title: E125_Hdac1&2_cKO_scRNAseq

data_processing:
Raw sequencing data (fastq files) were aligned to the reference genome mm10 (cellranger reference 2020-A, and Ensembl v98 gene annotation) using the Cell Ranger pipeline (v.7.1.0, 10x Genomics) with parameters: --include-introns=false –r2-length=91 –r1-length=28. After alignment, filtering, barcode counting, and UMI counting we use feature-barcode matrices for downstream analysis.
Downstream analysis were performed using R package Seurat
Assembly: mm10

extract_protocol:
Single cells isolated from the cerebral cortices of both wild-type (WT) and HDAC1/2 conditional knockout (cKO) mice at embryonic day 12.5 (E12.5) were processed using the Chromium 10x system for single-cell cDNA generation.
The libraries were then prepared employing the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, strictly adhering to the manufacturer’s instructions. Following the cDNA clean-up, the libraries were quantified using a BioAnalyzer then were sequenced on the Illumina NovaSeq 6000.

tag: tissue


title: reHMGA1-18HR-1

status: Public on Oct 01 2024

type: SRA

city: New York

first: Ting-Hsiang

last: Huang

state: New York

country: USA

institute: Memorial Sloan Ketteting Cancer Center

library_source: genomic

data_processing:
Image analysis and base calling were conducted by the Control Software (CS). Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification
Assembly: hg38
Supplementary files format and content: Bigwig files for each conditions.
Supplementary files format and content: A txt file for DESeq2 2-hr vs mock. A txt file for DESeq2 18-hr vs mock. A txt file for DESeq2 18-hr vs 2-hr.

molecule: genomic DNA

organism: Homo sapiens

source_name: skin

growth_protocol: Effects of recombinant HMGA1 on chromatin accessibility in A375 melanoma

extract_protocol:
Samples were further processed by Azenta. See below.
ATAC-seq library preparation and sequencing reactions were conducted at Azenta Life Sciences (South Plainfield, NJ, USA). Live cell samples were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries. The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: 2.5 x 10^5 cells were treated with reHMGA1 for 2- and 18-hrs. 2 biological replicates were prepared. After treatment, cells were resuspended in cryopreservation medium with 10% DMSO at -80 degree.

value: skin

tag: cell line

tag: cell type

value: melanoma

tag: treatment

value: recombinant HMGA1 (18hr)


title: reHMGA1-18HR-2


title: LS_H3K4me1

city: Guangzhou

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

country: China

institute: Southern Medical University

data_processing:
Reads containing barcodes were de-multiplexed to generate single cell profiles by custom scripts.
Trimmed paired-end reads were mapped to a mouse mm10 genome reference genome with bowtie2.
Duplicate reads were removed using picard. Only uniquely reads>1500 cells will be remained.
Peaks were called uing macs2 with nolambda、nomedel and broad.
Bigwig files were generated using the Deeptools BamCoverage，reads were normalized to 1000000.
Assembly: mm10
Supplementary files format and content: broadPeak
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: embryos

growth_protocol: Mouse embryos were dissected at time points of E6.0, E6.5, E7.0, E7.25 and E7.5, and the individual embryo was micro-dissected and staged as pre-streak (Pre_Ps), Early Streak (ES), Mid-Streak (MS), Late Streak (LS), No Allantoic Bud (OB), and Early Headfold (EHF) stages according to their morphology. Pre-PS, ES, MS and LS embryos were dissected to remove extra-embryo tissues.

extract_protocol:
The embryos were microdissected and digested with Collagenase I dissociation buffer at 37°C for 15-60 min to generate single-cell suspension. The dissociated single cells were collected by centrifugation at 600 g for 3 min. After incubation with Con-A beads, the cell-bead mixture was fixed with methyl alcohol and incubate on ice for 5 min.
Custom library preparation was performed by two steps of PCR amplification. The first step was performed by addition of 0.5 μL 25 μM Truseq connector primer (Connector primer F:5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGTCGGCAGCGTCTCCACGC-3′.Connector primer R:5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCTCGTGGGCTCGGCTGTCCCTGT-3′), 25 μL 2X Taq master mix and 16.5 μL 1mM MgCI2 to the 3 μL CoBATCH cell lysis in each tube and the reaction was set up by incubation at 72°C for 5 min, 95°C for 5 min, 13-16 cycles of amplification (95°C for 30 s, 63°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. The PCR enrichment was directly performed in the same tube as described above. Then 0.4 μL Exo1 was added and incubated at 37°C for 1 h followed by inactivation at 72°C for 20 min. The second PCR enrichment was performed by adding 0.7 μL 10 μM Truseq i5 primer (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′), 0.7 μL 25 μM i7 index primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′), 20 μL 2X Taq master mix and 8.6 μL 1 mM MgCI2 followed by incubation at 95°C for 5 min, 5-7 cycles of  95°C for 30 s, 63°C for 30 s, 72°C for 1 min, and final 72°C extension for 5 min. Finally, the PCR products were purified and selected by SPRI beads for 200-1000 bp.

value: embryos

tag: time point

tag: Stage

value: gastrulation

tag: gastrulation stage

value: LS

tag: strain

tag: chip antibody


title: mGCCtrl_HMD201207001_BC08

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

country: Japan

institute: Kyushu University

library_source: transcriptomic single cell

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

molecule: total RNA

source_name: ovary

growth_protocol: mouse lines used for this study were maintained on a mixed genetic background

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

value: ovary

tag: developmental stage

value: pre-granulosa cells

tag: subpopulation gc

tag: subpopulation oocyte

tag: genotype

value: Sf1-Cre;Wls flox/+;Ai9 (control)

tag: marker expression_tdtomato

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)

tag: intron ratio


title: MS_H3K4me1

tag: tissue

value: MS


title: reHMGA1-2HR-2

tag: cell line

value: recombinant HMGA1 (2hr)


title: mGCCtrl_HMD201207001_CB19

tag: cell type

value: ovarian surface epithelial cells


title: reHMGA1-2HR-1

tag: treatment


title: Pre_PS_H3K4me1

tag: time point


title: EHF_H3K27ac

tag: Stage

value: EHF


title: mGCCtrl_HMD201207001_AI01

value: early theca cells


title: ES_H3K4me1

tag: gastrulation stage

value: ES


title: mGCCtrl_HMD201207001_CL05


title: mGCCtrl_HMD201207001_AK05

value: interstitial cells


title: OB_H3K27ac

value: OB

tag: strain


title: MS_H3K27ac

tag: chip antibody


title: LS_H3K27ac


title: mGCCtrl_HMD201207001_AA11

tag: developmental stage

value: excluded by low quality


title: reHMGA1-Mock-1

value: skin

value: melanoma

value: untreated


title: PA7_9_3

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to human genome (hg38) by TopHat version 2.1.0 with default parameter. Aligned reads in bam file were sorted by genomic coordinate by samtools.
Gene differential expression (DE) analysis was conducted by Cuffdiff version 2.2.1
Assembly: hg38
Supplementary files format and content: tab delimated file containing gene expression for each gene in each sample

growth_protocol: The U373 human glioblastoma cells were propagated in DMEM/F12 (Corning, 10-013-CV) supplemented with 10% FBS (GenClone 25-550).

