title: Mated h90 fus1 III (F1III)

city: Lausanne

first: Aleksandar

last: Vjestica

state: Vaud

address: Genopode Building, University of Lausanne

department: Center for Integrative Genomics

institute: University of Lausanne

description: Library name: F1 III

data_processing:
QC performed with FastQC
trimming of low quality sequences performed with Trimmomatic
genome alignment performed with hisat2
conversion to BAM and indexing performed using samtools and bamtools
Assembly: ASM294v2.54
Supplementary files format and content: BAM files containing reads aligned to the genome

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Cells were grown exponentially in liquid MSL+N media.

extract_protocol:
Cells recovered from mating spots were resuspended in ice-cold DEPC-treated water, centrifuged at 1’000 g for 1 minute, the supernatant removed and cells snap-frozen in liquid nitrogen. Pellets were resuspended in 750 μL of extraction buffer (10 mM Tris-HCl, pH 7.5; 10 mM EDTA, pH 8.0; 0.5% SDS), mixed with an equal volume of acid-equilibrated phenol, and incubated at 65°C for 1 hour. The samples were cooled on ice and centrifuged at 16’000 g for 15 minutes at 4°C. The aqueous phase was sequentially extracted with phenol:chloroform:isoamyl alcohol (125:24:1; 77617-100ML, Merck, Darmstadt, Germany) and chloroform:isoamyl alcohol (24:1; 25666-100ML, Merck, Darmstadt, Germany), each using centrifugation at 16’000 g for 5 min at 4°C. RNA was precipitated at -20°C overnight using three volumes of absolute ethanol and 0.1 volumes of a 3M sodium acetate pH 5.2 solution, and recovered by centrifugation at 16’000 g for 10 min  at 4°C. The RNA pellet was washed with 70% ethanol pre-chilled to 4°C and re-suspended in DEPC-treated water. The RNA samples were further purified and subjected to DNAse treatment using the Monarch RNA purification kit (T2010S, New England Biolabs, Ipswich, USA), following manufacturer instructions. RNA samples were stored at -70°C until use.
Truseq Stranded RNA

treatment_protocol: Exponentially grown cells were diluted to density of O.D.600 = 1 and incubated at 30°C with 200 rpm agitation for 5 hours. The starved cells were collected by centrifugation, ~2·107 cells concentrated into 20 μL of media and spotted onto MSL-N solid media. After 10 hours of incubation at 25°C, mating efficiency reached approximately 80% and 6 mating spots (~1.2·108 cells) were harvested using inoculation loops, per biological replica (triplicates), for RNA extraction.

value: yeast

value: mated

tag: batch


title: liver biopsy [GSM5773950 re-analysis]

status: Public on Jul 03 2025

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: rejection archetype groups (nr,tcmr,nkrl,injury)

value: NKRL

tag: tissue

value: liver biopsy


title: ChIP for GFP in His2AvRFP; EGFP-Ez/+ (EGFP-Ez) embryos staged at NC14M replicate ID= rep2

type: SRA

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

country: USA

institute: Northwestern University

description:
Library name: EGFP-Ez_ChIP-GFP_NC14M_rep2
E(z) binding at NC14

library_source: genomic

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates
Duplicate-marked mapped reads were imported into R, discarding duplicates, and keeping only reads with map-quality scores of 10 or greater. Wiggle files were generated by calculating the average number of mapped reads within 10 bp windows, and normalizing to millions of reads in the overall sample. Peaks were called using MACS2. Broad polycomb domains were called using STAN.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: wiggle files for merged replicates are provided . Data represents counts per million normalized average reads per 10 bp genomic bin
Supplementary files format and content: Coverage files for merged replicates for all ChIP experiments are provided in bigwig format. Peak calls for Cg, GAF, Pho, and E(z) are provided in .bed format. Broad polycomb domains are provided in .bed format.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
For ChIP experiments, embryos were crosslinked (Heptane/PBS/formaldehyde, 15 minutes) and sorted by stage prior to homogenization in RIPA buffer and sonication. Sonicated chromatin samples were subjected to immunoprecipiation with the indicated antibodies.
ChIP libraries: following IP but prior to washes, antibody-chromatin complexes were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 40 minutes at 37 degrees C. Following tagmentation, beads were washed and subjected to PCR with barcoding primers (Buenrostro, 2013).

value: embryo

tag: genotype

value: His2AvRFP; EGFP-Ez/+

tag: chip antibody

value: GFP

tag: developmental stage


title: ChIP for GFP in His2AvRFP; EGFP-Ez/+ (EGFP-Ez) embryos staged at NC14M replicate ID= rep1

description:
Library name: EGFP-Ez_ChIP-GFP_NC14M_rep1
E(z) binding at NC14


title: milk somatic cells Polish White Improved goat_1

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

description: MSC_W_goat1 SRLV-seronegative goats (SRLV-SN)

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Capra hircus

source_name: milk somatic cells (MSC)

growth_protocol: not applicable

extract_protocol: isolation of total RNA from goat MSC  the RNeasy Lipid Tissue Mini Kit (Qiagen, USA); the RNA isolationfrom goat PNCB was conducted by using Total RNA mini Kit (A & A Biotechnology, POLAND)

treatment_protocol: MSC was protected with Qiazol reagent from the RNeasy Lipid Tissue Mini Kit Qiagen (Qiagen, USA); Blood from vein was mixed with erythrocyte lysis buffer RBCL and protected with fenozol from Total RNA mini Kit (A & A Biotechnology,POLAND)

tag: cell type

value: milk somatic cells (MSC)

tag: breed

value: female goat breed Polish White Improved the peak of 1st lactation

source_name: peripheral nuclear cells blood

value: peripheral nuclear cells

tag: sample type

value: common reference sample compsed of total RNAs isolated from peripheral nuclear cells blood  of  7 healthy goats in 4th lactation from both Polish breeds (PWI=4 & PFI=3) after the lactation cycle


title: Mated h90 fus1 II (F1II)

country: Switzerland

description: Library name: F1 II

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: Mated h90 fus1 I (F1I)

description: Library name: F1 I


title: liver biopsy [GSM5773952 re-analysis]

value: NR


title: liver biopsy [GSM5773956 re-analysis]

value: TCMR


title: Not mated heterothallic WT III (NMWT3)

description: Library name: NMWT3

value: nitrogen starved


title: ChIP for GFP in His2AvRFP; EGFP-Ez/+ (EGFP-Ez) embryos staged at NC14M replicate ID= rep3

description:
Library name: EGFP-Ez_ChIP-GFP_NC14M_rep3
E(z) binding at NC14


title: liver biopsy [GSM5773948 re-analysis]


title: ChIP for GFP in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep3

description:
Library name: EGFP-GAF_ChIP-GFP_NC14M_rep3
GAF binding at NC14

value: EGFP-GAF


title: D12

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

library_source: other

data_processing:
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1)
Pairwise alignmnet was conducted using blastn between the replicates from the same protein and between the replicates from the two proteins to evaluate for consistency and reliability between replicates.
Fastaptamer-Count tool in the FASTAptamer pipeline was used to count the reads for each sequence, normalize the read count for each sequence to reads per million (RPM), and rank order sequences by decreasing abundance.
The most abundant sequence was used as the seed sequence for the FASTAptamer-Cluster algorithm. This operation clustered sequences with an RPM ≥ 100 and a Levenshtein edit distance33 of ≤ 7 into the same cluster.FASTAptamer-Enrich was used to calculate a fold-enrichment for each sequence present in more than one sequencing round, with an RPM >1.2.
The mFold web server with default settings was used to predict RNA folding structures for the most enriched sequences. MEME was used to identify the top three protein binding motifs for the enriched sequences.
Supplementary files format and content: tab-delimited counts of each oligonucleotide found

molecule: other

organism: synthetic construct

source_name: not a cell: random 70-mer RNA library

extract_protocol:
RAPID-SELEX using PARP1 and MeCP2 and an RNA library (independent experiments for each protein) were used to select for RNAs that are high binders for this proteins. Proteins were bound to Ni-NTA-micro-columns and incubated with RNA library for 12 rounds. Each round consist of a non-amplification and an amplification cycles (after reverse transcribing of RNA to cDNA) to generate the selected RNAs with enriched specificity for next round of selection.
The RNA library was containing ~ 5 × 10^15 unique 120-mer sequences consisting of a random 70-mer flanked by constant regions at each end [5’ AAGCTTCGTCAAGTCTGCAGTGAA-N70-GAATTCGTAGATGTGGATCCATTCCC]. The RNA library contained (on average) of 4 to 6 copies of each unique sequence. RNAs from RAPID-SELEX rounds 3, 8, and 12, were cDNA converted and PCR amplified to form dsDNAs. These DNAs were subjected to to Illumina Hi-Seq 4000 platform according to the manufacturer’s instructions.

value: not a cell:random 70-mer RNA library

value: MECP2_rep2 _R12

tag: protein

tag: selex round


title: Not mated heterothallic WT II (NMWT2)

description: Library name: NMWT2

value: yeast


title: D10

value: MECP2_rep2 _R3


title: D11

value: MECP2_rep2 _R8


title: ChIP for GFP in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep1

description:
Library name: EGFP-GAF_ChIP-GFP_NC14M_rep1
GAF binding at NC14


title: ChIP for GFP in EGFP-GAF (EGFP-GAF) embryos staged at NC14M replicate ID= rep2

description:
Library name: EGFP-GAF_ChIP-GFP_NC14M_rep2
GAF binding at NC14


title: Not mated heterothallic WT I (NMWT1)

description: Library name: NMWT1


title: liver biopsy [GSM5773946 re-analysis]

value: liver biopsy


title: tuft cell, KO

city: Beijing

first: Jiali

last: Wang

address: Hai Dian

country: China

institute: Tsinghua University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads;  remove the contaminated reads for adapters and remove the low-quality reads.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HIAST2 v2.1.0.
we used HISAT to align the clean reads to the reference genome. We used Bowtie2 to aligh the clean reads to the reference genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM for each sample

organism: Mus musculus

source_name: small intestine

extract_protocol:
The RNA of sorted tuft cells  was extracted by TRIzol reagent (Invitrogen).
RNA-Seq library construction uses amplification of cDNA via SMART-SeqII combined with transposase-based library construction technique.

value: small intestine

value: tuft cells

value: Spibfl/flVillin-cre


title: D8

value: MECP2_rep1 _R8


title: liver biopsy [GSM5773945 re-analysis]


title: liver biopsy [GSM5773949 re-analysis]


title: tuft cell, WT

value: Spib+Villin-cre


title: D7

value: MECP2_rep1 _R3


title: ChIP for GFP in EGFP-Cg (EGFP-Cg) embryos staged at NC14 replicate ID= rep2

description:
Library name: EGFP-Cg_ChIP-GFP_NC14_rep2
Cg binding at NC14

value: embryo

value: EGFP-Cg

value: GFP


title: D6

value: PARP1_rep2 _R12


title: ChIP for GFP in Pho-sfGFP (Pho-sfGFP) embryos staged at NC14 replicate ID= rep2

description:
Library name: Pho-sfGFP_ChIP-GFP_NC14_rep2
Pho binding at NC14

value: Pho-sfGFP


title: Endometrial tissues, NER, rep2

city: Zhengzhou

first: Aiwu

last: Wei

address: No. 19, Renmin Road, Jinshui District

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

description: Library name: Samole 2

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and corresponding sequencing quality information.
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
Assembly: Rnor_6
Supplementary files format and content: diff_gene_of_all_groups.xlsx

organism: Rattus norvegicus

source_name: Uterus

growth_protocol: Female and male Sprague-Dawley (SD) rats (age 10 weeks) had free access to food and water. The rats were kept under temperature (23 ± 1°C), humidity (45%–55%), and 12 h light-dark cycle conditions.

