title: Nucleus pulposus cells from LSI #3, RNA-seq

description:
LSI_3
Sham_LSI_LSI_E_RPKM.txt

source_name: Nucleus pulposus tissue from LSI

value: Nucleus pulposus tissue from LSI

value: LSI


title: genomic DNA from ID 0018 for 'b' visit

status: Public on Jul 17 2024

type: genomic

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

description:
0018b
3998567059_R04C02

hyb_protocol: standard Illumina protocol

scan_protocol: illumina iScan

data_processing:
waterMelon
wateRmelon::dasen() normalised Average Beta

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral whole blood

label_protocol: KCL samples were profiled using the Illumina Infinium HumanMethylation450 BeadChip and UMC samples were profiled using the Illumina Infinium HumanMethylationEPIC BeadChip

extract_protocol: Approximately 500ng of blood-derived DNA from each sample was treated with sodium bisulfite in duplicate, using the EZ-96 DNA methylation kit (Zymo Research, CA, USA)

tag: visit

value: b

tag: institute

value: KCL

tag: age

tag: Sex

value: F

tag: bcell

tag: gran

tag: mono

tag: nk

tag: smokingscore


title: Nucleus pulposus cells from LSI #2, RNA-seq

type: SRA

city: Wuhan

first: Cao

last: Yang

state: Hubei

address: Jiefang average

country: China

institute: Wuhan Union Hospital

description:
LSI_2
Sham_LSI_LSI_E_RPKM.txt

library_source: transcriptomic

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were qualified using FastQC and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCH38.94 whole genome and Rattus_norvegicus.Rnor_6.0.
Read Per Kilobase of exon per Megabase of library size (RPKM)  were calculated using a procotol from Feng, Jianxing et al. Bioinformatics (Oxford, England) vol. 28,21 (2012): 2782-8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling of the meta-transcript and by the size of the library.
Assembly: Homo_sapiens.GRCh38.94; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: IVDD_Normal_RPKM.txt
Supplementary files format and content: Sham_LSI_LSI_E_RPKM.txt

molecule: total RNA

organism: Rattus norvegicus

growth_protocol: Nucleus pulposus cells were isolated from human or rat lumbar nucleus pulposus tissues

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent. Illumina TruSeq RNA Sample Pre Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
Libraries were prepared according to instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly, RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer. cDNA was synthed using dNTPs, DNA polymeraseI and RNaseH. Then cDNA was purified using AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols.

treatment_protocol: Nucleus pulposus tissues were digested with 0.4% type II collagenase for 4-6 hours.

tag: tissue

tag: cell type

value: Nucleus pulposus cells

tag: treatment


title: PHD2-KO-2

first: Hongyan

last: Deng

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
Fastp version 0.21.0 (https://github.com/OpenGene/fastp) was used to perform basic statistics on the quality of the raw reads.
The clean reads were mapped to the human reference genome (hg38) using Star version 2.7.9a (https://github.com/alexdobin/STAR).
RSEM version 1.3.3 (https://github.com/deweylab/RSEM) was used to calculate gene and transcript expression levels expressed as fragments per kilobase of transcript per million fragments mapped (FPKM).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: lung

growth_protocol: H1299 cells were cultivated in DMEM supplemented with 10% FBS and maintained at 37℃ in a humidified incubator containing 5% carbon dioxide.

extract_protocol:
Total RNA from PHD2-deficient or wildtype H1299 cells was purified using the RNeasy Mini Kit (QIAGEN, 74104).
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) according to the manufacturer’s protocol. Qualified libraries were pooled and sequenced on Illumina NovaSeq platforms using the PE150 strategy at Wuhan Benagen Technology Co., Ltd. (Wuhan, China).

value: lung

tag: cell line

value: non-small cell lung cancer cells

tag: genotype

value: PHD2 knockdown


title: NES, PRDM6, V5 CUT&RUN, Replicate 1

city: San Francisco

first: Bjoern

last: Schwer

state: CA

country: USA

institute: University of California, San Francisco

library_source: genomic

data_processing:
For data analysis, we used the nf-core framework CUT&RUN analysis pipeline (v3.0; https://github.com/nf-core/cutandrun/tree/3.0)19,20. In brief, adapter-trimmed reads (TrimGalore v0.6.6) were mapped to the human (hg38) and spike-in (S. cerevisiae, sacCer3) genome reference assemblies by Bowtie2 (v2.4.4). Duplicates were marked by Picard (v2.27.4). Reads were normalized against spike-in. CUT&RUN peaks were called by SEACR (v1.3) using stringent settings, and consensus peaks were identified as peaks that were present in all replicates per condition.
Assembly: hg38
Supplementary files format and content: bigwig files are replicate-merged and BPM-normalized
Supplementary files format and content: consensus.peaks.awk.bed files contain SEACR consensus peaks.
Library strategy: CUT&Run

source_name: Neuroepithelial stem cells

growth_protocol: For human neuroepithelial stem (NES) cells: NES cells were generated from human iPS cells (WTC10). NES cells were cultured on poly-L-ornithine/laminin-coated wells in NES cell medium (DMEM/F-12 with GlutaMAX, 1x N2 supplement, 0.05x B27 without vitamin A supplement, 1.6 g/L Glucose, 20 ng/mL EGF, 20 ng/mL FGF2) in a humidified 37 C incubator with 5% CO2. NES cells were fed daily, passaged every three to four days using TrypLE Express, and plated at 500,000-600,000 cells per well of a 6-well plate in 2 mL of NES cell medium.

extract_protocol:
Preparation of CUT&RUN libraries was done with the CUT&RUN assay kit (Cell Signaling Technology). Briefly, 250,000 NES cells per sample were fixed with 0.1% formaldehyde in PBS for 2 min and quenched with 1 M glycine for 5 min at room temperature. Cells were washed in 1x wash buffer containing spermidine and protease inhibitor cocktail, and incubated in antibody binding buffer containing spermidine, proteinase inhibitor cocktail, digitonin, and 10 µl of activated concanavalin A beads per sample for 16-18 h at 4 C. Per CUT&RUN reaction, 0.2 µg of H3K27me3 antibody (clone C36B11, #9733, Cell Signaling Technology) or 0.96 µg of V5 antibody (clone D3H8Q, #13202, Cell Signaling Technology) was used. pAG-MNase in 1x wash buffer containing spermidine, protease inhibitor cocktail, and digitonin was bound to the antibody for 1 h at 4 C. pAG-MNase was activated by adding 3 µL calcium chloride per sample and incubated for 30 min at 4 C. Digestion was stopped by adding 1x stop buffer (digitonin solution, RNase A, and 50 pg S. cerevisiae spike-in DNA (Cell Signaling Technology) for normalization) and samples were incubated for 10 min at 37 C. Samples were subjected to SDS and proteinase K treatment for 2 h at 65 C. Zymo DNA Clean and Concentrator (D4034) was used to clean up the samples.
NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) was used for library preparation. Library clean-up and size selection was done by using SPRI beads (103778-488, Bulldog Bio). Libraries were quantified and analyzed by Qubit and Tapestation 4200 (Agilent) analysis and sequenced for 38 cycles in paired-end mode on a NextSeq 500 (Illumina).

value: Neuroepithelial stem cells

tag: antibody

value: V5, clone D3H8Q, #13202, Cell Signaling Technology


title: OPM2, KRAS G12A, replicate 1

city: Würzburg

first: Larissa

middle: Anita

last: Haertle

state: Bavaria

address: Josef-Schneider-Str. 2, Haus C11

department: Medizinische Klinik und Poliklinik II

country: Germany

institute: Universitätsklinikum Würzburg (UWK)

data_processing:
Sequencing quality was evaluated via FastQC.
RNA-sequencing reads were mapped to the human genome using STAR.
The mapped reads were quantified by featureCounts (v. 1.6.3) from the Subread package
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited files including raw counts for each Sample
Supplementary files format and content: tab-delimited files including normalized counts (TPM) for each Sample

source_name: cell line

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1 mM sodium pyruvate, 2 mM glutamine, 100 U/ml penicillin, and 100 g/ml streptomycin and kept at 5% CO2 and 37°C. Cultures were regularly split (every 3-4 days) and routinely checked for mycoplasma negativity. OPM2 cells are semi-adherent and were scratched with a cell scraper before each splitting.

extract_protocol:
For the RNA-Seq analysis, the OPM2 KRAS WT and the OPM2-derived KRAS A146T and G12A cells were seeded in triplicates at a density of 100,000 cells/ml. Three days after seeding, two million cells were pelleted and stored at -80°C. The RNeasy Mini kit (Qiagen) was used to extract the RNA and the quality was checked with the 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent). The RIN was ~10 for all samples.
Libraries were prepared from 1000ng of total RNA using the TruSeq stranded mRNA kit (Illumina). Quantification was conducted with the Qubit 3.0 Fluorometer (ThermoFisher) and the 2100 Bioanalyzer with the DNA 1000 kit (Agilent). Pooled libraries were sequenced (single-end) on the NextSeq 500 (Illumina) using the High Output Kit v2.5 (75 Cycles).

value: cell line

value: Multiple Myeloma

value: KRAS G12A

value: no teatment


title: genomic DNA from ID 0018 for 'd' visit

description:
0018d
3998567059_R05C02

value: d


title: OPM2, KRAS wildtype, replicate 1

value: wildtype


title: genomic DNA from ID 0018 for 'a' visit

description:
0018a
3998567059_R03C02

value: a


title: NES, PRDM6, V5 CUT&RUN, Replicate 2


title: Nucleus pulposus cells from LSI #1, RNA-seq

description:
LSI_1
Sham_LSI_LSI_E_RPKM.txt

value: Nucleus pulposus tissue from LSI

value: LSI


title: PHD2-KO-1


title: Nucleus pulposus cells from LSI-E #3, RNA-seq

description:
LSI_E_3
Sham_LSI_LSI_E_RPKM.txt

source_name: Nucleus pulposus tissue from LSI-E

value: Nucleus pulposus tissue from LSI-E

value: LSI-E


title: PHD2-WT-3


title: Nucleus pulposus cells from sham operation #3, RNA-seq

description:
Sham_3
Sham_LSI_LSI_E_RPKM.txt

source_name: Nucleus pulposus tissue from sham operation

value: Nucleus pulposus cells

value: Sham operation


title: NES, EV, V5 CUT&RUN, Replicate 1

value: EV


title: genomic DNA from ID 0010 for 'd' visit

description:
0010d
3998567059_R01C02

value: KCL

value: F


title: PHD2-KO-3

value: lung

value: non-small cell lung cancer cells

value: PHD2 knockdown


title: PHD2-WT-2


title: genomic DNA from ID 0010 for 'b' visit

description:
0010b
3998567059_R06C01

value: b


title: NES, PRDM6, H3K27me3 CUT&RUN, Replicate 2

value: Neuroepithelial stem cells

value: H3K27me3, clone C36B11, #9733, Cell Signaling Technology


title: Nucleus pulposus cells from sham operation #2, RNA-seq

description:
Sham_2
Sham_LSI_LSI_E_RPKM.txt

value: Nucleus pulposus tissue from sham operation


title: Nucleus pulposus cells from sham operation #1, RNA-seq

description:
Sham_1
Sham_LSI_LSI_E_RPKM.txt


title: genomic DNA from ID 0010 for 'a' visit

description:
0010a
3998567059_R05C01

value: a


title: NES, PRDM6, H3K27me3 CUT&RUN, Replicate 1


title: PHD2-WT-1

value: wildtype


title: SUM225, Treated rep 3

city: Houston

first: Justin

last: Wong

state: TX

address: 1155 Pressler St

institute: MD Anderson Cancer Center

data_processing:
adapter trimming: cutadapt
read alignment: bowtie2 v2.3.4.2
mark duplicates: picard v2.9.0
peak calling: MACS2
differential atac-seq: DESeq2
Assembly: hg38
Supplementary files format and content: bigwig file of open chromatin regions

growth_protocol: SUM225 cells were maintained in Ham's F12 supplemented with 5% fetal bovine serum, 10mM HEPES, 1µg/mL hydrocortisone, 5µg/mL insulin and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Control and treated cells were harvested for transpostion reaction (Illumina, #FC-121-1030) and purified DNA using a Qiagen MinElute Cleanup Kit (Qiagen, #28204) .
ATAC libraries for ATAC-seq were prepared using KAPA HiFi™ Real-Time PCR Library Amplification Kit (KAPA Biosystems, # KK2700) following manufacturer's protocols.

