality bases and Illumina sequencing adapters
GRCh38v93 version of the human genome and transcriptome using the STAR RNA-seq alignment too
Gene counts were compiled using the HTSeq tool
Differential gene expression was assessed using R version 4.2.1 coupled with DESeq2
Assembly: GRCh38v93
Supplementary files format and content: RNAseqNormalizedCounts.xlsx - Colum headers reffer to sample - Row titles reffer to Ensembl gene IDs

source_name: Xenograft

extract_protocol:
RNEasy (qiagen)
KAPA Stranded mRNA-Seq Kit (Roche)

treatment_protocol: Cells were treated for 7 days with doxycycline before growth in culture or as xenografts

value: Xenograft

value: Doxycycline


title: XenoCFPACPlusDox4


title: 21d Nkapl KO1 DRIP input


title: 21d WT2 DRIP input

value: Wild-type


title: 7d-Dox_b2-20

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline. Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to hg38 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 1.5-fold change.

value: immortalized human astrocytes (IHA)

value: Astrocytes

value: WT IDH1

value: Dox


title: Phha_3857_72011

extract_protocol: DNA extracted using Zymo DNA miniprep


title: 7d-Dox_b2-19


title: Phha_2429_72011


title: XenoCFPACPlusDox3


title: XenoCFPACPlusDox2


title: 21d WT1 DRIP input

value: Testis

value: postnatal day 21


title: Phha_4543_12014


title: 21d WT2 RaseH DRIP


title: XenoCFPACPlusDox1


title: 7d-Dox_b2-18


title: 21d WT1 RaseH DRIP


title: 7d-Dox_b2-17


title: 7d-Dox_b1-13


title: noDox_b2-4

value: noDox


title: 21d Nkapl KO2 DRIP

value: Knockout


title: XenoCFPACMinusDox4


title: XenoCFPACMinusDox3


title: 21d Nkapl KO1 DRIP


title: Phha_4177_12013


title: noDox_b2-2


title: XenoCFPACMinusDox2


title: noDox_b2-1


title: 21d WT2 DRIP


title: 21d WT1 DRIP


title: XenoCFPACMinusDox1


title: noDox_b1-3


title: Phha_2079_72011


title: Phha_4679_12015


title: Phha_3856_72011


title: noDox_b1-2


title: XenoPancPlusDox5


title: XenoCFPACMinusDox5


title: 21d Nkapl TGdel/TGdel rep2

data_processing:
Clean data were obtained by trimming the adaptor sequence and removing sequences with low quality.
Clean reads were mapped to the mouse genome (mm10) with HISAT2 (v.2.1.0; Johns Hopkins University, Baltimore, MD, USA) with a GTF file download from the UCSC database (University of California, Santa Cruz).
The aligned reads of genes were counted using HTSeq followed by DESeq2 normalization to evaluate gene expression as normalized counts per million.
Assembly: mm10
Supplementary files format and content: Gene counts for every gene and every sample

extract_protocol:
Testes were collected from wild-type, Nkapl-KO, Sox30-KO, and Nkapl TGdel/TGdel mice, and RNA was harvested using Trizol reagent.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina).

value: TGdelete


title: Phha_2217_72011

value: Skin


title: 21d Nkapl TGdel/TGdel rep3


title: Phha_4546_12014

value: M


title: Phha_4724_42018


title: 21d Nkapl TGdel/TGdel rep1


title: noDox_b1-1


title: Phha_4666_12015


title: XenoPancPlusDox3


title: Phha_4959_12015


title: Cut&Run on IHA-7d-Dox using H3K27ac antibody

data_processing:
Reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20), and reads quality was evaluated using FastQC. Reads were mapped to human genome (hg19, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools. Broad peaks were called using epic2 against the corresponding HRP samples as background control. Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Assembly: hg19
Supplementary files format and content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins.
Supplementary files format and content: Peaks files were constructed using epic2 against HRP samples as background control.
Library strategy: Cut&Run