extract_protocol:
Total RNA was extracted and RNA quality was assessed by agarose electrophoresis, Nanodrop and Agilent 5400.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The rats in the LER and LIG groups were given hydroxyurea solution (450 mg/kg/d) by gavage for 10 d and adrenaline (0.3 mg/kg/d) by subcutaneous injection from the 4th day to the 10th day.   The control group received intragastric administration of equal saline for 10 d and subcutaneous injection of equal saline from the 4th day to the 10th day. After model generation, the female rats in each group were mated with male rats at a ratio of 2:1 at 5 pm every day.    The following morning, the presence or absence of vaginal plugs was observed at 9 am.    The day on which a vaginal plug appeared was considered as the day 0.5 of gestation (GD 0.5).    For the LIG group,  40 mg/kg LIG was given daily by gavage to each rat starting at GD 0.5.    And the control and LER group received intragastric administration of equal olive oil

value: Uterus

value: olive oil


title: D5

value: not a cell:random 70-mer RNA library

value: PARP1_rep2 _R8


title: liver biopsy [GSM5773943 re-analysis]

value: NKRL


title: Tuft cells, Day14_1

value: wildtype

value: Heligmosomoid polygyrus infection


title: Tuft cells, Day14_2

value: small intestine

value: tuft cells


title: D9

value: MECP2_rep1 _R12


title: liver biopsy [GSM5773942 re-analysis]

value: TCMR

value: liver biopsy


title: Tuft cells, Day6_2


title: GAERS_G90

city: Boston

first: Shamsuddin

last: Bhuiyan

state: MA

address: 60 Fenwood Rd, 7006, Hale

institute: Harvard Medical School and Brigham & Women's Hospital

description: Library name: Chip176_G90

data_processing:
Aligned and quantified using FLAIR
Assembly: Rnor6.0
Supplementary files format and content: counts

source_name: Thalamus

extract_protocol:
Targeted amplification using Cacna1e primers
The generated Cacna1e gene specific amplicons were processed as per the Oxford Nanopore Technologies (ONT) SQK-LSK108 adapter ligation procedure. In brief, DNA amplicon molecules were treated to generate A-tailed molecules allowing the ligation of ONT specific adapter onto the amplicon ends. These adapted molecules were then run on the ONT MinION device and signal data captured for base calling over a 48hr period. Sequence data was generated from the raw captured data using ONT specific software (Guppy 3.4) on a GPU enabled desktop PC.

value: Thalamus


title: D3

value: PARP1_rep1 _R12


title: NEC_P10

description: Library name: Chip170_N10


title: D4

value: PARP1_rep2 _R3


title: D2

value: PARP1_rep1 _R8


title: ChIP for GFP in EGFP-Cg (EGFP-Cg) embryos staged at NC14 replicate ID= rep1

description:
Library name: EGFP-Cg_ChIP-GFP_NC14_rep1
Cg binding at NC14

value: embryo

value: EGFP-Cg

value: GFP


title: Tuft cells, Day0_1


title: liver biopsy [GSM5773940 re-analysis]

value: NR


title: Tuft cells, Day0_2


title: 0 Day Post-Spinal Cord Injury IP Replicate 1

city: Shanghai

first: Liming

last: Cheng

address: Siping Road No.1239

institute: Tongji University

description:
0d-1.txt
Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 24 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level”, “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA. Differentially m6A-methylated RNAs or differentially expressed RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation or expression pattern among samples.

source_name: 0 Day Post-Spinal Cord Injury Spinal Cord

label_protocol: The “IP” RNA and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

extract_protocol: 1-3 μg total RNA and m6A spike-in control mixture were added to 300 μL 1IP buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/μL RNase Inhibitor) containing 2 μg anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 L Dynabeads™ M-280 Sheep Anti-Rabbit IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 μL 1IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 μL 1IP buffer and twice with 500 μL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/μL RNase Inhibitor). The enriched RNA was eluted with 200 μL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

value: spinal cord

tag: fraction

value: m6A methylated RNAs


title: GAERS_G10

description: Library name: Chip160_G10


title: D1

value: not a cell:random 70-mer RNA library

value: PARP1_rep1 _R3


title: liver biopsy [GSM5773939 re-analysis]

value: Injury


title: Topmouth culter, day 7, Control2

status: Public on Jul 02 2025

city: Hangzhou

first: 劳

last: 霁晖

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District

department: College of life sciences

institute: Zhejiang University

description:
Library name: TCCF2022_CK_2
TPM_allsample.csv for all RNA-Seq sample

data_processing:
RNA-seq raw data was processed with Fastp (v 0.19.5).
TopHat (v 2.1.1) was used to align reads to NCBI reference genome L_crocea_2.0 (GCA_000972845.2,).
After alignment, transcripts were assembled using Cufflinks (v 2.2.1).
To annotate the gene functions, the integrated gene set was aligned against public databases, including NR, Swiss-Port, Pfam, EggNOG, GO and KEGG with BLAST+ (v 2.9.0).
Gene expression was measured using RSEM (v 1.3.3) with expression values normalized into transcripts per million (TPM).
Assembly: DEseq2 (v 1.24.0) was used for differential expression analysis. When the log2FC cutoff value above 1 and P-adjust <0.05, genes were considered differentially expressed.
Supplementary files format and content: L_crocea_2.0 (GCA_000972845.2)
Supplementary files format and content: CSV files include TPM values for each Sample

organism: Culter alburnus

growth_protocol: TCCF2022 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) ，5ng/ml bFGF and 1×PS in humidified atmosphere with 5% CO2 at 27℃

extract_protocol:
RNA was harvested using Trizoln Kit
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

treatment_protocol: On the basis of the original culture medium, TCCF2022 cells were added with or without 5μM Forskolin, and half of the solution was changed every 3 days.

tag: cell line

value: fibroblasts

value: WT

value: 7 Days


title: NEC_P90

description: Library name: Chip158_N90


title: liver biopsy [GSM5773938 re-analysis]

value: TCMR

value: liver biopsy


title: Topmouth culter, day 7, Forskolin1

description:
Library name: TCCF2022_F_1
TPM_allsample.csv for all RNA-Seq sample

value: 5μM Forskolin


title: ChIP for GFP in Pho-sfGFP (Pho-sfGFP) embryos staged at NC14 replicate ID= rep1

description:
Library name: Pho-sfGFP_ChIP-GFP_NC14_rep1
Pho binding at NC14

value: Pho-sfGFP


title: Sample8-Stool-P2

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

description: Library name: Sample8

data_processing:
Data analysis was based on the pipeline described by Gömer et al. (29). Briefly, raw reads were trimmed using Trimmomatic 0.39 and quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Subsequently, a consensus reference sequence was generated from plasma samples by first mapping sample reads to a HEV-3c reference sequence (accession: FJ705359) and subsequently generating the consensus sequence using Sam2Consensus v2.0 (https://github.com/vbsreenu/Sam2Consensus). These sequences were subsequently utilised in downstream analysis as a reference for mapping via Tanoti and variant calling using Diversitools (https://github.com/josephhughes/DiversiTools) and vNvS tools (https://github.com/rjorton/vnvs). Amino acid substitutions were visualised on an alpha fold 2-based model, which employed the HEV-3 Kernow/p6 genomic content. The graphical visualization of the model was conducted in ChimeraX v1.7. Haplotypes were generated using CliqueSNV (https://github.com/vtsyvina/CliqueSNV), which were used for phylogenetic and genome linkage analysis. Phylogenetic trees were computed with IQ-tree2 (30) using the option best modelfind and 1000 bootstraps. To identify iSNVs for each haplotype, the patient's plasma consensus sequence was used as a reference sequence. Phylogenetic trees were visualised with in-house R scripts, utilising the following packages: tidyverse, tibble, treeio, ggtree, phytools and cowplot.
Assembly: Patient specific consensus mapping
Supplementary files format and content: .bam files

organism: Hepatitis E virus

source_name: Stool

extract_protocol:
Total RNA was extracted from plasma, stool suspension or urine using the Cobas AmpliPrep Total Nucleic Acid Isolation Kit (Roche, Basel, Switzerland).
Complementary DNA (cDNA) synthesis and amplicon generation were conducted in accordance with Todt et al. (6). Briefly, cDNA was synthesised from 2 to 8 μL of purified total RNA using the SuperScript III first-strand synthesis system (Life Technologies, Carlsbad, CA, USA). Amplicons were generated in a two-step touchdown PCR using TaKaRa Ex Taq Hot Start Version polymerase (Dalian, China). The NEBNext Ultra II FS DNA Library Preparation Kit (NEB) was used to prepare sequencing libraries according to the manufacturer's recommendations. Library quality was determined with the Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) and a 2100 Bioanalyzer Instrument (Agilent Technologies). All samples were normalised and quantified using the KAPA Library Quantification Kit for Illumina (Kapa Biosystems, Wilmington, MA, USA). Sequencing was conducted on a Illumina MiSeq using a 2 × 300 base pair (bp) paired-end sequencing protocol.

value: Stool

tag: donor


title: liver biopsy [GSM5773947 re-analysis]


title: liver biopsy [GSM5773936 re-analysis]


title: liver biopsy [GSM5773944 re-analysis]


title: Sample38-Stool-P1

description: Library name: Sample38


title: Topmouth culter, day 7, Forskolin3

description:
Library name: TCCF2022_F_3
TPM_allsample.csv for all RNA-Seq sample


title: liver biopsy [GSM5773937 re-analysis]

value: NKRL


title: Topmouth culter, day 7, Control3

description:
Library name: TCCF2022_CK_3
TPM_allsample.csv for all RNA-Seq sample


title: Topmouth culter, day 7, Forskolin2

description:
Library name: TCCF2022_F_2
TPM_allsample.csv for all RNA-Seq sample


title: Topmouth culter, day 7, Control1

description:
Library name: TCCF2022_CK_1
TPM_allsample.csv for all RNA-Seq sample


title: Sample5-Urine-P1

description: Library name: Sample5

source_name: Urine

value: Urine


title: liver biopsy [GSM5773941 re-analysis]


title: Sample4-Plasma-P2

description: Library name: Sample4

source_name: Plasma

value: Plasma


title: Sample26-Urine-P2

description: Library name: Sample26


title: Sample35-Stool-P2

description: Library name: Sample35


title: Sample30-Plasma-P2

description: Library name: Sample30


title: Sample1-Urine-P2

description: Library name: Sample1


title: Sample28-Plasma-P1

description: Library name: Sample28


title: Sample11-Stool-P1

description: Library name: Sample11


title: MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep3

city: New York

first: Yang

last: Luo

state: NY

address: 408 E 69th St

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

description: Library name: MCF7_shKDM6A_HA-KDM6A-NU_rep3

data_processing:
Read count extraction and quantification were performed using Salmon (v1.10.1) and imported with tximport (v1.22.0).
Differential gene expression analysis was performed with DESeq2 in R or Galaxy.
Assembly: hg38
Supplementary files format and content: csv files include DESeq2 analysis of pairwise comparison of MYC samples and of shCtrl vs shKDM6A MCF7 samples.