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Ambion). About 1 million cells were lysed in 1 mL of TRIzol followed by the addition of 0.2 mL (5:1 ratio) of chloroform. Samples were then centrifuged at 12,000 g for 15 min at 4℃. The top layer was transferred to a tube and the RNA was precipitated in 100% isopropanol (1:1 ratio), 3 M sodium acetate (10:1 ratio), and 4 μL of glycogen (5 mg/mL) for an hour at -20℃. The samples were then centrifuged at 15,000 RPM for 20 min at 4℃ and washed twice with 1 mL of 75% ethanol.
RNA was isolated as described above. About 1 μg of total RNA was sent to Admera Health for library construction. The NEBNext Poly(A) mRNA Magnetic Isolation Module was used to isolate intact poly(A)+ RNA followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. Library concentration was measured by qPCR, and library quality was evaluated by Tapestation High Sensitivity D1000 ScreenTapes (Agilent Technologies, CA, USA). Equimolar pooling of libraries was performed based on qPCR values.

treatment_protocol: For deletion of the NEAT1 PAS (ΔNEAT1 PAS), U373 cells that harbor Cas9 expression were transfected with two sgRNAs (sgRNA #1: 5’-ACTTTATTTGTGCTGTAAAG-3’; sgRNA #2: 5’-TACATCCAAAGTCGTTATGA-3’). For acute effects in bulk transfected cells, U373 cells were harvested 48 h after transfection for molecular analysis. Moreover, genetically edited clones harboring ΔNEAT1 PAS were isolated, and propagated for functional studies.

value: Glioblastoma


title: Pre_PS_H3K27ac

value: embryos

value: gastrulation


title: mGCCtrl_HMD201207001_CH15

value: ovary

value: granulosa cells

tag: subpopulation gc


title: OB_H3K4me1


title: 4NQO-induced oral cancer models with treatment of regorafenib (#4)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4). Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM25)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

molecule: polyA RNA

source_name: Oraol squamous cell carcinoma

growth_protocol: 6-week-old C57BL/6J mice were fed with 100 ug/ml of 4NQO (Sigma-Aldrich) in drinking water for 10 weeks and subsequently changed with fresh water until the experiment terminated

extract_protocol:
Total RNA was isolated by using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany)
Libraries were prepared using a TruSeq Stranded mRNA Preparation Kit (Illumina)

treatment_protocol: The mice were randomly divided into two groups to receive vehicle, regorafenib (5mg/kg/day), anti-PD1, or combination treatment until the experiment.

value: Oraol squamous cell carcinoma

value: C57BL/6J mice

value: Regorafenib


title: 4NQO-induced oral cancer models with treatment of regorafenib (#3)


title: ES_H3K27ac


title: 4NQO-induced oral cancer models with treatment of regorafenib (#2)


title: 4NQO-induced oral cancer models with treatment of regorafenib (#1)


title: mGCCtrl_HMD201207001_BK04

tag: subpopulation oocyte

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: PA7_9_2


title: PA7_9_1


title: 4NQO-induced oral cancer models with treatment of anti-PD1 + regorafenib (#5)


title: mOCCtrl_HMD201207001_DN22

tag: genotype


title: 4NQO-induced oral cancer models with treatment of anti-PD1 + regorafenib (#4)


title: 4NQO-induced oral cancer models with treatment of anti-PD1 + regorafenib (#1)


title: PA7_5_2


title: mOCCtrl_HMD201207001_DH04

tag: marker expression_tdtomato


title: 4NQO-induced oral cancer models with treatment of anti-PD1 + regorafenib (#2)


title: mGCCtrl_HMD201207001_CP09

tag: marker expression_kit-apc


title: 4NQO-induced oral cancer models with treatment of anti-PD1 (#2)


title: mOCCtrl_HMD201207001_DD14

value: oocytes

tag: cell size_(fsc1_area)


title: 4NQO-induced oral cancer models with treatment of anti-PD1 (#3)


title: ctr3


title: PA7_5_1


title: ctr2


title: 4NQO-induced oral cancer models with treatment of vehicle control (#3)

value: Vehicle


title: mGCCtrl_HMD201207001_AI05

value: interstitial cells

tag: intron ratio


title: mGCCtrl_HMD201207001_BC20

tag: tissue


title: 4NQO-induced oral cancer models with treatment of vehicle control (#2)


title: ctr1

tag: cell line


title: 4NQO-induced oral cancer models with treatment of vehicle control (#1)


title: reHMGA1-Mock-2

tag: cell type


title: 4NQO-induced oral cancer models with treatment of anti-CD40 agonist (#2)

tag: treatment

value: anti-CD40 agonist


title: mGCCtrl_HMD201207001_AO05


title: 4NQO-induced oral cancer models with treatment of anti-CD40 agonist (#3)


title: 4NQO-induced oral cancer models with treatment of anti-CD40 agonist  (#1)


title: mGCCtrl_HMD201207001_BO10


title: eGFP_parental_input_A498

city: Singapore

first: Xiaosai

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Assembly: hg19
Supplementary files format and content: ChIP-seq peaks are in macs2 narrowPeak format, including 10 columns: "chromosome"  "start coordinate" "end coordinate" "name" "score" "strand" "signalValue" "pValue" "qValue" "peak"

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature.
At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on Novaseq

treatment_protocol: Plasmid expressing guide RNA to insert a LAP tag downstream of the ZNF395 gene was a gift from Kevin White (https://www.encodeproject.org/genetic-modifications/ENCGM446NKU/). The sequence of the guide RNA was CAGCUCAGUCCAGAAAGCGC. Both 786-O and A498 cells were transfected using the Neon™ Transfection System (Invitrogen Life technologies) to express a EGFP tag for subsequent TF ChIP. Briefly, 1M cells were resuspended in 100 µL of resuspension buffer R along with 10 µg of donor plasmid and 1 µg of guide plasmid. Electroporation was performed at 1100V with 20ms pulse width for 2 pulses. Genomic DNA was harvested using DNeasy Blood & Tissue Kit (Qiagen) to validate the presence of GFP by PCR and sanger sequencing.

tag: chip target

value: none (input)

value: parental

value: input


title: PA7_5_3


title: 4NQO-induced oral cancer models with treatment of anti-PD1 + regorafenib (#3)


title: eGFP_parental_A498

value: GFP

value: GFP (AbCAM ab290)


title: HNSCC mouse models with treatment of regorafenib + anti-PD1 (#1)

source_name: Head and neck squamous cell carcinoma

growth_protocol: In subcutaneous moue model, 6×106 Sq-1979 cells immersed in Matrigel (Corning Life Sciences) were injected subcutaneously into 6-week-old male C3H/HeN mice.

treatment_protocol: After 20 days implantation, vehicle, regorafenib (5mg/kg/day), anti-PD1, or combination treatment was administrated through daily oral gavage until the experiment was terminated.

value: Head and neck squamous cell carcinoma

value: C3H/HeN mice


title: 4NQO-induced oral cancer models with treatment of anti-PD1 (#1)


title: HNSCC mouse models with treatment of regorafenib + anti-PD1 (#2)


title: mGCCtrl_HMD201207001_AG03

value: ovary


title: eGFP_ZNF395_input_A498

value: eGFP knock in at ZNF395


title: 4NQO-induced oral cancer models with treatment of vehicle control (#4)

value: Oraol squamous cell carcinoma


title: mOCCtrl_HMD201207001_DF18


title: Ctrl_rep3

city: Houston

first: Brendan

middle: H.

