title: ck_3

value: control


title: Meningioma 62 (RNA-seq)

status: Public on Jan 10 2022

type: SRA

city: San Francisco

first: Abrar

last: Choudhury

state: California

country: USA

institute: University of California, San Francisco

description:
Sex: 2
M62

library_source: transcriptomic

data_processing:
Standard Illumina software was used for basecalling
Sequenced reads were trimmed using Trimmomatic, then mapped to hg38 transcriptome using HISAT2 2.1.0
Exon level count data were extracted from the mapped reads using featureCounts
Transcripts per million (TPM) were calculated from the count data
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPMs for every gene and every sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Meningioma

extract_protocol:
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and RNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit v2 (CAT# RS-122-2001)

tag: tissue

value: meningioma

tag: institution

value: UCSF

tag: age

tag: grade


title: Meningioma 61 (RNA-seq)

description:
Sex: 1
M61


title: Meningioma 60 (RNA-seq)

description:
Sex: 1
M60


title: Meningioma 58 (RNA-seq)

description:
Sex: 2
M58


title: Meningioma 59 (RNA-seq)

description:
Sex: 2
M59


title: ck_2

city: Jinan

first: Luoyan

last: Zhang

address: wenhuadong 88

country: China

institute: shandong normal university

data_processing:
The RNA sample of every accession was sequenced by the Illumina NovaSeq 6000. cDNA library was constructed, and Illumina pair-end 150 bp sequencing (PE150)
Raw reads of fastq format were firstly processed through in-house perl scripts. In this step, adapt-er-containing reads, ploy-N-containing reads, and low-quality reads were removed from raw data, yielding clean reads. Meanwhile, Q20, Q30, GC-content, and sequence duplication levels of the clean data were determined.
Reference genome (ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/) and gene model annotation files (ftp://ftp.ensemblgenomes.org/pub/release39/plants/gtf/chlamydomonas_reinhardtii/Chlamydomonas_reinhardtii.v3.1.39.gtf.gz) were downloaded from the genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5), which was adopted to align paired-end clean reads to the reference genome.
For the prediction of novel transcripts, StringTie (v1.3.3b) was adopted to assemble the mapped reads of each sample as previously described (Pertea et al., 2015).
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Chlamydomonas reinhardtii

source_name: alga cells

growth_protocol: The wild-type C. reinhardtii strain GY-D55 was obtained from LeadingTec Co., Ltd. (http://www.leadingtec.cn/) and maintained in 150 mL of BG-11 medium on a shaking table at 120 rpm under the following conditions: photoperiod 16-8 h/light-dark, temperature 23℃, and light intensity 100 μmol m-2 s-1. Under the above-mentioned conditions, C. reinhardtii cells were cultured in BG11 medium for approximately 14 days until the cell density reached 2 × 106 cells/mL. The cells of the mid-logarithmic phase were used for salt stress treatment.

extract_protocol:
Briefly, 100 mL cell cultures from different groups were subjected to centrifugation at 3,000 g for 5 min, and the cell pellet was re-suspended in 25 mL RNAlater solution (Ambion). Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. The integrity of RNA was evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and the NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, 50 mL medium containing 800 mM NaCl was added to a 150-mL culture medium, the final NaCl concentration was 200 mM, and the pH of the medium was adjusted to 7.0. Cells cultured in the absence of NaCl were used as the control group. Each experiment was conducted in triplicate. The cells of C. reinhardtii were collected at eight pre-set time points after exposure to 200 mM NaCl: 2, 4, 8,12, 24, 48, 72, and 96 h.

tag: strain

tag: treatment


title: AGO2_KO2_XEN_day4

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D4B_GAGTGG

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR v2.5.0c allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts

organism: Mus musculus

growth_protocol: mESCs were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on gelatine coated plates.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mESCs were plated at a density of 1x104 cells per cm2 on gelatin-coated plates and cultured for 5 days in RPMI 1640 supplemented with 15% FBS, 1% Penicillin/Streptomycin, 0.1 mM 2-ß-mercaptoethanol, 0.1μM all-trans retinoic acid and 10ng/mL Activin A.

value: 129/Ola background

value: Embyronic stem cells; Blastocyste

tag: genotype/variation

value: AGO2 knock out cells


title: AGO2_KO1_XEN_day4

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D4A_CGTACG


title: AGO2_KO1_diff_XEN [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120837 for the convenient retrieval of the complete raw data from SRA.


title: AGO2_KO2_diff_XEN [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120838 for the convenient retrieval of the complete raw data from SRA.


title: Meningioma 57 (RNA-seq)

description:
Sex: 2
M57


title: ck_1


title: Meningioma 56 (RNA-seq)

description:
Sex: 2
M56


title: Salt_4h_1

value: 200mM NaCl 4h


title: Meningioma 55 (RNA-seq)

description:
Sex: 1
M55


title: AGO2_KO2_XEN_day3

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D3B_GTTTCG


title: Meningioma 53 (RNA-seq)

description:
Sex: 1
M53


title: Salt_2h_2

value: 200mM NaCl 2h


title: AGO2_KO2_XEN_day2

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D2B_GTGAAA


title: Salt_2h_1


title: Lico_Hipp_1

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according   to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2   mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for   15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper   aqueous phase where RNA remained was transferred into a new tube with equal volume of   supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix   was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the   pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated   water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using   a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: hippocampus

tag: genotype

value: Licochalcone A  treatment 30 days


title: Meningioma 51 (RNA-seq)

description:
Sex: 1
M51


title: Ctrl_Hipp_3

value: Normal Culture


title: Meningioma 52 (RNA-seq)

description:
Sex: 2
M52


title: Meningioma 5 (RNA-seq)

description:
Sex: 2
M5


title: AGO2_KO1_XEN_day2

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D2A_GTCCGC


title: Meningioma 6 (RNA-seq)

description:
Sex: 2
M6


title: Ctrl_Hipp_2


title: Meningioma 48 (RNA-seq)

description:
Sex: 2
M48


title: Meningioma 49 (RNA-seq)

description:
Sex: 2
M49


title: Meningioma 47 (RNA-seq)

description:
Sex: 1
M47


title: AGO2_KO2_XEN_day1

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D1B_CCGTCC


title: Meningioma 46 (RNA-seq)

description:
Sex: 2
M46


title: AGO2_KO1_XEN_day1

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D1A_ATGTCA


title: Meningioma 44 (RNA-seq)

description:
Sex: 2
M44


title: Meningioma 45 (RNA-seq)

description:
Sex: 1
M45


title: Elnf_P8_AscAo [ctrl]

city: Saint Louis

first: Chien-Jung

last: Lin

state: MO

address: 660 Euclid Ave CB 8228

department: Cell Biology and Physiology

data_processing:
Preprocessing was performed using Cell Ranger by the McDonnell Genome Institute. Downstream analysis was performed using Seurat (version 4.0.0).
Genome_build: mm9
Supplementary_files_format_and_content: TAR (of MTX, TSV)

source_name: P8 ascending aorta

growth_protocol: mice were housed and maintained per standard protocol in the Department of Comparative Medicine barrier facility at Washington University School of Medicine in St. Louis

extract_protocol:
P8 ascending aortae were dissected out and pooled on iced PBS, digestd in an enzymatic mix (collagenase I [657 U/mL], collagenase XI [187.5 U/mL], hyaluronidase [90 U/mL], Dnase I [90U/mL] in HBSS) for ~20 min, filtered through a 70 um strainer, and resuspended in RPMI 1640 with 5% FBS. FACS was performed to isolate live singlets with DAPI as negative viability marker. The sorted cells were resuspended in PBS/0.04% BSA for scRNA-seq library preparation using 10x Chromium 3' v3 kit.
10x Chromium 3' v3

treatment_protocol: Eln was inactivated in smooth muscle cells and derivatives using TaglnCre and LoxP-floxed alleles of Eln

value: ascending aorta

value: 1 Elnf/f and 2 Elnf/+

tag: Sex

value: pooled male and female


title: TaglnCreElnff_P8_AscAo [mut]

institute: Washington University School of Medicine in St. Louis

description: P8 ascending aortae were dissected out and pooled on iced PBS, digestd in an enzymatic mix (collagenase I [657 U/mL], collagenase XI [187.5 U/mL], hyaluronidase [90 U/mL], Dnase I [90U/mL] in HBSS) for ~20 min, filtered through a 70 um strainer, and resuspended in RPMI 1640 with 5% FBS. FACS was performed to isolate live singlets with DAPI as negative viability marker. The sorted cells were resuspended in PBS/0.04% BSA for scRNA-seq library preparation using 10x Chromium 3' v3 kit.

value: TaglnCre;Elnf/f


title: Lico_Hipp_2


title: AGO2_KO2_mESC [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120833 for the convenient retrieval of the complete raw data from SRA.


title: Meningioma 43 (RNA-seq)

description:
Sex: 2
M43


title: Meningioma 4 (RNA-seq)

description:
Sex: 1
M4


title: Sirt5-/- liver #3

first: Renqiang

last: Sun

address: 131,Dong'an Road

institute: Fudan university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter.
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances.
Differential gene expression analysis was done using R package DESeq2 v1.24.0.
Genome_build: not provided
Supplementary_files_format_and_content: WT_liver_vs_Sirt5_KO_liver.deseq2.annot.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Liver

extract_protocol:
Mouse liver tissues (~20 mg) were homogenized in 1 ml lysis buffer of Tissue RNA Purification Kit PLUS (EZBioscience), and total RNA was extracted according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 4-week-old male Sirt5+/+ and Sirt5-/- mice were injected with 50 μg PB[Act-RFP]DS or PB[CMV-myc-YAP5SA]DS and 10 μg Act-PBase plasmids.

value: Male

value: Liver

value: 20 days after YAP5SA-HDI


title: AGO2_KO1_mESC [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120832 for the convenient retrieval of the complete raw data from SRA.


title: Meningioma 54 (RNA-seq)

description:
Sex: 1
M54

value: meningioma


title: AGO2_KO1_XEN_day3

description:
reverse-stranded protocol
20160420.B-AGO2KO_XEN_D3A_GTGGCC


title: WT1_diff_XEN [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120835 for the convenient retrieval of the complete raw data from SRA.

value: wild type cells


title: WT2_diff_XEN [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2120836 for the convenient retrieval of the complete raw data from SRA.