growth_protocol: U2OS and MCF7 cells were maintained in DMEM high glucose media supplemented with 10% fetal bovine serum (FBS) and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using TRIzol, treated with DNase I (RNase free), and precipitated with sodium acetate before submission for sequencing.
RNA libraries for RNA-seq were prepared using NEB Next Ultra II RNA library prep kit with PolyA selection following manufacturer's protocol.

treatment_protocol:
U2OS cells were transfected with the cDNA vectors containing MYC coding sequence (-NU) or MYC coding sequence and its 3′UTR (-U). The GFP+ cells were sorted by FACS 24 hours after transfection.
MCF7 cells with stable KDM6A knockdown were generated and transfected with cDNA vectors containing the KDM6A (encoding UTX) coding sequence only (-NU) or containing the KDM6A coding sequence and its 3′UTR (-U). Cells were harvested 24 hours after transfection, side by side with the control MCF7 cells that express scrambled shRNA.

value: breast adenocarcinoma cell line

value: KDM6A knockdown

value: HA-KDM6A-NU transfection


title: MCF7 cells, shKDM6A + HA-KDM6A-U, Rep3

description: Library name: MCF7_shKDM6A_HA-KDM6A-U_rep3

value: HA-KDM6A-U transfection


title: MCF7 cells, shKDM6A + HA-KDM6A-U, Rep2

description: Library name: MCF7_shKDM6A_HA-KDM6A-U_rep2


title: MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep2

description: Library name: MCF7_shKDM6A_HA-KDM6A-NU_rep2


title: MCF7 cells, shKDM6A + HA-KDM6A-NU, Rep1

description: Library name: MCF7_shKDM6A_HA-KDM6A-NU_rep1


title: MCF7 cells, shCtrl, Rep3

description:
Library name: MCF7_shCtrl_rep3
log2FC showing changes from shKDM6A to shCtrl


title: MCF7 cells, shKDM6A, Rep1

description:
Library name: MCF7_shKDM6A_rep1
log2FC showing changes from shKDM6A to shCtrl


title: MCF7 cells, shKDM6A, Rep2

description:
Library name: MCF7_shKDM6A_rep2
log2FC showing changes from shKDM6A to shCtrl


title: MCF7 cells, shCtrl, Rep2

description:
Library name: MCF7_shCtrl_rep2
log2FC showing changes from shKDM6A to shCtrl


title: MCF7 cells, shKDM6A, Rep3

description:
Library name: MCF7_shKDM6A_rep3
log2FC showing changes from shKDM6A to shCtrl


title: Sample31-Urine-P1

description: Library name: Sample31


title: SafeHarbor_SafeHarbor_Control_exp_8_replicate_2

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

description: Library name: QJ118

data_processing:
Trimming with cutadapt
algnment to hg38 with STAR
Duplicates removed with picard tools MarkDuplicates
Counts generated with htseq-count
Assembly: hg38
Supplementary files format and content: CombinedCounts.csv; count matrix showing the raw data for each sample

source_name: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2

growth_protocol: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2 (Product Code JIPSC002072) iPSCs (iTF-iPSCs) were obtained from The Jackson Laboratory. iPSCs were maintained in mTeSR Plus Basal Medium (StemCell; Cat. No. 100-0276) on cell culture dishes pre-treated with Growth Factor Reduced, LDEV-free Matrigel Basement Membrane Matrix (Corning; Cat. No. 354230) diluted 1:100 in phenol-free DMEM/F12 basal medium (ThermoFisher; Cat. No. 11039021)

extract_protocol:
Norgen Total RNA Purification kit (Norgen; Cat. No. 37500) with the RNase-DNase I kit (Norgen; Cat. No. 25720)
Eukaryotic mRNA library preparation with poly A enrichment

treatment_protocol: iPSC cells were treated with day 0 differentiation (Essential 8 Basal Medium [ThermoFisher; Cat. No. A1517001] + 10 M Y-27632 dihydrochloride ROCK Inhibitor [StemCell; Cat. No. 72304] + 2g/mL Doxycycline [StemCell; Cat. No. 72742]. On day 2, medium was replaced with day 2 differentiation medium containing Advanced DMEM/F12 Medium as a base medium containing the following: 1X GlutaMAX (ThermoFisher; Cat. No. 35050061), 2μg/mL Doxycycline, 100 ng/mL Human IL-34 (Peprotech; Cat. No. 200-34), and 10 ng/mL Human GM-CSF (Peprotech; Cat. No. 300-03). On day 4, the medium was replaced with iTF-Microglia medium, containing Advanced DMEM/F12 (ThermoFisher; Cat. No. 12634010) as a base medium and the following: 1X GlutaMAX, 2μg/mL Doxycycline, 100 ng/mL Human IL-34, 10n/mL Human GM-CSF, 50 ng/mL Human M-CSF (Peprotech; Cat. No. 300-25), and 50 ng/mL Human TGFB1 (Peprotech; Cat. No. 100-21C). Cells were then transduced with lentivirus expreessing gRNAs

value: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2

value: iPSC

value: Doxycycline


title: SafeHarbor_SafeHarbor_Control_exp_8_replicate_1

description: Library name: QJ117


title: SafeHarbor_SafeHarbor_Control_exp_7_replicate_2

description: Library name: QJ116


title: MCF7 cells, shCtrl, Rep1

description:
Library name: MCF7_shCtrl_rep1
log2FC showing changes from shKDM6A to shCtrl

value: WT


title: SafeHarbor_SafeHarbor_Control_exp_7_replicate_1

description: Library name: QJ115


title: SafeHarbor_SafeHarbor_Control_exp_3_replicate_2

description: Library name: QJ110


title: SafeHarbor_SafeHarbor_Control_exp_4_replicate_1

description: Library name: QJ111


title: rs6509201_EXOC3L2_Variant_exp_8_replicate_2

description: Library name: QJ108


title: SafeHarbor_SafeHarbor_Control_exp_3_replicate_1

description: Library name: QJ109


title: rs6509201_EXOC3L2_Variant_exp_8_replicate_1

description: Library name: QJ107


title: sci-Plex-SHP2-Q510

first: Ross

middle: M

last: Giglio

institute: Columbia University

description:
Library name: Sample 2
sci-Plex transcriptomic profiling of SHP2 Q510 variants in HEK 293 cells

library_source: transcriptomic single cell

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in our manuscript as well as in Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq). Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 1, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only single hashes were used in these experiments). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out.txt files) for each nuclear transcriptome in the experiment. Tab-delimited columns of hashTable.out.txt files correspond to a sample id, the cell barcode identified for that hash, a "_" delimited string with condition metadata, an axis id for each hash (not used in these experiments), and umi counts for each hash. The first tab-delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. The first "_" delimited string corresponds to the SHP2 variant, the second corresponds to the EGF concentration, and the third corresponds to the combination of hash plate (e.g. 01, 02) and hash well e.g. (A01, B01). The hash well also corresponds to the orientation of the cells position for drugging. The associated CellLine.RT.Plate.csv file contains information for timepoint of harvesting post-EGF stimulation.
Assembly: GrCh38
Supplementary files format and content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: kindey, embryo

growth_protocol: Cells were cultured in a 37 °C tissue culture incubator with 5% CO2. Cells were discarded by passage 25 and tested for mycoplasma every 3 months. HEK 293 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. HEK 293 SHP2 knock-out cells were grown in DMEM with 10% FBS.

extract_protocol:
24 hours hours after drug exposure, cells were harvested following the sci-Plex protocols (Srivatsan, McFaline-Figueroa, Ramani et al. 2020 Science) as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
sci-RNA-seq3: Nuclei were subjected to a modified version of the three-level sci-RNA-seq described in Cao et al. 2019 Nature 566(7745) p. 496-502 that incorporates random hexamer priming as in Sziraki et al. 2023 Nature Genetics and Giglio et al. 2024 bioRxiv, see methods.

treatment_protocol: 10E6 HEK 293 SHP2KO cells were seeded in a 6-well plate, and transfected 24 hours later with 2 μg DNA in 200 μL empty DMEM using 6 μL of polyethylenimine (PEI). Early the next morning, each well was trypsinized and reseeded into a 96-well plate to a final density of 10,000 cells per well. 12 hours after re-seeding, cells were checked for adherence and culture media was aspirated. Cells were serum- starved overnight in DMEM + 0.2%FBS. After 12 hours of serum-starvation, EGF was added to the cells in DMEM + 0.2% FBS to a final concentration of: 1000 ng/mL, 500 ng/mL, 250 ng/mL, 100 ng/mL, 50 ng/mL, 25 ng/mL, 12.5 ng/mL, 0 ng/mL (unstimulated).