extract_protocol:
Cut&Run assay was done as described in (Meers et al., 2019; Skene and Henikoff, 2017) with slight modifications as follows: Cells were harvested and counted, with 200,000 cells taken per reaction. Permeabilized cells, bound to Concanavalin A-coated beads (Bangs Laboratories, BP531), were mixed with individual primary antibody (diluted 1:150-1:200) and incubated overnight at 4°C while rotating. Secondary antibody anti-rabbit HRP was used as a negative control. pAG-MNase enzyme (generated in the Department of Life Sciences Core Facilities, WIS, using Addgene plasmid 123461) was added to each sample followed by incubation step of 1 h at 4°C. Targeted digestion was done by 15 min incubation on ice block (0°C) under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609).
Libraries were prepared from 1-20ng of DNA as previously described [61]. Briefly, DNA Fragments were repaired by T4 DNA polymerase (NEB, M0203), and T4 polynucleotide kinase (T4 PNK, NEB, M0201) was used to add a phosphate group at the 5′ ends. An adenosine base was then added by Klenow fragments (NEB, M0212) to allow efficient ligation, using T4 quick ligase (NEB, M2200), of sequencing adapters, which contain a T-overhang. DNA fragments were amplified by PCR reaction (Pfu Ultra II fusion, Agilent Technologies, 600670), which also introduced the Illumina-P5 adapter at one end of the molecule. SPRI beads were used to purify proper sized DNA fragments after each enzymatic step. Libraries were quantified by Qubit (ThermoFisher Scientific) and proper fragment range (200-400bp) was verified by TapeStation (Agilent). Sequencing was done on a Next-Seq 500 instrument (Illumina) using a Nextseq 150 cycles mid output kit, allocating 10M reads per sample (paired end sequencing).


title: XenoPancPlusDox2


title: 21d Nkapl-WT rep3 (NE)


title: Cut&Run on IHA-7d-Dox using H4K16ac antibody


title: XenoPancPlusDox1


title: XenoPancPlusDox4


title: 21d Nkapl-WT rep2 (NE)


title: Cut&Run on IHA-7d-Dox using H3K9ac antibody


title: Phha_4536_12014


title: 21d Nkapl-WT rep1 (NE)


title: Phha_4601_12015


title: Cut&Run on IHA-2d-Dox using H4K16ac antibody


title: XenoPancMinusDox5


title: Phha_2200_12013


title: 21d Sox30-KO rep3


title: Phha_2486_72011


title: 21d Sox30-KO rep2


title: Cut&Run on IHA-2d-Dox using H3K27ac antibody


title: XenoPancMinusDox4


title: XenoPancMinusDox3


title: Cut&Run on IHA-2d-Dox using H3K9ac antibody


title: 21d Sox30-KO rep1


title: Cut&Run on IHA-noDox using IgG control antibody (2nd HRP)


title: XenoPancMinusDox2


title: Phha_4544_12014


title: 21d Sox30-WT rep3


title: Phha_2130_72011


title: XenoPancMinusDox1


title: Cut&Run on IHA-noDox using H4K16ac antibody


title: 21d Sox30-WT rep2


title: Phha_4532_12014


title: XenoBXPC3PlusDox5


title: Cut&Run on IHA-noDox using H3K27ac antibody


title: 21d Sox30-WT rep1


title: XenoBXPC3PlusDox4


title: 21d Nkapl-KO rep3


title: Cut&Run on IHA-noDox using H3K9ac antibody


title: Phha_4703_12015


title: Phha_2430_72011


title: XenoBXPC3PlusDox3


title: truncated_SK3_base_rep3

city: NanJING

first: CHEN

last: XIN

state: JiangSu

address: N0.2 SiPai Road

institute: Southeast University

description:
Library name: sample21
Column name in counts_all.csv: SK3_B_3

data_processing:
Sample quality and yield were monitored by a Bioanalyzer (Agilent). The DNA were sequenced from 43bp-end with both i5 and i7 indices (6 bp each) using an Illumina HiSeqTM 2500. During library construction and sequencing, investigators were blinded to samples. Raw reads were filtered with Trimmomatic software 17 and aligned to the GRCm38 mm10 assembly reference genome with hisat2 18. The R package DESeq2 was used to identify differentially expressed genes (DEGs) with option “counts > 5”. Genes with p-value < 0.05 (Benjamini-Hochberg correction) and fold-change (log2scale) ≥1 or ≤-1  were considered as significant difference. Gene ontology (GO) analysis was performed by DAVID (6.8) online with DEGs defined with FDR < 0.01.
Assembly: GRCm38 mm10 assembly reference genome
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: excel file inlcudes normalized counts matrix of differentially expressed genes upon conditions