value: 129/Ola background


title: Meningioma 234 (RNA-seq)

description:
Sex: 2
M234

value: UCSF


title: Sirt5-/- liver #1


title: Meningioma 231 (RNA-seq)

description:
Sex: 1
M231


title: Meningioma 235 (RNA-seq)

description:
Sex: 2
M235


title: Meningioma 232 (RNA-seq)

description:
Sex: 2
M232


title: Meningioma 230 (RNA-seq)

description:
Sex: 2
M230


title: Meningioma 233 (RNA-seq)

description:
Sex: 1
M233


title: Sirt5-/- liver #2


title: Meningioma 3 (RNA-seq)

description:
Sex: 2
M3


title: WT1_XEN_day4

description:
reverse-stranded protocol
20160420.B-E14_XEN_D4A_AGTCAA

value: Embyronic stem cells; Blastocyste


title: Sirt5+/+ liver #2


title: Meningioma 23 (RNA-seq)

description:
Sex: 1
M23


title: Meningioma 227 (RNA-seq)

description:
Sex: 2
M227


title: WT2_XEN_day3

description:
reverse-stranded protocol
20160420.B-E14_XEN_D3B_CTTGTA


title: Meningioma 226 (RNA-seq)

description:
Sex: 2
M226


title: Meningioma 224 (RNA-seq)

description:
Sex: 1
M224


title: Meningioma 225 (RNA-seq)

description:
Sex: 1
M225


title: Meningioma 222 (RNA-seq)

description:
Sex: 2
M222


title: D20-LN-TCR(Vac+aPDL1)

city: Philadelphia

first: Bo

last: Li

state: PA

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: The Children’s Hospital of Philadelphia, University of Pennsylvania

description:
TCR library (10X Genomics)
A9LnTCR_S1_L001

data_processing:
The Cell Ranger (v2.1.1) Software Suite was used to process the raw sequence data into gene expression profiles. The fastq files for each sample were processed with Cell Ranger count, which was used to align to mm10 reference genome, filter and quantify.
For scTCR-seq data, TCR reads were aligned to the mm10 reference genome and TCR annotation was performed using the 10x cellranger vdj pipeline.
Low quality T cells were filtered if no matched TCR (either α or β chain) was detected or the number of expressed genes (UMI count >0) was smaller than a predefined cutoff value.
The Cd3 expression was defined as the average UMI counts of Cd3d, Cd3e, Cd3g, and those cells with Cd3 expression > 0 were kept for subsequent analysis.
The count table of cells was log-normalized implemented in the R package Cell RangerTM R Kit.
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix text files, cell information text files

source_name: MC38 tumor model

extract_protocol:
10x Genomic single cell 5’ VDJ library, Gel Bead & Multiplex Kit and Chip Kit
Single-cell gene expression and TCR libraries were generated according to the manufacturer’s instructions.

tag: cell type

value: T cell

value: neoantigen vaccine + aPD-L1

tag: time

value: Day 20

value: lymph node


title: D20-TM-TCR(Vac+aPDL1)

description:
TCR library (10X Genomics)
F7TmTCR_S7_L001

value: tumor


title: Sirt5+/+ liver #3


title: WT2_XEN_day2

description:
reverse-stranded protocol
20160420.B-E14_XEN_D2B_TAGCTT


title: Meningioma 217 (RNA-seq)

description:
Sex: 1
M217


title: WT2_XEN_day1

description:
reverse-stranded protocol
20160420.B-E14_XEN_D1B_ACTTGA


title: WT1_XEN_day2

description:
reverse-stranded protocol
20160420.B-E14_XEN_D2A_GATCAG


title: D20-TM-TCR(Vac)

description:
TCR library (10X Genomics)
A12TmTCR_S7_L001

value: neoantigen vaccine


title: Meningioma 216 (RNA-seq)

description:
Sex: 2
M216


title: Meningioma 221 (RNA-seq)

description:
Sex: 1
M221


title: Meningioma 219 (RNA-seq)

description:
Sex: 2
M219


title: Meningioma 228 (RNA-seq)

description:
Sex: 2
M228


title: Sirt5+/+ liver #1


title: Meningioma 215 (RNA-seq)

description:
Sex: 2
M215


title: D20-LN-TCR(aPDL1)

description:
TCR library (10X Genomics)
A7LnTCR_S10_L001


title: D20-LN-TCR(Vac)

description:
TCR library (10X Genomics)
A11LnTCR_S4_L001


title: WT2_XEN_day4

description:
reverse-stranded protocol
20160420.B-E14_XEN_D4B_AGTTCC


title: D20-TM-TCR(aPDL1)

description:
TCR library (10X Genomics)
B1TmTCR_S5_L001


title: Meningioma 212 (RNA-seq)

description:
Sex: 2
M212


title: D20-TM-TCR

description:
TCR library (10X Genomics)
C6tmTCR_S8_L004

value: naïve


title: WT1_XEN_day3

description:
reverse-stranded protocol
20160420.B-E14_XEN_D3A_GGCTAC


title: Meningioma 210 (RNA-seq)

description:
Sex: 2
M210


title: Meningioma 21 (RNA-seq)

description:
Sex: 2
M21


title: WT1_XEN_day1

description:
reverse-stranded protocol
20160420.B-E14_XEN_D1A_CAGATC


title: WT_1_mESC [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2082855 for the convenient retrieval of the complete raw data from SRA.

value: Passage 33


title: WT_2_mESC [re-used]

description:
reverse-stranded protocol
This is duplicated sample record of GSM2082856 for the convenient retrieval of the complete raw data from SRA.

value: Passage 42


title: D20-SP-TCR

description:
TCR library (10X Genomics)
C5spTCR_S7_L004

value: spleen


title: Meningioma 209 (RNA-seq)

description:
Sex: 2
M209


title: Meningioma 208 (RNA-seq)

description:
Sex: 2
M208


title: Meningioma 218 (RNA-seq)

description:
Sex: 2
M218


title: Meningioma 206 (RNA-seq)

description:
Sex: 1
M206


title: Meningioma 203 (RNA-seq)

description:
Sex: 2
M203


title: Meningioma 207 (RNA-seq)

description:
Sex: 2
M207


title: Meningioma 213 (RNA-seq)

description:
Sex: 2
M213


title: Meningioma 205 (RNA-seq)

description:
Sex: 2
M205


title: D10-LN-TCR

description:
TCR library (10X Genomics)
D1LNTCR_S1_L001

value: Day 10


title: Meningioma 202 (RNA-seq)

description:
Sex: 2
M202


title: D10-SP-TCR

description:
TCR library (10X Genomics)
B3spTCR_S1_L004


title: DNA_WT

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

library_source: genomic

data_processing:
After removal of the adaptor sequences, the 49 bp reads from each sample were aligned to genome reference (mm9) as well as the size-selected MspI fragments generated by our in silico simulation. Because of the strand specificity of DNA methylation, two rounds of alignments were carried out, i.e. the bisulfite converted reads were aligned to the genome sequences termed the “T genome” with each cytosine converted to thymine and in the meanwhile the reads were also aligned to the genome sequences termed the “A genome” with each guanine converted to adenosine. The alignments were carried out with BAMAP aligner allowing up to two mismatches for successful mapping.
Genome_build: mm9
Supplementary_files_format_and_content: Methylation data for both WT and KO samples were summarized in two separates tab-delimited text files containing the following informations for each covered cytosine : chromosome ID (c1), genomic position (C2), strand (c3), sequence context (C4), base pattern (c5), number of methylated reads (c6) and number of unmethylated reads (c7).

molecule: genomic DNA

source_name: Mouse embryonic fibroblasts

extract_protocol:
Genomic DNA samples were purified from subconfluent MEFs by phenol extraction and ethanol precipitation.
Bisulfite-converted genomic DNA libraries were prepared according to the previously described methods. Briefly, genomic DNA was digested with MspI (New England Biolabs), followed by end-repair and addition of 3′ A overhangs. Methylated adaptors (Illumina) with a 3′ T overhang were ligated to the A tailed DNA fragments. For reduced representation, 40 to 220 bp (pre-adaptor-ligation size) fragments were excised from 2% TAE agarose gels and bisulfite-converted with EZ DNA methylation Gold kit (Zymo Research). Bisulfite converted libraries were amplified by PCR.

value: Mouse embryonic fibroblasts

value: MBD4 WT

value: Embryos were isolated from the uteri of day 12.5 postcoitus pregnant mice


title: D10-TM-TCR

description:
TCR library (10X Genomics)
B4tmTCR_S2_L004


title: Meningioma 214 (RNA-seq)

description:
Sex: 1
M214

value: meningioma


title: D20-TM-GEX(Vac+aPDL1)

description:
5' gene expression library (10X Genomics)
E9TmGEX_S5_L001


title: D20-LN-GEX(Vac+aPDL1)

description:
5' gene expression library (10X Genomics)
A3LnGEX_S2_L001


title: Meningioma 200 (RNA-seq)

description:
Sex: 2
M200

value: UCSF


title: W3.5_rep3

city: Fort Collins

first: Carl

last: VanGessel

state: CO

address: Colorado State University

institute: Colorado State University

data_processing:
RNA-seq reads were trimmed and checked for quality Phred scores above 30 using Fastp v0.20.1
Trimmed reads were aligned to a version of the IWGSC RefSeq v1.0 genome assembly consisting of A and B chromosome pseudomolecules and Unanchored scaffolds not assigned to any chromosome (ABU) using STAR 2.7.5 aligner (outFilterMismatchNoverReadLmax = 0.04, alignIntronMax = 10,000)
Transcript levels were quantified by featureCounts using 190,391 gene models from the ABU IWGSC RefSeq v1.1 annotations
Genome_build: IWGSC RefSeq v1.0, ABU
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Triticum turgidum subsp. durum

source_name: W3.5_apical meristem

growth_protocol: Plants were grown in controlled conditions in PGR15 growth chambers (Conviron, Manitoba, Canada) under a long day photoperiod (16 h light/8 h dark) at 23 ℃ day/17 ℃ night temperatures and a light intensity of ~260 µM m-2 s-1. Developing apical meristems were harvested under a dissecting microscope using a sterile scalpel and placed immediately in liquid nitrogen. All samples were harvested within a one-hour period of the day 4 h after the lights were switched on (+/- 30 min) to account for possible differences in circadian regulation of gene expression.

extract_protocol:
Tissues were ground into a fine powder in liquid nitrogen and total RNA was extracted using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO).
Libraries were barcoded to allow multiplexing and all samples were sequenced using the 100 bp single read module across two lanes of a HiSeq3000 sequencer at the UC Davis Genome Center.

tag: variety

value: Kronos

tag: waddington stage

value: apical meristem


title: W3.5_rep4


title: W3.5_rep2


title: SPJ649_WT_LG6_K9me2_rep2

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

description: ChIP-seq

data_processing:
Sequencing reads were de-multiplexed and aligned to the S. pombe reference genome (ASM294v2), obtained from Pombase 46 with Bowtie2 using default parameters. Peaks were called with MACS2 and only peaks appearing in both replicates were included for downstream analysis. Genome-wide coverage was calculated with deepTools2 and normalized to counts per million (CPM). ChIP-seq experiments were performed in duplicates for each genotype.
Genome_build: ASM294v2.29
Supplementary_files_format_and_content: bigwig:coverage tracks