treatment_protocol: SUM225 cells were treated with an AKT inhibitor MK2206 (SelleckChem, #S1078) at 1 µM or vehicle control for 24 h.

value: Breast adenocarcinoma derived from ductal carcinoma in situ recurrence

value: AKT inhibitor (MK2206)


title: genomic DNA from ID 0010 for 'e' visit

description:
0010e
3998567059_R02C02

value: e


title: genomic DNA from ID 0008 for 'e' visit

description:
0008e
3998567059_R04C01

value: M


title: NES, PRDM6, Replicate 3

data_processing:
The nf-core framework best-practice ATAC-seq analysis pipeline (nf-core/atacseq v1.2.1) was used for sequence processing and data analysis. In brief, adapters were trimmed by TrimGalore (v0.6.4_dev)34 and adapter-trimmed reads were mapped to the hg38 reference assembly by BWA (v0.7.17)35. Duplicates were marked and removed by Picard (v2.23.1). ATAC-seq peaks were called by MACS2 (v2.2.7.1) and differential analysis of ATAC-seq peaks present in all three biological replicates per group (PRDM6 or EV NES cells) was performed by DiffBind (v3.6.5) and DESeq2.
Assembly: hg38
Supplementary files format and content: peaks.xls files contain the MACS2 peak calling output.
Supplementary files format and content: bigwig files contain replicate-merged ATAC-seq signal.
Supplementary files format and content: peaks.bed files contain ATAC-seq consensus peaks

extract_protocol:
Preparation of ATAC-seq libraries and sequencing was performed as described [PMCID: PMC7580199 DOI: 10.1016/j.xpro.2020.100079], with slight modifications. In brief, 100,000 cells per sample were harvested and lysed in ATAC-seq lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1 % (w/v) IGEPAL CA-630).
The transposition reaction was performed using Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) and 4.7 µL TDE1 Tagment DNA enzyme per sample in a 50-µL total reaction volume. Zymo DNA Clean and Concentrator Kit was used for cleanup of the transposition reaction. Quantitive PCR and limited-cycle PCR was performed using NEBNext Ultra II master mix (New England Biolabs), SYBR green and 0.5 µM of sample-specific P5/P7 barcoded primer mix (New England Biolabs). Bead clean-up and purification was performed using SPRI beads (Beckman Coulter). Agilent TapeStation 4200 was used to check for quality of sequencing libraries.


title: NES, EV, V5 CUT&RUN, Replicate 2

value: V5, clone D3H8Q, #13202, Cell Signaling Technology


title: genomic DNA from ID 0009 for 'b' visit

description:
0009b
3998567059_R03C01


title: SUM225, Treated rep 2


title: SUM225, Treated rep 1


title: 34605 CD56bright CD8-

city: St. Louis

first: Todd

last: Fehniger

state: MO

address: 660 S Euclid Ave, Campus Box 8007

department: Oncology

institute: Washington University School of Medicine

description:
group_cd56bright_CD8_Differential_Expression_GEO
all.gene_moderated_log2cpm.tsv

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
Assembly: GRCh38
Supplementary files format and content: tab-delimitted text file containing counts of protein-coding genes and differential expression between CD8+ and CD8- in each sample
Supplementary files format and content: tab-delimitted text file containing log-normalized counts per million for each sample

source_name: peripheral blood

growth_protocol: freshly isolated peripheral blood NK cells were rested overnight in 1 ng/mL IL-15, then sorted the following day and immediately resuspended in trizol and frozen at -80 degrees C until RNA extraction

extract_protocol:
RNA was isolated using the Direct-zol RNA MicroPrep kit (zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood

value: natural killer cells


title: 34605 CD56dim CD8-

description:
group_cd56dim_CD8_Differential_Expression_GEO
all.gene_moderated_log2cpm.tsv


title: NES, PRDM6, Replicate 2


title: NES, PRDM6, Replicate 1


title: 34605 CD56dim CD8+


title: 34605 CD56bright CD8+


title: genomic DNA from ID 0008 for 'b' visit

description:
0008b
3998567059_R02C01

value: KCL


title: genomic DNA from ID 0008 for 'a' visit

description:
0008a
3998567059_R01C01


title: NES, EV, Replicate 3

value: EV


title: SUM225, Control rep 3

value: Vehicle


title: SUM225, Control rep 2


title: 11689 CD56dim CD8-


title: genomic DNA from ID 0006 for 'd' visit

description:
0006d
3998567005_R05C02

value: d


title: SUM225, Control rep 1


title: NES, EV, Replicate 1


title: 11689 CD56bright CD8-


title: NES, EV, Replicate 2


title: genomic DNA from ID 0006 for 'b' visit

description:
0006b
3998567005_R04C02

value: b


title: MCF7 cells, palbociclib, rep3

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

institute: University medical center Mainz

data_processing:
Data processing was carried out by the bioinformatics core facility of the IMB Mainz
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (2.7.3a)
Read count extraction and normalization were performed using the subread package
DGE analysis was based on DEseq2, FC filter of 1 and adjusted p-value of 0.01
Assembly: hg38
Supplementary files format and content: *.bw files include the tracks

growth_protocol: MCF7 breast cancer cells were obtained from CLS Cell Lines Service GmbH (Eppelheim) were cultivated in DMEM-F12 HAM, 5% fetal bovine serum. Cells were cultured in a humid atmosphere at 37°C; 5% CO2.

extract_protocol:
RNA was iosolated using the NucleoSpin® RNA Kit (Macherey-Nagel, Düren, Germany).
NGS library prep was performed by the core facility genomics of the IMB Mainz, with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation, following the ReferenceGuide (June 2020). Libraries were prepared with a starting amount of 1000 ng and amplified in 9 PCR cycles.

treatment_protocol: 1 day post seeding, the cells were exposed to PD-0332991 [1 µM] and incubated for 120 h

value: breast cancer cell line

value: palbociclib [1 µM]


title: genomic DNA from ID 0005 for 'd' visit

description:
0005d
3998567005_R01C02


title: genomic DNA from ID 0006 for 'a' visit

description:
0006a
3998567005_R03C02


title: 11642 CD56dim CD8-


title: 11642 CD56dim CD8+


title: genomic DNA from ID 0005 for 'a' visit

description:
0005a
3998567005_R05C01


title: MCF7 cells, palbociclib, rep2


title: 11642 CD56bright CD8-


title: 11642 CD56bright CD8+


title: Control , Cont 3

type: RNA

city: ankara

first: nevin

last: belder

address: gumusdere

country: Turkey

institute: ankara university

description: Gene expression data from CD34+ cells healthy control group

hyb_protocol: Following fragmentation, 15 μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on Human GeneChip HG-U133 Plus 2.0 arrays (Affymetrix).  The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: CD34+ cells from healthy control group

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen, Carlsbad, CA).

value: Bone marrow/blood

value: CD34+ cells

tag: disease state

value: Control

tag: β-catenin level


title: genomic DNA from ID 0003 for 'e' visit

description:
0003e
3998567005_R04C01

tag: visit


title: 11689 CD56dim CD8+


title: MCF7 cells, untreated control, rep1

value: control


title: MCF7 cells, untreated control, rep2


title: 3743 CD56dim CD8-


title: AML patient group with high β-catenin levels , AML9

description: Gene expression data from CD34+ cells from AML patient

source_name: CD34+ cells from AML patient

value: AML

value: high


title: genomic DNA from ID 0003 for 'd' visit

description:
0003d
3998567005_R03C01

tag: institute

value: M


title: 3743 CD56dim CD8+


title: Control, Cont 2


title: MCF7 cells, ionizing radiation, rep 3

description: Highoutput FC, 2x150 cycles

data_processing:
Data processing was carried out by the core facility genomics at the IMB Mainz, using NGSpipe2go
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (2.7.3a)
Read count extraction and normalization were performed using the subread package
DGE analysis was based on DEseq2, FC filter of 1 and adjusted p-value of 0.01
Assembly: hg38
Supplementary files format and content: *.fastq.gz files include the raw data
Supplementary files format and content: *.raw_readcounts.tsv files include the readcounts

molecule: polyA RNA

source_name: MCF7 (RRID:CVCL_0031)

extract_protocol:
RNA was iosolated using the NucleoSpin® RNA Kit (Macherey-Nagel, Düren, Germany). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles
NGS library prep was performed with by the core facility genomics of the IMB Mainz, utilizing Illumina's TruSeq stranded mRNA LT Sample Prep Kit following TruSeqStrandedmRNAReferenceGuide (Oct.2017)

treatment_protocol: MCF7 cells were exposed 24 h after seeding with benzoapyrene [1 µM] or ionizing radiation (5 Gy) or nothing

value: MCF7 (RRID:CVCL_0031)

value: ionizing radiation [5 Gy]


title: genomic DNA from ID 0003 for 'b' visit

description:
0003b
3998567005_R02C01

tag: age


title: genomic DNA from ID 0005 for 'b' visit

description:
0005b
3998567005_R06C01

tag: Sex


title: AML patient group with low β-catenin levels , AML14

value: low


title: AML patient group with low β-catenin levels , AML17


title: Control , Cont 1


title: MCF7 cells, untreated control, rep3


title: MCF7 cells, ionizing radiation, rep 2

description: Highoutput FC, 2x150 cycles


title: genomic DNA from ID 0003 for 'a' visit

description:
0003a
3998567005_R01C01

value: a

value: KCL

tag: bcell


title: GFP control biol rep 3

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped using STAR guided by GTF and DamID reads were mapped using bowtie2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: Dm6 (Drosophila melanogaster)
Supplementary files format and content: Big Wig (.bw)