source_name: cochlea

extract_protocol:
polyA RNA was extracted by smart-seq2-used lysis buffer (0.1% Triton X-100, 5 mM dNTPs, 2.5 μM Oligo-dT30VN (5’-AAGCAGTAGTATCAAVGCAGAGTACT30VN-3’, where ‘N’ is any base and ‘V’ is either A, C or G) and 1U/μl RNase inhibitor (Takara, 2313A))
cDNA libraries were constituted by the Smart-seq2 method. (Picelli, S., Bjorklund, A.K., Faridani, O.R., Sagasser, S., Winberg, G., and Sandberg, R. (2013). Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098. 10.1038/nmeth.2639.)

value: cochlea

value: spiral ganglion neuron

value: dominant-negative effect of mSK3

value: biological replicate3 in basal region in truncated_SK3


title: 21d Nkapl-KO rep1


title: Phha_4680_12015


title: XenoBXPC3PlusDox2

value: Xenograft

value: Doxycycline


title: truncated_SK3_base_rep2

description:
Library name: sample20
Column name in counts_all.csv: SK3_B_2

value: biological replicate2 in basal region in truncated_SK3


title: XenoBXPC3PlusDox1


title: 21d Nkapl-WT rep3

value: Wild-type


title: Phha_4547_12014


title: XenoBXPC3MinusDox5


title: Phha_2218_72011


title: XenoBXPC3MinusDox4


title: truncated_SK3_apex_rep2

description:
Library name: sample17
Column name in counts_all.csv: SK3_A_2

value: biological replicate2 in apical region in truncated_SK3


title: 21d Nkapl-WT rep2


title: Phha_2388_72011


title: Phha_4677_12015


title: truncated_SK3_apex_rep1

description:
Library name: sample16
Column name in counts_all.csv: SK3_A_1

value: biological replicate1 in apical region in truncated_SK3


title: 21d Nkapl-KO rep2

value: Testis


title: Phha_4540_12014


title: XenoBXPC3MinusDox3


title: XenoBXPC3MinusDox2


title: 21d Nkapl-WT rep1

value: postnatal day 21


title: DN-mHCN2_base_rep3

description:
Library name: sample15
Column name in counts_all.csv: DN-mHCN2_B_3

value: dominant-negative effect of mHCN2

value: biological replicate3 in basal region in DN-mHCN2


title: Phha_3860_72011


title: KO_input

data_processing:
Reads were aligned to the mouse reference genome mm10 with BOWTIE software (bowtie2 version 2.3.4.3), followed by the removal of those reads that with low mapping quality and duplicated through sample amplification or sequencing.
Peak calling was carried out by using MACS2 (version 2.1.2, with options'-mfold 5, 50-p 0.0001'), on ChIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0).
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Fresh testes were collected from wild-type and Nkapl KO mice at postnatal day 21, ground into powder in liquid N2, and crosslinked by 1% formaldehyde, followed by quenching with glycine solution. Chromatin was fragmented by sonication in ChIP SDS lysis buffer (50 mM Tris-HCl, pH=8; 10 mM EDTA, pH=8; 1% SDS) using the Covaris-S220 sonicator. Crosslinked chromatin was incubated with indicated antibodies in ChIP dilution buffer (50 mM HEPES, pH7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxycholate) with protease inhibitors overnight. Crosslinking was reversed overnight at 65°C, and DNA was extracted by using phenol/chloroform/isoamyl alcohol.
Precipitated DNA was amplified for deep-sequencing. For ChIP-seq, equal DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers.