last: Lee

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Sequencing reads were mapped to Mus_musculus.GRCm38.
Differential expression analysis of the transcriptome data was performed using the R package DESeq2.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: text tiles include raw count for the corresponding samples

source_name: Tibia

extract_protocol:
Snap-frozen tibias were pulverized using Tissuelyser II (Qiagen). Total RNA was extracted using cold chloroform and precipitated in cold ethanol. RNA samples were further purified with the Direct-zol RNA Kit (Zymo Research). RNA quality and quantity were measured by Bioanalyzer (Agilent Technologies).
Strand specific cDNA libraries were generated with polyA selection using the Illumina TruSeq RNA Sample Prep Kit v2

value: Tibia

value: Atrxf/y


title: Ctrl_rep2


title: HNSCC mouse models with treatment of regorafenib (#3)

value: Regorafenib


title: eGFP_ZNF395_A498


title: Ctrl_rep1


title: eGFP_parental_input_786-O


title: HNSCC mouse models with treatment of regorafenib (#2)


title: AtrxKO_rep3

value: Osterix-Cre; Atrxf/y


title: mGCCtrl_HMD201207001_CF21

value: ovarian surface epithelial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_BG02

value: interstitial cells


title: mGCCtrl_HMD201207001_AK01


title: eGFP_ZNF395_input_786-O

value: none (input)


title: HNSCC mouse models with treatment of regorafenib + anti-PD1 (#3)


title: HNSCC mouse models with treatment of anti-PD1 (#3)


title: mGCCtrl_HMD201207001_BM06

value: granulosa cells


title: eGFP_ZNF395_786-O


title: mGCCtrl_HMD201207001_BM14


title: HNSCC mouse models with treatment of anti-PD1 (#2)


title: AtrxKO_rep1


title: AtrxKO_rep2


title: GS ATP 15 d - biol rep2

city: Suwon

first: Jiawei

last: An

state: Kyunggi-do

address: 206, World cup-ro

country: South Korea

institute: Ajou University

data_processing:
The cDNA library was sequenced using the NovaSeq platform (Illumina).
Sequence quality was verified using FastQC v0.11.7.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for all samples.

source_name: brain striatum

extract_protocol:
Total cellular RNA was obtained using RNeasy kits (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
Illumina-compatible libraries were constructed using a TruSeq RNA library preparation kit (Illumina, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized with intraperitoneal injections of 2.5% tribromoethanol (250 mg/kg; Sigma, St. Louis, MO, USA), and placed in a stereotactic apparatus (David Kopf Instruments, Tujunga, CA, USA). Brain injury was produced by unilateral administration of 0.8 μl ATP (500 mM Sigma), a component of DAMPs produced under pathological conditions, into the striatum (from bregma: AP, +1.0 mm; ML, -1.9 mm; DV, -3.2 mm), based on stereotactic coordinates in The Atlas of the Mouse Brain (Paxinos and Franklin, second edition). ATP was injected at a rate of 0.2 μl/min using a Hamilton syringe equipped with a 33gauge needle attached to a syringe pump (KD Scientific, New Hope, PA, USA); the needle was left in place for an additional 10 min prior to removal to prevent leakage through the needle track.

value: brain striatum

value: GS

value: ATP injury

tag: time


title: GS ATP 15 d - biol rep1


title: HNSCC mouse models with treatment of vehicle (#3)

value: Head and neck squamous cell carcinoma

value: Vehicle


title: mGCCtrl_HMD201207001_BC22

value: ovary


title: mGCCtrl_HMD201207001_BI04


title: HNSCC mouse models with treatment of anti-PD1 (#1)

value: C3H/HeN mice


title: AGS cells, WT3

city: Fuzhou

first: Shun

last: Hu

state: Fujian

address: Chazhong Road

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
Relatively accurate and effective data are obtained by mass cutting through trimmatic (Version 0.36).
Assembly: hg19
Supplementary files format and content: raw counts of each samples

source_name: AGS

growth_protocol: SNU-719 (EBV-positive gastric cancer cell line), AGS, AGS-NC (EBV-negative gastric cancer cell line) and AGS-OE (lentivirus-transfected miR-BART1-3p overexpression cell line in our laboratory) were cultured in PMI-1640 and F12, respectively. 5% fetal bovine serum and penicillin and streptomycin (100U/mL) were added to the medium prior to use.

extract_protocol:
Total RNA was extracted from cells using a high purity RNA extraction kit (TRIzol) according to the manufacturer's protocol. The OD260 and OD280 values and ratios of 1 μl extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
Through the high-throughput sequencing laboratory of Shanghai Shengong Bioengineering Co., LTD., library construction was conducted to detect the gene expression profiles of SNU719, AGS-OE (miR-BART1-3p overexpressed gastric cancer cells) and AGS-NC, and the differentially expressed genes and the associated genes of miR-BART1-3p in gastric cancer were obtained.

value: AGS

value: gastric cancer cells

value: WT


title: MYC_786-O

value: parental 786-O

value: c-Myc (Santa Cruz, sc-764, Lot no.:#D0612)


title: AGS cells, WT2


title: WT ATP 15 d - biol rep2


title: HNSCC mouse models with treatment of vehicle (#2)


title: eGFP_parental_786-O

value: GFP

value: parental

value: GFP (AbCAM ab290)


title: WT ATP 15 d - biol rep1


title: AGS cells, WT1


title: HNSCC mouse models with treatment of regorafenib (#1)

value: Regorafenib


title: 408_mouse_10d_sorted_KO_bio_rep3

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

country: Germany

institute: DKFZ

data_processing:
Reads were aligned to the GRCm38mm10 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Assembly: Grcm38mm10
Supplementary files format and content: res_p95h_het_ctr_annotation.txt

source_name: reporter positive cells from back skin

extract_protocol:
RNA was extracted with Trizol following manufacturer's instructions
For SRSF2 knock out mice and controls RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Gold library prep kit. For SRSF2 P95H mutant mice and controls RNA sequencing libraries were prepared using stranded Total RNA prep with Ribo-zero plus kit.

treatment_protocol: mouse back skin was treated topically every other day for a given period of time with 4-hydroxy tamoxifen

value: reporter positive cells from back skin

value: 4-hydroxy tamoxifen

value: 10 days


title: mOCCtrl_HMD201207001_DJ16

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: GS ATP 3 d - biol rep2

value: brain striatum

value: GS

value: ATP injury

value: 3 d


title: mGCCtrl_HMD201207001_BO04

value: ovary

value: ovarian surface epithelial cells


title: HNSCC mouse models with treatment of vehicle (#1)

value: Head and neck squamous cell carcinoma

value: C3H/HeN mice

value: Vehicle


title: SNU719 cells, S2

value: gastric cancer cells

value: control


title: GS ATP 3 d - biol rep1


title: SNU719 cells, S1


title: WT ATP 3 d - biol rep2

value: WT


title: mGCCtrl_HMD201207001_CB09

value: granulosa cells


title: WT ATP 3 d - biol rep1


title: 407_mouse_10d_sorted_CTR_bio_rep3

value: reporter positive cells from back skin

value: ctr

value: 4-hydroxy tamoxifen


title: mGCCtrl_HMD201207001_AO11

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mOCCtrl_HMD201207001_DB12

value: oocytes


title: 360_mouse_10d_sorted_CTR_bio_rep2

value: 10 days


title: AGS cells, OE_3

value: AGS

value: miR-BART1-3p overexpressed


title: AGS cells, OE_2


title: mGCCtrl_HMD201207001_BE08

value: ovary


title: GS ATP 6 h - biol rep1

value: brain striatum

value: GS

value: ATP injury

value: 6 h


title: SNU719 cells, S3

value: gastric cancer cells


title: mGCCtrl_HMD201207001_AC11

value: pre-granulosa cells


title: HFD, LKO, female8 RNA-seq

city: Lincoln

first: Xinghui

last: Sun

state: NE

address: 1901 Vine Street

department: Biochemistry

institute: University of Nebraska - Lincoln

description:
L2399
femaleLKOvsFlox_counts.csv

data_processing:
Data QC including error rate distribution, GC-content distribution, and data filtering
mapping to reference genome (mm10)
gene expression quantification
differential expression analysis
functional analysis
Assembly: mm10
Supplementary files format and content: Comma Separated Values Files includes raw counts for each sample

source_name: liver

growth_protocol: Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water, or a HFD with 60 kcal% fat (Research Diets, D12492) and water.