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in YEA or moved to YEA low glucose media (0.1% glucose, 3% glycerol) for 6 hours while in mid-log phase

extract_protocol:
Log-phase yeast cells were crosslinked with 1% formaldehyde for 20 minutes with shaking at room temperature, followed by 5 minutes quenching with 125mM glycine. Cells were harvested, washed with PBS (phosphate-buffered saline) and flashfrozen with liquid nitrogen. The thawed pellet was washed and then resuspended in ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% Deoxycholate, 1mM PMSF). Ice-cold glass beads were added and the mixtures were vigorously disrupted in a bead-beater with four 30-seconds rounds. The lysates were collected and NP buffer was added (10 mM Tris, pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2). MNase was added to the reaction and the reactions were incubated at 37°C for 20 minutes. MNase amount was titrated empirically so that the chromatin was digested to yield mainly mono- and di-nucleosomes. The reaction was stopped by the addition of 0.5 M EDTA, and the tubes were placed on ice. 5X ChIP lysis buffer was added to the reaction, mixed by short vertexing, and the tubes were incubated on ice for 30 minutes. The reactions were then cleared by centrifugation at 16,000 x g for 10 minutes. A small fraction of the cleared supernatant was reserved as input and the rest was used for immunoprecipitation. The protocols for immunoprecipitation, reverse-crosslinking, and DNA precipitation are the same as in the previous ChIP section. The precipitated DNA was treated with RNAase A (EN0531, Thermo Fisher Scientific) for 1 hour at 37°C. DNA concentration was determined with the Qubit dsDNA HS Assay Kit (Q33230, Thermo Fisher Scientific). 1-5 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). Libraries were pooled and sequenced with single-end sequencing on a NextSeq500/550 at the JP Sulzberger Genome Center at Columbia University.
1-5 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB).

value: WT

tag: medium

value: YEA LG

tag: antibody


title: SPJ649_WT_Input

description: ChIP-seq

value: YEA


title: SPJ649_WT_LG6_input

description: ChIP-seq


title: W3.25_rep4

source_name: W3.25_apical meristem


title: Meningioma 20 (RNA-seq)

description:
Sex: 2
M20


title: DNA_KO

value: MBD4 KO


title: D20-TM-GEX(Vac)

description:
5' gene expression library (10X Genomics)
A6TmGEX_S12_L001

value: T cell

value: neoantigen vaccine

value: Day 20

value: tumor


title: SPJ649_WT_K9me2_rep2

description: ChIP-seq


title: D20-LN-TCR

description:
TCR library (10X Genomics)
E5LNTCR_S4_L001

value: naïve

value: lymph node


title: Meningioma 2 (RNA-seq)

description:
Sex: 1
M2


title: W3.25_rep3


title: SPJ649_WT_K9me2_rep1

description: ChIP-seq


title: D20-LN-GEX(Vac)

description:
5' gene expression library (10X Genomics)
A5LnGEX_S9_L001


title: Meningioma 199 (RNA-seq)

description:
Sex: 2
M199


title: Meningioma 201 (RNA-seq)

description:
Sex: 1
M201


title: W3.25_rep2


title: HEK293T KD - recovery

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
Library strategy: Oxford Nanopore Long-read sequencing
The library were sequencd using MinKNOW v20.10.3 with real-time basecalling using Guppy v4.2.2.
Sequencing adapters were trimmed using Porechop v0.2.4 from quality filtered reads and the reads were mapped using minimap2. For fusion analysis, the reads were splitted into 0.2kb bins followed by aligning to hg38 using bowtie2 v2.3.5.1.
Genome_build: hg38

source_name: HEK293T (stable cell line; CGGBP1-targetting shRNA)

growth_protocol: Human primary fibroblasts [Coriell Cell Repository GM02639] and HEK293T CT and KD [lentivirally transduced shRNA system as described in PMID 31547883] were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.

extract_protocol:
Human primary fibroblasts [Coriell Cell Repository GM02639] were harvested from two T25 flasks for each sample. HEK293T CT and KD cells were harvested from two 10cm dishes for each sample. Genomic DNA was extracted using standard phenol:chloroform:isoamyl alcohol extraction method followed by ethanol precipitation and dissolution in nuclease-free water. For TP53BP1 ChIP-seq was performed as described elsewhere [PMID 31547883] except for the following modifications: The antibody used was NB100-304 (Novus Biologicals) against TP53BP1.
As per the Ligation Sequencing Kit SQK-LSK109 from Oxford Nanopore Technologies

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-silencing (KD) [Origene Lentiviral system TL313955V]. For stable transduction, control and CGGBP1 shmiR transduced cells were selected with 10 ug/ml puromycin. Human primary fibroblast (GM02639) cells were cultured at 37°C, heat stressed at 40°C for 24h with 1°C increment per day and recovered at 37°C post-heat stress for 24 h. The CT and KD cells were cultured at 37°C, heat stressed at 42°C for 24h and recovered at 37°C post-heat stress for 24h.

tag: transduction

value: CGGBP1-targetting shRNA


title: Meningioma 198 (RNA-seq)

description:
Sex: 2
M198


title: HEK293T KD - 42°C


title: W3.0_rep4

source_name: W3.0_apical meristem


title: W3.5_rep1


title: D20-TM-GEX

description:
5' gene expression library (10X Genomics)
C4tmTran_S6_L004


title: Meningioma 197 (RNA-seq)

description:
Sex: 2
M197


title: D20-LN-GEX(aPDL1)

description:
5' gene expression library (10X Genomics)
A1LnGEX_S6_L001


title: W3.25_rep1


title: HEK293T KD - 37°C


title: W3.0_rep3


title: D20-SP-GEX

description:
5' gene expression library (10X Genomics)
C3spTran_S5_L004

value: spleen


title: HEK293T CT - recovery

source_name: HEK293T (stable cell line; non-targetting shRNA)

value: non-targetting shRNA


title: Meningioma 193 (RNA-seq)

description:
Sex: 2
M193

value: meningioma


title: Meningioma 194 (RNA-seq)

description:
Sex: 2
M194

value: UCSF


title: SPJ649_WT_LG6_K9me2_rep1

description: ChIP-seq


title: D20-LN-GEX

description:
5' gene expression library (10X Genomics)
E3LNGEX_S3_L001


title: HEK293T CT - 42°C


title: W3.0_rep1

value: Kronos


title: W3.0_rep2

value: apical meristem


title: Meningioma 192 (RNA-seq)

description:
Sex: 1
M192


title: D10-TM-GEX

description:
5' gene expression library (10X Genomics)
B6tmTran_S4_L004

value: Day 10


title: W2_rep4

source_name: W2.0_apical meristem


title: HEK293T CT - 37°C


title: Meningioma 191 (RNA-seq)

description:
Sex: 2
M191


title: D20-TM-GEX(aPDL1)

description:
5' gene expression library (10X Genomics)
B2TmGEX_S11_L001


title: D10-SP-GEX

description:
5' gene expression library (10X Genomics)
B5spTran_S3_L004


title: Meningioma 190 (RNA-seq)

description:
Sex: 2
M190


title: D10-LN-GEX

description:
5' gene expression library (10X Genomics)
D3LNGEX_S1_L001


title: GM02639 - recovery

source_name: Primary fibroblast

value: Human primary fibroblasts [Coriell Cell Repository GM02639]


title: GM02639 - 37°C


title: Meningioma 188 (RNA-seq)

description:
Sex: 2
M188


title: BM differentiated, IL4-treated #3

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

data_processing:
Sequenced reads were mapped to GRCm38 (Ensembl version 94) using STAR 2.6.1d with default parameters
STAR 2.6.1d was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.94.gtf.
Genome_build: Genome_build:  GRCm38 version 94
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample

source_name: Differentiated Hoxb8 BM cells

growth_protocol: 10^6 Hoxb8 progenitors were cultured per T75 cell culture flask in 13 ml of RPMI 1640 (Sigma R 8758) supplemented with 10% FCS (BIO-SELL S0615), 1% penicillin/streptomycin (Sigma P 4333), 1μM β-estradiol (Sigma E2257), 30 μM 2-Mercapto-Ethanol (Sigma M3148) and 6% SCF-containing supernatant, the cells were collected the next day for RNA sequencing (Hoxb8 progenitors). For the generation of differentiated macrophages, 2*10^6 Hoxb8 progenitors were seeded in 20 ml of  RPMI 1640 (Sigma R 8758) supplemented with 10% FCS (BIO-SELL S0615), 1% penicillin/streptomycin (Sigma P 4333), 30 μM 2-Mercapto-Ethanol (Sigma M3148) and 6% SCF-containing supernatant  and 10 ng/ml M-CSF (Immuno Tools 12343115)) at 37°C/5% CO2. Cell culture medium was changed every second day till day 5 (differentiated Hoxb8 cells).

extract_protocol:
Tryzol was used for RNA extraction and samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies) using RNA Nano/HS LabChip Kits (Agilent Technologies).
Library preparation was performed with the Illumina TruSeq® Stranded mRNA technology, according to the manufacturer´s protocol. The protocol started with an RNA fragmentation step. afterwards, cDNA was generated. After purification of the amplified cDNA samples, quality control of each single sample was carried out using the 2100 Bioanalyzer DNA HS LabChip (Agilent Technologies).  Amplified cDNA samples revealed typical electropherograms showing a broad fragment distribution between 230 bp – 600 bp with a peak around 300 bp for all samples. The electropherograms for all cDNA libraries are provided in the folder 19153_QC/Libraries in the files19153_DNA_1000&HS.pdf  Furthermore, all libraries were quantified using the highly sensitive fluorescent dye-based Qubit®ds DNA HS Assay Kit (Thermo Fisher Scientific). All single libraries were pooled into a sequencing library with an equal DNA amount per sample was used.Cartridge loading was conducted following the manufactures recommendations for NovaSeq 6000 according to the standard workflow using a SP flowcell.

treatment_protocol: untreated, or treated with 100 ng/ml IL4/ or 100 ng/ml LPS as indicated

value: BM

tag: progenitor

value: NO

tag: date


title: W1_rep3

source_name: W1.0_apical meristem

tag: tissue


title: W2_rep3


title: W1_rep4


title: W2_rep1


title: Meningioma 189 (RNA-seq)

description:
Sex: 1
M189

tag: institution

tag: age


title: W2_rep2


title: BM differentiated, LPS-treated #3

value: LPS


title: Meningioma 186 (RNA-seq)

description:
Sex: 2
M186

tag: grade


title: BM differentiated, untreated #3

tag: treatment


title: W1_rep2


title: Meningioma 19 (RNA-seq)

description:
Sex: 2
M19


title: W1_rep1


title: YS differentiated, LPS-treated #3

source_name: Differentiated Hoxb8 YS cells

value: YS


title: Meningioma 185 (RNA-seq)

description:
Sex: 2
M185

source_name: Meningioma


title: YS progenitors, untreated #3

source_name: Hoxb8 YS progenitors

value: YES


title: GM02639 - 40°C


title: YS differentiated, LPS-treated #2


title: Meningioma 184 (RNA-seq)

description:
Sex: 2
M184


title: BM differentiated, IL4-treated #2


title: Meningioma 183 (RNA-seq)

description:
Sex: 2
M183


title: Meningioma 182 (RNA-seq)

description:
Sex: 1
M182


title: Meningioma 181 (RNA-seq)

description:
Sex: 1
M181


title: Meningioma 180 (RNA-seq)

description:
Sex: 2
M180


title: Meningioma 18 (RNA-seq)

description:
Sex: 1
M18


title: Meningioma 187 (RNA-seq)

description:
Sex: 2
M187


title: Meningioma 179 (RNA-seq)

description:
Sex: 2
M179


title: BM differentiated, IL4-treated #1


title: YS differentiated, untreated #3


title: YS differentiated, LPS-treated #1


title: BM differentiated, LPS-treated #1


title: BM differentiated, LPS-treated #2


title: YS differentiated, IL4-treated #3


title: BM differentiated, untreated #2


title: YS progenitors, untreated #2


title: YS differentiated, untreated #2


title: YS progenitors, untreated #1


title: BM progenitors, untreated #3

source_name: Hoxb8 BM progenitors


title: A253-siSETX_rep2

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description:
Submaxillary salivary gland
Carcinoma; Epidermoid
RNA extracted 48 hours post transfection.