value: Knockout

tag: chip antibody


title: truncated_SK3_base_rep1

description:
Library name: sample19
Column name in counts_all.csv: SK3_B_1

tag: tissue

value: biological replicate1 in basal region in truncated_SK3


title: CellsCFPacPlusDox3

source_name: Cell Culture

value: Cell Culture


title: truncated_SK3_apex_rep3

description:
Library name: sample18
Column name in counts_all.csv: SK3_A_3

value: cochlea

value: biological replicate3 in apical region in truncated_SK3


title: KO_SOX30

value: SOX30 (ABclonal, A11759)


title: XenoBXPC3MinusDox1


title: KO_HDAC3

value: HDAC3 (Abcam, ab7030)


title: CellsCFPacPlusDox2


title: DN-mHCN2_base_rep2

description:
Library name: sample14
Column name in counts_all.csv: DN-mHCN2_B_2

value: spiral ganglion neuron

value: biological replicate2 in basal region in DN-mHCN2


title: DN-mHCN2_apex_rep4

description:
Library name: sample12
Column name in counts_all.csv: DN-mHCN2_A_4

value: biological replicate4 in apical region in DN-mHCN2


title: DN-mHCN2_base_rep1

description:
Library name: sample13
Column name in counts_all.csv: DN-mHCN2_B_1

value: biological replicate1 in basal region in DN-mHCN2


title: Phha_4702_12015

value: Skin

value: M


title: Phha_2075_72011


title: Phha_4537_12014


title: CellsCFPacPlusDox1

value: Doxycycline


title: KO_Pol ll

value: Testis

value: postnatal day 21

value: Pol II (Millipore, 05-623)


title: Pol ll_WT

value: Wild-type


title: DN-mHCN2_apex_rep3

description:
Library name: sample11
Column name in counts_all.csv: DN-mHCN2_A_3

value: dominant-negative effect of mHCN2

value: biological replicate3 in apical region in DN-mHCN2


title: Phha_4539_12014

source_name: AllBat clock age 4.362295698454


title: SOX30_WT_rep2

source_name: Testis


title: DN-mHCN2_apex_rep2

description:
Library name: sample10
Column name in counts_all.csv: DN-mHCN2_A_2

value: cochlea

value: biological replicate2 in apical region in DN-mHCN2


title: DN-mHCN2_apex_rep1

description:
Library name: sample9
Column name in counts_all.csv: DN-mHCN2_A_1

value: biological replicate1 in apical region in DN-mHCN2


title: Phha_4543_12015


title: CellsCFPacMinusDox3

value: Cell Culture


title: SOX30_WT_rep1

value: SOX30 (ABclonal, A11759)


title: CellsCFPacMinusDox1


title: HDAC3_WT_rep2

value: HDAC3 (Abcam, ab7030)


title: Phha_2104_72011


title: HDAC3_WT_rep1


title: Phha_4548_12014


title: Phha_2077_72011


title: control_base_rep3

description:
Library name: sample7
Column name in counts_all.csv: CTRL_B_3

value: spiral ganglion neuron

value: WT

value: biological replicate3 in basal region in WT


title: control_base_rep2

description:
Library name: sample6
Column name in counts_all.csv: CTRL_B_2

value: biological replicate2 in basal region in WT


title: NKAPL_WT

value: NKAPL (Abclonal, E10124)


title: Phha_2216_72011

value: Skin

value: M


title: CellsPancPlusDox2

value: Doxycycline


title: control_apex_rep4

description:
Library name: sample4
Column name in counts_all.csv: CTRL_A_4

value: biological replicate4 in apical region in WT


title: CellsPancPlusDox1


title: CellsCFPacMinusDox2


title: control_base_rep1

description:
Library name: sample5
Column name in counts_all.csv: CTRL_B_1

value: biological replicate1 in basal region in WT


title: Phha_1852_72011

source_name: AllBat clock age 7.82876910713


title: control_base_rep4

description:
Library name: sample8
Column name in counts_all.csv: CTRL_B_4

value: biological replicate4 in basal region in WT


title: CellsPancMinusDox2


title: control_apex_rep3

description:
Library name: sample3
Column name in counts_all.csv: CTRL_A_3

value: cochlea

value: biological replicate3 in apical region in WT


title: RFP MTF rep2

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Reads, excluding the rRNA seqeunces, were mapped to the genome (Ensembl R64-1-1 release101) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalize.
Assembly: R64-1-1
Supplementary files format and content: tab separated RSEM results