organism: Drosophila melanogaster

source_name: third instar larval wing disc

extract_protocol:
To prepare genomic DNA for DamID, 100 pairs of eye discs were homogenized in 200 µl ice-cold 0.1M Tris pH 9/0.1M EDTA/1%SDS (solution A). Another 300 µl of ice-cold solution A was added and the samples were incubated for 25 min at 70°C. 70 µl of 8 M potassium acetate was added and samples were incubated on ice for 30 min. The samples were centrifuged at 4°C at 14000 rpm for 15 min and the supernatants were extracted with an equal volume of phenol-chloroform solution (Sigma-Aldrich 77618 phenol-chloroform-isoamyl alcohol mixture 49.5:49.5:1), followed by a chloroform extraction. DNA was precipitated from the supernatant with 0.5 volume of isopropanol, incubated at room temperature for 5-10 min and centrifuged for 15 min at 4°C. The pellet was washed with 1 ml of 70% ethanol, air-dried and resuspended in 50 µl water overnight. To prepare RNA for RNA-Seq, RNA was extracted using Trizol (Invitrogen) followed by genomic DNA elimination and further purification with a Qiagen RNeasy Plus Micro kit. RNA quality and quantity was assessed using a Bio-analyzer 2100 (Agilent) prior to library preparation. To prepare single cells, eye discs were dissected into ice cold Rinaldini solution with 1.9 μM Actinomycin-D. Single cells were dissociated from eye discs mechanically by pipetting and enzymatically with Collagenase (100 mg/ml; Sigma-Aldrich #C9697) and Dispase (1 mg/ml; Sigma-Aldrich #D4818). Dissociated single cells were filtered and washed once with 0.05% Bovine Serum Albumin (BSA) in Rinaldini solution. Cells were resuspended in 0.05% BSA in Rinaldini solution to a concentration of 1000-1200 cells/μl. Only samples with over 95% viability (assayed with Hoechst propidium iodide) were used for scRNA-seq.
DamID libraries were prepared as described (Marshall, O. J., Southall, T. D., Cheetham, S. W. & Brand, A. H. Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nat Protoc 11, 1586-1598 (2016).) RNA-Seq libraries were constructed using Illumina TruSeq Stranded mRNA (Cat #20020595), with 250 ng of total RNA as input, and 10 cycles of PCR amplification. scRNA-Seq library was prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit 3v31.

value: third instar larval wing disc

value: wing disc cell

value: FRT82; UAS-GFP clones


title: MCF7 cells, ionizing radiation, rep 1

description: Highoutput FC, 2x150 cycles

value: breast cancer cell line


title: AML patient group with low β-catenin levels , AML13


title: 596 CD56dim CD8-

value: peripheral blood

value: natural killer cells


title: 3743 CD56bright CD8+


title: GFP control biol rep2


title: AML patient group with unchanged β-catenin levels , AML19

value: Bone marrow/blood

value: CD34+ cells

value: unchanged


title: MCF7 cells, untreated control (radiation), rep 3

description: Highoutput FC, 2x150 cycles


title: 596 CD56dim CD8+


title: MCF7 cells, untreated control (radiation), rep 2

description: Highoutput FC, 2x150 cycles


title: AML patient group with high β-catenin levels , AML8

value: AML


title: 596 CD56bright CD8-


title: GFP control biol rep 1


title: 3743 CD56bright CD8-


title: AML patient group with high β-catenin levels , AML6

value: high


title: MCF7 cells, untreated control (radiation), rep 1

description: Highoutput FC, 2x150 cycles


title: 527 CD56dim CD8-


title: UAS-RasV12 biol rep 3

value: FRT82; UAS-GFP, UAS-RasV12 clones


title: UAS-RasV12 biol rep 2


title: AML patient group with low β-catenin levels , AML12


title: MCF7 cells, benzoapyrene, rep 2

description: Highoutput FC, 2x150 cycles

value: MCF7 (RRID:CVCL_0031)

value: benzoapyrene [1 uM]


title: 527 CD56dim CD8+


title: UAS-RasV12 biol rep 1


title: MCF7 cells, benzoapyrene, rep 1

description: Highoutput FC, 2x150 cycles


title: UAS-Gl&RasV12 biol rep 3

value: FRT82; UAS-GFP, UAS-Gl, UAS-RasV12 clones


title: AML patient group with low β-catenin levels , AML11

value: low


title: AML patient group with low β-catenin levels , AML7


title: 527 CD56bright CD8-


title: 596 CD56bright CD8+


title: AML patient group with low β-catenin levels , AML10


title: AML patient group with unchanged β-catenin levels , AML18


title: MCF7 cells, untreated control, rep 3

description: Highoutput FC, 2x150 cycles


title: MEL290 (treated with 0.04μM JQ-1) - 2

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d).
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Homo sapiens.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was isolated with EZ-press RNA Purification Kit (B0004D, EZBioscience) and submitted to the Personalbio Laboratory for stranded library preparation.
Sequencing libraries were generated by using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and the quality was assessed on the Agilent Bioanalyzer 2100 system. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: cell line

value: human uveal melanoma cell line

value: WT


title: UAS-Gl biol rep 3

value: third instar larval wing disc

value: wing disc cell

value: FRT82; UAS-GFP, UAS-Gl clones


title: MCF7 cells, palbociclib, rep1

value: breast cancer cell line

value: palbociclib [1 µM]


title: UAS-Gl&RasV12 biol rep 2


title: AML patient group with unchanged β-catenin levels , AML16

value: Bone marrow/blood

value: CD34+ cells


title: MCF7 cells, untreated control, rep 2

description: Highoutput FC, 2x150 cycles


title: 527 CD56bright CD8+

value: peripheral blood

value: natural killer cells


title: M2,6KO_1_HAC

city: Boston

first: Qi

last: Liu

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: M2,6KO HAC Cleaved

data_processing:
Adapter sequences were trimmed and low quality sequences (Q20) were discarded using trim_galore. For tRNA chemical sequencing data, clean reads were mapped to the mature tRNA sequences downloaded from GtRNAdb using Bowtie with a maximum of two mismatches allowed. The alignments were then processed to record the read depth of each site on tRNAs using Bedtools. Based on tRNA mapping bam files and read depth information, cleavage score and cleavage score ratio between input and chemically-treated sample using the program cleavage_score.R (https://github.com/rnabioinfor/TRAC-Seq). Based on 21 bp sequences around m7G sites, the enriched motifs were analyzed by MEME with a maximum 7bp width. To conduct tRNA expression analysis for Input samples, we used the programs ARM-Seq data analysis pipeline.
Assembly: hg19
Supplementary files format and content: Cleavage Ratios from HAC-seq analysis
Library strategy: HAC-Seq

growth_protocol: All HEK293T WT and KO cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 10-cm dishes.

extract_protocol:
m3C HAC-Seq was performed as previously described (Cui et al., 2021). Small RNAs (smRNAs) were isolated by using the miRVana miRNA Isolation Kit (Thermo Fisher Scientific). Isolated small RNAs were first treated 10% hydrazine in 3M NaCl on ice for 4 h. Then RNAs were precipitated with ethanol. The RNA pellet was next resuspended in aniline cleavage buffer (H2O:glacial acid:aniline = 7:3:1) and incubated at room temperature in the dark for 2 h to induce the m3C-site-specific cleavage. After ethanol precipitation, HAC-treated RNA samples and untreated control RNA samples were demethylated with 80 pmol of recombinant wild-type AlkB and 160 pmol of recombinant D135S AlkB proteins in 100 ul of demethylation buffer for 2 h before cDNA library preparation. cDNA libraries were constructed by using the NEBNext Small RNA Library Prep Set (New England Biolabs) and sequenced with Illumina Nextseq 500.
NEBNext Small RNA Library Prep Set (New England Biolabs)

treatment_protocol: HEK293T WT and KO cells were generated by using the CRISPR/Cas9 technology. For knocking out METTL2 genes, sgRNAs were designed to target both METTL2A and METTL2B. Cells were transfected with pX459 vectors containing sgRNAs for KO cells or pX459 empty vectors for WT cells. Cells were selected with puromycin (2.5ug/mL) for 24 h and then switched to complete medium without puromycin for screening single clones.

value: METTL2A/2B and METTL6 KO

tag: agent

value: HAC treated


title: UAS-Gl&RasV12 biol rep 1


title: MCF7 cells, untreated control, rep 1

description: Highoutput FC, 2x150 cycles

value: MCF7 (RRID:CVCL_0031)


title: MEL290 (treated with 0.04μM JQ-1) - 1


title: UAS-Gl, cic biol rep 3

value: FRT82, cicQ219X; UAS-GFP, UAS-Gl clones


title: M2,6KO_2_HAC

description: M2,6KO HAC Cleaved


title: UAS-Gl, cic biol rep 2


title: UAS-Gl biol rep 2


title: AML patient group with unchanged β-catenin levels , AML15

value: AML

value: unchanged


title: M2,6KO_1_ctrl

description: M2,6KO untreated control

value: untreated control


title: CV0987 venom gland ATACseq

city: Arlington

first: Siddharth

last: Gopalan

address: 501 S. Nedderman Dr, Life Sciences Building RM 337

department: Biology

institute: University of Texas at Arlington

data_processing:
Broadly, ATAC-seq steps followed methods previously published (Perry et al., 2022; GSM5183958)
Assembly: UTA_CroVir_3.0 (GCA_003400415.2)
Supplementary files format and content: All sample files except for CV1084 (which was of lower quality, and excluded from the study), bigwig (.bw) are provided. These files allow one to visualize chromatin accessibility peaks mapped across the reference genome build.

organism: Crotalus lutosus

source_name: venom gland

extract_protocol:
Venom gland samples were extracted, snap frozen with liquid nitrogen, and sent to Active Motif for ATAC-seq data generation.
ATAC-seq libraries were prepared by Active Motif (Carlsbad, CA). ATAC-seq libraries were sequenced on an Illumina NextSeq500 using 42 bp paired-end reads.