extract_protocol:
Total RNAs were extracted from mouse liver tissues after homogenization using TRIzol Reagent (Thermo Fisher, 15596026) according to the manufacturer’s instructions.
Directional mRNA library preparation (poly A enrichment) by Novogene

treatment_protocol: Male and female matrin-3 floxed mice and littermate LKO  mice were fed a 60% HFD (Research Diets, D12492) at 7 weeks of age for 16 weeks.

tag: Sex

value: female

value: liver

value: liver-specific knockout

value: 60% HFD for 16 weeks


title: AGS cells, NC_3

value: negtive control


title: WT ATP 6 h - biol rep2

value: WT


title: 372_mouse_10d_sorted_CTR_bio_rep1

value: reporter positive cells from back skin

value: ctr

value: 4-hydroxy tamoxifen


title: mGCCtrl_HMD201207001_CB23

value: ovarian surface epithelial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: HFD, LKO, female7 RNA-seq

description:
L2388
femaleLKOvsFlox_counts.csv


title: 402_mouse_10d_sorted_KO_bio_rep2

value: 10 days


title: WT ATP 6 h - biol rep1

value: brain striatum


title: AGS cells, NC_2

value: AGS


title: GS intact - biol rep2

value: GS


title: 398_mouse_10d_sorted_KO_bio_rep1


title: mGCCtrl_HMD201207001_CF03

value: ovary

value: interstitial cells


title: mOCCtrl_HMD201207001_DF14

value: oocytes


title: HFD, LKO, female6 RNA-seq

description:
L2390
femaleLKOvsFlox_counts.csv

value: female

value: liver


title: mOCCtrl_HMD201207001_DD22


title: GS ATP 6 h - biol rep2

value: ATP injury

value: 6 h


title: GS intact - biol rep1


title: 120mM_high_glucose_medium,rep2 [ATAC-seq]

city: xi'an

first: guangbo

last: tang

address: xianning road

institute: xi'an jiaotong university

data_processing:
sequence reads were mapped to hg38 using bowtie2(version 2.2.1)
duplicated reads were removed by picard MarkDuplicateds
reads mped to mitochondrion were removed using samtools view
peaks were called by MACSs
Assembly: hg38
Supplementary files format and content: tab-delimited text files of peaks information for each Sample

source_name: Human peritoneum

extract_protocol:
DNA was extracted from cells using proteinase K treatment and used for the construction of sequencing libraries.
ATAC-seq libraries for ATAC-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina from Vazyme  following manufacturer's protocols.

value: Human peritoneum

value: HPMCs

value: Human peritoneum derived cell


title: AGS cells, NC_1

value: gastric cancer cells

value: negtive control


title: AGS cells, OE_1

value: miR-BART1-3p overexpressed


title: WT intact - biol rep2

value: WT


title: mGCCtrl_HMD201207001_CN03

value: ovarian surface epithelial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: 120mM_high_glucose_medium,rep1 [ATAC-seq]


title: mGCCtrl_HMD201207001_CB11

value: granulosa cells


title: HFD, LKO, female5 RNA-seq

description:
L2392
femaleLKOvsFlox_counts.csv

value: liver-specific knockout

value: 60% HFD for 16 weeks


title: WT intact - biol rep1

value: brain striatum


title: HFD, floxed, female3 RNA-seq

description:
L2385
femaleLKOvsFlox_counts.csv

value: female

value: floxed


title: control_medium,rep2 [ATAC-seq]

value: control  medium


title: control_medium,rep1 [ATAC-seq]


title: HFD, floxed, female4 RNA-seq

description:
L2416
femaleLKOvsFlox_counts.csv

value: liver


title: mGCCtrl_HMD201207001_BE06

value: ovary


title: 120mM_high_glucose_medium,rep2

data_processing:
Trimmed sequence reads were mapped to hg38 using hisat2(version 2.2.1)
Read count extraction and normalization were performed using stringtie (version 2.1.7)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

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

value: Human peritoneum

value: HPMCs


title: HFD, floxed, female1 RNA-seq

description:
L2417
femaleLKOvsFlox_counts.csv


title: mOCCtrl_HMD201207001_DD20

value: oocytes


title: 120mM_high_glucose_medium,rep1

value: Human peritoneum derived cell


title: HFD, LKO, male8 RNA-seq

description:
L2396
maleLKOvsFlox_counts.csv

value: male


title: HFD, floxed, female2 RNA-seq

description:
L2387
femaleLKOvsFlox_counts.csv


title: mOCCtrl_HMD201207001_DB20

value: excluded by low quality


title: control_medium,rep2


title: HFD, LKO, male7 RNA-seq

description:
L2395
maleLKOvsFlox_counts.csv


title: mOCCtrl_HMD201207001_DJ18


title: HFD, LKO, male6 RNA-seq

description:
L2405
maleLKOvsFlox_counts.csv


title: mGCCtrl_HMD201207001_AM15

value: ovarian surface epithelial cells


title: HFD, LKO, male5 RNA-seq

description:
L2403
maleLKOvsFlox_counts.csv


title: WildType RCA replicate 3

type: RNA

first: Luke

last: Brewster

state: GA

address: 101 Woodruff Circle

department: Surgery

description: wt 3R

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: right (non-ligated) carotid artery

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Partial Carotid ligation was performed on the left common carotid artery of the mouse while the right common carotid artery was left untouched. Induction of disturbed blood flow was confirmed by ultrasound.  One-day post ligation, the carotid arteries were explanted and the RNA extraction was performed to investigate the global changes in gene expression using illumina microarray.

extract_protocol: RNA was extracted with Qiagen miREasy Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tag


title: mGCCtrl_HMD201207001_CN11

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Ribo-seq_293AD, F-YAP 5SA, serum-deprived, rep1

city: Daejeon

first: Daehee

last: Hwang

address: Yuseong-gu, Daehak-ro 291 Basic Science Bldg. (E6-6) #413

department: Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
Raw reads were trimmed using Cutadapt (v4.2)
Index building and alignment were preformed using STAR (v2.7.10a)
Read counts were generated using HTSeq (v2.0.2)
DEGs were obtained using deltaTE
Analysis of RPFs were performed using Ribo-TISH (v0.1.9)
Assembly: hg38
Supplementary files format and content: Anotated table containing fold-changes and FDR values comparing YAP 5SA vs. Vec (.txt)
Supplementary files format and content: Anotated table containing fold-changes and FDR values comparing YAP 5SA vs. Vec under serum-deprivation conditions (.txt)
Library strategy: Ribo-seq

growth_protocol: 293AD cells were cultured in DMEM (Welgene) supplemented with 10% FBS and penicillin-streptomycin