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: fmt1 S. cerevisiae expressing EcFMT or EcFMTR42L were grown at 30°C in SC-media until A600 of ~0.5

extract_protocol:
~50 A260 unit of cell lysates were supplemented with RNase I and incubated 1 hr at room temperature with gentle rotation. Resulting samples were layered onto 10%-50% sucrose gradient and centrifuged at 39,000 rpm at 4 °C for 2.5 hr using SW-41 Ti rotor. Resulting sucrose gradients were monitor and digested 80S fractions were collected, followed by centrifugal filtration. Sequentially, samples were mixed with release buffer and incubated on ice for 10 min, followed by centrifugation and transferred the flowthrough into a new sterile tube. The flowthroughs were adjusted to 1% SDS, followed by the addition of 1 volume of Acid-Phenol:Chloroform (pH4.5), vortex, incubation at 65°C for 5 min, and incubation on ice for 1 min. Resulting samples were centrifuged at 12,000xg at 4°C for 5 min, and resulting aqueous top was transferred to new sterile 1.5 ml tubes. RNA from the resulting samples were ethanol precipitated by adding NaOAc (pH 5.5) containing 1/100 volume Glycoblue, followed by 2.5 volumes of 100% ethanol and incubation at -20°C overnight.
Harvested RNA fragments were dephosphorylated, following adaptor ligation using 3’-adaptor. The Ligated RNAs were reverse transcribed using RT-primer, circularized and PCR-amplified for 12. Following PCR products are purified and subjected to 150bp-double end sequencing using the Illumina Nextseq 1000 system.
RIBO-Seq

treatment_protocol: Cells were rapidly vacuum filtered and snap frozen in liquid nitrogen. Frozen cells were resuspended in the ribosome lysis buffer, followed by mechanical disruption using bead beater.

value: budding yeast


title: Phha_2200_72011


title: RFP MTF rep1


title: HSPA8KO-8K-K-3A

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

description: Library name: Sample 6

data_processing:
Clc Geromics Workbench y 11.0.1
Secuence reads were trimmed for adaptor secuencelow-auality seouence usina ClC oenomic benchwork (parameter- Quality limit: 0.05)
Timmed seuence reads were mapped to GrCM38/mm10 using CLC genomic benchwok (parameters-msmath cost 2 insertion ost-3 deleton cost 3 length fector: 0.8 simlarity facton:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Kidney

growth_protocol: The sample size for the animal studies was calculated based on a survey of data from published research or preliminary studies. Hspa8flox/flox (C57BL/6J-Hspa8em1flox/Cya; Strain No. CKOCMP-15481-Hspa8-B6J-VA) and Cdh16-Cre mice (Cat#: C001452) obtained from Cyagen Biosciences (Guangzhou) Inc (Guangzhou, Guangdong, China). C57BL/6J mice and Pkr-/- (C57BL/6JGpt-Eif2ak2em4Cd2637/Gpt; Strain No. T015370) mice based on C57BL/6J background were purchased from Gempharmatech Co. Ltd (Jiangsu, Nanjing, China). These mice were maintained in SPF units of the Animal Center of First Affiliated Hospital of Southern University of Science and Technology with a 12 h light cycle from 8 a.m. to 8 p.m., 23 ± 1 °C, 60 – 70 % humidity. Mice were allowed to acclimatize to their housing environment for 7 days before the experiments. At the end of the experiments, all mice were anesthetized and euthanized in a CO2 chamber, followed by the collection of kidney tissues. All animals were randomized before treatment. Mice were treated in a blinded fashion as the drugs used for treating animals were prepared by researchers who did not carry out the treatments. No mice were excluded from the statistical analysis.