value: venom gland


title: MEL290 (treated with DMSO) - 2

value: cell line

value: human uveal melanoma cell line

value: WT

value: DMSO


title: UAS-Gl biol rep 1

value: third instar larval wing disc

value: wing disc cell

value: FRT82; UAS-GFP, UAS-Gl clones


title: MEL270 (treated with DMSO) - 2


title: M6KO_1_HAC

description: M6KO HAC Cleaved

value: METTL6 KO


title: AML patient group with high β-catenin levels , AML5

value: Bone marrow/blood

value: CD34+ cells

value: high


title: AML patient group with high β-catenin levels , AML3


title: M2,6KO_2_ctrl

description: M2,6KO untreated control

value: METTL2A/2B and METTL6 KO


title: MEL270 (treated with 0.04μM JQ-1) - 2


title: AML patient group with high β-catenin levels , AML4


title: AML patient group with high β-catenin levels , AML2


title: UAS-Gl&RasV12, pnt biol rep 3

value: FRT82, pntdelta88; UAS-GFP, UAS-Gl, UAS-RasV12 clones


title: UAS-Gl, cic biol rep 1

value: FRT82, cicQ219X; UAS-GFP, UAS-Gl clones


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-hairpin inhibitor IVC, rep 4

city: Rishon LeZiyyon

first: Noam

last: Meiri

address: 68 HaMakkabbim Road

country: Israel

institute: Agricultural Research Organization, The Volcani Center

data_processing:
Raw fastq data were aligned to the rat (Rnor6) reference genome using STAR (v 2.7.9a)
SAMtools collectionwas used to sort, remove PCR duplicates (rmdup), index BAM files (index), and calculate library statistics (flagstat)
Mapped reads were processed by HTseq (v 0.13.5), with the following parameters: 'htseq-count -s no --mode=union’
Read count matrix was assembled and pair-wise differential gene expression analysis was performed using DESeq2
Assembly: Rnot6
Supplementary files format and content: Read count for each sample

organism: Rattus rattus

source_name: Hypothalamic arcuate nucleus

extract_protocol:
Coronal brain sections of the hypothalamus were sliced using a cryostat (-2.3 to -4.5 mm Bregma, using Paxison and Watson coordinates) and the ARC was extracted with a 1 mm disposable Miltex biopsy punch plunger (Bar Noar Ltd). Punches from each hemisphere were immersed in RNA Save (Biological Industries, Kibbutz Beit-Haemek, Israel) for downstream RNA extraction. RNA was isolated using TriReagent (Molecular Research Center, Cincinnati, OH) in DIO/voluntary running experiment. RNA was isolated using RNA/DNA Purification Micro Kit (Cat. 50300) (Norgen BioTek Corporation, Thorold, ON, Canada) in miR-injection experiment.
A bulk adaptation of the MARS-Seq protocol was used

value: Hypothalamic arcuate nucleus

value: Female

tag: diet

value: Chow

value: MiRIDIAN hsa-miR-211-hairpin inhibitor IVC administration


title: MEL270 (treated with 0.04μM JQ-1) - 1

value: cell line

value: human uveal melanoma cell line


title: M6KO_2_ctrl

description: M6KO untreated control

value: untreated control


title: UAS-Gl&RasV12, pnt biol rep 2

value: third instar larval wing disc


title: M6KO_1_ctrl

description: M6KO untreated control


title: MEL270 (treated with DMSO) - 1

value: WT

value: DMSO


title: UAS-Gl&RasV12, pnt biol rep 1

value: wing disc cell


title: M6KO_2_HAC

description: M6KO HAC Cleaved

value: METTL6 KO

value: HAC treated


title: MS751 cells, siDDX24-1, Day2

city: Zhuhai

first: Baibin

last: Wang

address: The Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
RNA-Seq reads were adaptor trimmed and the data quality was assessed with the fastp (v 0.23.2) software before any data filtering criteria was applied.
Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using HISAT2 (v 2.0.4).
The mapped reads were assembled into transcripts or genes by using StringTie software (v 1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf).
For quantification purpose, the relative abundance of the transcript/gene was measured by a normalized metrics.
Assembly: GRCh38.91
Supplementary files format and content: tab-delimited text files include read count values for each Sample

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

extract_protocol:
RNA was extracted from tissues by using TRIzol reagent kit (Ambion, Invitrogen, USA) according to the reagent protocols. A total amount of 1 μg RNA per sample was used as the input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol:
Transfection was performed by Lipofectamine 3000 reagent with 5μL 20μM siRNA for  2 days.
5μL 20μM siRNA (RiboBio), and 5μL Lipofectamine 3000 reagent  (Thermo) in the presence of 2mL DMEM containing 10% FBS until day 2.

value: Squamous cell carcinoma line of cervix

value: DDX24 knockdown

value: siDDX24-1 transfection

tag: time

value: Day 2


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-hairpin inhibitor IVC, rep 2

value: Hypothalamic arcuate nucleus


title: M2KO_2_HAC

description: M2KO HAC Cleaved

value: METTL2A/2B KO


title: Egfr control, biol rep 3

source_name: third instar larval eye disc

value: third instar larval eye disc

value: eye disc cells

value: 18 degrees


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-hairpin inhibitor IVC, rep 1

value: Female

value: Chow

value: MiRIDIAN hsa-miR-211-hairpin inhibitor IVC administration


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-hairpin inhibitor IVC, rep 3


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-mimic IVC, rep 4

value: MiRIDIAN hsa-miR-211-mimic IVC administration


title: SiHa cells, siDDX24-1, Day2

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

source_name: SiHa

value: SiHa


title: MCF7 cells, benzoapyrene, rep 3

description: Highoutput FC, 2x150 cycles

value: MCF7 (RRID:CVCL_0031)

value: breast cancer cell line

value: benzoapyrene [1 uM]


title: MS751 cells, siControl, Day2

value: Squamous cell carcinoma line of cervix

value: WT

value: siControl transfection


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-mimic IVC, rep 3


title: Egfr control, biol rep 1


title: AML patient group with high β-catenin levels , AML1

value: Bone marrow/blood

value: CD34+ cells

value: AML

value: high


title: M2,6KO_RPF_3

data_processing:
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequence which were retrieved from Ensembl (Release 91) (https://useast.ensembl.org/Mus_musculus/Info/Index) and GtRNAdb databases , respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse gene models (GENCODE, mm10) using Bowtie with a maximum one mismatch allowed .The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 1.5 fold change of TE to define the differential translation genes.
Assembly: hg19
Supplementary files format and content: xlsx
Library strategy: Ribo-Seq

growth_protocol: All HEK293T WT and KO cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 15-cm dishes.

extract_protocol:
Cells were lyzed in Mammalian Polysome Buffer (Illumina) containing cyclohexamide to pause translation. Input mRNAs and RPFs were isolated according to the TruSeq Ribo Profile pipline (Illumina) with modifications. Ribosomal RNAs were depleted and  cDNA libraries were constructed by using the NEBNext Small RNA Library Prep Set (New England Biolabs).
NEBNext Small RNA Library Prep Set (New England Biolabs)

treatment_protocol: HEK293T WT and KO cells were generated by using the CRISPR/Cas9 technology. All three genes METTL2A, METTL2B, and METTL6 were knocked out for generating the M2,6KO cells . Cells were transfected with pX459 vectors containing sgRNAs for KO cells or pX459 empty vectors for WT cells. After 24 h transfection, cells were selected with puromycin (2.5ug/mL) for another 2 days and then switched to complete medium without puromycin for screening single clones.

value: METTL2A/2B and METTL6 KO

tag: sample type

value: RPF


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-mimic IVC, rep 2

tag: tissue

value: Hypothalamic arcuate nucleus

value: Female


title: MEL290 (treated with DMSO) - 1

value: cell line

tag: cell type

value: human uveal melanoma cell line

value: DMSO


title: M2KO_2_ctrl

description: M2KO untreated control

value: METTL2A/2B KO

value: untreated control


title: Egfr mutant, biol rep 3

value: third instar larval eye disc

value: eye disc cells

tag: treatment

value: 24 h at 29 degrees


title: SiHa cells, siControl, Day2

tag: cell line

value: SiHa

value: Squamous cell carcinoma line of cervix

value: WT

value: siControl transfection

value: Day 2


title: WSH female arcuate nucleus, MiRIDIAN hsa-miR-211-mimic IVC, rep 1

value: Chow

value: MiRIDIAN hsa-miR-211-mimic IVC administration


title: Egfr control, biol rep 2

tag: genotype

value: 18 degrees


title: M2KO_1_ctrl

description: M2KO untreated control


title: M2,6KO_RPF_1

value: METTL2A/2B and METTL6 KO

value: RPF


title: Egfr mutant, biol rep 2


title: M2,6KO_RPF_2


title: WT_1_HAC

description: WT HAC Cleaved

value: HAC treated


title: WSH female arcuate nucleus, HF voluntary running, rep 3

value: Hypothalamic arcuate nucleus

value: Female

value: 60% HFD

value: HFD, voluntary wheel running


title: WSH female arcuate nucleus, HF voluntary running, rep 4


title: Egfr mutant, biol rep 1

value: third instar larval eye disc

value: eye disc cells


title: M2KO_1_HAC

description: M2KO HAC Cleaved

value: METTL2A/2B KO


title: elav>Pnt-Dam DamID-Seq biol rep 3

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped using STAR guided by GTF and DamID reads were mapped using bowtie2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: Dm6 (Drosophila melanogaster)
Supplementary files format and content: Big Wig (.bw)
Library strategy: DamID-Seq

value: photoreceptors

value: elav-GAL4; UAS-Pnt-Dam


title: WT_2_ctrl

description: WT untreated control

value: WT

value: untreated control


title: WSH female arcuate nucleus, HF voluntary running, rep 2


title: WT_1_ctrl

description: WT untreated control


title: WT_RPF_2


title: elav>Pnt-Dam DamID-Seq biol rep 2

value: elav-GAL4; UAS-PntDam


title: WSH female arcuate nucleus, HF voluntary running, rep 1


title: WT_RPF_1


title: WSH female arcuate nucleus, HF sedentary, rep 3

value: HFD, sedentary


title: M2,6KO_input_3

data_processing:
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequence which were retrieved from Ensembl (Release 91) (https://useast.ensembl.org/Mus_musculus/Info/Index) and GtRNAdb databases , respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse gene models (GENCODE, mm10) using Bowtie with a maximum one mismatch allowed .The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 1.5 fold change of TE to define the differential translation genes.
Assembly: hg19
Supplementary files format and content: xlsx

value: Input


title: WT_2_HAC

description: WT HAC Cleaved


title: M2,6KO_input_2

value: METTL2A/2B and METTL6 KO


title: WSH female arcuate nucleus, HF sedentary, rep 1


title: WSH female arcuate nucleus, HF sedentary, rep 2


title: elav>Pnt-Dam DamID-Seq biol rep 1


title: elav>Gl-Dam DamID-Seq biol rep 3

value: elav-GAL4; UAS-Gl-Dam


title: WT_RPF_3

value: RPF


title: elav>Gl-Dam DamID-Seq biol rep 1


title: M2,6KO_input_1


title: elav>Gl-Dam DamID-Seq biol rep 2


title: WT_input_3


title: WSH female arcuate nucleus, chow sedentary, rep 3

value: Hypothalamic arcuate nucleus

value: Chow

value: Chow, sedentary


title: elav>Dam DamID-Seq biol rep 3

value: elav-GAL4; UAS-Dam


title: WT_input_2


title: WSH female arcuate nucleus, chow sedentary, rep 2

value: Female


title: elav>Dam DamID-Seq biol rep 2

value: third instar larval eye disc


title: WT_input_1


title: WSH female arcuate nucleus, chow sedentary, rep 1


title: elav>Dam DamID-Seq biol rep 1


title: M178R

city: Ann Arbor

first: Tristan

last: Maerz

state: MI

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

data_processing:
Sequencing was performed using the DNA nanoball (DNB)-Seq platform (BGI), with 100 bp paired-end reads, >40M clean reads per sample. Reads were aligned to the Mus musculus reference genome (GCF_000001635.26_GRCm38.p6) using Hisat4. Aligned reads were mapped to reference genes using Bowtie5, and RSEM6 was used to generate final read counts.
Assembly: GCF_000001635.26_GRCm38.p6 (mm10) mus musculus
Supplementary files format and content: .xlsx files; count matrix, fpkm matrix, mouse identifiers, gene info

organism: Mus musculus

source_name: Knee Synvoium

extract_protocol:
Whole synovium, including Hoffa’s fat pad, was microdissected from male and female Sham, 7d and 28d ACLR, and contralateral knee joints, then immediately placed in TRIzol on ice. Samples were homogenized in TRIzol using an automated tissue homogenizer. RNA was isolated using Qiagen RNeasy Micro kits, and all samples were confirmed to have RNA integrity number (RIN) values > 6.5.
Libraries were constructed according to the standard BGI protocol, where the insert is flanked by adaptors: 5' read 1 or 3' read 2, index sequence, and BGI barcode primer

value: Knee Synvoium

tag: strain

value: ACLR

tag: time point


title: DCIS-38N

hyb_protocol: Each target gene of interest was detected using a pair of reporter-capture probes to target a 100 bp sequence. Hybridization between target mRNA and reporter-capture probe pairs was incubated at 65°C for 20 h using CT1000 Touch Thermal Cycler (Bio-Rad, CA) according to manufacturer protocol.