value: kindey, embryo

value: HEK 293

value: epithelial

value: SHP2 KO

value: EGF stimulation


title: MCF7 cells, shKDM6A + HA-KDM6A-U, Rep1

description: Library name: MCF7_shKDM6A_HA-KDM6A-U_rep1


title: SafeHarbor_SafeHarbor_Control_exp_4_replicate_2

description: Library name: QJ112


title: rs6509201_EXOC3L2_Variant_exp_6_replicate_1

description: Library name: QJ105


title: EXOC3L2_EXOC3L2_Promoter_exp_8_replicate_2

description: Library name: QJ104


title: EXOC3L2_EXOC3L2_Promoter_exp_6_replicate_1

description: Library name: QJ101


title: EXOC3L2_EXOC3L2_Promoter_exp_6_replicate_2

description: Library name: QJ102


title: rs6979218_SPDYE3_Variant_exp_6_replicate_2

description: Library name: QJ98


title: rs6979218_SPDYE3_Variant_exp_8_replicate_2

description: Library name: QJ100


title: EXOC3L2_EXOC3L2_Promoter_exp_8_replicate_1

description: Library name: QJ103


title: ZNF594_ZNF594_Promoter_exp_4_replicate_2

description: Library name: QJ86


title: SPDYE3_SPDYE3_Promoter_exp_7_replicate_2

description: Library name: QJ94


title: rs77972827_ZNF594_Variant_exp_6_replicate_2

description: Library name: QJ92


title: ZNF594_ZNF594_Promoter_exp_4_replicate_1

description: Library name: QJ85


title: ZYX_ZYX_Promoter_exp_4_replicate_2

description: Library name: QJ79


title: rs12703526_EPHA1,ZYX_Variant_exp_3_replicate_1

description: Library name: QJ82


title: ZNF594_ZNF594_Promoter_exp_6_replicate_2

description: Library name: QJ88


title: SPDYE3_SPDYE3_Promoter_exp_8_replicate_1

description: Library name: QJ95


title: SPDYE3_SPDYE3_Promoter_exp_8_replicate_2

description: Library name: QJ96


title: ZNF594_ZNF594_Promoter_exp_6_replicate_1

description: Library name: QJ87


title: rs77972827_ZNF594_Variant_exp_4_replicate_1

description: Library name: QJ89


title: rs6979218_SPDYE3_Variant_exp_6_replicate_1

description: Library name: QJ97


title: rs77972827_ZNF594_Variant_exp_4_replicate_2

description: Library name: QJ90


title: rs12703526_EPHA1,ZYX_Variant_exp_5_replicate_2

description: Library name: QJ84


title: SPDYE3_SPDYE3_Promoter_exp_7_replicate_1

description: Library name: QJ93


title: rs12703526_EPHA1,ZYX_Variant_exp_3_replicate_2

description: Library name: QJ83


title: ZYX_ZYX_Promoter_exp_6_replicate_2

description: Library name: QJ81


title: rs77972827_ZNF594_Variant_exp_6_replicate_1

description: Library name: QJ91


title: ZYX_ZYX_Promoter_exp_4_replicate_1

description: Library name: QJ78


title: rs6509201_EXOC3L2_Variant_exp_6_replicate_2

description: Library name: QJ106


title: rs6979218_SPDYE3_Variant_exp_8_replicate_1

description: Library name: QJ99


title: EPHA1_EPHA1_Promoter_exp_6_replicate_1

description: Library name: QJ77


title: rs72838287_BIN1_Variant_exp_7_replicate_1

description: Library name: QJ73


title: rs72838287_BIN1_Variant_exp_3_replicate_2

description: Library name: QJ72


title: rs72838287_BIN1_Variant_exp_7_replicate_2

description: Library name: QJ74


title: EPHA1_EPHA1_Promoter_exp_4_replicate_2

description: Library name: QJ76


title: rs72838287_BIN1_Variant_exp_3_replicate_1

description: Library name: QJ71


title: ZYX_ZYX_Promoter_exp_6_replicate_1

description: Library name: QJ80


title: BIN1_BIN1_Promoter_exp_3_replicate_2

description: Library name: QJ67


title: BIN1_BIN1_Promoter_exp_7_replicate_1

description: Library name: QJ69


title: BIN1_BIN1_Promoter_exp_7_replicate_2

description: Library name: QJ70


title: rs13230744_STAG3_Variant_exp_5_replicate_2

description: Library name: QJ63


title: BIN1_BIN1_Promoter_exp_5_replicate_2

description: Library name: QJ68


title: rs13230744_STAG3_Variant_exp_7_replicate_1

description: Library name: QJ64


title: BIN1_BIN1_Promoter_exp_3_replicate_1

description: Library name: QJ66


title: STAG3_STAG3_Promoter_exp_7_replicate_2

description: Library name: QJ60


title: STAG3_STAG3_Promoter_exp_5_replicate_2

description: Library name: QJ58


title: STAG3_STAG3_Promoter_exp_3_replicate_2

description: Library name: QJ57


title: rs184017_APOE_Variant_exp_6_replicate_2

description: Library name: QJ55


title: rs184017_APOE_Variant_exp_6_replicate_1

description: Library name: QJ54


title: rs13230744_STAG3_Variant_exp_7_replicate_2

description: Library name: QJ65


title: EPHA1_EPHA1_Promoter_exp_4_replicate_1

description: Library name: QJ75


title: APOE_APOE_Promoter_exp_8_replicate_1

description: Library name: QJ46


title: STAG3_STAG3_Promoter_exp_3_replicate_1

description: Library name: QJ56


title: APOE_APOE_Promoter_exp_7_replicate_2

description: Library name: QJ45


title: rs184017_APOE_Variant_exp_4_replicate_1

description: Library name: QJ52


title: STAG3_STAG3_Promoter_exp_7_replicate_1

description: Library name: QJ59


title: rs12721109_APOE_Variant_exp_8_replicate_2

description: Library name: QJ51


title: rs13230744_STAG3_Variant_exp_3_replicate_1

description: Library name: QJ61


title: rs184017_APOE_Variant_exp_4_replicate_2

description: Library name: QJ53


title: rs12721109_APOE_Variant_exp_8_replicate_1

description: Library name: QJ50


title: rs12721109_APOE_Variant_exp_7_replicate_1

description: Library name: QJ48


title: APOE_APOE_Promoter_exp_7_replicate_1

description: Library name: QJ44


title: APOE_APOE_Promoter_exp_8_replicate_2

description: Library name: QJ47


title: APOE_APOE_Promoter_exp_6_replicate_2

description: Library name: QJ43


title: APOE_APOE_Promoter_exp_6_replicate_1

description: Library name: QJ42


title: rs13230744_STAG3_Variant_exp_3_replicate_2

description: Library name: QJ62


title: rs72847948_HLA-DRB1_Variant_exp_6_replicate_2

description: Library name: QJ39


title: APOE_APOE_Promoter_exp_4_replicate_2

description: Library name: QJ41


title: APOE_APOE_Promoter_exp_4_replicate_1

description: Library name: QJ40


title: rs12721109_APOE_Variant_exp_7_replicate_2

description: Library name: QJ49


title: rs9271607_HLA-DRB1_Variant_exp_6_replicate_2

description: Library name: QJ35


title: rs72847948_HLA-DRB1_Variant_exp_4_replicate_2

description: Library name: QJ37


title: rs9271607_HLA-DRB1_Variant_exp_6_replicate_1

description: Library name: QJ34


title: rs9271607_HLA-DRB1_Variant_exp_4_replicate_2

description: Library name: QJ33


title: rs72847948_HLA-DRB1_Variant_exp_4_replicate_1

description: Library name: QJ36


title: rs28732235_HLA-DRB1_Variant_exp_6_replicate_2

description: Library name: QJ31


title: rs28732235_HLA-DRB1_Variant_exp_4_replicate_2

description: Library name: QJ29


title: rs28732235_HLA-DRB1_Variant_exp_6_replicate_1

description: Library name: QJ30


title: rs9270887_HLA-DRB1_Variant_exp_3_replicate_2

description: Library name: QJ25


title: rs9270887_HLA-DRB1_Variant_exp_8_replicate_1

description: Library name: QJ27


title: rs9270887_HLA-DRB1_Variant_exp_8_replicate_2

description: Library name: QJ28


title: rs9271176_HLA-DRB1_Variant_exp_8_replicate_2

description: Library name: QJ23


title: rs9270887_HLA-DRB1_Variant_exp_5_replicate_2

description: Library name: QJ26


title: rs9271176_HLA-DRB1_Variant_exp_3_replicate_2

description: Library name: QJ21


title: rs9270887_HLA-DRB1_Variant_exp_3_replicate_1

description: Library name: QJ24


title: rs9271176_HLA-DRB1_Variant_exp_8_replicate_1

description: Library name: QJ22


title: rs9271176_HLA-DRB1_Variant_exp_3_replicate_1

description: Library name: QJ20


title: HLA-DRB1_HLA-DRB1_Promoter_exp_8_replicate_1

description: Library name: QJ18


title: HLA-DRB1_HLA-DRB1_Promoter_exp_5_replicate_2

description: Library name: QJ17


title: HLA-DRB1_HLA-DRB1_Promoter_exp_3_replicate_2

description: Library name: QJ16


title: HLA-DRB1_HLA-DRB1_Promoter_exp_8_replicate_2

description: Library name: QJ19


title: rs72847948_HLA-DRB1_Variant_exp_6_replicate_1

description: Library name: QJ38


title: rs9271607_HLA-DRB1_Variant_exp_4_replicate_1

description: Library name: QJ32


title: HLA-DRB1_HLA-DRB1_Promoter_exp_3_replicate_1

description: Library name: QJ15


title: rs4575098_ADAMTS4,FCGR3B_Variant_exp_7_replicate_2

description: Library name: QJ14


title: rs4575098_ADAMTS4,FCGR3B_Variant_exp_3_replicate_1

description: Library name: QJ11


title: rs4575098_ADAMTS4,FCGR3B_Variant_exp_3_replicate_2

description: Library name: QJ12


title: FCGR3B_FCGR3B_Promoter_exp_7_replicate_2

description: Library name: QJ8


title: FCGR3B_FCGR3B_Promoter_exp_8_replicate_2

description: Library name: QJ10


title: FCGR3B_FCGR3B_Promoter_exp_8_replicate_1

description: Library name: QJ9


title: ADAMTS4_ADAMTS4_Promoter_exp_7_replicate_1

description: Library name: QJ5


title: rs4575098_ADAMTS4,FCGR3B_Variant_exp_7_replicate_1

description: Library name: QJ13


title: FCGR3B_FCGR3B_Promoter_exp_7_replicate_1

description: Library name: QJ7


title: ADAMTS4_ADAMTS4_Promoter_exp_7_replicate_2

description: Library name: QJ6


title: ADAMTS4_ADAMTS4_Promoter_exp_3_replicate_2

description: Library name: QJ2


title: ADAMTS4_ADAMTS4_Promoter_exp_5_replicate_1

description: Library name: QJ3


title: Macrophage, 14P TAM, rep 4

city: Birmingham

first: Christopher

middle: D

last: Willey

state: AL

address: 1700 6th Avenue South

department: Radiation Oncology

institute: University of Alabama at Birmingham

description: Library name: TAM_14P_1031

data_processing:
Sequencing was performed using biological quadruplicate for each polarization state on a NovaSeq X Plus Series using 150bp paired end reads at 150M read depth.
Assembly: Reads were aligned to the human genome Gencode vH43 using STAR (2.7.10b). BAM files were indexed with Samtools (v1.17). Aligned transcripts were quantified using Salmon (v1.10).
Supplementary files format and content: Quantified Salmon reads are provided as a raw counts matrix.

source_name: primary

growth_protocol: Cell culture Patient-derived xenograft (PDX) media: Dulbecco's Modified Eagle Medium (DMEM)/F12 50/50 (#10-090-CV, Corning, USA), B27 supplement minus Vitamin A (50X) (#12587010, Gibco, USA), 1% penicillin-streptomycin (#30-001-CI, Corning, USA), 1% sodium pyruvate (#5000CI, Corning, USA), EGF (20 ng/mL) (#PHG0311, Gibco, USA), FGF (20 ng/mL) (#PHG0261, Gibco, USA). TheraPEAK™ X-VIVO™-15 Serum-free Hematopoietic Cell Medium (X-Vivo): TheraPEAK™ X-VIVO™-15 Serum-free Hematopoietic Cell Medium (#BEBP02-055Q, Lonza, Switzerland) supplemented with 1% GlutaMAX (#35050-061, Gibco, USA), 1% penicillin-streptomycin (#30-001-CI, Corning, USA), and 1% sodium pyruvate (#5000CI, Corning, USA).  GBM patient-derived xenolines. The JX14P xenoline was originally obtained from Mayo Clinic and maintained in the UAB Brain Tumor Model Core and was approved for use on a UAB IRB approved protocol (IRB-300002910). The matched acquired radiation-resistant PDX line (JX14P-RT) development has been previously described [43, 44]. PDX authentication is routinely confirmed using short tandem repeat (STR). Cell lines are maintained in PDX media as defined above.  Heat-inactivation of human serum Matched fresh whole blood was collected in serum clot activator tubes and allowed to clot for an hour. Afterwards, the tubes were centrifuged at 650 x g for 10 minutes, and the serum was collected. The serum was then incubated at 56°C for 30 minutes to heat-inactivate complement factors.  PBMC isolation and macrophage differentiation Up to 15 mL of Fresh whole blood from healthy donors was collected in EDTA tubes and diluted with 15 mL phosphate-buffered saline (PBS) in a 50 mL conical tube. 10 mL of Lymphoprep (#18060, StemCell Technologies, Canada) was carefully layered underneath using a 10 mL serological pipette. The tubes were centrifuged at 650 x g for 30 minutes with no brake. The buffy coat was collected and transferred to a new 50 mL tube containing RPMI media (#A1049101, Gibco, USA), then centrifuged for 5 minutes at 650 x g to pellet the cells. The pellet was washed twice with PBS and plated in a 15 cm2 dish with RPMI 1640 supplemented with 10% matched donor serum and 50 ng/mL human M-CSF (#11792-HNAH1, SinoBiological, China). The media was replenished with 50 ng/mL of M-CSF on days 3 and 5. On day 7, the cells were washed three times with PBS and lifted for downstream experiments. After replating, the cells were cultured in a 1:1 mixture of PDX and X-VIVO media supplemented with 25 ng/mL M-CSF.