data_processing:
Demultiplexed and trimmed fastq's are generated from Illumina BaseSpace with FastqGeneration app.
Alignment and raw counts are generated with nf-core/rnaseq v3.3 pipeline. The pipeline are running with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: *salmon.gene_counts.tsv: Tab-delimited text files include raw counts.

source_name: squamous carcinoma

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen) and purified from DNA contamination through a DNase I (Qiagen, IT) digestion step. Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated in triplicate using 400ng of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA).

tag: cell line

value: Squamous Cell Carcinoma tumor cell line

tag: sirna

value: siSETX


title: Ker-CT-siSETX_rep1

description:
skin; Foreskin
normal
RNA extracted from transfected Ker-CT treated for three days with CaCl2.

source_name: keratinocytes

value: Ker-CT

value: hTERT-immortalized human keratinocytes


title: A253-siSETX_rep1


title: Ker-CT-sip63_rep2


title: Ker-CT-SCR_rep2

value: SCR


title: A253-siSETX_rep3


title: Ker-CT-sip63_rep1


title: Ker-CT-siSETX_rep2


title: Ker-CT-SCR_rep3


title: Ker-CT-sip63_rep3


title: Ker-CT-siSETX_rep3


title: Meningioma 174 (RNA-seq)

description:
Sex: 2
M174


title: Meningioma 171 (RNA-seq)

description:
Sex: 1
M171


title: Meningioma 175 (RNA-seq)

description:
Sex: 2
M175


title: Meningioma 176 (RNA-seq)

description:
Sex: 1
M176


title: Meningioma 178 (RNA-seq)

description:
Sex: 2
M178


title: Meningioma 173 (RNA-seq)

description:
Sex: 2
M173


title: A253-sip63_rep3


title: Ker-CT-SCR_rep1


title: A253-sip63_rep2


title: Meningioma 170 (RNA-seq)

description:
Sex: 1
M170


title: A253-sip63_rep1


title: Meningioma 17 (RNA-seq)

description:
Sex: 2
M17


title: YS differentiated, IL4-treated #2


title: BM progenitors, untreated #2


title: BM progenitors, untreated #1


title: A253-SCR_rep3


title: Meningioma 169 (RNA-seq)

description:
Sex: 1
M169


title: YS differentiated, untreated #1


title: Meningioma 168 (RNA-seq)

description:
Sex: 2
M168


title: Meningioma 164 (RNA-seq)

description:
Sex: 2
M164


title: A253-SCR_rep2


title: Meningioma 166 (RNA-seq)

description:
Sex: 1
M166


title: BM differentiated, untreated #1


title: A253-SCR_rep1


title: Meningioma 163 (RNA-seq)

description:
Sex: 1
M163


title: Meningioma 167 (RNA-seq)

description:
Sex: 2
M167


title: YS differentiated, IL4-treated #1


title: WT_Strep_Cycling_5M_mock-IP

city: Santa Cruz

first: Seth

last: Rubin

state: CA

address: 1156 High Street

department: Chemistry

institute: UC Santa Cruz

description: Strep-precipitation

data_processing:
bwa-mem aligner was used directly on paired end fq.gz files to generate sam alignements using the hg38 reference genome
samtools was used to generate sorted bam files which were visualized using IGV desktop browser
macs2 was utilized in -BAMPE mode to call MNase-ChIP peaks using a braod-cutoff of 0.1. A mock-IP dataset (empty Strep-EmptyVector plasmid transfection followed by Strep precipitation) was used as a control.
macs2 peaks with greater than 4.7-fold enrichment were intersected against knownGenes using UCSC Genome TableBrowser tool to generate filtered annotated peaks. These peaks were then further classified as being DREAM genes (or not) using an annotations provded in the manuscript. Atrifacts, duplicates and intergenic peaks were either filtered out from the annotated peaks or marked with an '*'
Genome_build: hg38
Supplementary_files_format_and_content: raw macs2 peaks (.broadPeak)
Supplementary_files_format_and_content: txt file of filtered annotated peaks in a modified bed format: chr, start, end, geneName, fold-enrichment, length, pileup, -log10(Pvalue),-log10(Qval)

growth_protocol: Cells were grown in DMEM with 10% FBS at 37C and 5% CO2.

extract_protocol:
Harvested cells were lysed in a buffer containing 50mM TrispH8.0, 150mMNaCl, 1%TritonX-100, 0.1%sodium deoxycholate, 5mM CaCl2 and subjected to MNase-digestion. Digested input samples were subjected to RNase (37C) and Proteinase-K treatment at (65C o/n) prior to DNA purification by SPRI beads. For the Strep-precipitated samples, digested chromatin was bound to StrepTactin-XT beads (IBA-Lifesciences) , washed in RIPA buffers and the bead suspension was resuspended in a buffer containing 10 mM Tris pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.6% SDS prior to RNase and Proteinase-K treatment as above.
NEB Next Ultra II Library Prep Protocol
MNase-ChIP seq

treatment_protocol: 24hours after plasmid transfection, cells were treated for an additional 48 hours with either 10uM Nutlin-3a dissolved in DMSO or a solvent control.

tag: transfection

value: Strep-EmptyVector

value: untreated

tag: digestion

value: 5U MNase


title: LIN37_KO_Strep_Arrested_5M_mock-IP

description: Strep-precipitation

value: 10uM Nutlin-3a


title: Meningioma 165 (RNA-seq)

description:
Sex: 2
M165

value: meningioma

value: UCSF


title: WT_Strep_Arrested_1M_mock-IP

description: Strep-precipitation

value: 1U MNase


title: LIN37_KO_Strep_Arrested_1M_mock-IP

description: Strep-precipitation


title: Skeletal muscle FoxM1-dNdK #1

city: Porto

first: Elsa

last: Logarinho

state: Porto

address: Rua Alfredo Allen, 208

country: Portugal

data_processing:
Raw reads were mapped to mm10 (GRCm38.p6) mouse genome and gene counts were obtained with STAR v2.5.2b.
Gene counts were normalized using RLE method and log-transformed using edgeR (3.28.1) package in R.
Only genes covered by 10 reads or more in the analyzed samples were used for downstream analysis.
Differential expressions were calculated with limma (3.42.2) package in R.
STAR --runThreadN 30 --outSAMtype BAM Unsorted --outSAMmultNmax 1 --quantMode GeneCounts --genomeDir {genomedir} --genomeLoad NoSharedMemory --readFilesCommand gunzip -c --readFilesIn {file.fastq} --outFileNamePrefix {file.fastq}
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Genecounts, table

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA was isolated from snap-frozen samples of tissues, after mechanical homogenization, using RNeasy Fibrous Tissue Mini Kit (muscle, aorta; QIAGEN) according to the manufacturer's protocol. Ion Torrent sequencing libraries were prepared according to the AmpliSeq Library prep kit protocol and as previously published (Papp et al. 2018 PLoS One)
10ng of total RNA was reverse transcribed, the resulting cDNA was amplified for 12 cycles by adding PCR Master Mix, and the AmpliSeq Mouse transcriptome gene expression primer pool (targeting 20,767 well-annotated RefSeq genes + 3,163 XM and XR genes) (based on GRCm38/mm10). Amplicons were digested with the proprietary FuPa enzyme, then barcoded adapters were ligated onto the target amplicons. The library amplicons were bound to magnetic beads, and residual reaction components were washed off. Libraries were amplified, re-purified and individually quantified using Agilent TapeStation High Sensitivity tape.

tag: strain

tag: genotype

value: 88 weeks

value: Gastrocnemius muscle


title: Skeletal muscle FoxM1-dNdK #3


title: Skeletal muscle Rosa26 #4


title: Meningioma 162 (RNA-seq)

description:
Sex: 2
M162


title: 19-T4_S5_ATAC-Seq

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 to mm10 using STAR guided by GTF and ATAC-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ATAC-Seq peak calling was performed using MACS
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw), Count Tables (.txt)

source_name: control thoracic motor neurons replicate 2

extract_protocol: DNA was extracted from purified dissected mouse embryonic MNs. Cells were aliquoted and washed twice in ice-cold 1Ã— PBS. Cell pellets were resuspended in 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 (v/v), 0.1% tween20, 0.01% Digitonin and 1% BSA, centrifuged at 500 g for 5 min at 4°C. Pellets were resuspended in 12.5 ul of 2Ã— tagmentation DNA buffer, 1.25 ul Tn5 (Nextera DNA Sample Preparation Kit, FC-121€“1030) and 11.25 ul of water, and incubated at 37°C for 30 min. The sample was purified using the MinElute PCR Purification Kit (Qiagen, 28004). PCR enrichment of the library was performed with custom-designed primers and 2Ã— NEB Master Mix. A qPCR reaction with 1Ã— SYBR Green (Invitrogen), custom-designed primers and 2Ã— NEB Master Mix (New England Labs, M0541) was performed to determine the optimal number of PCR cycles (one third of the maximum measured fluorescence) (Buenrostro et al., 2013). The libraries were purified using the AMPure XP beads (Beckman Coulter, A63880). High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify the fragment length distribution of the library. Library quantification was performed using the KAPA Library Amplification kit on a Roche LightCycler 480. The libraries were sequenced on an Illumina NovaSeq (100 cycles, paired-end)

value: thoracic motor neurons

value: control


title: 19-L4_S6_ATAC-Seq

source_name: control lumbar motor neurons replicate 2

value: lumbar motor neurons


title: 19-B4_S4_ATAC-Seq

source_name: control brachial motor neurons replicate 2

value: brachial motor neurons


title: Meningioma 161 (RNA-seq)

description:
Sex: 1
M161


title: 16-T2_S11_ATAC-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 2

value: Ring1 mutant


title: 16-T6_S2_ATAC-Seq

source_name: control thoracic motor neurons replicate 1


title: 16-L6_S3_ATAC-Seq

source_name: control lumbar motor neurons replicate 1


title: LIN37_KO_Strep-LIN9_Arrested_5M_Rep2_INPUT


title: LIN37_KO_Strep-LIN9_Arrested_1M_INPUT


title: Meningioma 160 (RNA-seq)

description:
Sex: 2
M160


title: LIN37_KO_Strep-LIN9_Arrested_5M_Rep1_INPUT


title: 16-L4_S12_ATAC-Seq

source_name: Ring1 mutant lumbar motor neurons replicate 2


title: Skeletal muscle Rosa26 #2


title: Skeletal muscle FoxM1-dNdK #2


title: WT_StrepLIN9_Cycling_5M_Rep1_INPUT


title: Meningioma 159 (RNA-seq)