extract_protocol:
RNA was havested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manutacturer's protocols

value: Kidney

value: Hspa8 knockout

value: 8-week-old mice fed with normal chow


title: Phha_4697_12015


title: CellsPancPlusDox3

value: Cell Culture


title: CellsPancMinusDox1


title: RFP MTFi rep2


title: control_apex_rep2

description:
Library name: sample2
Column name in counts_all.csv: CTRL_A_2

value: spiral ganglion neuron

value: WT

value: biological replicate2 in apical region in WT


title: CellsPancMinusDox3


title: RFP MTFi rep1


title: HSPA8KO-8K-K-1A

description: Library name: Sample 4


title: Striga leaf 2

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing:
ShortStack version 4.4.0 was used for small RNA annotation. FASTQ files were processed and trimmed using autotrim option and default alingment settings in ShortStack.
Assembly: GCA_902706635.1
Supplementary files format and content: Raw counts text file

organism: Striga hermonthica

source_name: Leaf stage 6

growth_protocol: Striga hermonthica was grown on host Oryza sativa ssp. Japonica variety KitaakeX under 16 hour light conditions in a quarantine facility at 30°C for 45 days.

extract_protocol:
Total RNA was extracted using Zymo Quick-RNA Plant Miniprep Kit
sRNA-seq libraries were prepared as described in McGuire et al., (2020)
small RNA-seq

value: Leaf stage 6

value: kibos


title: CellsBXPC3PlusDox2


title: control_apex_rep1

description:
Library name: sample1
Column name in counts_all.csv: CTRL_A_1

value: biological replicate1 in apical region in WT


title: Striga leaf 1


title: C57-8W-K-3A

description: Library name: Sample 3


title: Phha_4546_12015

city: College Park

first: Gerald

last: Wilkinson

address: Biology-Psychology Building

institute: University of Maryland

value: Skin

value: M


title: CellsBXPC3PlusDox1

value: Doxycycline


title: C57-8W-K-1A

description: Library name: Sample 1


title: CellsBXPC3MinusDox3


title: HSPA8KO-8K-K-2A

description: Library name: Sample 5


title: Striga haustorium stage 6 1

source_name: Haustorium stage 6

value: Haustorium stage 6


title: CellsBXPC3MinusDox2


title: Striga haustorium 3

source_name: Haustorium

value: Haustorium


title: Striga haustorium 1


title: CellsBXPC3MinusDox1


title: R71000057 AATD CD45neg

city: Philadelphia

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the STARSolo 2.7.9a and downstream analysis performed using Seurat v4
Assembly: GRCh38

source_name: Peripheral lung tissue

extract_protocol:
Peripheral samples: 2cm deep from the pleura, airway or vessel visible structures >2mm removed. Proximal airway: 5 generations of airway from main stem bronchus.Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two or one biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina Hiseq 2500 with 2 × 100 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.
Libraries were prepared according to the manufacturer’s protocol using Chromium Single Cell 3’ v2 chemistry.

value: Peripheral lung tissue

tag: disease

value: AATD

value: Male


title: WT Naïve T cells

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

institute: Seoul National University

description: Library name: WT Naïve

data_processing:
During data processing, genes with zero read counts in more than one sample were excluded. The remaining data were log2-transformed and normalized using the TMM (Trimmed Mean of M-values) method.
Differential expression analysis was performed using edgeR’s exactTest, with p-values adjusted for false discovery rate (FDR) using the Benjamini-Hochberg algorithm.
Genes with a fold change ≥2 and raw p-value <0.05 were selected as differentially expressed genes (DEGs).
Hierarchical clustering of DEGs was conducted using the complete linkage method and Euclidean distance.
Gene enrichment, functional annotation, and pathway analysis for the significant genes were performed using gProfiler and the KEGG pathway database. All data analysis and visualization were carried out using R version 3.6.0.
Assembly: mm10
Supplementary files format and content: xlsx file includes FPKM, TPM, average, read count, etc for each sample.

source_name: spleen

extract_protocol:
Using anti-CD8 microbeads, CD8 T cells were isolated from the C57BL/6 spleens by magnetic sorting and sorted into naïve (CD44-CD49d-), TM (CD44hiCD49d+) and VM (CD44hiCD49d-) on the basis of Ly6C and Sca-1 expression. RNA was extracted using an Isolate II RNA mini kit.
The library was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, followed by paired-end sequencing (101 bp) on an Illumina platform. Initial sequence quality was assessed using FastQC (v0.11.7), and preprocessing was performed with Trimmomatic (v0.38) to remove adapter sequences and trim bases with a quality score below 3 from the ends. A sliding window approach (window size = 4, mean quality ≥ 15) was used to remove low-quality regions, and reads shorter than 36 bp were discarded, resulting in high-quality, clean data for downstream analysis.