extract_protocol:
5 x 105 PBMC-derived Macrophages were plated in a 6-well plate. Afterwards, they were either maintained as resting, M0, or polarized towards M1, M2, JX14P-TAM, or JX14P-RT TAM states. Total RNA was extracted using a Qiagen RNeasy mini kit (#74104, Qiagen, Netherlands).
Samples were submitted to Novogene (Novogene Co., Ltd., Beijing, China) for DNase digestion, quality control assessment, library preparation, and sequencing. RNA Integrity was assessed using RNA ScreenTape (Agilent Technologies TapeStation), with all RNA integrity numbers greater than 9.0. Ribosomal RNA was depleted before conducting stranded library preparation.

treatment_protocol: M1 polarization Resting macrophages were stimulated with 20 ng/mL IFNγ (#300-02-500UG, Gibco, USA) and 1 µg/mL of lipopolysaccharide (#00-4976-03, ThermoFisher, USA) for 24 hours to induce a pro-inflammatory phenotype. M2 polarization Resting macrophages were stimulated with 20 ng/mL of IL-4 (204-IL, R&D Systems, USA) and IL-13 (#213-ILB, R&D Systems, USA) for 72 hours to induce an anti-inflammatory phenotype. TAM polarization Resting macrophages were indirectly co-cultured with GBM PDX xenolines using transwell inserts with 3 µm pores (#353096, Corning, USA) for 72 hours, as previously described [45]. Macrophages were seeded in the lower well and GBM was seeded in the upper insert.

value: Macrophage

tag: ifny conc_ng_per_ml

tag: lps conc_ug_per_ml

tag: il-4 conc_ng_per_ml

tag: il-13 conc_ng_per_ml

tag: polarization start

tag: expt start_date

tag: serum

tag: conc

tag: rin

tag: prep date

tag: expt type

value: novel


title: Macrophage, M2, rep 4

description: Library name: M2_1031

tag: cell type

value: classical


title: Macrophage, M1, rep 4

description: Library name: M1_1031


title: Macrophage, 14P-RT TAM, rep 4

description: Library name: TAM14PRT1031


title: Macrophage, 14P-RT TAM, rep 3

description: Library name: TAM14PRT_968


title: Macrophage, 14P TAM, rep 3

description: Library name: TAM_14P_968


title: ADAMTS4_ADAMTS4_Promoter_exp_3_replicate_1

description: Library name: QJ1

tag: genotype

tag: treatment


title: Macrophage, M2, rep 3

description: Library name: M2_968


title: Macrophage, M0, rep 4

description: Library name: M0_1031

value: baseline


title: Macrophage, M0, rep 3

description: Library name: M0_968


title: Macrophage, M1, rep 3

description: Library name: M1_968


title: Macrophage, 14P-RT TAM, rep 2

description: Library name: TAM14PRT_258


title: Tuft cells, Day6_1

tag: tissue

value: small intestine

value: tuft cells

value: wildtype

value: Heligmosomoid polygyrus infection


title: Macrophage, 14P TAM, rep 2

description: Library name: TAM_14P_258


title: ADAMTS4_ADAMTS4_Promoter_exp_5_replicate_2

description: Library name: QJ4

tag: cell line

value: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2


title: Macrophage, M2, rep 2

description: Library name: M2_258


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 5, rep 4

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

institute: University of Manitoba

description: Library name: D40.s5.r4

data_processing:
Reads were aligned with HISAT2 (Kim et al., 2019), v2.2.1, paired-end mode
Gene counts were quantified using featureCounts (Liao et al., 2014), v2.0.6, paired-end mode, reverse stranded
Raw gene counts were batch corrected with ComBat-seq (Zhang et al., 2020), correcting for both water status (well-watered vs growth-limiting drought) and temperature (30°C vs 40°C)
For FPKMs, mean fragment size was calculated with Picard, v3.1.0, and FPKM values were then calculated with countToFPKM R package (Alhendi, 2019), v1.0
Assembly: MSU release 7.0 Oryza sativa Nipponbare reference genome (Ouyang et al., 2007; Kawahara et al., 2013)
Supplementary files format and content: 2025.Robertson_Wilkins.RawGeneCounts.csv: csv file containing raw gene counts of all genes for each sample (counted with featureCounts)
Supplementary files format and content: 2025.Robertson_Wilkins.BatchCorrectedGeneCounts.csv: csv file containing batch corrected raw counts of all genes for each sample (adjusted with ComBat-seq R package)
Supplementary files format and content: 2025.Robertson_Wilkins.BatchCorrectedFPKM.csv: csv file containing batch corrected FPKM counts of all genes for each sample (fragment size calculated with Picard, FPKMs calculated with countToFPKM R package (Alhendi, 2019))

organism: Oryza sativa

source_name: Mature 3rd leaf

growth_protocol: Pregerminated rice seeds were planted into potting mix with gravimetric soil water contents (SWC; g water / g dry soil) of 3 g/g (well-watered) or 1.5 g/g (growth-limiting drought). The seedlings were grown in a Conviron growth chamber with a 12-hour daylength with 500 µmol light intensity, 30°C/25°C day/night temperature, and 80% humidity. Pots were weighed and rewatered daily to maintain SWCs until the third leaves of the rice seedlings were fully elongated (10 days for 3 g/g, 12 days for 1.5 g/g). Prior to collection, half of the pots were heat shocked at 40°C for 30 minutes, resulting in 4 total conditions: well-watered, drought, heat shock, and drought + heat shock. Third, fully elongated leaves from each condition were collected at midday (6 ZT). Leaf blades were removed by a razorblade at the sheath collar and dissected into seven equal-length segments.. We kept the center 5 segments (segments 2-6) and discarded the tip-most and base-most segments (segments 1 and 7). We collected 4 replicates per condition, each containing matched segments from 3 leaves.

extract_protocol:
Leaf segments from the above conditions were flash frozen in liquid nitrogen and stored at -80°C. Tissue was ground to a powder in a bead mill (30s, 6m/s), and total RNA was extracted with a Qiagen RNeasy Plant Mini Kit.
Total RNA was sent to Génome Québec (Montreal, Quebec) for library construction and sequencing, using Nextera XT library preparation and sequencing of 100bp paired-end reads on a NovaSeq 6000.

value: Mature 3rd leaf

tag: soil water_content_(g_water_/_g_soil)

tag: temperature at_collection_(°c)

tag: leaf segment_(base_=_s2)

tag: replicate

tag: batch


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 6, rep 4

description: Library name: D40.s6.r4


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 3, rep 4

description: Library name: D40.s3.r4


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 2, rep 4

description: Library name: D40.s2.r4


title: Macrophage, M0, rep 2

description: Library name: M0_258

tag: ifny conc_ng_per_ml

tag: lps conc_ug_per_ml

tag: il-4 conc_ng_per_ml

tag: il-13 conc_ng_per_ml

tag: polarization start


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 6, rep 3

description: Library name: D40.s6.r3


title: Macrophage, 14P-RT TAM, rep 1

description: Library name: TAM14PRT_215

tag: expt start_date

tag: serum

tag: conc

tag: rin

tag: prep date


title: Macrophage, M2, rep 1

description: Library name: M2_215

tag: cell type

tag: expt type


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 3, rep 3

description: Library name: D40.s3.r3

tag: tissue

tag: soil water_content_(g_water_/_g_soil)


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 5, rep 3

description: Library name: D40.s5.r3

tag: temperature at_collection_(°c)

tag: leaf segment_(base_=_s2)


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 4, rep 3

description: Library name: D40.s4.r3

tag: replicate

tag: batch


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 2, rep 3

description: Library name: D40.s2.r3


title: Macrophage, M0, rep 1

description: Library name: M0_215

tag: ifny conc_ng_per_ml

tag: lps conc_ug_per_ml


title: Macrophage, M1, rep 1

description: Library name: M1_215

tag: il-4 conc_ng_per_ml

tag: il-13 conc_ng_per_ml


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 5, rep 2

description: Library name: D40.s5.r2


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 4, rep 2

description: Library name: D40.s4.r2


title: iMSC_Input

first: Wenpeng

last: Song

state: Beijing

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

institute: Capital Medical University

data_processing:
For the processing of OCT4 ChIP-seq data, raw reads were trimmed with Trim-Galore software (version 0.4.5). Trimmed reads were mapped to the human (Homo sapiens) hg38 genome obtained from UCSC genome browser database using Bowtie2 (version 2.5.4). Duplicated reads were discarded by MarkDuplicates.jar program in Picard tools (version 1.119). Then, reads were sorted with SAMtools (version 1.2.0). MACS2 (version 1.1) was used to call peak with the parameters set to ‘-f BAMPE -p 0.05 -g hs’. The genomic annotation of ChIP-seq peaks were produced using the ChIPseeker v1.26.0 R package. BAM files were converted to bigWig files with CPM normalization using deepTools bamCoverage tool (version 3.3.5) and bigWig files were visualized in the WashU epigenome browser.
Assembly: hg38
Supplementary files format and content: narrowPeaks

source_name: PSCs

extract_protocol:
ChIP-seq was performed to investigate the binding of specific transcription factors (OCT4) across the genome. Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 125 mM glycine. The cells were then washed with cold PBS, harvested, and lysed in lysis buffer containing protease inhibitors. The chromatin was sheared to an average fragment size of 200-400 bp using a Covaris S220 (Covaris, Massachusetts, USA). The sheared chromatin was incubated overnight at 4°C with protein A/G magnetic beads pre-bound to specific antibodies against the target protein (OCT4). After immunoprecipitation, the beads were washed, and the bound DNA-protein complexes were eluted and reverse cross-linked.
For ChIP-seq library preparation, The DNA fragments were end-repaired and A-tailed. Then, the DNA fragments with A tail were ligated with sequencing adaptors. The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system (Agilent, California, USA) and quantified by qPCR (1.5nM). After library quality control, different libraries are pooled according to their effective concentrations and the required amount of data for sequencing on the Illumina platform, generating paired-end reads of 150 bp. The basic principle of sequencing is synthesis while sequencing. In the sequencing flow cell, four fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added for amplification. With each complementary strand extension in a sequencing cluster, the incorporation of a fluorescently labeled dNTP releases corresponding fluorescence. The sequencing instrument captures the fluorescence signals, and computer software converts these signals into sequencing peaks, thus obtaining the sequence information of the target fragments.

value: PSCs

tag: chip antibody


title: iMSC_IP

value: OCT4(Abcam, ab181557)