scan_protocol: The hybridized transcriptome probes were imaged and counted using a digital analyzer for image acquisition and data processing (nCounter Digital Analyzer) as per the manufacturer’s protocol.

data_processing: nSolver software normalization process

source_name: Normal mammary tissues

extract_protocol: 48 samples from patients with 40 DCIS and 8 matched normal mammary tissues were macrodissected from FFPE slides and isolated for RNA using Rneasy FFPE kit (Qiagen, #73504) following the manufacture's protocol.

treatment_protocol: Tissue has been macrodissected and target area was collected for RNA extraction.

value: Normal mammary tissues

tag: tumor grade


title: ato>Pnt-Dam DamID-Seq biol rep 3

value: MF

value: ato-GAL4; UAS-Pnt-Dam


title: M178L

value: Contra


title: ato>Pnt-Dam DamID-Seq biol rep 2

value: ato-GAL4; UAS-PntDam


title: M176R


title: ato>Gl-Dam DamID-Seq biol rep 3

value: ato-GAL4; UAS-Gl-Dam


title: M176L


title: DCIS-36N


title: M175

value: Sham


title: ato>Pnt-Dam DamID-Seq biol rep 1


title: DCIS-35N


title: M174R


title: ato>Gl-Dam DamID-Seq biol rep 2


title: DCIS-30N


title: DCIS-28N


title: DCIS-26N


title: M174L


title: ato>Dam DamID-Seq biol rep 3

value: ato-GAL4; UAS-Dam


title: M173R


title: ato>Dam DamID-Seq biol rep 2


title: DCIS-17N


title: L20057

first: Bogdan

last: Czerniak

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

hyb_protocol: MAUI Hybridization System,  BioMicro Systems,  02-A002-03

scan_protocol: DNA Microarray Scanner, Agilent, G2565B

data_processing: Raw values were trimmed to exclude 4295 random probes. Raw values were log2-transformed, and samples were median centered. The median-centered log2 values were then quantile-normalized in R (normalize.quantiles).

source_name: Homo Sapiens

label_protocol: Cy3 9mer Wobble TriLink, Biotechnologies, 50 O.D., N46-0001-50

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

value: Low Grade Bladder Cancer


title: H20296

value: High Grade Bladder Cancer


title: H64407A


title: L20129


title: DCIS-38T

source_name: DCIS

value: DCIS

tag: tumor size


title: DCIS-39T

value: 5 mm


title: M170

value: Male


title: L20031


title: M169R


title: ato>Dam DamID-Seq biol rep 1


title: L20013


title: MSC_TNF_2

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
FASTQ files were generated by CASAVA.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized
Assembly: GRCh38 (Human); mRatBN7.2 (Rat)
Supplementary files format and content: ExpectedCounts.txt.gz: Text file, mapping read counts
Supplementary files format and content: MedianNorm_TPMs.txt.gz: text file, normalized TPM values

source_name: Bone marrow

extract_protocol:
MSCs were grown to confluence in 75-cm2 filter cap cell culture flasks, washed with PBS, and the media was replaced with StemPro MSC serum-free media (SFM) CTS (Gibco Life Technologies, Gaithersburg, MD). Cells were incubated 18-24 hours upon which the conditioned culture media (CM) was collected and exosomes were isolated by differential ultracentrifugation essentially as previously described.21  The CM was centrifuged using a Beckman Coulter Allegra® X-15R centrifuge (2000 g at 4°C for 20 minutes) to remove any detached cells, apoptotic bodies, and cell debris. Clarified supernatant CM was then centrifuged in a Beckman Coulter Optima™ L-80XP Ultracentrifuge (100,000 g at 4°C for 2 hours) with a SW 28 rotor to pellet exosomes. The supernatant was carefully removed, and exosome pellets were re-suspended in PBS and pooled. Exosomes were characterized using a Thermo NanoDrop spectrophotometer for protein and RNA concentration. Particle diameter and concentration were evaluated via IZON qNano Nanoparticle Characterization instrument (Zen-bio Inc, Research Triangle Park, NC).
Total RNAs were isolated from Human MSCs and MSCs-derived exosomes, as well as rat medial collateral ligaments (MCLs) (post-injury day 14) using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column Dnase digestion (Qiagen #79254). One hundred nanograms of total RNA were used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol
mRNA-seq: RNAs were selected using the NEB Next Poly A+ Isolation Kit (NEB #E7490S/L).  Poly A+ fractions were eluted, primed, and fragmented for 7 minutes at 85°C.  First stand cDNA synthesis was performed using SmartScribe Reverse Transcriptase (Takara Bio USA #639538), and RNA was removed.  cDNA fragments were purified with Ampure XP beads (Beckman Coulter #A63881). The 5’ adapter was ligated, and 18 cycles of amplification were performed. These final indexed cDNA libraries were quantified, normalized, multiplexed, and run as single-end reads on the HiSeq 3000; small RNA-seq: Total RNAs were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254). One hundred nanograms of total RNA was used to prepare sequencing libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB #E7560S). The 3’ adapter was ligated and the reverse transcription primer hybridized.  The 5’ adapter was ligated and cDNA synthesis was performed using ProtoScript II Reverse Transcriptase.  PCR amplification was performed with 15 cycles and purified with Qiaquick PCR Purification Kit (Qiagen # 28106).  cDNA libraries were then size-selected using AMpure XP beads (Beckman Coulter #A63881).

value: Bone marrow

value: Mesenchymal stromal cells

value: TNF-α


title: MSC_TNF_3


title: DCIS-37T


title: MSC_TNF_1


title: M169L

value: Knee Synvoium


title: M171

value: Female


title: DCIS-40T

value: 3 mm


title: ato>Gl-Dam DamID-Seq biol rep 1

value: third instar larval eye disc

value: MF


title: L20225


title: L20099


title: H20056


title: DCIS-22N

value: Normal mammary tissues


title: L20280


title: M167R

value: ACLR


title: MSC_Control_2

value: No treatment


title: MSC_Control_3


title: L20131


title: M173L

value: Contra


title: M167L


title: DCIS-35T


title: DCIS-36T

value: 8 mm


title: MSC_Control_1


title: DCIS-34T

value: 9 mm


title: H20333

value: High Grade Bladder Cancer


title: M166R


title: DCIS-33T

value: DCIS

value: 6 mm


title: MSC_CRX_3

value: Bone marrow


title: M166L

value: Male


title: MSC_CRX_2

value: Mesenchymal stromal cells


title: M165

value: Knee Synvoium

value: Sham


title: NU26

value: Normal Ureter


title: MSC_CRX_1


title: DCIS-32T

value: 10 mm


title: M164


title: H40251


title: H20258


title: M163R


title: DCIS-30T


title: M163L


title: TNF_MSC_2

value: TNF-α


title: DCIS-29T


title: TNF_MSC_3


title: DCIS-31T

value: 3 mm


title: H20328


title: TNF_MSC_1


title: M161R

value: Female

value: ACLR


title: DCIS-28T


title: M161L

value: Contra


title: H20254


title: Contr_MSC_2

value: No treatment


title: DCIS-27T


title: DCIS-26T


title: M160R


title: Contr_MSC_3


title: Contr_MSC_1


title: M160L


title: DCIS-25T


title: DCIS-24T

value: 4 mm


title: CRX_MSC_3


title: NU21


title: M158R


title: DCIS-23T


title: NU25


title: M157R


title: M158L


title: H20242

value: High Grade Bladder Cancer


title: DCIS-22T

value: DCIS

value: 8 mm


title: NU28


title: DCIS-21T

value: 1 mm


title: TNF_Exo9

value: Bone marrow


title: TNF_Exo8

value: Mesenchymal stromal cells


title: T16

value: Low Grade Bladder Cancer


title: UC15

value: Bladder Cancer Cell Line


title: M157L

value: Knee Synvoium


title: DCIS-20T


title: M155

value: Sham


title: DCIS-19T


title: M154R

value: Male


title: MSC_Exo3


title: T45


title: CRX_MSC_2


title: TNF_Exo7

value: TNF-α


title: CRX_MSC_1


title: DCIS-17T

value: 5 mm


title: MSC_Exo1


title: DCIS-16T


title: T8


title: NU204

value: Normal Urothelium Cell Line


title: KO3-DSS

city: Arcadia

first: Mark

last: Boldin

state: California

address: 1500 Duarte Road

institute: City of Hope Beckman Research Institute

data_processing:
Reads were mapped to GRCm38 (mm10).dna.chromosome with Tophat-2.1.1 to generate counts
edgeR (v.3.30.3) was used to perform differential expression analysis
Assembly: GRCm38 (mm10).dna.chromosome

source_name: colon

extract_protocol:
miRNeasy kits
The KAPA mRNA HyperPrep kit was used for sequencing library preparation
polyA enriched stranded RNA-seq library

treatment_protocol: Cells were isolated from mice which were treated with 3% DSS for 3 days