value: spleen

value: Virtual memory T cells

value: Wild-type (WT)


title: WT Ly6C- Sca-1+ Virtual memory T cells

description: Library name: WT P-10


title: WT Ly6C- Sca-1- Virtual memory T cells

description: Library name: WT P-9


title: WT Ly6C+ Sca-1+ Virtual memory T cells-2

description: Library name: WT P8-2


title: CellsBXPC3PlusDox3

value: Cell Culture

tag: cell line


title: WT True memory T cells

description: Library name: WT TM

tag: cell type


title: WT Ly6C+ Sca-1- Virtual memory T cells-2

description: Library name: WT P7-2


title: R710000551 AATD CD45neg Rep2

description: 10x Genomics

value: Female


title: shSCUBE3_02

type: RNA

city: SHANGHAI

first: CAIYUN

last: ZHANG

address: CHANGHAI ROAD NO. 168

institute: CHANGHAI HOSPITAL

description: Gene expression from data CAL-27 cells infected with shSCUBE3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeview human PathArrayTM.

scan_protocol: Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing:
The normalization/processing algorithm used in our data is log2-RMA. The statistical  significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.
|Fold Change| ≥ 1.3 and FDR < 0.05 as significant.

label: Biotin

source_name: GeneChip primeview human (CAL-27 cells with SCUBE3 shRNA lentiviral transfection)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in DMEM medium (Gibco) supplemental with 10% fetal bovine serum  (Gibco), placing in a 37°C incubator containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CAL-27 cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or shSCUBE3 lentivirus, culturing in DMEM medium (Gibco) supplemental with 10% fetal bovine serum in a 6-well dish with 2×105 cells per well.

value: tongue squamous cell carcinoma (TSCC) cell lines

value: CAL-27 cells


title: 21d Nkapl-WT eCLIP rep1

city: Nanjing

first: Chen

last: Xu

address: 101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
The adapters and 3' adapter-dimers were trimmed with cutadapt (V1.14), and PCR duplicates were removed with a custom python script.
The reads aligned to the repeat elements from UCSC with STAR (V2.7.6a) were filtered out before mapping to mm10 reference genome (GENCODE vM23).
Assembly: mm10
Supplementary files format and content: bigWig files

molecule: nuclear RNA

extract_protocol:
Fresh testes were collected from wild-type mice at P21, and the subsequent PBS suspension containing seminiferous tubules was crosslinked by UV-irradiation three times at 254 nm (400 mJ/cm2) and lysed in eCLIP lysis buffer with RNase I (LifeTech) and Turbo DNase (LifeTech). NKAPL-RNA complexes were immunoprecipitated with anti-NKAPL antibodies and protein A dynabeads. 2% of lysates were used as input and processed in parallel with immunoprecipitated samples. NKAPL-RNA complexes were dephosphorylated, and ligated with 3′ RNA adapter. NKAPL-RNA complexes were separated and transferred for RNA extraction. RNAs were reverse transcribed before stand-specific eCLIP library construction.
RNAs were reverse transcribed with AffinityScript (Agilent) followed by treatment with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. The DNA adapter was ligated to the 3' end of cDNA with T4 RNA Ligase (NEB). Samples were cleaned up with MyOne Silane Dynabeads (Thermofisher) and subject to quantitative PCR to determine the appropriate number of PCR cycles. Libraries were amplified with Q5 Polymerase (NEB). Amplified PCR products were separated on 3% low-melting temperature agarose gel (Seakem GTG LMP), and size-selected libraries were purified with a MinElute gel extraction kit (Qiagen).