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 3, rep 2

description: Library name: D40.s3.r2


title: JN-DSRCT-1_shWT1-CDS_dox_metastasis

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

description:
matrix.mtx
features.tsv
barcodes.tsv
object.rds

data_processing:
After alignment and counting with STARsolo (STAR 2.7.11b), quality control and analysis were done using Seurat and SingleCellExperiment packages. Cells discarded by SeuratWrappers::RunMiQC with posterior cutoff of 0.8 and scuttle::quickPerCellQC functions were discarded, as well as genes expressed in less than 2 cells. Normalization, scaling and centering was performed using Seurat::SCTransform, taking into account the potential confounders of ribosomal and mitochondrial gene expression, cell cycle state, expression of housekeeping and dissociation-associated genes as well as the cell line and shRNA version. Signatures were scored with the ssGSEA implementation of the irGSEA package.
Assembly: hg38v40
Supplementary files format and content: Output of STARsolo: Count matrix (matrix.mtx), gene names (features.tsv) and cell identities (barcodes.tsv) as tab-seperated files.
Supplementary files format and content: Processed Seurat object as an rds file.

source_name: xenografted tumor metastasis

growth_protocol: One million DSRCT cells harboring either shRNA against WT1-CDS or WT1-UTR were resuspended in PBS and mixed with Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix in 1:1 proportion, and slowly injected in the peritoneum of 10–12 weeks old NOD/scid/gamma (NSG) mice

extract_protocol:
Xenografted tumors (≤ 200 mg) were harvested, rapidly cooled in ice-cold PBS and kept on ice until further processing. Sections were minced with a scalpel and transferred to gentleMACS C tubes with 5 mL of ice-cold protease cocktail, consisting of cold-active Bacillus licheniformis protease (10 mg/mL), calcium chloride (5 mM), DNase I (125 U/mL) in PBS and incubated for 10 min at 4°C with rocking, followed by two runs of m_brain_03 program and 5 min incubation at 4°C. After filtering (70 µm) and protease stopping with HBSS + 10% FCS, the cells were resuspended in ice-cold HBSS supplemented with 2% bovine serum albumin. Human cells were identified based on an antibody panel and sorted into a DNA low-binding 384-well plate containing 1.2 µL of lysis mix per well (0.095% Triton X-100, 1 U/µL RNase Inhibitor, 2,5 mM dNTPs, 2.5 µM Oligo-dT primer (AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN).
Lysed cells were thawed and incubated for 3 min at 72°C to complete lysis. After 2 min incubation on ice, reverse transcription and template switching mix (10 U/µL Maxima H-, 1.4 U/µL RNase Inhibitor, 1X Maxima H- buffer, 4.5 µM template switching oligo (AAGCAGTGGTATCAACGCAGAGTACATrGrG+G) and 11,25% poly-ethylenglycol 8000 in nuclease-free water) was added and the plates were incubated for 90 min at 42°C, followed by an enzyme inactivation at 70°C for 15 min. PCR amplification with 21 cycles was conducted by adding 3 µL KAPA HiFi HotStart ReadyMix and 0.05 µL IS PCR primer (10 µM) to each well and incubating according to the manufacturer’s protocol with 67°C annealing temperature and 6 min extension time. After clean-up with 5 µL AmpureXP beads at a beads ratio of 0.8, cDNA was diluted to 1-3 ng/µL and fragmentation of full-length cDNA was performed using 1.2 µL Tn5 tagmentase in tagmentation buffer per well (10 mM Tris-HCl pH 7.5, 10 mM magnesium chloride, 50% dimethylformamide) with 0.4 µL cDNA by incubating for 10 min at 55°C. After stopping the incubation by adding 0,4 µL sodium dodecyle sulfate, barcoding oligos with illumina sequencing barcodes were added, and library amplification was conducted by adding 2.7 µL KAPA HiFi HotStart ReadyMix with 0.3 µL dimethyl-sulfoxide and incubating according to the manufacturer’s protocol with 12 cycles of 63°C annealing temperature and 30 s extension time. After pooling and clean-up with AmpureXP beads at a beads ratio of 0.9, the pooled library was diluted to 10 nM for sequencing on the NextSeq 550 sequencing platform.

treatment_protocol: Seven-weeks after injection, mice were randomized in two groups and they were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of WT1 (DOX (+)), or 5% sucrose (control, DOX (−)) for 96h. At the experimental endpoint mice were sacrificed by cervical dislocation.

value: xenografted tumor metastasis

tag: cell line

value: Desmoplastic small round cell tumor

tag: genotype

tag: treatment

value: doxycycline


title: JN-DSRCT-1_shWT1-CDS_nodox_metastasis

value: sucrose


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 2, rep 2

description: Library name: D40.s2.r2


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 4, rep 4

description: Library name: D40.s4.r4


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 6, rep 1

description: Library name: D40.s6.r1


title: Macrophage, M1, rep 2

description: Library name: M1_258

tag: polarization start

tag: expt start_date

tag: serum

tag: conc

tag: rin

tag: prep date


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 5, rep 1

description: Library name: D40.s5.r1

tag: tissue

tag: soil water_content_(g_water_/_g_soil)

tag: temperature at_collection_(°c)

tag: leaf segment_(base_=_s2)


title: SK-DSRCT-2_shWT1-UTR_dox_metastasis

tag: cell type


title: JN-DSRCT-1_shWT1-CDS_nodox_primary

source_name: xenografted tumor

value: xenografted tumor


title: Macrophage, 14P TAM, rep 1

description: Library name: TAM_14P_215

value: Macrophage

tag: ifny conc_ng_per_ml

tag: lps conc_ug_per_ml

tag: il-4 conc_ng_per_ml

tag: expt type


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 4, rep 1

description: Library name: D40.s4.r1

tag: replicate

tag: batch


title: SK-DSRCT-2_shWT1-UTR_nodox_primary

tag: cell line

tag: genotype

tag: treatment


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 2, rep 1

description: Library name: D40.s2.r1


title: SK-DSRCT-2_shWT1-UTR_dox_primary


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 6, rep 2

description: Library name: D40.s6.r2


title: Leaf, well-watered, 30-min heat shock, segment 5, rep 4

description: Library name: W40.s5.r4

value: 3 g/g


title: Leaf, well-watered, 30-min heat shock, segment 4, rep 4

description: Library name: W40.s4.r4


title: Leaf, well-watered, 30-min heat shock, segment 3, rep 4

description: Library name: W40.s3.r4


title: PTPRZ_het_ctrl_TECs_r5

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

description: Library name: PTPRZ_het_ctrl_r5

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (version 0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Transcript abundance estimates were computed with Salmon (version 1.10.2) with a transcriptome index generated from GENCODE version M32 and subsequently summarized to gene level with the tximeta R package (version v1.22.1).
The exploration, modeling, and interpretation of the expression data follows the protocols defined by Ludt et al (2022). All downstream analyses were performed in R (version 4.4.1) and Bioconductor v3.20.
Exploratory data analysis was performed with the pcaExplorer package (version 2.31.0). Principal Component Analysis plots were performed including the top 500 most variable genes.
Differential expression analysis was performed with DESeq2 package (version 1.45.3), setting the false discovery rate (FDR) cutoff to 0.05. Accurate estimation of the effect sizes (described as log2 fold change) was performed using the apeglm shrinkage estimator.
Further analyses included Gene Ontology pathway enrichment by topGO, setting all expressed genes as background dataset, and were performed using the ideal package (version 1.29.0). The enrichment results were further processed with the GeneTonic package (version 2.9.0) for visualization and summarizing. Gene expression profiles were plotted as heatmaps (color-coded standardized Z scores for the expression values, after variance stabilizing transformation to enable comparison across samples.
Assembly: GRCm39, GENCODE M32
Supplementary files format and content: comma-delimited text file include the raw expression values for all genes as a count matrix, used for the statistical modeling

source_name: renal tubular epithelial cell (TEC)

growth_protocol: Primary renal TEC were isolated from kidneys and grown in DMEM/HamsF12 1:1 media containing 10% FBS, anibiotics, HEPES, EGF (epidermal growth factor), Prostaglandine E2, Trijod-Thyronine, Hydrocortisone, L-Epinephrine, Insuline-Transferrine-Sodium-Selenite.

extract_protocol:
RNA was isolated using the innuPREP RNA Mini Kit 2.0 (Ist-Innuscreen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNASeq were prepared using the NEBNext UltraTM II Directional RNA library preparation Kit (New England Biolaps).

treatment_protocol: Tubular epithelial cells were stimulated with LPS (100 ng/mL) and IFNy (10 ng/mL) for 24 h. Untreated cells were used as control.

tag: strain

value: renal tubular epithelial cell (TEC)