value: colon

value: colonocytes

value: C15ORF48/miR-147 KO

value: DSS


title: DCIS-18T

value: DCIS

value: 2 mm


title: A45

value: Adjacent to Tumor


title: M150R

value: ACLR


title: CRX_Exo6

value: Bone marrow

value: Mesenchymal stromal cells


title: UC13

value: Bladder Cancer Cell Line


title: KO2-DSS


title: UC14


title: DCIS-14T


title: M153R

value: Knee Synvoium


title: UC17


title: CRX_Exo5


title: T5

value: High Grade Bladder Cancer


title: T20


title: MSC_Exo2

value: No treatment


title: UC16


title: A20


title: UC9


title: DCIS-15T


title: CRX_Exo4


title: M150L

value: Male

value: Contra


title: UC12


title: KO5


title: MSC_Exosomes_TNFa.93436

value: TNF-α


title: M147R


title: KO1-DSS

value: colon


title: DCIS-13T


title: DCIS-12T


title: UC3


title: KO4

value: colonocytes


title: MSC_Exosomes_TNFa.93433


title: M147L


title: DCIS-11T

value: 5 mm


title: M146R

value: Female


title: M153L


title: M154L


title: KO2

value: C15ORF48/miR-147 KO


title: WT3-DSS

value: WT

value: DSS


title: MSC_Exosomes_TNFa.93430


title: DCIS-10T

value: DCIS

value: 1 mm


title: MSC_Exosomes_Control.93438

value: Bone marrow

value: Mesenchymal stromal cells


title: M149

value: Knee Synvoium

value: Sham


title: M146L


title: DCIS-09T


title: WT2-DSS


title: NU22

value: Normal Ureter


title: MSC_Exosomes_Control.93435

value: No treatment


title: M145


title: MSC_Exosomes_Control.93432


title: UC1

value: Bladder Cancer Cell Line


title: M144


title: WT3


title: DCIS-07T


title: MSC_Exosomes_CRX.93437


title: MSC_Exosomes_CRX.93431


title: M143L

value: Contra


title: M142R

value: ACLR


title: WT1

value: colon

value: colonocytes


title: DCIS-05T

value: 8 mm


title: MSC_Exosomes_CRX.93434


title: DCIS-08T

value: 7 mm


title: WT1-DSS

value: WT


title: M142L

value: Female


title: DCIS-06T

value: DCIS


title: M143R


title: WT2


title: RNA-Seq_HEK293T_siKDM1A_rep2

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using STAR version 2.7.10.
Assembly: hg19

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: Normal condition

value: Human embryonic kidney 293T cells

value: KDM1A knock down


title: DCIS-03T


title: DCIS-04T


title: gene expression - CELL_MIX_nc886

city: Seoul

first: GyeongJin

last: Shin

state: Seoul

address: 222, Banpo-daero, Seocho-gu

department: Biomedicine and Health Sciences, Microbiology

country: South Korea

institute: The Catholic University of Korea

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v5.0.0 multi pipeline with GRCh38-2020-A and vdj-GRCh38-alts-ensembl-5.0.0 reference genomes.
Assembly: GRCh38
Supplementary files format and content: vcf file, R object file

source_name: WPMY-1, Hep3B-886, and HEK293T

extract_protocol:
WPMY-1 and Hep3B cell lines were purchased from the American Type Culture Collection (Manassas, VA). To create Hep3B cells (designated "Hep3B-886") we used a lenticiral plasmd "pLL3.7.Puro.U6:nc886". This vector, a modification of the original lentiviral vector pLL3.7 (Addgene, Watertown, MA) was engineered to carry the nc886 gene (102 nts) under the control of the U6 promoter. Total RNA from these cell lines was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA).
For the generation of a nc886 feature library, a gene-specific primer was designed to have 3' nc886 sequences, flanked by a feature barcode and a sequencing adaptor.
The sequence is 5’-CGGAGATGTGTATAAGAGACAGNNNNNNNNNNGTATGTCCGCTCGATNNNNNNNNNAGGGTCAGTAAGCACCCGCG-3'. The first underlined 22 nts represent a Read2N adaptor (10X genomics); the second 15 nts, a feature barcode (TotalSeqTM-C0182, BioLegend); and the third 20 nts, complementary 3’ nc886 sequences. The three nucleotide blocks are separated by 10 or 9 nts spacer sequences. Reverse transcription by this nc886-GSP will generate a 1st strand cDNA consisting of CCC-nc886-spacer-feature barcode-spacer-Read2N sequences. Second strand synthesis will be accomplished by the template switching oligos (TSOs) attached to the gel bead of 5’ scRNA-seq reagent.
Single cell suspensions of WPMY-1, Hep3B-886, and HEK293T cell lines were mixed in equal numbers and subjected to scRNA-Seq using Chromium Next GEM Single Cell V(D)J Reagent Kits v2 (10× Genomics, Pleasanton, CA). We set the cell recovery rate to 5000 per library and followed the manufacturer’s instructions with a slight modification.
During the GEM generation & barcoding step, we added 0.1 µM nc886-gene specific primer to the master mix. In addition to the 5’ gene expression (GEX) library, nc886 feature library was constructed using the 5' Feature Barcode Kit (10× Genomics). Both libraries were sequenced on an Illumina Hiseq X as 100 bp paired-end.

value: WPMY-1, Hep3B-886, and HEK293T

tag: library type

value: gene expression


title: DCIS-02T

value: 12 mm


title: RNA-Seq_HEK293T_siKDM1A_rep1


title: antibody capture - paired_mm1_nc886_feature

description: 10x Genomics

value: antibody capture


title: UC6


title: M140R

value: Knee Synvoium


title: RNA-Seq_HEK293T_siGATAD2A_rep2

value: GATAD2A knock down


title: No-degenerated nucleus pulposus cells #3, RNA-seq

city: Wuhan

first: Cao

last: Yang

address: Jiefang average

institute: Wuhan Union Hospital

description:
Normal_3
IVDD_Normal_RPKM.txt

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were qualified using FastQC and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCH38.94 whole genome and Rattus_norvegicus.Rnor_6.0.
Read Per Kilobase of exon per Megabase of library size (RPKM)  were calculated using a procotol from Feng, Jianxing et al. Bioinformatics (Oxford, England) vol. 28,21 (2012): 2782-8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling of the meta-transcript and by the size of the library.
Assembly: Homo_sapiens.GRCh38.94; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: IVDD_Normal_RPKM.txt
Supplementary files format and content: Sham_LSI_LSI_E_RPKM.txt

source_name: No-degenerated nucleus pulposus tissue

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent. Illumina TruSeq RNA Sample Pre Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
Libraries were prepared according to instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly, RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer. cDNA was synthed using dNTPs, DNA polymeraseI and RNaseH. Then cDNA was purified using AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols.

value: No-degenerated nucleus pulposus tissue

value: Nucleus pulposus cells


title: M140L

value: Contra


title: Wufeng B,treated,48h,3

city: Nanchang

first: shaochun

address: Jiaoqiao town

institute: Jiangxi Agricultural University

data_processing:
Fastp( version 0.19.7 ) was used to quality control the raw data to obtain clean reads
Assembly: the indica reference genome (Oryza_indica.ASM465v1.dna.toplevel. fa),the  Japonica reference genome(Oryza sativa Japonica IRGSP-1.0)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Indica Group

source_name: leaf

extract_protocol:
Total RNA was isolated according to the protocol of Trizol Reagent kit and purification (Invitrogen)
The experimental samples were constructed and sequenced by cDNA library of Beijing Novogene using Novaseq 6000 platform.

value: leaf

value: MESOPHYLL cell

value: Wufeng B

value: 48h with Guy11


title: M139

value: Female

value: Sham


title: No-degenerated nucleus pulposus cells #2, RNA-seq

description:
Normal_2
IVDD_Normal_RPKM.txt


title: Wufeng B,treated,48h,2


title: DCIS-01T

city: Houston

first: Justin

last: Wong

address: 1155 Pressler St

institute: MD Anderson Cancer Center

value: DCIS

value: 5 mm


title: RNA-Seq_HEK293T_siGATAD2A_rep1

value: Human embryonic kidney 293T cells


title: RNA-Seq_HEK293T_siHDAC2_rep1

value: HDAC2 knock down


title: No-degenerated nucleus pulposus cells #1, RNA-seq

description:
Normal_1
IVDD_Normal_RPKM.txt


title: Degenerated nucleus pulposus cells #3, RNA-seq

description:
IVDD_3
IVDD_Normal_RPKM.txt

source_name: Degenerated nucleus pulposus tissue

value: Degenerated nucleus pulposus tissue


title: M138

value: Male


title: Wufeng B,treated,36h,3

value: 36h with Guy11


title: RNA-Seq_HEK293T_siHDAC2_rep2


title: M137R

value: Knee Synvoium

value: ACLR


title: Degenerated nucleus pulposus cells #2, RNA-seq

description:
IVDD_2
IVDD_Normal_RPKM.txt

value: Nucleus pulposus cells


title: Wufeng B,treated,48h,1


title: M137L

value: Contra


title: RNA-Seq_HEK293T_siCHD4_rep2

value: CHD4 knock down


title: M135R


title: Wufeng B,treated,36h,1

value: leaf

value: MESOPHYLL cell


title: ChIP-Seq_MCF7_GATAD2A

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Assembly: hg38
Supplementary files format and content: bigWig, dense data

extract_protocol:
For ChIP assays, cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 15 mins at RT (CARM1 (CST, 12495) and GATAD2A (Abcam, ab87663)). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 2 hrs. After washing and elution, the cross-linked protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

value: Human breast cancer cell MCF7


title: Degenerated nucleus pulposus cells #1, RNA-seq

description:
IVDD_1
IVDD_Normal_RPKM.txt


title: Wufeng B,treated,36h,2

value: Wufeng B


title: RNA-Seq_HEK293T_siCARM1_rep2

value: CARM1 knock down


title: Wufeng B,treated,24h,3

value: 24h with Guy11


title: ChIP-Seq_MCF7_CARM1


title: RNA-Seq_HEK293T_siCHD4_rep1


title: M135L


title: M134

value: Sham


title: ChIP-Seq_HEK293T_3×HA_GATAD2A_7R/K

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Assembly: hg19

extract_protocol:
For ChIP assays, cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 15 mins at RT (HA-tagged proteins (Abcam, ab9110), CHD4 (Abcam, ab70469), HDAC2 (Santa Cruz Biotechnology,  sc7899), GATAD2A (Abcam, ab87663), and KDM1A (Bethyl Laboratory, A300-215A). Fixation was stopped by adding glycine (0.125 M) and incubating for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300-500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4 ℃, followed by incubation with protein G magnetic beads (Biorad) for an additional 2 hrs. After washing and elution, the cross-linked protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to either qPCR analysis or high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

value: Human embryonic kidney 293T cells

tag: chip antibody


title: M133

tag: Sex


title: RNA-Seq_HEK293T_siCTL_rep2

value: WT

value: siCTL


title: ChIP-Seq_HEK293T_3×HA_GATAD2A_WT


title: Wufeng B,treated,24h,2


title: Wufeng B,treated,24h,1


title: RNA-Seq_HEK293T_siCTL_rep1


title: ChIP-Seq_HEK293T_KDM1A


title: Wufeng B,treated,12h,3

value: 12h with Guy11


title: M131L

value: Male


title: Wufeng B,treated,12h,1


title: Wufeng B,treated,12h,2


title: ChIP-Seq_HEK293T_HDAC2

value: Santa Cruz;sc7899


title: ChIP-Seq_HEK293T_GATAD2A


title: M131R

value: Knee Synvoium

value: ACLR


title: ChIP-Seq_HEK293T_CHD4


title: M130L

value: Contra


title: ChIP-Seq_HEK293T_3×HA_CARM1_rep2


title: M130R


title: Wufeng B,untreated,0h,3

value: 0h with Guy11


title: PI_adult_HA_1

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Chip-seq coverage tracks (BedGraph) were obtained using deepTools (Ramírez et al. 2014) bamCoverage function with bin width 50 bp and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by MACS2, IDR and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from two- to three-day-old adult flies. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (rabbit anti-Mzfp1, 1:100) or G (rat anti-Mzfp1, 1:100) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes and anti-HA Magnetic beads (Pierce) were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes.