extract_protocol:
293AD cells stably expressing empty vector or YAP 5SA subjected to serum deprivation were preincubated with cycloheximide (100 μg/ml, Sigma) for 10 min. The cells were then lysed in 600 μl of lysis buffer [Tris-Cl pH 7.4 (10 mM, Duchefa), MgCl2 (5 mM, Junsei), KCl (100 mM, Junsei), Triton-X-100 (1%, Sigma), cycloheximide (100 μg/ml, Sigma), dithiothreitol (1 mM, Sigma), RiboLock RNase inhibitor (0.2 U/μl, Thermofisher), and EDTA-free protease inhibitor cocktail (1x, Roche)]. Then 300 μl of the cell lysates were treated with RNase I (5 U/μl, Ambion) for 45 min at room temperature for Ribo-seq library construction. The remaining 300 μl cell lysates were aliquoted for mRNA-seq library construction. RNase I-treated cell lysates were then placed in the Illustra MicroSpin S-400 HR Columns (GE Healthcare) and centrifuged at 600 x g for 2 min. Next, RiboMinus TM Eukaryote System v2 (Thermofisher) was used for the removal of ribosomal RNAs. For processing 5- and 3-end of ribosome protected fragments (RFPs) for subsequent library construction, Antarctic phosphatase (NEB) and T4 polynucleotide kinase (NEB) were treated, followed by size selection of 26-32 nt RPFs using a 12% TBE-urea gel system (National Diagnostics).
Library construction was performed using the TruSeq Small RNA Kit (Illumina)

treatment_protocol: Overnight serum-deprivation was performed by replacing growth medium with serum-free medium (same as growth medium, but without FBS)

value: embryonic kidney

tag: expressing

value: F-YAP 5SA

value: Overnight (14 h) serum deprivation

tag: molecule subtype = RPF (ribosome-protected fragment) RNA


title: HFD, floxed, male4 RNA-seq

description:
L2404
maleLKOvsFlox_counts.csv

value: 60% HFD for 16 weeks


title: mGCCtrl_HMD201207001_BI10

tag: developmental stage

tag: subpopulation gc


title: Ribo-seq_293AD, F-YAP 5SA, serum-deprived, rep2


title: Ribo-seq_293AD, F-YAP 5SA, rep2


title: FibVKO RCA replicate 1

description: ko 1R


title: HFD, floxed, male3 RNA-seq

description:
L2393
maleLKOvsFlox_counts.csv

tag: genotype


title: mGCCtrl_HMD201207001_CL03

value: pre-granulosa cells

tag: subpopulation oocyte

tag: marker expression_tdtomato


title: HFD, floxed, male2 RNA-seq

description:
L2711
maleLKOvsFlox_counts.csv

value: floxed


title: Ribo-seq_293AD, F-YAP 5SA, rep1


title: WildType LCA replicate 1

description: wt 1L

source_name: left (ligated) carotid artery


title: Ribo-seq_293AD, Vec, serum-deprived, rep2

value: vector


title: HFD, floxed, male1 RNA-seq

description:
L2710
maleLKOvsFlox_counts.csv

value: liver


title: control_medium,rep1

value: control  medium


title: FibVKO LCA replicate 1

description: ko 1L


title: FibVKO RCA replicate 2

description: ko 2R


title: WildType RCA replicate 1

description: wt 1R


title: FibVKO RCA replicate 3

description: ko 3R


title: mGCCtrl_HMD201207001_AE09

value: ovary

value: early theca cells

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)


title: WildType LCA replicate 2

description: wt 2L


title: FibVKO LCA replicate 3

description: ko 3L


title: Ribo-seq_293AD, Vec, rep2


title: Il1b+p53

first: Timothy

last: Wang

state: NY

address: 1130 Saint Nicholas Avenue

institute: Columbia university

data_processing:
Raw fastq files were processed by cellranger count https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count to generate single cell feature counts for each library.
Assembly: GRCm38
Supplementary files format and content: filtered feature-barcode matrices generated using cellranger.

source_name: Stomach

extract_protocol:
Samples were subjected to scRNA seq library construction on the 10X Genomics platform using Chromium™ Single Cell 3' v3 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol.
scRNA seq library construction was performed according to the 10X Genomics's instructions.

tag: tissue

value: Stomach

tag: agent


title: mGCCtrl_HMD201207001_BC14

tag: cell type

tag: intron ratio


title: mOCCtrl_HMD201207001_DP16

value: oocytes


title: FibVKO LCA replicate 2

description: ko 2L


title: Ribo-seq_293AD, Vec, serum-deprived, rep1

tag: cell line

tag: treatment


title: mGCCtrl_HMD201207001_AG17


title: mGCCtrl_HMD201207001_CP01


title: WildType LCA replicate 3

description: wt 3L


title: Ribo-seq_293AD, Vec, rep1


title: mGCCtrl_HMD201207001_CJ05

value: granulosa cells


title: Il1b_1


title: 293AD, F-YAP 5SA, serum-deprived, rep2

data_processing:
Raw reads were trimmed using Cutadapt (v4.2)
Index building and alignment were preformed using STAR (v2.7.10a)
Read counts were generated using HTSeq (v2.0.2)
DEGs were obtained using deltaTE
Assembly: hg38
Supplementary files format and content: Anotated table containing fold-changes and FDR values comparing YAP 5SA vs. Vec (.txt)
Supplementary files format and content: Anotated table containing fold-changes and FDR values comparing YAP 5SA vs. Vec under serum-deprivation conditions (.txt)

extract_protocol:
293AD cells stably expressing empty vector or YAP 5SA subjected to serum deprivation were preincubated with cycloheximide (100 μg/ml, Sigma) for 10 min. The cells were then lysed in 600 μl of lysis buffer [Tris-Cl pH 7.4 (10 mM, Duchefa), MgCl2 (5 mM, Junsei), KCl (100 mM, Junsei), Triton-X-100 (1%, Sigma), cycloheximide (100 μg/ml, Sigma), dithiothreitol (1 mM, Sigma), RiboLock RNase inhibitor (0.2 U/μl, Thermofisher), and EDTA-free protease inhibitor cocktail (1x, Roche)]. Then 300 μl of the cell lysates were treated with RNase I (5 U/μl, Ambion) for 45 min at room temperature for Ribo-seq library construction. The remaining 300 μl cell lysates were aliquoted, and total RNA was extracted using TRIzol reagent (Invitrogen)
Library construction was performed using the TruSeq Stranded mRNA Kit (Illumina)


title: 293AD, F-YAP 5SA, serum-deprived, rep1


title: mGCCtrl_HMD201207001_AK09

value: interstitial cells


title: CTRL_1

value: CTRL


title: WildType RCA replicate 2

description: wt 2R


title: mGCCtrl_HMD201207001_AO01

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: 293AD, F-YAP 5SA, rep2

value: embryonic kidney


title: Il1b_2


title: Tumor, PD-L1KO2

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The raw reads in fastq format was generated using cellranger mkfastq and count matrix was generated by cellranger count acording to cellranger v7.0.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissues were dissected from mice and digested with collagenase to make single cells.
scRNA-seq libraries were generataed using 10X 3’ single cell mRNAseq V3 reagents according to manufacturer's protocol.