value: ctrl

tag: animal id


title: PTPRZ_KO_LPSIFNy_TECs_r5

description: Library name: PTPRZ_KO_LPSIFNy_r5

value: LPSIFNy


title: Leaf, well-watered, 30-min heat shock, segment 6, rep 4

description: Library name: W40.s6.r4


title: PTPRZ_KO_ctrl_TECs_r5

description: Library name: PTPRZ_KO_ctrl_r5


title: Leaf, well-watered, 30-min heat shock, segment 2, rep 4

description: Library name: W40.s2.r4


title: Leaf, well-watered, 30-min heat shock, segment 6, rep 3

description: Library name: W40.s6.r3


title: SK-DSRCT-2_shWT1-UTR_nodox_metastasis


title: PTPRZ_het_LPSIFNy_TECs_r5

description: Library name: PTPRZ_het_LPSIFNy_r5


title: PTPRZ_het_LPSIFNy_TECs_r4

description: Library name: PTPRZ_het_LPSIFNy_r4


title: PTPRZ_KO_LPSIFNy_TECs_r4

description: Library name: PTPRZ_KO_LPSIFNy_r4


title: Leaf, well-watered, 30-min heat shock, segment 5, rep 3

description: Library name: W40.s5.r3


title: Leaf, well-watered, 30-min heat shock, segment 4, rep 3

description: Library name: W40.s4.r3


title: PTPRZ_het_ctrl_TECs_r4

description: Library name: PTPRZ_het_ctrl_r4


title: JN-DSRCT-1_shWT1-CDS_dox_primary


title: PTPRZ_KO_LPSIFNy_TECs_r3

description: Library name: PTPRZ_KO_LPSIFNy_r3


title: Leaf, growth-limiting-drought, 30-min heat shock, segment 3, rep 1

description: Library name: D40.s3.r1


title: Leaf, well-watered, 30-min heat shock, segment 6, rep 2

description: Library name: W40.s6.r2


title: PTPRZ_KO_ctrl_TECs_r3

description: Library name: PTPRZ_KO_ctrl_r3


title: Leaf, well-watered, 30-min heat shock, segment 3, rep 3

description: Library name: W40.s3.r3


title: PTPRZ_het_LPSIFNy_TECs_r3

description: Library name: PTPRZ_het_LPSIFNy_r3


title: PTPRZ_het_ctrl_TECs_r3

description: Library name: PTPRZ_het_ctrl_r3


title: PTPRZ_KO_ctrl_TECs_r4

description: Library name: PTPRZ_KO_ctrl_r4


title: PTPRZ_KO_LPSIFNy_TECs_r2

description: Library name: PTPRZ_KO_LPSIFNy_r2


title: Leaf, well-watered, 30-min heat shock, segment 4, rep 2

description: Library name: W40.s4.r2


title: Leaf, well-watered, 30-min heat shock, segment 2, rep 3

description: Library name: W40.s2.r3


title: PTPRZ_KO_ctrl_TECs_r2

description: Library name: PTPRZ_KO_ctrl_r2


title: Leaf, well-watered, 30-min heat shock, segment 6, rep 1

description: Library name: W40.s6.r1


title: Leaf, well-watered, 30-min heat shock, segment 5, rep 1

description: Library name: W40.s5.r1


title: PTPRZ_KO_LPSIFNy_TECs_r1

description: Library name: PTPRZ_KO_LPSIFNy_r1


title: Leaf, well-watered, 30-min heat shock, segment 2, rep 2

description: Library name: W40.s2.r2


title: PTPRZ_het_LPSIFNy_TECs_r2

description: Library name: PTPRZ_het_LPSIFNy_r2


title: PTPRZ_KO_ctrl_TECs_r1

description: Library name: PTPRZ_KO_ctrl_r1


title: Leaf, well-watered, 30-min heat shock, segment 3, rep 2

description: Library name: W40.s3.r2


title: PTPRZ_het_LPSIFNy_TECs_r1

description: Library name: PTPRZ_het_LPSIFNy_r1


title: PTPRZ_het_ctrl_TECs_r2

description: Library name: PTPRZ_het_ctrl_r2


title: Leaf, well-watered, 30-min heat shock, segment 2, rep 1

description: Library name: W40.s2.r1


title: Leaf, well-watered, 30-min heat shock, segment 4, rep 1

description: Library name: W40.s4.r1


title: Leaf, well-watered, 30-min heat shock, segment 3, rep 1

description: Library name: W40.s3.r1


title: PTPRZ_het_ctrl_TECs_r1

description: Library name: PTPRZ_het_ctrl_r1


title: Leaf, growth-limiting-drought, ambient temp, segment 6, rep 4

description: Library name: D30.s6.r4


title: B6_ctrl_r2

description: Library name: B6_ctrl_r2

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow derived macrophages (BMDM) were differentiated from BM-cells for 6 days under the presence of M-CSF (10 ng/mL)

treatment_protocol: To obtain M1 Macrophages they were treated with LPS (100 ng/mL) and IFNy (10 ng/mL) for 24 h, to obtain M2 Macrophages they were treated with IL-4 (20 ng/mL) for 24 h.

value: Bone Marrow Derived Macrophages

value: BMDM


title: B6_LPSIFNy_r2

description: Library name: B6_LPSIFNy_r2

value: BMDM M1


title: Leaf, growth-limiting-drought, ambient temp, segment 4, rep 4

description: Library name: D30.s4.r4


title: Leaf, growth-limiting-drought, ambient temp, segment 3, rep 4

description: Library name: D30.s3.r4


title: Leaf, growth-limiting-drought, ambient temp, segment 2, rep 4

description: Library name: D30.s2.r4


title: Leaf, growth-limiting-drought, ambient temp, segment 6, rep 3

description: Library name: D30.s6.r3


title: B6_LPSIFNy_r1

description: Library name: B6_LPSIFNy_r1


title: B6_IL4_r1

description: Library name: B6_IL4_r1

value: BMDM M2


title: Leaf, growth-limiting-drought, ambient temp, segment 5, rep 3

description: Library name: D30.s5.r3

value: Mature 3rd leaf


title: B6_ctrl_r1

description: Library name: B6_ctrl_r1


title: Leaf, well-watered, 30-min heat shock, segment 5, rep 2

description: Library name: W40.s5.r2


title: Leaf, growth-limiting-drought, ambient temp, segment 4, rep 3

description: Library name: D30.s4.r3


title: PTPRZ_KO_LPSIFNy_r2

description: Library name: PTPRZ_KO_LPSIFNy_r2


title: PTPRZ_KO_ctrl_r2

description: Library name: PTPRZ_KO_ctrl_r2


title: Leaf, growth-limiting-drought, ambient temp, segment 6, rep 2

description: Library name: D30.s6.r2


title: PTPRZ_KO_IL4_r1

description: Library name: PTPRZ_KO_IL4_r1


title: Leaf, growth-limiting-drought, ambient temp, segment 2, rep 3

description: Library name: D30.s2.r3


title: Leaf, growth-limiting-drought, ambient temp, segment 5, rep 2

description: Library name: D30.s5.r2


title: Leaf, growth-limiting-drought, ambient temp, segment 5, rep 4

description: Library name: D30.s5.r4


title: B6_IL4_r2

description: Library name: B6_IL4_r2


title: NF_EV6

city: guangzhou

first: Yun

last: Li

state: Guangdong

address: 58 Zhongshan Road Ⅱ

institute: sun-yat sen university

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 6

hyb_protocol: Then biotinylated cRNA targets hybridized with the Microarray slides at 65℃ for 17 hours

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner  (G5761A)

data_processing:
Feature Extraction software (version 12.0.3.1, Agilent Technologies) was used to process the original images and extract the raw data. Genespring software (version 14.8, Agilent Technologies) was then used for quantile standardization and subsequent processing. The standardized data were filtered, and at least one group of probes marked as 100% detected in each group of samples used for comparison was retained for subsequent analysis.
The raw data were imported into Genespring software (version 14.8, Agilent) and standardized using the quantile method to obtain the results, which included the raw signal value, standardized signal value, detection status, and detailed annotation information.

source_name: Normal fibroblasts-derived exosomes, LSCC patient 6

label_protocol: fluorescent dye Cyanine-3-CTP (Cy3) was used for labeling, and then purified using QIAGEN RNeasy Kit. Finally, rolling hybridization was performed at 65℃ for 17h, and after elution, the original image was scanned using Agilent Scanner G5761A (Agilent Technologies).

extract_protocol: Total RNA of the sample was extracted using Trizol (Invitrogen) reagent. Total RNA of the sample was quantified using NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was tested by Agilent Bioanalyzer 2100 (Agilent Technologies). The purity of Total RNA will affect the labeling efficiency of the probe and the results of chip hybridization, so QIAGEN RNeasy Kit was used to purify the total RNA. 250ng of the purified Total RNA was taken for labeling and amplification. First, the AffinityScript-RT kit and Ptomoter Primer were used to reverse transcribe RNA into the first chain of cDNA, and then the Anti-sense Promoter was used to generate the second chain of cDNA, and T7 RNA polymerase was added to amplify the second chain of cDNA to generate cRNA.

treatment_protocol: After primary CAFs/NFs reached 80% confluence and were cultured with exosome-free FBS for 48 h, exosomes were collected by standard centrifugation.

value: exosome

tag: gender

value: male


title: CAF_EV6

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 6

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 6

tag: tissue


title: perirenal adipose tissue, buffalo-6 [miRNA-seq]

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

description:
Library name: 9342-shenzhouzhiB
Column name in miRNA_count_all_samples.txt:shenzhouzhiB_9342

data_processing:
Raw data were filtered with Fastp (v0.20.1) to remove reads with low quality or adapter.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Botie2
In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA.
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is:C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
DESeq2 version 1.24.0 was used to normalize gene readcounts and compute differential expression
Assembly: MiRbase v22（BAT）Due to the lack of a curated buffalo miRNA database, miRNA annotation was inferred from Bos taurus (cattle) entries in miRBase release 22.
Supplementary files format and content: Matrix table with normalized gene counts for every miRNA and every sample

organism: Bubalus bubalis

source_name: adipose tissue

growth_protocol: Buffaloes were weaned at 3 months of age, started to fatten at 15 months of age, and slaughtered at 20 months of age.

extract_protocol:
Total RNA was isolated using RNeasy Lipid Tissue Mini Kit (QIAGEN, GER) according to the manual instruction.
Approximately 2 μg of total RNA per sample was used for library construction according to the protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

value: adipose tissue

tag: tissue type

value: perirenal adipose tissue


title: perirenal adipose tissue, buffalo-5 [miRNA-seq]

description:
Library name: 7121-shenzhouzhiB
Column name in miRNA_count_all_samples.txt:shenzhouzhiB_7121


title: Leaf, growth-limiting-drought, ambient temp, segment 2, rep 2

description: Library name: D30.s2.r2

tag: soil water_content_(g_water_/_g_soil)

tag: temperature at_collection_(°c)


title: PTPRZ_KO_IL4_r2

description: Library name: PTPRZ_KO_IL4_r2

tag: cell type


title: NF_EV5

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 5

source_name: Normal fibroblasts-derived exosomes, LSCC patient 5


title: perirenal adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-shenzhouzhiA
Column name in miRNA_count_all_samples.txt:shenzhouzhiA_7034


title: Leaf, growth-limiting-drought, ambient temp, segment 6, rep 1

description: Library name: D30.s6.r1

tag: leaf segment_(base_=_s2)


title: CAF_EV5

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 5

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 5


title: perirenal adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-shenzhouzhiB
Column name in miRNA_count_all_samples.txt:shenzhouzhiB_1783


title: perirenal adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-shenzhouzhiA
Column name in miRNA_count_all_samples.txt:shenzhouzhiA_1277


title: Leaf, growth-limiting-drought, ambient temp, segment 3, rep 2

description: Library name: D30.s3.r2


title: perirenal adipose tissue, buffalo-2 [miRNA-seq]

description:
Library name: 1745-shenzhouzhiA
Column name in miRNA_count_all_samples.txt:shenzhouzhiA_1745


title: pericardial adipose tissue, buffalo-6 [miRNA-seq]

description:
Library name: 9342-xinbaozhiB
Column name in miRNA_count_all_samples.txt:xinbaozhiB_9342

value: pericardial adipose tissue


title: Leaf, growth-limiting-drought, ambient temp, segment 3, rep 3

description: Library name: D30.s3.r3


title: NF_EV4

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 4

source_name: Normal fibroblasts-derived exosomes, LSCC patient 4


title: PTPRZ_KO_LPSIFNy_r1

description: Library name: PTPRZ_KO_LPSIFNy_r1


title: Leaf, growth-limiting-drought, ambient temp, segment 5, rep 1

description: Library name: D30.s5.r1


title: pericardial adipose tissue, buffalo-5 [miRNA-seq]

description:
Library name: 7121-xinbaozhiA
Column name in miRNA_count_all_samples.txt:xinbaozhiA_7121


title: Leaf, growth-limiting-drought, ambient temp, segment 4, rep 1

description: Library name: D30.s4.r1


title: PTPRZ_KO_ctrl_r1

description: Library name: PTPRZ_KO_ctrl_r1


title: CAF_EV4

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 4

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 4


title: Leaf, growth-limiting-drought, ambient temp, segment 4, rep 2

description: Library name: D30.s4.r2


title: pericardial adipose tissue, buffalo-2 [miRNA-seq]

description:
Library name: 1745-xinbaozhiA
Column name in miRNA_count_all_samples.txt:xinbaozhiA_1745


title: pericardial adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-xinbaozhiB
Column name in miRNA_count_all_samples.txt:xinbaozhiB_7034


title: pericardial adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-xinbaozhiB
Column name in miRNA_count_all_samples.txt:xinbaozhiB_1783