description:
Sex: 1
M159


title: Meningioma 158 (RNA-seq)

description:
Sex: 2
M158


title: WT_Strep-LIN9_Arrested_5M_Rep2_INPUT


title: 16-B6_S1_ATAC-Seq

source_name: control brachial motor neurons replicate 1


title: Skeletal muscle Rosa26 #1


title: WT_Strep_Arrested_5M_mock-IP

description: Strep-precipitation


title: Meningioma 157 (RNA-seq)

description:
Sex: 2
M157


title: Aorta FoxM1-dNdK #2

source_name: Aorta

value: Aorta


title: Aorta FoxM1-dNdK #1


title: 14-T4_S8_ATAC-Seq

source_name: Ring1 mutant thoracic motor neurons replicate 1


title: Meningioma 155 (RNA-seq)

description:
Sex: 2
M155


title: Meningioma 156 (RNA-seq)

description:
Sex: 2
M156


title: Aorta Rosa26 #4


title: WT_Strep-LIN9_Arrested_1M_INPUT


title: 16-B4_S10_ATAC-Seq

source_name: Ring1 mutant brachial motor neurons replicate 2


title: 14-B4_S7_ATAC-Seq

source_name: Ring1 mutant brachial motor neurons replicate 1


title: 14-L4_S9_ATAC-Seq

source_name: Ring1 mutant lumbar motor neurons replicate 1


title: Aorta Rosa26 #3


title: WT_Strep-LIN9_Arrested_5M_Rep1_INPUT


title: Meningioma 153 (RNA-seq)

description:
Sex: 2
M153

source_name: Meningioma


title: HM-1_tumor_Cd276KO, biological rep3

city: Kyoto

first: Taito

last: Miyamoto

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

country: Japan

institute: Kyoto University

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The raw sequencing reads were trimmed using Trim Galore (RRID: SCR_011847). The resulting sequence reads were aligned to the mouse reference genome of GRCm38/mm10 using STAR (Dobin A et al., Bioinformatics, 2013).
Read counts per each gene according to the GENCODE mouse reference annotation were calculated using HTSeq (Anders S et al., Bioinformatics, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for every gene in each sample.

growth_protocol: HM-1 and ID8 cells were cultured in MEM alpha and RPMI 1640 medium respectively, supplemented with 10% (v/v) heat-inactivated foetal bovine serum, 100 IU/ml penicillin and 100 μg/ml streptomycin in an atmosphere containing 5% CO2 at 37 °C. A total of 1×106 HM-1 cells were intradermally inoculated to B6C3F1 mice, and the tumors were collected at day 10.

extract_protocol:
Total RNA was extracted from cell lines or frozen tumors using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue/cell type

value: ovarian cancer tumors

tag: genotype/variation


title: LIN37_KO_Strep-4xLIN9_Arrested_5M

description: Strep-precipitation


title: Skeletal muscle Rosa26 #3


title: Aorta Rosa26 #2


title: LIN37_KO_Strep-LIN9_Arrested_5M_Rep2

description:
Strep-precipitation
LIN37_KO_Strep-LIN9_Arrested_5M_Rep2.broadPeak
TopMACS_KO_Strep-LIN9_Arrested_5M_R2_txt.bed.txt


title: Meningioma 152 (RNA-seq)

first: Abrar

last: Choudhury

description:
Sex: 2
M152

data_processing:
Standard Illumina software was used for basecalling
Sequenced reads were trimmed using Trimmomatic, then mapped to hg38 transcriptome using HISAT2 2.1.0
Exon level count data were extracted from the mapped reads using featureCounts
Transcripts per million (TPM) were calculated from the count data
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPMs for every gene and every sample

extract_protocol:
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and RNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit v2 (CAT# RS-122-2001)


title: Aorta Rosa26 #1


title: LIN37_KO_Strep-LIN9_Arrested_1M

description:
Strep-precipitation
LIN37_KO_Strep-LIN9_Arrested_1M.broadPeak
TopMACS_KO_Strep-LIN9_Arrested_1M_txt.bed.txt


title: Meningioma 150 (RNA-seq)

description:
Sex: 2
M150


title: HM-1_tumor_Cd276KO, biological rep2


title: HM-1_tumor_Cd276KO, biological rep1


title: Meningioma 15 (RNA-seq)

description:
Sex: 1
M15


title: HM-1_tumor_control, biological rep3


title: LIN37_KO_Strep-LIN9_Arrested_5M_Rep1

description:
Strep-precipitation
LIN37_KO_Strep-LIN9_Arrested_5M_Rep1.broadPeak
TopMACS_KO_Strep-LIN9_Arrested_5M_R1_txt.bed.txt


title: HM-1_tumor_control, biological rep2


title: SiCD_B_pool2

city: Rehovot

first: Naama

last: Teboul

address: Hankin 18

department: Plant sciences and genetics

country: Israel

institute: Hebrew University

description:
C5
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG

data_processing:
FastQ files, generated from raw data obtained from Illumina sequencing, were processed and filtered with publically available tools. Quality evaluation of each sample was manually inspected using FastQC v0.11.4
Barcode removal and trimming of low-quality reads were conducted using Trim Galore with a Phred score threshold of 25
Paired end reads were mapped to the sesame reference genome S_indicum_v1.0  using STAR aligner
Mapped reads were further processed for visualization with Samtools Utilities v 0.1.19
Uniquely mapped reads per gene were counted using HTSeq-count for both strands
Transcriptional data visualization and analysis of differentially expressed genes was conducted using DESeq2 R package
Filtering DEG -> Only top 100 DEG were opted after a sort based on the most significant genes
Genome_build: Paired end reads were mapped to the sesame reference genome S_indicum_v1.0 (genome assembly GCF_000512975.1) using the STAR aligner
Supplementary_files_format_and_content: normalized count data was conducted with the DESeq2 package.  Since we used a bulk segregant assay, a strict false discovery rate (FDR) adjusted P-value threshold of Padj<1.3×10e-24 was determined to detect significantly differentially expressed genes (DEGs).

organism: Sesamum indicum

source_name: young leaf tissue of 17-day old seedlings

growth_protocol: Seeds were germinated in a tray with a growing mixture (Green 90, Even Ari, Israel)  growth room at a temperature of 28C/22C, 12h/12h day/night, at 50-60% relative humidity.

extract_protocol:
RNA extraction was conducted via Tri reagent method (Plant RNA reagent Invitrogen, USA), followed by purification using Plant/Fungi Total RNA Purification Kit (Norgen Biotek Corp., Canada) and on column DNAse treatment (Qiagen, Germany).
Six pair-end (100bp) bar-coded cDNA libraries were prepared for multiplex sequencing on the Illumina HiSeq 2500 sequencer (Technion Genome Center, Haifa, Israel) using the TruSeq RNA sample preparation kit ver. 2 (Illumina, San Diego, CA), according to manufacturer’s standard protocols.
Bulk segregant RNA-seq

treatment_protocol: Recombinant inbred lines from containing either SiCD-A or SiCD-B allele

value: SiCD_B allele

tag: developmental stage

value: 17-day old seedlings

value: leaf

tag: replicate


title: SiCD_B_pool3

description:
C6
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG


title: WT_StrepLIN9_Cycling_5M_Rep2

description: Strep-precipitation

value: untreated

value: 5U MNase


title: WT_StrepLIN9_Cycling_5M_Rep1

description:
Strep-precipitation
WT_Strep-LIN9_Cycling_5M.broadPeak
TopMACS_WT_Strep-LIN9_Cycling_5M_R1_txt.bed.txt


title: SiCD_B_pool1

description:
C4
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG


title: ID8_cell_Cd276KO, biological rep3

value: ovarian cancer cells


title: SiCD_A_pool3

description:
O3
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG

value: SiCD_A allele


title: SiCD_A_pool2

description:
O2
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG


title: HM-1_tumor_control, biological rep1


title: Meningioma 144 (RNA-seq)

city: San Francisco

institute: University of California, San Francisco

description:
Sex: 2
M144

value: meningioma

value: UCSF


title: Meningioma 145 (RNA-seq)

description:
Sex: 1
M145


title: ID8_cell_Cd276KO, biological rep2


title: WT_Strep-LIN9_Arrested_1M

description:
Strep-precipitation
WT_Strep-LIN9_Arrested_1M.broadPeak
TopMACS_WT_Strep-LIN9_Arrested_1M_txt.bed.txt

value: 10uM Nutlin-3a

value: 1U MNase


title: WT_Strep-LIN9_Arrested_5M_Rep2

description:
Strep-precipitation
WT_Strep-LIN9_Arrested_5M_Rep2.broadPeak
TopMACS_WT_Strep-LIN9_Arrested_5M_R2_txt.bed.txt


title: Meningioma 143 (RNA-seq)

description:
Sex: 2
M143


title: WT_Strep-LIN9_Arrested_5M_Rep1

description:
Strep-precipitation
WT_Strep-LIN9_Arrested_5M_Rep1.broadPeak
TopMACS_WT_Strep-LIN9_Cycling_5M_R1_txt.bed.txt


title: Meningioma 142 (RNA-seq)

description:
Sex: 2
M142


title: ID8_cell_control, biological rep3

value: control


title: MYC_KD2

first: Yumin

last: Han

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Sequenced reads were aligned to Ensemble database with STAR.
Gene expression values were normalized to obtain RPKM values using RSEM.
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample .

extract_protocol:
Cells were lysed in Trizol reagent and total RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: stomach cancer cell line


title: MYC_KD1


title: Meningioma 141 (RNA-seq)

description:
Sex: 1
M141


title: ID8_cell_control, biological rep2


title: C_M_pre_8

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads (~35.3 M/sample) were aligned to human genome (Ensembl GRCh38, release 98) using STAR v2.7.2b resulting in ~26.5 M/sample uniquely aligned reads.
2) Gene read coverages (~22 M/sample) were computed with featureCounts v1.6.2 using same human genome annotation.
3) Differential expression analysis was performed using edgeR v3.28.1 with "y ~ 0 + group" design (group represents the combinations of "Disease" and "Cell Type" together) while filtering low count reads using built-in function filterByExpr (n = 17,689 genes) and blocking for patient IDs with voomLmFit function.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: counts.tsv: Text file in tab-separated format with gene coverages in units of read counts.
Supplementary_files_format_and_content: logCPM_filtered_batchCorrected.tsv: Text file in tab-separated format with gene coverages in units of log2 counts per million (CPM). The logCPM values are batch corrected for "Patient IDs". See "data processing step 3" for details.

source_name: muscle (vastus lateralis)

growth_protocol: Myotubes were grown in α-MEM with 10% v/v fetal bovine serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B, and later differentiated for 6 days in α-MEM with 2% v/v horse serum, 0.5% v/v penicillin-streptomycin and 0.5% v/v amphotericin B.