value: Tumor

value: primary cells

value: Epithelial and immune cells

value: Cd274 KO


title: Tumor, PD-L1KO1


title: mOCCtrl_HMD201207001_DF10

value: excluded by low quality


title: mGCCtrl_HMD201207001_CF07


title: mOCCtrl_HMD201207001_DN16


title: 293AD, Vec, serum-deprived, rep1

value: vector

value: Overnight (14 h) serum deprivation


title: 293AD, Vec, serum-deprived, rep2


title: CTRL_2


title: Tumor, WT2

value: WT


title: mGCCtrl_HMD201207001_AE07

value: ovary


title: 293AD, Vec, rep2


title: miR-223-/y Chronic AOM/DSS 3

city: Maynooth

first: Eoin

middle: N

last: McNamee

state: Co Kildare

address: Rm 2.19 Bioscience bldg

department: Biology

country: Ireland

institute: Maynooth University

data_processing:
Illumina Casava 1.8 version base recognition
The procedure of raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined);(3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping: Used HISAT2 version 2.0.5 with the default parameters
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.The FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential Analaysis: Used DESeq2 version 1.20.0, parameters |log2(FoldChange)| >= 1 & padj <= 0.05
ClusterProfiler (version 3.8.1) was used for enrichment analysis. Padj < 0.05
GSEA (version 3.0) was used for GSEA analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes the correlation values for each sample

source_name: Colon

growth_protocol: miR-223 and C57BL/6J mice where bred in-house. After weaning for 21 days mice where co-housed until they where 8 weeks old.

extract_protocol:
Total RNA was ioslated from snap-frozen colonic tissue using Qiazol Reagent and Qiagen RNeasy kit (cat no. 74106) was followed as per manufactors instructions.
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 using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Mice were injected intraperitoneally with 10mg/kg of azoxymethane (AOM). After three days, dextran sodium sulphate (DSS) (2% w/v)  was administered in drinking water ad libitum for 7 days. This was followed by a two week recovery period where DSS was removed. This cycle of DSS was performed three times and then mice where culled.

value: Colon

value: miR223 Knockout

value: Azoxymethane (AOM)/Dextran Sodium Sulfate (DSS)


title: Tumor, WT1


title: mGCCtrl_HMD201207001_AE21

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

value: ovarian surface epithelial cells


title: 293AD, Vec, rep1


title: miR-223-/y Chronic AOM/DSS 2


title: mGCCtrl_HMD201207001_BG04

value: granulosa cells


title: 293AD, F-YAP 5SA, rep1

value: F-YAP 5SA


title: Prostate cancer - DACTPL rep3

city: Baltimore

first: Roshan

last: Chikarmane

state: Maryland

address: 30 W Biddle Street, Apt 1103B

department: Pharmacology

institute: Johns Hopkins University

data_processing:
rsem-1.2.09 was used for running the alignments to hg19 as well as generating transcript expression levels  for each gene, measured in expected counts and transcripts per million (TPM)
DESeq2 was used for differential expression analysis between treatment groups; TPM was used as an input
R version 4.0.4 was used to convert TPM to z-scores
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of z-score, expected counts, and TPM for each gene and sample. Table of fold changes and statistical results comparing treatment groups for each gene.

source_name: Prostate cancer

growth_protocol: All cells were incubated at 37°C & 5% CO2 in ATCC-recommended medium and grown to 80-90% confluence before addition of treatment.

extract_protocol:
Following the 20-day treatment period, total RNA was extracted and purified for using Qiagen Allprep method.
250-500ng of total RNA was subjected to library synthesis using the Illumina TruSeq Stranded Total RNA Sample Preparation kit. Quantification of the libraries is performed by qPCR with the NEBNext Library Quant Kit or by the Agilent Bioanalyzer, and equimolar concentrations of each library were pooled together. Cluster generation was performed on the cBot with Illumina’s TruSeq PE Cluster Kit v3, and sequencing performed on an Illumina HS2500 platform for a 100bp x 100bp, paired end sequencing with both the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit v3 (200 cycles).

treatment_protocol: DU145 cells were exposed to either 2 nM triptolide alone, 33 nM decitabine alone, or both 2 nM triptolide and 3 nM decitabine once daily for 3 days, followed by 17 more days of treatment-free growth.

value: 2 nM triptolide + 33 nM decitabine (20 days)

tag: disease state

value: prostate cancer, CNS metastasis


title: mGCCtrl_HMD201207001_BA20

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: miR-223-/y Chronic AOM/DSS 1


title: WT Chronic AOM/DSS 3


title: Prostate cancer - DACTPL rep2


title: mGCCtrl_HMD201207001_BI14

value: pre-granulosa cells


title: WT Chronic AOM/DSS 2


title: mOCCtrl_HMD201207001_DP22

value: oocytes


title: Prostate cancer - DAC rep3

value: 33 nM decitabine (20 days)


title: mOCCtrl_HMD201207001_DJ12


title: Prostate cancer - DAC rep2


title: WT Control 3

value: Untreated


title: mGCCtrl_HMD201207001_CD05


title: mOCCtrl_HMD201207001_DL20

value: excluded by low quality


title: Prostate cancer - DACTPL rep1


title: Prostate cancer - DAC rep1


title: WT Control 1


title: mGCCtrl_HMD201207001_AG05


title: Prostate cancer - TPL rep2

value: 2 nM triptolide (20 days)


title: WT Control 2


title: Prostate cancer - TPL rep3


title: MEF-KDM6A-WT-rep3

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 transcriptome with STAR, and gene expression was quantified with RSEM.
Differential gene expression analysis was performed with DESeq2.
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Raw counts of

source_name: Mouse embryonic fibroblast

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher Scientific) and then purify on RNA Clean and Concentrator column (Zymo Research).
polyA selection

treatment_protocol: Interferon alpha 200nM for 18h

value: Mouse embryonic fibroblast

value: Kdm6a wild type

tag: biorep


title: mOCCtrl_HMD201207001_DH22

first: Tappei

source_name: ovary

value: ovary


title: mGCCtrl_HMD201207001_AI15

value: early theca cells


title: MEF-KDM6A-WT-rep1


title: MEF-KDM6A-WT-rep2


title: Prostate cancer - Ctrl rep2

value: Vehicle (DMSO; 20 days)


title: MEF-KDM6A-WT-KRAS-rep3

value: Kdm6a wild type KRAS G12V


title: Prostate cancer - Ctrl rep3


title: WT Chronic AOM/DSS 1

value: Colon

value: Azoxymethane (AOM)/Dextran Sodium Sulfate (DSS)


title: mGCCtrl_HMD201207001_CP05

value: granulosa cells


title: mGCCtrl_HMD201207001_CN15


title: Mel 3

city: Shanghai

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

institute: Fudan University

description: Mel treatment

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: T24 cells

growth_protocol: T24 Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Yeasen),100 units/ml penicillin, and 100 μg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37°C。

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: T24 Cells were treated with or without melittin for 24 hours

value: human bladder cancer cells

value: treated with Mel

value: bladder cancer


title: MEF-KDM6A-WT-KRAS-rep2


title: MEF-KDM6A-WT-KRAS-rep1


title: mGCCtrl_HMD201207001_CJ11

last: Mishina

address: 744 Motooka Nishi-ku

institute: Kyushu University

value: interstitial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: human ATRT cell line, CHLA04

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

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

data_processing: Minfi R package (1.36.0); only probes with detection p value < 0.01 in all samples were kept; probes from X and Y chromosomes were removed; probes with SNPs in CpG site were removed; final probe set had n = 813.439 probes

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were grown under optimized conditions in DMEM/F12 supplemented with B27, EGF, FGF (CHLA02, CHLA04, CHLA05, CHLA06), IMDM supplemented with 10% FCS and 1x IST (CHLA266, BT12), or RPMI supplemented with 10% FCS (BT16).