value: Testis

value: postnatal day 21

value: Wild-type

value: NKAPL (ABclonal, E10124)


title: WT Ly6C+ Sca-1+ Virtual memory T cells-1

description: Library name: WT P8-1


title: C57-8W-K-2A

description: Library name: Sample 2

value: Kidney

value: WT

tag: treatment

value: 8-week-old mice fed with normal chow


title: shSCUBE3_01


title: R710000551 AATD CD45neg Rep1

description: 10x Genomics

value: Peripheral lung tissue


title: shSCUBE3_03


title: 21d Nkapl-WT input


title: Striga haustorium stage 6 2

value: Haustorium stage 6

value: kibos


title: shCtrl_03

description: Gene expression from data CAL-27 cells infected with shCtrl

source_name: GeneChip primeview human (CAL-27 cells with SCUBE3 shRNA negative control lentiviral transfection)


title: WT Ly6C+ Sca-1- Virtual memory T cells-1

description: Library name: WT P7-1

value: spleen


title: sEVs from old-passage 10 ASCs

status: Public on Dec 11 2024

city: Tokyo

first: Toshiya

last: Tsubaki

address: 7-3-1 Hongo, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Sample 5

data_processing:
The raw data were mapped to a reference genome (GCF_000001405.38_GRCh38.p12) using Bowtie2 (ver. 2.2.9) after adapter sequences were removed using SOAPnuke (ver. 1.5.6). Expression values were calculated using the following formula: Expression = (the number of UMI reads that are mapped to the small RNA * 1,000,000) / the UMI number of total clean reads in the sample.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-delimited text file includes rae read counts for each Sample

source_name: small extracellular vesicles

growth_protocol: ASCs were cultured in MSC NutriStem® XF Basal Medium (NutriStem, Sartorius Stedim Biotech, Lower Saxony, Germany) supplemented with 2% fetal bovine serum (FBS) and 0.1% penicillin-streptomycin at 37°C in an incubator with humidified 5% CO2.

extract_protocol:
The precipitated sEVs (sEV extraction) were lysed with TRI reagent (Molecular Research Center, Inc., Cincinnati, OH, USA), and RNA was extracted using the Direct-zol RNA kit.
Outsourced to BGI Japan Co., Ltd.

treatment_protocol: ASCs were seeded into 15-cm dishes and cultured to 80% confluence. The medium was then replaced with sEV collection medium (NutriStem:DMEM = 1:1). After 48 h, the culture supernatant was collected. The supernatant was centrifuged at 2000 g for 10 min to remove cell debris and filtered using a 0.22 µm filter (Thermo Fisher Scientific, Massachusetts, USA). The filtered supernatant was ultrafiltered using Vivaspin®20 Membrane: 100,000 MWCO PES (Sartorius Stedim Biotech, Lower Saxony, Germany). Exosomes were purified from the ultrafiltered supernatant using Exoquick TC (System Biosciences, Palo Alto, CA, USA).

value: small extracellular vesicles

value: mesenchymal stem cells


title: WT-7pm

city: Worcester

first: Patrick

last: Sheehan

address: 364 Plantation Ave.

department: Neurobiology

institute: University of Massachusetts Medical School

description:
Library name: WT-7pm
WT-7pm-cortex

data_processing:
Sample processing was performed using the Cell Ranger Single-Cell Software.  Seurat v4.9 was used for analysis.
Assembly: Mouse Ensembl release 101 primary assembly
Supplementary files format and content: Processed matrix, barcodes and feature files are included for import into Seurat

source_name: Cortex

extract_protocol:
Brain was frozen prior to extraction of nuclei.
Nuclei were sequenced using the Chromium Single Cell 3’ Reagent Kit from 10x Genomics.

treatment_protocol: Mice were placed in constant darkness 24 hours prior to sacrificing.

value: Cortex


title: WT-7am

description:
Library name: WT-7am
WT-7am-cortex


title: sEVs from young-passage 10 ASCs

description: Sample 2


title: sEVs from young-passage 15 ASCs

description: Sample 3


title: 21d Nkapl-WT eCLIP rep2


title: amniotic fluid fetal cells_Fetal_AF117816

city: Zhangzhou

first: Shurong

last: Hong

department: Department of molecular genetic center

institute: Zhangzhou Municipal Hospital of Fujian Province and Zhangzhou Affiliated Hospital of Fujian Medical University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing: The array image was acquired using Affymetrix GeneChip Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 4.0).

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from amniotic fluid fetal cells using the QIAamp DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: amniotic fluid fetal cells


title: shCtrl_01

value: tongue squamous cell carcinoma (TSCC) cell lines


title: shCtrl_02

value: CAL-27 cells