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA universal kit (Qiagen).
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold.

treatment_protocol: No treatment applied.

tag: group

tag: participant id

tag: disease

value: CTRL

value: muscle

tag: gender

value: female

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: Meningioma 14 (RNA-seq)

description:
Sex: 1
M14

tag: tissue

tag: institution

tag: age

tag: grade


title: C_M_pre_6


title: P_M_pre_24

value: PCOS


title: Meningioma 139 (RNA-seq)

description:
Sex: 2
M139


title: Meningioma 146 (RNA-seq)

description:
Sex: 2
M146


title: Meningioma 147 (RNA-seq)

description:
Sex: 2
M147


title: HM-1_cell_Cd276KO, biological rep3

tag: strain

tag: cell line

tag: tissue/cell type

tag: genotype/variation


title: P_M_pre_13

tag: group

tag: cell type


title: ID8_cell_control, biological rep1


title: IL-27-p28-GFP, HTO

city: San Diego

first: John

middle: R

last: Teijaro

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

data_processing:
Libraries were sequenced using Illumina NextSeq500. Demultiplexing of BCL files was performed using 10X Genomics cellranger mkfastq version 4.0.0 with the following parameters in csv format: Lane, Sample, Index 1,NS870_cDNA,SI-GA-G4  2,NS870_cDNA,SI-GA-G4  3,NS870_cDNA,SI-GA-G4  4,NS870_cDNA,SI-GA-G4  1,NS870_HTOs,SI-GA-A5  2,NS870_HTOs,SI-GA-A5  3,NS870_HTOs,SI-GA-A5  4,NS870_HTOs,SI-GA-A5
Cell demultiplexing, barcode counting and gene counting were performed using 10X Genomics cellranger count version 4.0.0 using parameters --expect-cells=30000 --transcriptome=./refdata-gex-mm10-2020-A.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are the unaltered output of cellranger count in the form of matrix of counts, list of cell barcodes and list of features (genes and hashtags) counted per cell.

source_name: splenocytes

growth_protocol: Tg(Il27-Gfp) mice were infected with 2x10^6 pfu LCMV Clone 13 intravenously.

extract_protocol:
Splenocytes were harvested and live single cells sorted by flow cytometry, then subjected to antibody hashing using TotalSeq-B hashing antibodies (Biolegend) according to the manufacturer's instructions. Hashtag-stained cells were subsequently processed using the 10X Genomics Chromium controller.
Single-cell transcriptome and barcode libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1

tag: infection

value: LCMV Clone 13


title: WT1

city: Shanghai

tag: genotype


title: IL-27-p28-GFP, mRNA-derived cDNA


title: SiCD_A_pool1

description:
O1
all_merge_normalized.txt
all_merge.txt
all_merged_norm_log2FC_anno
DEG

tag: developmental stage

value: 17-day old seedlings

tag: replicate


title: WT2


title: Meningioma 137 (RNA-seq)

description:
Sex: 2
M137


title: P_M_pre_11

tag: participant id

tag: disease

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)


title: Meningioma 135 (RNA-seq)

description:
Sex: 1
M135

tag: tissue

tag: institution

tag: age

tag: grade


title: HM-1_cell_Cd276KO, biological rep1

tag: strain

tag: cell line

tag: tissue/cell type

tag: genotype/variation


title: WT_Strep-4xLIN9_Arrested_5M

description:
Strep-precipitation
WT_Strep-4xLIN9_Arrested_5M.broadPeak
TopMACS_WT_Strep-4xLIN9_Arrested_5M_txt.bed.txt

tag: transfection

tag: treatment

tag: digestion


title: HM-1_cell_Cd276KO, biological rep2


title: 27_mb286_RNA-Seq

source_name: iHoxc13 ESC-MN replicate 2

extract_protocol: Cells were collected prior to TF induction (day 2 of RA/SAG differentiation) and 48h after Doxycycline (Dox) treatment. RNA was extracted by using TRIzol LS Reagent (Life Technologies) and purified using the RNAeasy mini kit (Qiagen). Agilent High Sensitivity RNA Screentape (Agilent, 5067-5579) was used to check RNA integrity. 500ng of RNA was used to prepare RNA-seq libraries and spiked-in with ERCC Exfold Spike-in mixes (Thermo Fisher, 4456739). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594). Library size was verified using High Sensitivity DNA ScreenTape (Agilent, 5067-5584). The KAPA library amplification kit was used on Roche Lightcycler 480 for library quantification before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2mM L-glutamine, 0.1mM B-mercaptoethanol and penicillin-streptomycin (Gibco),) at 37°C, 5%CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 uM all-trans retinoic acid and 0.5 uM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 ug/mL of Doxycycline (Sigma, D9891) on day 2. For RNA-seq experiments, 3.5x10^5 mESCs were plated in 100mm suspension dishes (Corning).

value: ESC-MN

tag: genotype

value: expressing Hoxc13


title: Meningioma 134 (RNA-seq)

description:
Sex: 2
M134


title: HM-1_cell_control, biological rep3


title: ID8_cell_Cd276KO, biological rep1


title: P_M_pre_7

tag: group

tag: participant id

tag: disease

tag: cell type

tag: body fat (%)

tag: lean mass (%)


title: HM-1_cell_control, biological rep2


title: C_c_pre_7

source_name: myotubes obtained from vastus lateralis

value: myotubes

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)


title: T_D7_4

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Normalizations were performed  using iDEGES/edgeR
Genome_build: mm10

source_name: Adhesion tissue at day7 after adhesion induction

growth_protocol: C57/Black6 (B6) mice (male, eight weeks) were obtained from CLEA Japan (Tokyo, Japan). Mice were mainained in an air-conditioned animal room with  a conventional  diet and water.

extract_protocol:
Total RNA was isolated according to the manufacturer’s instructions for the ISOGEN II reagent. Purified total RNA was quantified using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA integrity score was evaluated using the Bioanalyzer RNA 6000 Nano Assay Kit (Agilent Technologies, Santa Clara, CA, USA).
RNA-Seq libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit for Illumina and  NEBNext rRNA Depletion Kit V2(Human/Mouse/Rat) according to the manufacturer's instructions and subsequently validated for an average size of about 305-360 bp using  the Agilent DNA1000 kit.

treatment_protocol: After laparotomy with minimal incision, 300 µL of a saline-based talc solution (2.5 mg/g) (Unitalc; Nobelpharma, Tokyo, Japan) was injected into the pericardial cavity via the diaphragm using a 27G needle.

tag: strain

tag: tissue

value: Adhesion tissue

tag: Stage


title: Meningioma 132 (RNA-seq)

description:
Sex: 2
M132

tag: institution

tag: age

tag: grade


title: HM-1_cell_control, biological rep1

tag: cell line

tag: tissue/cell type

value: ovarian cancer cells

tag: genotype/variation


title: T_D3_4

source_name: Adhesion tissue at day3 after adhesion induction


title: C_c_pre_6

tag: group

tag: participant id

tag: disease


title: P_c_pre_24

tag: cell type

tag: body fat (%)

tag: lean mass (%)


title: RNA-seq_HiII_3_0mm_b

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: RNA-seq, HiII hybrid fertile anther, 3.0 mm, replicate 2

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
Supplementary_files_format_and_content: Text containing distinct RNAs with their raw abundance after removing the adapter sequences

organism: Zea mays

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ103-12

extract_protocol:
TRI Reagent® (Sigma-Aldrich) follow instruction from manufacturer
For sRNA library preparation, 20- to 30-nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, lnc.) were used for ultra-low amount of total RNA starting from 100 ng. For RNA-seq, 2 µg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs) was used for library construction with 500 ng of treated RNA.

value: Dissected whole anthers

tag: genotype

value: BHLH122//BHLH122 BHLH51//BHLH51


title: T_D1_4

source_name: Adhesion tissue at day0


title: Meningioma 130 (RNA-seq)

description:
Sex: 2
M130

value: meningioma

value: UCSF


title: P_c_pre_11

tag: gender

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)


title: H_D3_4

source_name: Whole heart tissue at day3 after adhesion induction

tag: strain

tag: tissue

value: Heart

tag: Stage


title: Meningioma 13 (RNA-seq)

description:
Sex: 1
M13

tag: institution

tag: age

tag: grade


title: H_D0_3

source_name: Whole heart tissue at day0


title: H_D7_4

source_name: Whole heart tissue at day7 after adhesion induction


title: RNA-seq_HiII_3_0mm_a

description: RNA-seq, HiII hybrid fertile anther, 3.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ104-6


title: RNA-seq_HiII_2_0mm_a

description: RNA-seq, HiII hybrid fertile anther, 2.0 mm, replicate 1


title: Meningioma 128 (RNA-seq)

description:
Sex: 1
M128


title: P_c_pre_10

tag: group


title: Meningioma 127 (RNA-seq)

description:
Sex: 2
M127


title: C_M_pre_5

tag: participant id


title: RNA-seq_HiII_1_5mm_b

description: RNA-seq, HiII hybrid fertile anther, 1.5 mm, replicate 2


title: shJMJD1A-AGE group 3

city: guangzhou

first: Ming

last: WANG

state: Guangdong

address: 1838 Guangzhou Avenue North, Baiyun District

institute: School of Traditional Chinese Medicine, Southern Medical University

data_processing:
NEBNext® UltraTM RNA Library Preparation Kit for   Illumina® to generate a sequencing library
The libraries were pooled in equimolar amounts and sequenced using a 2×132 bp chemical method
Quality control of RNA-seq raw paired data was performed using FastQC and MultiQC
Trim Galore was used to trim adapters, reads with low quality (<50) and short length (<75 bp)
RNA-seq reads were mapped to Homo sapiens genome Ensembl GRCh38 using Hisat2 (version 2.1.0) with default codes
The read counts of each gene were summarized using featureCounts . Raw read counts were imported into R studio and analyzed by using R package of DESeq2
Genes with  foldchange > 2 and false discovery rate (FDR) p-value < 0.05 adjusted by using ClusterProfile method were considered as differentially expressed genes (DEGs).
Supplementary_files_format_and_content: count

source_name: Renal tubular epithelial cells

growth_protocol: HK-2 cells from an immortalized human proximal tubular epithelial cell line were obtained from the ATCC, which was grown in the MEM and supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, Calif., USA). The cells were placed in a CO2 incubator at 37 °C and will be taken for the subsequent experimental logarithmic phase.

extract_protocol:
RNAex Pro Reagent (AG, hunan, China) was used to extract total RNA from HK-2 cells according to   the instructions provided by the manufacturer. A total amount of 2 μg isolated RNA per sample was   used for DNA library preparation.
Use NEBNext® UltraTM RNA Library Preparation Kit for   Illumina® to generate a sequencing library (Neb, Ipswich, Massachusetts, USA) in accordance with the manufacturer's instructions.