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: male

value: human ATRT cell line


title: Mel 2

description: Mel treatment


title: MEF-KDM6A-KO-rep3

value: Kdm6a knock out


title: human ATRT cell line, BT12

value: female


title: human ATRT cell line, BT16


title: mGCCtrl_HMD201207001_BK08

city: Fukuoka


title: MEF-KDM6A-KO-rep2

value: Mouse embryonic fibroblast


title: Prostate cancer - DAC_20d_rep2

hyb_protocol: Genomic DNA was bisulfite converted using the Zymo Research EZ DNA methylation approach according to the manufacturer’s instructions, amplified, and hybridized to Illumina Infinium Human Methylation Beadchip using the standard Illumina protocol

scan_protocol: Array were imaged using the Illumina BeadArray Reader using the recommended Illumina iScan settings

data_processing: R version 4.0.4 was used to generate raw and normalized beta values. Normalization included preprocessing for Illumina methylation microarrays as used in Genome Studio followed by subset-quantile within array normalization (SWAN).

label_protocol: Standard Illumina Protocol for Cy5 and Cy3 labelling

extract_protocol: Genomic DNA was extracted with DNeasy kit according manufacturer’s protocol.

treatment_protocol: DU145 cells were exposed to either 2 nM triptolide alone, 33 nM decitabine alone, or both 2 nM triptolide and 3 nM decitabine once daily for 3 days, followed by  2 more days (5 days total) or 17 more days (20 days total) of treatment-free growth.

value: 2 nM triptolide

tag: time

value: 20 days

value: prostate cancer, CNS metastasis


title: Mel 1

description: Mel treatment


title: Prostate cancer - TPL rep1

value: 2 nM triptolide (20 days)


title: Prostate cancer - DACTPL_20d_rep2

value: 2 nM triptolide+ 33 nM decitabine


title: human ATRT cell line, CHLA02


title: human ATRT cell line, CHLA05


title: Brain_CR_2

city: Kyoto

first: Yutaro

last: Tomobe

address: 54 Kawaharacho Shogoin Sakyoku

department: Pediatrics

institute: Graduate School of Medicine, Kyoto University

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software.
Trimmed reads were mapped to a reference rat genome (mRatBN7.2) using STAR (version 2.7.10a).
Reads of annotated genes were counted using featureCounts (version 2.0.1).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Rattus norvegicus

source_name: whole brain

extract_protocol:
RNA was extracted using a TRIzol method (Invitrogen). 1.0 μg of total RNA was used for the construction of sequencing library.
RNA library were prepared with QIAseq Stranded RNA Lib Kit UDI (QIAGEN) and MGIEasy Universal Library Conversion Kit (App-A) (MGI).

value: whole brain

value: caloric restriction


title: MEF-KDM6A-KO-rep1


title: Prostate cancer - TPL_20d_rep2

value: 33 nM decitabine


title: Prostate cancer - Ctl_20d_rep2

value: Vehicle (DMSO)


title: Brain_CR_3


title: mGCCtrl_HMD201207001_BG16

value: ovary

tag: developmental stage


title: mOCCtrl_HMD201207001_DL10

value: oocytes

tag: subpopulation gc


title: Prostate cancer - TPL_20d_rep1


title: mGCCtrl_HMD201207001_BC16

value: pre-granulosa cells

tag: genotype

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Brain_CR_1


title: human ATRT cell line, CHLA266

value: human ATRT cell line


title: Ctrl 3

description: no treatment

value: human bladder cancer cells

value: no treatment

value: bladder cancer


title: Brain_ctrl_3

value: control


title: Ctrl 2

description: no treatment


title: human ATRT cell line, CHLA06

value: female


title: Ctrl 1

description: no treatment


title: MEF-KDM6A-KO-KRAS-rep3

value: Mouse embryonic fibroblast

value: Kdm6a knock out KRAS G12V


title: MEF-KDM6A-KO-KRAS-rep2


title: Prostate cancer - DACTPL_5d_rep2

value: 2 nM triptolide+ 33 nM decitabine

value: 5 days

value: prostate cancer, CNS metastasis


title: Prostate cancer - Ctrl rep1

value: Vehicle (DMSO; 20 days)


title: Brain_ctrl_2

value: whole brain


title: MEF-KDM6A-KO-KRAS-rep1


title: mOCCtrl_HMD201207001_DP12

value: ovary

tag: subpopulation oocyte


title: mGCCtrl_HMD201207001_BA14

value: excluded by low quality

tag: marker expression_tdtomato


title: Prostate cancer - Ctl_5d_rep2

value: Vehicle (DMSO)


title: IL-27 Pump Treated TxA23

city: St. Louis

first: Richard

last: DiPaolo

state: MO

address: 1100 S Grand Ave

institute: Saint Louis Univeristy

description: three females

data_processing:
Files were run through cellranger 3.0.0 using the cellranger count function and replicates were combined using cellranger aggr.
Assembly: UCSC Genome Browser assembly ID: mm10
Supplementary files format and content: The processed data files contain up to three aggregated replicates for each treatment condition.

source_name: Stomach Flush

extract_protocol:
Immune cells were flushed from the gastric mucosa and CD45+ propidium iodide-cells were isolated. These cell suspensions then were washed once and loaded onto the 10× Genomics Chromium Controller to follow the 10X 5'v1.1 protocol
Library construction followed the 10x Genomics 5' v1.1 GEX Library Construction protocol.

treatment_protocol: Mini osmotic pumps loaded with PBS or 4 μg/mL recombinant, covalently linked p28-EBI3 (rIL27), were implanted subcutaneously into TxA23 mice at 3 months of age and left for 1 month.

value: Stomach Flush

value: Immune


title: Brain_ctrl_1


title: mOCCtrl_HMD201207001_DB24

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)

tag: marker expression_kit-apc


title: Water deficit, Day 10, Young, Rep 3

city: Leiden

first: Salma

last: Balazadeh

address: Slviusweg 72

country: Netherlands

institute: Leiden University

data_processing:
Read trimming, and alignment an mapping of reads were performed in CLC Genomics workbench (QIAGEN). Reads were aligned to the Solanum lycopersicum SL4.00 genome release, using ITAG4.1 gene annotation data, using the following parameters: Mismatch cost: 2, insertion cost: 3, deletion cost: 3. Normalization and differential expression analyses were performed using the DESeq2 package in R (4.3.1).
Assembly: Solanum lycopersicum SL4.00
Supplementary files format and content: comma separated values (.csv) file, contains raw readcounts for each sample

organism: Solanum lycopersicum

source_name: Whole developing leaf

growth_protocol: Solanum lycopersicum cv Moneymaker plants were germinated on full-strength Murashige-Skoog medium containing 3% sucrose. After three weeks, the most developed seedlings were transferred into 3 L pots containing potting soil, vermiculite and sand in a 25:8:2 ratio, supplemented with 3 tablespoons osmocote fertilizer. Plants were maintained at 70% relative humidity, with a long day (16h/8h) day/night cycle at at 200 µmol/m2/s light intensity.