value: whole organism

tag: development stage

value: adult

tag: antibody source

value: IgG


title: PI_adult_HA_2


title: Wufeng B,untreated,0h,2

value: leaf

value: MESOPHYLL cell

value: Wufeng B


title: p60_tnf_ko_3: Amplicon sequencing of genomic DNA, TNFR1ko P60, replicate 3

city: Basel

first: Simona

last: Baghai Sain

address: Schanzenstrasse 44

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

library_source: other

data_processing:
library strategy: Amplicon sequencing of genomic DNA
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. The number of sgRNAs in each sample was counted by the count command from the MAGeCK package.
processed data files format and content: Count matrix of sgRNAs (represented by the gene symbol of their target gene). Gene symbols on rows, samples on columns.
Assembly: mm10

molecule: other

source_name: mouse epidermis

extract_protocol:
P60 back skin was harvested with surgical scissors and placed dermis-facing up on a styrofoam tray with pins. Fat and subcutis were scraped off with a scalpel. Fat-free skin was then washed, dermis-side facing down in 1xPBS. Skin was then placed in the same orientation in 0.5% Trypsin-EDTA (10X, Gibco; 15400054) and incubated at 37°C on an orbital shaker for 25 (females) or 50 min (males). Using a glass microscopy slide, skin was secured to the bottom of the dish and scraped again with a scalpel until it started to break. Excess cold PBS with 2% chelexed FBS (FBS(-)) was added to neutralize trypsin. Cell suspension was strained on ice first through a 70 µm filter, washed with an additional 15 mL of cold 1X PBS with 2% FBS(-) and then filtered through a 40 µm filter. Cell suspension was spun down at 400 x g for 10 min. Genomic DNA was extracted with Qiagen DNEasy genomic DNA isolation kit.
The sgRNA region was  amplified in a nested PCR. In PCR1, we used 12.5 µl KAPA HiFi HotStart ReadyMix (Roche, 07958935001), 0.75 µl forward primer (5‘ CTTGTGGAAAGGACGAAACACCG 3’, 10μM), 0.75 µl reverse primer (5‘ GTGTCTCAAGATCTAGTTACGCCAAGC 3’ 10μM), 1 µl of extracted genomic  DNA (with a concentration between 50-100 ng/μl) and 10 μl nuclease-free water for a total volume of 25 μl per tumor. PCR1 was performed using the following conditions: Initial denaturation at 98°C for 2:30 min, followed by 22 cycles of denaturation 98°C -– 20 s, annealing 62°C -– 30 s, extension 72°C -– 30 s. PCR1 products for each tumor were individually column-purified with a GenElute™ PCR Clean-Up Kit (Sigma-Aldrich NA1020-1KT). For PCR2, 1 μl of cleaned up PCR1 was used as template along with 0.75 μl forward barcoded i5 primer (see Supplementary Information Table 1, 10 μM), 0.75 μl reverse barcoded i7 primer (see table, 10 μM), 10 μl nuclease free-water, along with 12.5 μl of KAPA HiFi HotStart ReadyMix for a total volume of 25 μl. Eight different i5 and i7 primers allowed for a total of 64 different combinations. PCR2 was performed under following conditions: Initial denaturation at 95°C for 3 min, followed by 32 cycles of denaturation 98°C -– 30 s, annealing 62°C – 30 s, extension 72°C – 30 s. PCR2 products for a maximum of 64 individually barcoded tumor amplifications were pooled and cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to manufacturer’s instructions before sequencing.

value: mouse epidermis

value: Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J (Jackson lab #026179) x Tnfr1 KO (Jackson lab #003243)

tag: age

value: 60 days post natal


title: Wufeng B,untreated,0h,1


title: ChIP-Seq_HEK293T_3×HA_CARM1_rep1

value: Human embryonic kidney 293T cells


title: p60_tnf_ko_4: Amplicon sequencing of genomic DNA, TNFR1ko P60, replicate 4


title: Mzfp1_wt_y1w1118_adult_anti_Mzfp1_1


title: Changhui T025,treated,48h,3

value: Changhui T025

value: 48h with Guy11


title: RNA-Seq_HEK293T_siCARM1_rep1

value: CARM1 knock down


title: Mzfp1_wt_y1w1118_adult_anti_Mzfp1_2


title: Mzfp1_delta42_adult_HA_anti_Mzfp1_2

value: y[1] M{RFP[3xP3.PB] GFP[E.3xP3]=vas-int.Dm}ZH-2A w[*]; M{3xP3-RFP.attP}ZH-86Fb


title: Mzfp1_delta42_adult_HA_anti_Mzfp1_1


title: p60_tnf_ko_2: Amplicon sequencing of genomic DNA, TNFR1ko P60, replicate 2


title: in vitro keratinocytes, mCherry positive, anti-TNFalpha treatment, replicate 2

description:
Primary mouse epidermal keratinocytes, sorted for mCherry positive (i.e. with construct for TNFalpha overexpression). Treated with anti-TNFalpha antibody.
keratinocytes_rnaseq_salmon_counts.csv.gz

data_processing:
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. Quality control of the paired-end bulk RNA-seq data was performed using the FastQC program. Adapter trimming of the Illumina Universal Adapter (AGATCGGAAGAG) was carried out with Cutadapt. Transcript-level quantification was performed with Salmon using the GENCODE Mouse M25 reference transcriptome.
processed data files format and content: Expression matrix with Salmon counts. Gene symbols are on rows, samples are on columns. Additional sample information in 'bulk_sequencing_keratinocytes_and_immune_depletion_Info.txt'.
Assembly: mm10

extract_protocol:
mCherry positive keratinocytes cells were FAC- sorted on a BD ARIA II directly into TriZol LS and column purified with a Direct-zol™ RNA Miniprep kit (Zymo Research).
Sequencing libraries from 1000ng of RNA per sample were prepared with the TrusSeq mRNA library kit and sequenced on a NovaSeq X 2x150bp at the Functional Genomics Center Zurich.

value: cultured primary mouse epidermal keratinocytes

value: keratinocytes derived from Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J overexpressing TNF-a

value: passage 20


title: in vitro keratinocytes, mCherry negative, anti-TNFalpha treatment, replicate 2

description:
Primary mouse epidermal keratinocytes, sorted for mCherry negative (i.e. no construct for TNFalpha overexpression). Treated with anti-TNFalpha antibody.
keratinocytes_rnaseq_salmon_counts.csv.gz

extract_protocol:
mCherry negative keratinocytes cells were FAC- sorted on a BD ARIA II directly into TriZol LS and column purified with a Direct-zol™ RNA Miniprep kit (Zymo Research).
Sequencing libraries from 1000ng of RNA per sample were prepared with the TrusSeq mRNA library kit and sequenced on a NovaSeq X 2x150bp at the Functional Genomics Center Zurich.


title: Mzfp1_deltaM2_adult_HA_anti_Mzfp1_2

value: whole organism


title: Changhui T025,treated,36h,3

value: 36h with Guy11


title: Changhui T025,treated,36h,2


title: in vitro keratinocytes, mCherry positive, anti-TNFalpha treatment, replicate 1


title: in vitro keratinocytes, mCherry positive, replicate 2

description:
Primary mouse epidermal keratinocytes, sorted for mCherry positive (i.e. with construct for TNFalpha overexpression)
keratinocytes_rnaseq_salmon_counts.csv.gz


title: Changhui T025,treated,36h,1


title: in vitro keratinocytes, mCherry negative, anti-TNFalpha treatment, replicate 1


title: in vitro keratinocytes, mCherry negative, replicate 2

description:
Primary mouse epidermal keratinocytes, sorted for mCherry negative (i.e. no construct for TNFalpha overexpression)
keratinocytes_rnaseq_salmon_counts.csv.gz


title: Changhui T025,treated,24h,3

value: 24h with Guy11


title: Mzfp1_wt_adult_HA_anti_Mzfp1_2

value: adult


title: y1w1118_wt_2

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The processed reads were aligned to the version dm6 of the Drosophila melanogaster genome using the splice-aware STAR algorithm (Dobin et al. 2013).
The gene read counts were calculated using the STAR quantMode option (--quantMode GeneCounts).
Assembly: dm6
Supplementary files format and content: Processed data are gene counts obtained using STAR quantMode.

extract_protocol:
50 ng of total RNA was used for isolation of mRNA using oligo(dT) Magnetic beads (NEB, USA) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared with the NEBNext® Ultra RNA Library Prep kit  (NEB, USA) per the manufacturer's instructions. Purified mRNA was used as a started material for library preparation. After first and second strands synthesis cDNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Indexed adapters were ligated, after which the material was purified with Ampure XP beads (Beckman Coulter). PCR amplification was performed using indexed primers for 12 cycles using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads, quantified using fluorometry with DS-11 (DeNovix, USA) and its quality was assessed on a Bioanalyzer 2100 system (Agilent).  Diluted libraries were clustered on a pair-read flowcell and sequenced using a NovaSeq 6000 system (Illumina, USA).

treatment_protocol: Total RNA was isolated using the TRI reagent (Molecular Research Center, USA) according to the manufacturer’s instructions. 100 mg of 3rd instar larvae was used for extraction procedure.

value: larvae


title: Mzfp1_wt_adult_HA_anti_Mzfp1_1


title: p60_tnf_ko_1: Amplicon sequencing of genomic DNA, TNFR1ko P60, replicate 1


title: Changhui T025,treated,24h,2

value: leaf

value: MESOPHYLL cell


title: Changhui T025,treated,48h,2


title: y1w1118_wt_1


title: in vitro keratinocytes, mCherry positive, replicate 1

value: mouse epidermis


title: Changhui T025,treated,24h,1


title: in vitro keratinocytes, mCherry negative, replicate 1


title: Changhui T025,treated,48h,1


title: Changhui T025,treated,12h,3

value: 12h with Guy11


title: Changhui T025,treated,12h,2


title: Mzfp1_attP_3


title: Mzfp1_deltaM2_adult_HA_anti_Mzfp1_1


title: Mzfp1_attP_2


title: Mzfp1_attP_1


title: Changhui T025treated,12h,1


title: CV1082 venom gland ATACseq

data_processing:
Broadly, ATAC-seq steps followed methods previously published (Perry et al., 2022; GSM5183958)
Assembly: UTA_CroVir_3.0 (GCA_003400415.2)
Supplementary files format and content: All sample files except for CV1084 (which was of lower quality, and excluded from the study), bigwig (.bw) are provided. These files allow one to visualize chromatin accessibility peaks mapped across the reference genome build.