treatment_protocol: The confluent cells were cultured in 400ug/ml AGEs for 72 h

tag: cell line

tag: shRNA


title: P_M_pre_10

tag: disease

tag: cell type

tag: body fat (%)


title: Meningioma 126 (RNA-seq)

description:
Sex: 1
M126


title: 26_mb285_RNA-Seq

source_name: iHoxc13 ESC-MN replicate 1

tag: genotype


title: Meningioma 133 (RNA-seq)

description:
Sex: 2
M133


title: Meningioma 125 (RNA-seq)

description:
Sex: 2
M125


title: Meningioma 124 (RNA-seq)

description:
Sex: 2
M124


title: P_M_pre_27

tag: gender

tag: height (m)

tag: lean mass (%)


title: P_M_pre_26

tag: weight (kg)

tag: body mass index (kg/m2)


title: RNA-seq_HiII_1_0mm_b

description: RNA-seq, HiII hybrid fertile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ106-6

tag: tissue

tag: Stage


title: RNA-seq_HiII_1_5mm_a

description: RNA-seq, HiII hybrid fertile anther, 1.5 mm, replicate 1


title: RNA-seq_HiII_1_0mm_a

description: RNA-seq, HiII hybrid fertile anther, 1.0 mm, replicate 1


title: RNA-seq_122ms_3mm_b

description: RNA-seq, bhlh122-1 sterile anther, 3.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ108-10


title: shCtrl-Normal group 2

value: shCtrl-Normal


title: shJMJD1A-AGE group 2


title: Meningioma 122 (RNA-seq)

description:
Sex: 2
M122

source_name: Meningioma

tag: institution

tag: age


title: shJMJD1A-AGE group 1


title: Meningioma 129 (RNA-seq)

description:
Sex: 2
M129

tag: grade


title: P_M_pre_1

source_name: muscle (vastus lateralis)

tag: group

tag: participant id


title: shCtrl-Normal group 3

tag: cell line

tag: shRNA


title: RNA-seq_HiII_2_0mm_b

description: RNA-seq, HiII hybrid fertile anther, 2.0 mm, replicate 2


title: C_c_pre_5

tag: disease

value: CTRL

tag: cell type


title: RNA-seq_122ms_3mm_a

description: RNA-seq, bhlh122-1 sterile anther, 3.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ105-8

tag: genotype


title: shCtrl-Normal group 1


title: Meningioma 120 (RNA-seq)

description:
Sex: 2
M120


title: RNA-seq_122ms_2mm_b

description: RNA-seq, bhlh122-1 sterile anther, 2.0 mm, replicate 2


title: C_c_pre_4

tag: gender

tag: body fat (%)


title: Meningioma 12 (RNA-seq)

description:
Sex: 2
M12


title: RNA-seq_122ms_2mm_a

description: RNA-seq, bhlh122-1 sterile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile siblingZQQ105-8


title: C_M_pre_4

value: muscle

tag: height (m)

tag: lean mass (%)


title: C_c_pre_3

source_name: myotubes obtained from vastus lateralis

value: female

tag: weight (kg)

tag: body mass index (kg/m2)


title: shCtrl-AGEs group 2

value: shCtrl-AGE


title: C_M_pre_3


title: shCtrl-AGEs group 1


title: RNA-seq_122ms_1_5mm_b

description: RNA-seq, bhlh122-1 sterile anther, 1.5 mm, replicate 2

tag: tissue

tag: Stage


title: C_c_pre_2

tag: age


title: Meningioma 123 (RNA-seq)

description:
Sex: 1
M123

tag: institution

tag: grade


title: RNA-seq_122ms_1_5mm_a

description: RNA-seq, bhlh122-1 sterile anther, 1.5 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ103-7


title: P_c_pre_26

tag: group

tag: participant id

value: PCOS


title: Meningioma 115 (RNA-seq)

description:
Sex: 2
M115


title: S372

city: Shenzhen

first: Peikai

last: Chen

address: 1 Haiyuan Rd

institute: The University of Hong Kong - Shenzhen Hospital

description: c.G2299A, p.G767S

data_processing:
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files in Excel include FPKM values for each Sample for all genes

source_name: OI patient with mutations on Collagen 1

extract_protocol:
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: OI

value: osteoblasts

value: M

tag: site

value: Right tibia

tag: mutant genes


title: Meningioma 116 (RNA-seq)

description:
Sex: 2
M116


title: Control 1 Tacrolimus single cell RNA

city: Pala Alto

first: Karim

last: Sallam

address: 300 Pasteur Dr, Rm S102C

institute: Stanford University

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to find cluster and generate UMAPs
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

source_name: Human Cardiac Organoids

growth_protocol: Cardiac Organoids maintained in RPMI/B27 + EGM2 Media (ratio 2:1)

extract_protocol:
Digestion using liberase followed by cell pellet
10x geonmics 3' sc-RNA (v3 chemistry)

treatment_protocol: DMSO, Sirolimus 50nM, Tacrolimus 1uM for 5 days

tag: cell type

value: iPSC-derived cardiomyocytes, endothelial cells and fibroblasts

tag: agent

value: Tacrolimus


title: Control 2 Tacrolimus single cell RNA


title: Meningioma 114 (RNA-seq)

description:
Sex: 2
M114


title: RNA-seq_122ms_1mm_c

description: RNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ106-11

value: Dissected whole anthers

tag: genotype


title: S503

description: c.G1964A, p.G655E

tag: gender

value: F

value: Femur


title: RNA-seq_122ms_1mm_a

description: RNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling, ZQQ106-12


title: Meningioma 113 (RNA-seq)

description:
Sex: 1
M113

value: meningioma

value: UCSF


title: RNA-seq_51ms_3_0mm_c

description: RNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-4


title: Control 2 Sirolimus single cell RNA

value: Sirolimus


title: Control 3 Sirolimus single cell RNA


title: shCtrl-AGEs group 3

tag: cell line

tag: shRNA


title: P_c_pre_27

tag: disease

value: myotubes

tag: height (m)

tag: weight (kg)

tag: body mass index (kg/m2)

tag: body fat (%)

tag: lean mass (%)


title: S502

description: c.G1093A, p.G365S

tag: age

value: left radial/ulnar


title: RNA-seq_51ms_3_0mm_b

description: RNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ105-2

tag: tissue

tag: Stage


title: Meningioma 112 (RNA-seq)

description:
Sex: 1
M112

tag: institution

tag: grade


title: Control 1 Sirolimus single cell RNA

tag: cell type


title: B23

description: c.G1045A, p.G349S (Het)

tag: disease state

tag: site

tag: mutant genes


title: Meningioma 119 (RNA-seq)

description:
Sex: 2
M119


title: Meningioma 111 (RNA-seq)

description:
Sex: 2
M111


title: RNA-seq_51ms_3_0mm_a

description: RNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-9

tag: genotype


title: Control 3 Untreated single cell RNA

tag: agent

value: Control


title: Meningioma 110 (RNA-seq)

description:
Sex: 2
M110


title: Meningioma 117 (RNA-seq)

description:
Sex: 2
M117


title: RNA-seq_51ms_2_0mm_b

description: RNA-seq, bhlh51-1 sterile anther, 2.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-10


title: Control 3 Tacrolimus single cell RNA


title: Control 2 Untreated single cell RNA


title: S144

description: c.G1138A, p.G380S

tag: gender

value: Fibula


title: B14

source_name: non-OI individual with bilateral limb discrepancy

value: non-OI

value: Left fibula


title: Meningioma 106 (RNA-seq)

description:
Sex: 2
M106


title: B15

source_name: Healthy individual, fractured

value: Healthy

value: osteoblasts

value: Right humerus


title: RNA-seq_51ms_1_5mm_b

description: RNA-seq, bhlh51-1 sterile anther, 1.5 mm, replicate 2


title: Meningioma 105 (RNA-seq)

description:
Sex: 2
M105


title: RNA-seq_51ms_1_5mm_a

description: RNA-seq, bhlh51-1 sterile anther, 1.5 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-3


title: S501

description: c.G1084A, p.G362S

value: OI

value: Left femur


title: LSD1i_rep3

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

institute: European Institute of Oncology

data_processing:
basecall was performed using CASAVA v1.8
Sequenced reads were mapped to hg18 using STAR 2.6.1a
Reads counts were performed using FeatureCount v1.6.4 and differential expressed genes were calculated using edgeR
Genome_build: hg18
Supplementary_files_format_and_content: featureCount tab-delimited output text files include reads count values for each Sample

source_name: human GBM TIC GBM#22

growth_protocol: GBM TICs  were grown in DMEM/F12 medium supplemented with  B27 supplement (Life Technologies), 20 ng/ml epidermal growth factor, 10 ng/ml basic fibroblast growth factor, 2mM L-Glutamine, penicillin (50 units/ml) and streptomycin (100 mg/ml).

extract_protocol:
Total RNA was extracted from GBM TICs using Quick-RNA Miniprep Kit (Zymo Research)
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: GBM TICs were plated at 250000 cells/ml and treted as indicated in each sample for 24 hours.

tag: cell line

value: primary GBM tumor initiating cell line

tag: treatment


title: RNA-seq_122ms_1mm_b

description: RNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ108-10

value: Dissected whole anthers


title: vehicle_rep3

value: vehilce (DMSO)


title: Mesangial cell ANGPT2 treatment-3

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

description: ANGPT2 treatment-3

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human mesangial cell line

growth_protocol: Immortalized human mesangial cell line was purchased from the CELL SYSTEMS (WA, USA) were cultured with DMEM medium supplemented with 10% FBS at 37°C in 5% CO2 incubator for growth.

extract_protocol:
The cells were homogenized with Trizol (Invitrogen) and the total RNA was extracted following the manual instruction.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated.

treatment_protocol: Then treated with 500 ng/ml recombinant ANGPT2 (MCE, HY-P7510) or left untreated with only vehicle for 24 hours.

value: Human mesangial cell line


title: LSD1i_rep2


title: RNA-seq_51ms_1_0mm_b

description: RNA-seq, bhlh51-1 sterile anther, 1.0 mm, replicate 2


title: Mesangial cell ANGPT2 treatment-2

description: ANGPT2 treatment-2


title: Meningioma 104 (RNA-seq)

description:
Sex: 1
M104

source_name: Meningioma

value: meningioma

value: UCSF


title: RNA-seq_51ms_2_0mm_a

description: RNA-seq, bhlh51-1 sterile anther, 2.0 mm, replicate 1


title: vehicle_rep2


title: RNA-seq_51ms_1_0mm_a

description: RNA-seq, bhlh51-1 sterile anther, 1.0 mm, replicate 1


title: Meningioma 103 (RNA-seq)

description:
Sex: 2
M103


title: LSD1i_rep1


title: Mesangial cell Control-3


title: Meningioma 102 (RNA-seq)

description:
Sex: 2
M102


title: vehicle_rep1


title: Mesangial cell Control-2


title: Meningioma 101 (RNA-seq)

description:
Sex: 2
M101


title: small RNA_HiII_3_0mm_2

description: sRNA-seq, HiII hybrid fertile anther, 3.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ103-12

value: BHLH122//BHLH122 BHLH51//BHLH51


title: Meningioma 108 (RNA-seq)

description:
Sex: 1
M108


title: small RNA_HiII_2_0mm_1

description: sRNA-seq, HiII hybrid fertile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ104-6


title: small RNA_HiII_3_0mm_1

description: sRNA-seq, HiII hybrid fertile anther, 3.0 mm, replicate 1


title: Control 1 Untreated single cell RNA

value: iPSC-derived cardiomyocytes, endothelial cells and fibroblasts


title: sh71_2

value: sh71 (LSD1 silencing)


title: Meningioma 10 (RNA-seq)

description:
Sex: 2
M10


title: small RNA_HiII_2_0mm_2

description: sRNA-seq, HiII hybrid fertile anther, 2.0 mm, replicate 2


title: sh71_1


title: Meningioma 107 (RNA-seq)

description:
Sex: 2
M107


title: Mesangial cell Control-1

value: Control


title: Podocyte ANGPT2 treatment-3

description: ANGPT2 treatment-3

source_name: Human podocyte cell line

growth_protocol: Immortalized human podocytes from Dr. Saleem M’s laboratory (University of Bristol, Bristol, UK) were cultured with RPMI1640 medium supplemented with 10% FBS, 1% Pen/Strep and 1% ITS at 33°C in 5% CO2 incubator for growth, followed by trypsinization, replating and culture at 37°C for 10 days to obtain differentiated cells.