title: NF_EV3

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 3

source_name: Normal fibroblasts-derived exosomes, LSCC patient 3


title: pericardial adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-xinbaozhiB
Column name in miRNA_count_all_samples.txt:xinbaozhiB_1277


title: omental adipose tissue, buffalo-6 [miRNA-seq]

description:
Library name: 9342-liuweimozhiA
Column name in miRNA_count_all_samples.txt:liuweimozhiA_9342

value: omental adipose tissue


title: CAF_EV3

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 3

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 3


title: Leaf, well-watered, ambient temp, segment 6, rep 4

description: Library name: W30.s6.r4


title: omental adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-liuweimozhiA
Column name in miRNA_count_all_samples.txt:liuweimozhiA_7034


title: NF_EV2

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 2

source_name: Normal fibroblasts-derived exosomes, LSCC patient 2


title: omental adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-liuweimozhiB
Column name in miRNA_count_all_samples.txt:liuweimozhiB_1783


title: Leaf, well-watered, ambient temp, segment 5, rep 4

description: Library name: W30.s5.r4


title: CAF_EV2

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 2

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 2


title: omental adipose tissue, buffalo-2 [miRNA-seq]

description:
Library name: 1745-liuweimozhiB
Column name in miRNA_count_all_samples.txt:liuweimozhiB_1745


title: omental adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-liuweimozhiB
Column name in miRNA_count_all_samples.txt:liuweimozhiB_1277


title: Leaf, well-watered, ambient temp, segment 4, rep 4

description: Library name: W30.s4.r4

source_name: Mature 3rd leaf


title: Leaf, well-watered, ambient temp, segment 3, rep 4

description: Library name: W30.s3.r4


title: Leaf, growth-limiting-drought, ambient temp, segment 3, rep 1

description: Library name: D30.s3.r1


title: inguinal adipose tissue, buffalo-6 [miRNA-seq]

description:
Library name: 9342-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_9342

value: inguinal adipose tissue


title: inguinal adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_1783


title: inguinal adipose tissue, buffal0-5 [miRNA-seq]

description:
Library name: 7121-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_7121


title: CAF_EV1

description: Gene expression in cancer-Associated Fibroblast-derived exosome of LSCC patient 1

source_name: Cancer-Associated Fibroblast-derived exosome, LSCC patient 1


title: inguinal adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_7034


title: NF_EV1

description: Gene expression in Normal fibroblasts-derived exosome of LSCC patient 1

source_name: Normal fibroblasts-derived exosomes, LSCC patient 1


title: inguinal adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_1277


title: SNU719, siH2AZ3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 6_siH2A-ZC_04-14-2023_S6

data_processing:
Reads were aligned using Bowtie2  against hg19 version of the human genome, and RNA-Seq by Expectation Maximization (RSEM) was used to quantify
Assembly: hg19 and NC_007605.1 version of EBV
Supplementary files format and content: tab-delimited text file includes raw counts of each sample for hg19 and NC_007605.1 version of EBV

extract_protocol:
RNeasy Kit mini (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: Gastric Cancer cell line

value: H2Az Knockdown

value: siRNA knockdown


title: Leaf, growth-limiting-drought, ambient temp, segment 2, rep 1

description: Library name: D30.s2.r1


title: Leaf, well-watered, ambient temp, segment 6, rep 3

description: Library name: W30.s6.r3

value: 3 g/g


title: SNU719, siH2AZ2

description: Library name: 5_siH2A-ZB_04-14-2023_S5


title: Leaf, well-watered, ambient temp, segment 5, rep 3

description: Library name: W30.s5.r3


title: inguinal adipose tissue, buffalo-2 [miRNA-seq]

description:
Library name: 1745-fugugouzhiB
Column name in miRNA_count_all_samples.txt:fugugouzhiB_1745


title: sternum subcutaneous adipose tissue, buffalo-5 [miRNA-seq]

description:
Library name: 7121-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_7121

value: sternum subcutaneous adipose tissue


title: omental adipose tissue, buffalo-5 [miRNA-seq]

description:
Library name: 7121-liuweimozhiB
Column name in miRNA_count_all_samples.txt:liuweimozhiB_7121


title: sternum subcutaneous adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_7034


title: SNU719, siH2AZ1

description: Library name: 4_siH2A-ZA_04-14-2023_S4


title: sternum subcutaneous adipose tissue, buffalo-2 [miRNA-seq]

description:
Library name: 1745-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_1745


title: Leaf, well-watered, ambient temp, segment 4, rep 3

description: Library name: W30.s4.r3


title: SNU719, siControl3

description: Library name: 3_zControl3_04-14-2023_S3

value: Control


title: sternum subcutaneous adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_1783


title: sternum subcutaneous adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_1277


title: Leaf, well-watered, ambient temp, segment 3, rep 3

description: Library name: W30.s3.r3


title: Leaf, well-watered, ambient temp, segment 2, rep 4

description: Library name: W30.s2.r4


title: back subcutaneous adipose tissue, buffalo-6 [miRNA-seq]

description:
Library name: 9342-beizhiB
Column name in miRNA_count_all_samples.txt:beizhiB_9342

value: back subcutaneous adipose tissue


title: Leaf, well-watered, ambient temp, segment 2, rep 3

description: Library name: W30.s2.r3


title: back subcutaneous adipose tissue, buffalo-4 [miRNA-seq]

description:
Library name: 7034-beizhiA
Column name in miRNA_count_all_samples.txt:beizhiA_7034


title: SNU719, siControl1

description: Library name: 1_zControl1_04-14-2023_S1


title: SNU719, siControl2

description: Library name: 2_zControl2_04-14-2023_S2


title: back subcutaneous adipose tissue, buffalo-5 [miRNA-seq]

description:
Library name: 7121-beizhiB
Column name in miRNA_count_all_samples.txt:beizhiB_7121


title: Leaf, well-watered, ambient temp, segment 6, rep 2

description: Library name: W30.s6.r2


title: sternum subcutaneous adipose tissue, buffalo-6 [miRNA-seq]

description:
Library name: 9342-xiongzhiB
Column name in miRNA_count_all_samples.txt:xiongzhiB_9342


title: back subcutaneous adipose tissue, buffalo-1 [miRNA-seq]

description:
Library name: 1277-beizhiB
Column name in miRNA_count_all_samples.txt:beizhiB_1277


title: back subcutaneous adipose tissue, buffalo-3 [miRNA-seq]

description:
Library name: 1783-beizhiB
Column name in miRNA_count_all_samples.txt:beizhiB_1783


title: Leaf, well-watered, ambient temp, segment 5, rep 2

description: Library name: W30.s5.r2


title: Leaf, well-watered, ambient temp, segment 4, rep 2

description: Library name: W30.s4.r2


title: BT935 patient-derived GBM cells, 5d TMZRT treatment

first: Tanveer

last: Sharif

state: MB

address: 727 McDermot Avenue

data_processing:
Fastq files were generated from raw sequencer output using the mkfastq command of cellranger 7.1.0
Cell-containing droplets were identified and quantified using the count command of cellranger 7.1.0
Assembly: mm10
Supplementary files format and content: HDF5 format files containing filtered feature-barcode matrices generated by 10X Cellranger (v7.0.0)

source_name: Glioblastoma brain tumor

growth_protocol: Patient-derived GBM cells were maintained in serum-free DMEM/F12 medium supplemented with 1X N2 supplement, 1X SM1 supplement, 20 ng/mL EGF, 10 ng/mL bFGF, 2 µg/mL of Heparin, and 1X antibiotic-antimycotic and propagated as non-adherent neurospheres.

extract_protocol:
Cellular populations consisting of single cells were submitted for Single cell 3’ RNA-Seq using 10X Genomics Chromium (10X Genomics) and Illumina next generation sequencing technologies (Illumina Nextseq 500 Sequencer). Input cells were quantitated and checked for viability assessment using the Countess II cell counter (Thermo Fisher). Following cell counting and viability assessment, the suspended cells were loaded on a Chromium controller Single-Cell instrument to generate Barcoded single-cell Gel Bead-In-Emulsions using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1. GEMs were broken and the barcoded cDNA were amplified using the C1000 Touch Thermal cycler with 96- Well Reaction Module.
The amplified barcoded cDNA was then fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3′ RNA-Seq libraries using the Single Index Kit T (10X Genomics). The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit and the fragment size distribution of the libraries were determined using the AATI Fragment analyzer High Sensitivity NGS kit (Aligent). Pooled libraries were then sequenced using Illumina Nextseq. All samples were sequenced to an approximately 20,000 reads per cell for V3.1 Kit as per 10x Genomics recommendation.

treatment_protocol: GBM cells received 25 µM of temozolomide and controls received equal volumes of DMSO vehicle. Immediately following TMZ treatment, cells were exposed to 1 Gy of X-ray irradiation using the Rad Source 2000 and incubated at 37°C in a 5% CO2 incubator for 1 hour. To mimic the exposure time of chemotherapy received by patients, where the half-life of TMZ is approximately 1-2 hours in circulation, the drug treatment was washed out of the patient-derived GBM cells after 1 hour and replaced with fresh media. The concurrent chemoradiotherapy treatment regimen was repeated daily for 5 consecutive days. After the 5th treatment day, patient-derived GBM cells received a 2-day treatment holiday prior to collection and subsequent analysis.

value: Glioblastoma brain tumor

value: Tumor cell

value: 5d TMZRT


title: BT935 patient-derived GBM cells, 3d TMZRT treatment

value: 3d TMZRT


title: BT935 patient-derived GBM cells, 7d TMZRT treatment (Resistant)

value: 7d TMZRT (Resistant)


title: Npy1R-3

first: KLaus

last: Schmitz-Abe

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

description: Library name: Samples C3

data_processing:
fastq file to bam file to count file Rsubread (Counts.xlsx) Default parameters
Count file to Gene differential expression file edgeR (version 3.28) Default parameters
Count file to Gene differential expression file DESeq2 (version 1.26.0) Default parameters
Count file to Gene differential expression file Lima (version 3.42.2) Default parameters
Join results VExP Pipeline
Assembly: GRCm38/mm10 (UCSC reference) Mus musculus
Supplementary files format and content: vcf files and excel file

growth_protocol: Treg cell and microglia were cell sorted from CNS were cell sorted using Sony MA900 and Snap Freezed before RNA extraction

extract_protocol:
CNS cell were stain with CD4 CD45, Notch3, Npy1R and CD11b and cell sorted (Sony MA900)
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

treatment_protocol: 8 weeks old Foxp3YFPCRE and Foxp3YFPCre Notch3Fl/FL mice were immunized with MOG35-55 using Hooke laboratory Kit

value: treg Cells

value: WT


title: Notch3+-1

description: Library name: Samples C5


title: Notch3+-2

description: Library name: Samples C6


title: Leaf, well-watered, ambient temp, segment 3, rep 2

description: Library name: W30.s3.r2

value: Mature 3rd leaf


title: Npy1R-4

description: Library name: Samples C4


title: BT935 patient-derived GBM cells, 1d TMZRT treatment

value: 1d TMZRT


title: Leaf, well-watered, ambient temp, segment 2, rep 2

description: Library name: W30.s2.r2


title: BT935 patient-derived GBM cells, 0d TMZRT treatment (Naïve)

value: 0d TMZRT (Naive)