organism: Crotalus viridis

extract_protocol:
Venom gland samples were extracted, snap frozen with liquid nitrogen, and sent to Active Motif for ATAC-seq data generation.
ATAC-seq libraries were prepared by Active Motif (Carlsbad, CA). ATAC-seq libraries were sequenced on an Illumina NextSeq500 using 42 bp paired-end reads.

value: venom gland


title: CV1095 venom gland ATACseq


title: PI_adult_HA

tag: protein

value: IgG

value: HA


title: Changhui T025,untreated,0h,2

value: Changhui T025

value: 0h with Guy11


title: Changhui T025,untreated,0h,3


title: PI_embryo_rabbit

value: embryo


title: CV1086 venom gland ATACseq


title: CV1090 venom gland ATACseq


title: Mzfp1_deltaZf_adult_HA_1

description:
Mzfp1_deltaZf_adult_HA.bedGraph
Mzfp1_deltaZf_adult_HA.narrowPeak

value: y[1] M{RFP[3xP3.PB] GFP[E.3xP3]=vas-int.Dm}ZH-2A w[*]; M{3xP3-RFP.attP}ZH-86Fb


title: Mzfp1_deltaZf_adult_HA_2


title: Changhui T025,untreated,0h,1


title: Wufengyou T025,treated,48h,3

value: Wufengyou T025

value: 48h with Guy11


title: CV0857 venom gland ATACseq


title: CV1096 venom gland ATACseq


title: CV1089 venom gland ATACseq


title: Wufengyou T025,treated,36h,3

value: 36h with Guy11


title: Mzfp1_deltaM2_adult_HA_2

description:
Mzfp1_deltaM2_adult_HA.bedGraph
Mzfp1_deltaM2_adult_HA.narrowPeak


title: Mzfp1_delta42_adult_HA_1

description:
Mzfp1_delta42_adult_HA.bedGraph
Mzfp1_delta42_adult_HA.narrowPeak


title: CV1081 venom gland ATACseq


title: Mzfp1_delta42_adult_HA_2


title: Mzfp1_deltaM2_adult_HA_1


title: Wufengyou T025,treated,48h,1


title: Wufengyou T025,treated,36h,2


title: siPTPN14+PDGF-BB 2

city: Tianjin

first: Qiannan

last: Ma

address: 22 Qiqiangtai Road

institute: Tianjin Medicial University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: HA-VSMCs

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HA-VSMCs


title: siPTPN14+PDGF-BB 3


title: PI_embryo_rat


title: Mzfp1_wt_adult_HA_2

description:
Mzfp1_wt_adult_HA.bedGraph
Mzfp1_wt_adult_HA.narrowPeak

value: adult


title: Wufengyou T025,treated,36h,1


title: siPTPN14+PDGF-BB 1


title: CV1087 venom gland ATACseq

source_name: venom gland


title: siPTPN14 3


title: Wufengyou T025,treated,24h,3

value: 24h with Guy11


title: Mzfp1_embryo_rat

description:
Mzfp1_embryo_rat.bedGraph
Mzfp1_embryo_rat.narrowPeak


title: Mzfp1_wt_adult_HA_1


title: siPTPN14 2


title: Wufengyou T025,treated,24h,2

value: leaf


title: Wufengyou T025,treated,48h,2

value: MESOPHYLL cell


title: Mzfp1_embryo_rabbit

description:
Mzfp1_embryo_rabbit.bedGraph
Mzfp1_embryo_rabbit.narrowPeak


title: Wufengyou T025,treated,12h,3


title: siPTPN14 1


title: KO biol rep 3

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Paired-end sequencing reads using publicly available Drop-seq Toolssoftware
each mRNA read was tagged with its nucleus barcode and unique molecular identifier and aligned using STAR
digital expression matrices were assembled using a list of UMIs in each gene and within each cell
Raw digital expression matrices were combined and loaded into the R package Seurat
QC, filtering and DE analysis was done using the Seurat R package
Assembly: mm10
Supplementary files format and content: txt file containing raw digital expression matrices

molecule: nuclear RNA

source_name: Cortex

extract_protocol:
Cortical tissue was mechanically homogenized in a sucrose solution and nuclei were isolated through a sucrose gradient and ultracentrifugation
Nuclei were captured and libraries were prepared for sequencing using the sNucDrop-seq protocol described in Hu et al. 2017
single-nucleus Drop-seq

value: Cortex


title: Wufengyou T025,treated,24h,1


title: siNC+PDGF-BB 3


title: XX2_24M,replicate2,snRNA_seq

city: chengdu

first: yujie

last: wu

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

description: 10x Genomics

data_processing:
We used the Singleron GEXSCOPE® Single Nucleus RNA Library Kit for sequencing the obtained samples, and all experimental protocols were strictly carried out in accordance with the GEXSCOPE Single Nucleus Transcriptome Library Kit manual provided by Singleron.
NOT PROVIDED
Supplementary files format and content: Tab-separated values files and matrix files

source_name: VAT

extract_protocol: The single-nucleus suspension was adjusted to a concentration of 3-4 × 10^5 nuclei/mL in PBS. This suspension was loaded onto a microfluidic chip, utilizing the GEXSCOPE® Single NucleusRNA-seq Kit (Singleron Biotechnologies). Following the manufacturer’s guidelines (Singleron Biotechnologies), we proceeded to construct the snRNA-seq libraries. These libraries were sequenced on an Illumina HiSeq X10 platform, using 150 bp paired-end reads.

value: VAT

tag: time

value: 24 months

value: Adipocytes


title: KO biol rep 2

tag: tissue


title: KO biol rep 1


title: siNC+PDGF-BB 1

tag: cell type


title: Wufengyou T025,treated,12h,2

last: Liu

tag: treatment

value: 12h with Guy11


title: FGG2_24M,replicate2,snRNA_seq

description: 10x Genomics

source_name: SAT

value: SAT


title: Wufengyou T025,treated,12h,1

tag: cell line


title: WT biol rep 3

tag: genotype

value: WT


title: Wufengyou T025,untreated,0h,2

value: 0h with Guy11


title: siNC+PDGF-BB 2


title: siNC 3


title: FGG3_2M,replicate2,snRNA_seq

description: 10x Genomics

value: 2 months


title: siNC 2


title: WT biol rep 2


title: siNC 1


title: FGG1_2M,replicate1,snRNA_seq

description: 10x Genomics


title: Wufengyou T025,untreated,0h,1

value: Wufengyou T025


title: Spinal cord, Q33;TDP-43 animal (4578)

status: Public on Jul 16 2024

city: Utrecht

first: R. Jeroen

last: Pasterkamp

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Data was filtered and trimmed using trim_galore (v 0.4.1).
mRNAs were mapped to the mouse genome mm10 using Tophat2 and gene expression was quantified using featureCounts software with gene annotation from Gencode release M19
Counts were normalized and differential expression analysis was performed using DESeq2 in R with an FDR < 0.05.
Differential exon usage was tested using the bioconductor package DEXseq (Simon Anders et al., 2008) with an FDR <0.1
Assembly: mm10
Supplementary files format and content: counts, DE, DEX

source_name: Whole spinal cord

extract_protocol:
Total RNA was isolated using QIAzol Lysis reagent (Qiagen) and miRNeasy mini kit (Qiagen) with DNA digestion on-column, according to the manufacturer's instructions. RNA concentration and integrity was validated using the RNA 6000 Nano Kit on a 2100 Bioanalyser (Agilent), with RIN values for all extractions above 7.5.
Samples were rRNA depleted and prepared for sequencing using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara).
Library size and purity control was performed on a 2100 Bioanalyzer (Agilent) using a High-Sensitivity DNA-Chip. Library concentration was measured using a KAPA Library Quantification Kit.  Prepared libraries were sequenced on three lanes PE100 with 20% in lane control on HiSeq4000

value: Whole spinal cord

value: Knock-in hATXN2-Q33; hTDP-43 (Double mutant, Heterozygous)

value: Untreated


title: Spinal cord, Q33;TDP-43 animal (4577)


title: Spinal cord, Q33;TDP-43 animal (4539)


title: Spinal cord, Q22;TDP-43 animal (4307)

value: Knock-in hATXN2-Q22; hTDP-43 (Double mutant, Heterozygous)


title: XX1_24M,replicate1,snRNA_seq

description: 10x Genomics


title: Spinal cord, TDP-43 animal (9285)

value: Knock-in hTDP-43 (Heterozygous)


title: Spinal cord, Q22;TDP-43 animal (4230)


title: Spinal cord, Q22;TDP-43 animal (4221)


title: Wufengyou T025,untreated,0h,3

value: leaf


title: Spinal cord, TDP-43 animal (9413)


title: Spinal cord, TDP-43 animal (8859)


title: Spinal cord, Q33 animal (8695)

value: Knock-in hATXN2-Q33 (Heterozygous)


title: Spinal cord, Q33 animal (8620)


title: Spinal cord, Q33 animal (8610)


title: Spinal cord, Q22 animal (4712)

value: Knock-in hATXN2-Q22 (Heterozygous)


title: FGG1_24M,replicate1,snRNA_seq

description: 10x Genomics


title: Spinal cord, NTg animal (1217)

value: Non-transgenic (C57BL/6)


title: Spinal cord, Q22 animal (5178)


title: Spinal cord, Q22 animal (5079)


title: Spinal cord, NTg animal (1226)


title: Spinal cord, NTg animal (1212)


title: WT biol rep 1

value: Cortex


title: Buffer

city: Chengdu

first: Danian

last: Chen

address: 37 Guoxue Xiang Street

institute: West China Hospital, Sichuan University

data_processing:
the sequencing quality was first assessed using FastQC, and poor-quality 5′ end reads were trimmed using a Perl script and then mapped onto the rat genome using TopHat2, allowing for up to 2 mismatches as default settings.
Reads mapped onto multiple genomic locations were discarded, and a custom R script was used to calculate the fragments per kilobase million (FPKM) of each gene and obtain the expression profile of each sample
Assembly: rn6
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample
Supplementary files format and content: The tab-delimited text file includes RPKM values for each sample

source_name: Retina

extract_protocol:
Total RNAs were extracted from dissected rat retinas using TRIzol (Thermo Fisher) and treated with RNAse-free DNAse I (New England Biolabs) to remove genomic DNA. The yield of total RNA was assessed using NanoDrop Microvolume Spectrophotometers (NanoDrop Technologies).
The cDNA libraries were prepared using an Illumina TruSeq RNA sample preparation kit, and the quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: STZ was prepared in citrate buffer (pH 4.5) to 60mg/ml. For intravitreal (IVIT) injection, freshly made STZ solution was diluted to 1μg/μl, 5μg/μl, and 10μg/μl, respectively. One microliter (1μl) STZ, citrate buffer, or saline was injected into the vitreous at P1, retinas were harvested at P4.

value: Retina

value: Intravitreal injection of citrate buffer (pH 4.5)


title: Stz

value: Intravitreal injection of STZ (10ug)


title: Saline

value: WT

value: Intravitreal injection of Saline