treatment_protocol: Then the differentiated podocytes were either treated with 500 ng/ml recombinant ANGPT2 (MCE, HY-P7510) or left untreated with only vehicle for 24 hours.

value: Human podocyte cell line


title: shNT_2

value: shRNA non targeting


title: shNT_1


title: small RNA_HiII_1_5mm_1

description: sRNA-seq, HiII hybrid fertile anther, 1.5 mm, replicate 1


title: Podocyte ANGPT2 treatment-1

description: ANGPT2 treatment-1


title: Podocyte ANGPT2 treatment-2

description: ANGPT2 treatment-2


title: SK-N-Be2C TWIST1_KO, Clone 3, Batch 1 [BegT3_1]

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

data_processing:
fastq files were mapped with STAR version 2.5.2b on both the Human genome version Hg19 and the Mouse genome version Mm10, simultaneously. The following options were changed from the default parameters: --outSAMmultNmax 50; --outFilterMatchNminOverLread 0.4;   --quantMode TranscriptomeSAM.
Transcriptome annotations in gtf format for both organisms were downloaded from the gencode website (https://www.gencodegenes.org/). Reads mapped on either the Human or the Mouse transcriptome were then parsed and split in one file per organism with an in-house perl script. Reads with matches on both Human and Mouse were discarded from the Mouse file. Per-gene quantification was then calculated independently for each organism using rsem version 1.3.0.
Mouse and Human data were analyzed independently, but following the same protocol. Genes with a log2 (rpkm) value above 1 in at least one sample were kept
Differential analysis was performed using the raw data counts in DESeq2 package version 1.26.0. For each comparison, the cutoffs for fold-change and adjusted p-values to call differentially transcribed genes were set to 1 and 0.05, respectively
Genome_build: Hg19/Mm10
Supplementary_files_format_and_content: The two supplemental tab-delimited text files Hs_GeneMat_raw_counts.txt and Mm_GeneMat_raw_counts.txt contain the rsem raw counts for Homo sapiens and Mus musculus.

source_name: SK-N-Be2C TWIST1_KO Cell-line

growth_protocol: SK-N-Be2c either WT or TWIST1_KO cells have been cultured at the density of 2x10^5 cells/ml in DMEM containing 1% P/S and 10% FBS. SK-N-Be2c -derived xenograft have been obtained upon orthotopical injection of 5x10^5 cells in the left adrenal gland of mice. Xenograft have been grown since their size reached 1000 mm3.

extract_protocol:
Total RNA from cell lines and tumors was extracted using RNeasy or miRNeasy mini kit (Qiagen, Hilden, Germany), respectively according to manufacturer instructions. RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was verified using the Agilent 2100 Bioanalyzer system (Agilent Technologies).
RNAseq was performed at the iGE3 Genomics platform (University of Geneva). The total RNA ribo-zero gold kit from Illumina was used for the library preparation with 1 µg or 500 ng of total RNA as input for cells (n=3 biological replicates/group) and tumors (n=4/group), respectively. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on 1.5 lanes for cells and 1.5 lanes for tumors of a Single-read Illumina Flow cell. Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: cell-line

tag: sample type

value: cell line


title: Mesangial cell ANGPT2 treatment-1

description: ANGPT2 treatment-1


title: Podocyte Control-3


title: SK-N-Be2C TWIST1_KO, Clone 2, Batch 2 [BegT2_2]


title: Podocyte Control-2


title: small RNA_HiII_1_0mm_1

description: sRNA-seq, HiII hybrid fertile anther, 1.0 mm, replicate 1


title: small RNA_122ms_3mm_1

description: sRNA-seq, bhlh122-1 sterile anther, 3.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ105-8


title: inib_2_5 input

data_processing:
Basecalls was performed using CASAVA software v1.8 and quality check  performed with fastqc version 0.10
ChIP-seq reads were aligned to the hg18 genome assembly using bowtie v1.0.1 with the option (-m 1 –v 2)
peaks were called using MACS version 1.4.1 with threshold of 10-5. For LSD1 ChIP the threshold was set to 10-10
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing chromosome coordinates of peaks and MACS score

extract_protocol:
Cells were cross-linked in culture medium with 1% formaldehyde in PBS and the reaction was stopped after 10 min at RT by adding 0.125 M glycine for 5 min at 4°C. The cells were washed twice with PBS and collected by centrifugation. Pellets were stored at -80° in SDS buffer (50 mM Tris•HCl pH 8.1, 0.33% SDS, 150mM NaCl, 5 mM EDTA, and protease inhibitor cocktail). Fixed cells were resuspended in IP buffer (100mM tris ph 8.6 0.3% SDS 1.7% TRITON x-100 and 5mM EDTA). Chromatin was then fragmented to obtain ~200 bp in average size length by using a Branson Sonifier 250. Chromatin pre-clearing was obtained with protein A-sepharose beads (Amersham).  For histone modification 250ug of chromatin were incubated with 2ug of primary antibody; for LSD1, 2mg of chromatin were incubated with 10ug of primary antibody. Before IP 2.5% of input was stored prior to the decrosslinking procedure. After overnight IP,  protein G magnetic beads have been added to the samples and incubated for 4 hours.  Decrosslinking was performed for all the IP samples and corresponding inputs, overnight in 0.1%SDS and 0.1% NaCOH3. The day after, the enriched DNA was treated with proteinase K at 56°C for 40 min and purified with a DNA purification kit (Qiagen).
The obtained DNA was then quantified with Qubit and processed for ChIP-Seq library preparation (as described for the Illumina protocol). For libraries preparation, 2ng of immunoprecipitated DNA was used.

treatment_protocol: NB4 cells were plated at 500000 cells/ml and treted as indicated in each sample for 24 hours.

tag: antibody used


title: SK-N-Be2C TWIST1_KO, Clone 1, Batch 1 [BegT1_1]


title: CHIP_LSD1i


title: ChIP_LSD1_vehicle

value: vehicle (DMSO)


title: Meningioma 100 (RNA-seq)

description:
Sex: 2
M100

tag: age


title: small RNA_122ms_3mm_2

description: sRNA-seq, bhlh122-1 sterile anther, 3.0 mm, replicate 2

tag: tissue


title: small RNA_122ms_2mm_2

description: sRNA-seq, bhlh122-1 sterile anther, 2.0 mm, replicate 2

tag: Stage


title: Podocyte Control-1


title: H3K4me3_LSD1i


title: SK-N-Be2C TWIST1_KO, Clone 1, Batch 2 [BegT1_2]


title: small RNA_HiII_1_5mm_2

description: sRNA-seq, HiII hybrid fertile anther, 1.5 mm, replicate 2


title: DMSO input


title: small RNA_122ms_2mm_1

description: sRNA-seq, bhlh122-1 sterile anther, 2.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile siblingZQQ105-8


title: SK-N-Be2C WT, Clone 3, Batch 1 [BeC3_1]

source_name: SK-N-Be2C WT Cell-line

value: wild-type


title: SK-N-Be2C WT, Clone 3, Batch 2 [BeC3_2]


title: small RNA_122ms_1_5mm2

description: sRNA-seq, bhlh122-1 sterile anther, 1.5 mm, replicate 2


title: Meningioma 1 (RNA-seq)

description:
Sex: 1
M1

tag: institution


title: H3K4me3_DMSO


title: SK-N-Be2C WT, Clone 2, Batch 2 [BeC2_2]


title: small RNA_122ms_1_5mm1

description: sRNA-seq, bhlh122-1 sterile anther, 1.5 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ103-7


title: SK-N-Be2C WT, Clone 2, Batch 1 [BeC2_1]


title: H3K4me2_LSD1i


title: LSD1_ChIP_input


title: small RNA_122ms_1mm_3

description: sRNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling ZQQ106-11


title: H3K4me2_DMSO


title: SK-N-Be2C WT, Clone 1, Batch 2 [BeC1_2]


title: small RNA_122ms_1mm_2

description: sRNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 2


title: small RNA_122ms_1mm_1

description: sRNA-seq, bhlh122-1 sterile anther, 1.0 mm, replicate 1

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh122-1 sterile sibling, ZQQ106-12


title: Meningioma 6 BTI (scRNA-seq)

description:
Sex: 2
Gender: 3

data_processing:
Library demultiplexing, read alignment to the hg38 human reference genome, identification of empty droplets, and UMI quantification was performed using CellRanger v3.0.2
Single cell UMI count data were processed in R v3.6.1 with the Seurat v3.0.1 package using the sctransform workflow, with scaling based on regression of UMI count and percentage of reads attributed to mitochondrial genes per cell.
Genome_build: hg38
Supplementary_files_format_and_content: matrix.mtx.gz (Matrix table with the number of unique molecular identifiers for every feature (gene) by row and every barcode (cell) by column)
Supplementary_files_format_and_content: barcodes.tsv.gz (Sequences corresponding to every barcode in the matrix table)
Supplementary_files_format_and_content: features.tsv.gz (Sequences corresponding to every feature in the matrix table)

extract_protocol:
Fresh meningiomas were dissociated into single cells by mincing and then treating with collagenase, trypsin, and RBC lysis buffer. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.

value: meningioma brain-tumor interface


title: SK-N-Be2C TWIST1_KO, Clone 2, Batch 1 [BegT2_1]


title: small RNA_HiII_1_0mm_2

description: sRNA-seq, HiII hybrid fertile anther, 1.0 mm, replicate 2

source_name: Whole anthers, provided by Walbot lab at Stanford, fromHiII hybrid fertile silbing ZQQ106-6


title: small RNA_51ms_3_0mm_3

description: sRNA-seq, bhlh51-1 sterile anther, 3.0 mm, replicate 3

source_name: Whole anthers, provided by Walbot lab at Stanford, frombhlh51-1 sterile sibling ZQQ103-4


title: Meningioma 6 (scRNA-seq)

description:
Sex: 2
Gender: 3


title: SK-N-Be2C WT, Clone 1, Batch 1 [BeC1_1]


title: H3K4me1_DMSO


title: SK-N-Be2C TWIST1_KO, Xenograft 3 [TBegT3]

organism:
Homo sapiens
Mus musculus

source_name: SK-N-Be2C TWIST1_KO Xenograft

value: Tumor from Xenograft