extract_protocol:
Total RNA has been extracted using TriZol, following the manufacturer's instructions
Library preparation was performed in-house by BGI genomics (P_Standard library & Seq (PE100), library was validated on the Agilent Technologies 2100 bioanalyzer)

treatment_protocol: Well watered plants were watered every other day to soil capacity. Water deficit plants were subjected to complete water withholding

value: Whole developing leaf

value: WT (cv MoneyMaker)

value: Water deficit


title: K27me3-MEF-KDM6A-WT

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 genome with Bowtie2.
Peak calling was performed with MACS v2.1.2
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Peak locations from MACS peak calling

extract_protocol:
For crosslinking, cells were pelleted and resuspended in PBS containing 1% fresh formaldehyde for 8 min at room temperature with rotation. Crosslinking was quenched by addition of 1/10 volume of 1.25M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in lysis buffer (10% glycerol, 1% Triton TX-100, 0.1 mM EDTA, 14mM NaCl 25mM Hepes pH 7.5) and incubated for 5 minutes on ice. Cell nuclei were pelleted and incubated 5 min in wash buffer (0.1 mM EDTA, 20mM NaCl, 2mM Tris-HCl pH 7.5). Cell nuclei were pelleted and resuspended in 1 ml sonication buffer (1 mM EDTA, 10mM Tris-HCl pH 7.5) at a concentration equivalent to 10x106 cells per ml. Samples were sonicated in 1ml in AFA fiber Covaris tubes using the Covaris E220 (Woburn, MA) for 30 minutes using the following settings: 15% Duty Cycle, 200 cycles/burst, and Peak incidence 140. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in 2X ChIP dilution buffer (2% Triton X-100, 2mM EDTA, 300mM NaCl, 30mM Tris-HCl pH 8). Sheared chromatin samples were block with 20 µl Protein A/G Dyna beads (Invitrogen) for 2h at 4°C with rotation. Immunoprecipitations were performed overnight (16 hours, 4°C, with rotation) with the following antibodies: H3K27Ac (Acitve Motif #39133), H3K27me3 (Cell Signaling Technologies #9733), KDM6A (Cell Signaling Technologies #33510). Samples were washed once with ChIP dilution buffer(1% Triton X-100, 1mM EDTA, 150mM NaCl, 15mM Tris-HCl pH 8), low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 100mM NaCl, 20mM Tris-HCl pH 8), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), LiCl wash buffer (1% deoxycholate, 1% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and Tris buffer (10mM Tris-HCl pH 7.5). For library construction, beads were incubated in 15 µl Tagmentase buffer with 1µl Tagment enzyme (Illumina Nextera DNA library Prep kit #15028212) and incubated at 37°C for 10 min. Immediately after, beads were washed once in 1ml ChIP dilution buffer and in 1 ml TE (10mM Tris-HCl pH 7.5, EDTA 1mM) prior to incubation in reverse crosslinking buffer (300mM NaCl, 10 mM EDTA, 0.5% SDS, 20mM Tris-HCl pH 8) for 4 hours at 65°C with shaking. Finally, proteinase K digestion was performed for 1h at 55°C with shaking prior to DNA purification using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205, Irvine, CA).
Libraries were generated by amplification of ChIP DNA using KAPA HiFi Hotstart Library Amp kit (Roche #07959028001, Indianapolis, IN) and size selected for between 200 bp and 700 bp using Ampure beads XP (Beckman Coulter, Brea, CA). Library were quantified and QC using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA) and sequenced on an Ilumina Hi-Seq 3000 with 150 bp pair-end reads.

value: Mouse embryonic fibroblast

value: Kdm6a wild type

tag: ip antibody


title: Water deficit, Day 10, Young, Rep 2

tag: tissue


title: mGCCtrl_HMD201207001_BE20

value: interstitial cells

tag: cell size_(fsc1_area)


title: Prostate cancer - DAC_5d_rep2

value: 2 nM triptolide

value: 5 days


title: K27me3-MEF-KDM6A-KO-KRAS

value: Kdm6a knock out KRAS G12V


title: Mouse (WT-S-5) with NAc transduced with HSV-ZFP189WT, Saline group, Day 7

city: Richmond

first: Joseph

middle: Anthony

last: Picone

state: Virginia

address: 1217 E Marshall St,

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genomes using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 Only unique reads within exon regions were counted.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: Fastq and hitcounts in .txt

source_name: Microdissected Nucleus accumbens

extract_protocol:
Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelectTM−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were multiplexed and clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

value: Microdissected Nucleus accumbens

tag: strain

value: Saline + ZFP189WT


title: K27me3-MEF-KDM6A-WT-KRAS

value: Kdm6a wild type KRAS G12V


title: Prostate cancer - Ctl_20d_rep1

value: Vehicle (DMSO)

value: 20 days

value: prostate cancer, CNS metastasis


title: mGCCtrl_HMD201207001_CB15

value: ovary

tag: cell type

value: excluded by low quality

tag: intron ratio


title: Prostate cancer - DACTPL_5d_rep1

tag: treatment

value: 2 nM triptolide+ 33 nM decitabine

tag: cell line


title: Prostate cancer - TPL_5d_rep1

value: 33 nM decitabine

tag: disease state


title: Prostate cancer - DAC_20d_rep1


title: Water deficit, Day 10, Young, Rep 1

value: Whole developing leaf

value: WT (cv MoneyMaker)

value: Water deficit


title: Prostate cancer - DACTPL_20d_rep1


title: Prostate cancer - DAC_5d_rep1


title: mOCCtrl_HMD201207001_DN18

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Mouse (WT-S-3) with NAc transduced with HSV-ZFP189WT, Saline group, Day 7


title: mGCCtrl_HMD201207001_CN05

value: interstitial cells


title: Control, Day 10, Young, Rep 2

value: Control


title: mGCCtrl_HMD201207001_CD17


title: Control, Day 10, Young, Rep 3


title: Mouse (WT-S-4) with NAc transduced with HSV-ZFP189WT, Saline group, Day 7

value: Microdissected Nucleus accumbens


title: K27me3-MEF-KDM6A-KO

value: Mouse embryonic fibroblast

value: Kdm6a knock out


title: K27ac-MEF-KDM6A-WT-KRAS

value: Kdm6a wild type KRAS G12V


title: Mouse (WT-S-1) with NAc transduced with HSV-ZFP189WT, Saline group, Day 7

value: Saline + ZFP189WT


title: Control, Day 10, Young, Rep 1


title: Mouse (WT-S-2) with NAc transduced with HSV-ZFP189WT, Saline group, Day 7


title: mGCCtrl_HMD201207001_CH09


title: Prostate cancer - Ctl_5d_rep1

value: Vehicle (DMSO)

value: 5 days

value: prostate cancer, CNS metastasis


title: K27ac-MEF-KDM6A-WT

value: Kdm6a wild type


title: mGCCtrl_HMD201207001_AO15

value: ovary

value: granulosa cells


title: K27ac-MEF-KDM6A-KO-KRAS

value: Kdm6a knock out KRAS G12V


title: mGCCtrl_HMD201207001_BO22


title: Water deficit, Day 10, Mature, Rep 3

source_name: Single leaflet of mature leaf

value: Single leaflet of mature leaf

value: WT (cv MoneyMaker)

value: Water deficit


title: Mouse (WT-M-5) with NAc transduced with HSV-ZFP189WT, Morphine group, Day 7

value: Morphine + ZFP189WT


title: Mouse (WT-M-4) with NAc transduced with HSV-ZFP189WT, Morphine group, Day 7


title: Water deficit, Day 10, Mature, Rep 2


title: Prostate cancer - TPL_5d_rep2

value: 33 nM decitabine


title: PBS Pump Treated TxA23

description: one male and one female

value: Stomach Flush

value: Immune

value: PBS


title: K27ac-MEF-KDM6A-KO

value: Mouse embryonic fibroblast

value: Kdm6a knock out


title: Mouse (WT-M-3) with NAc transduced with HSV-ZFP189WT, Morphine group, Day 7

value: Microdissected Nucleus accumbens


title: RGCs of  UTX-AAV2-GFP mice (P42) 3

city: Beijing

first: Tao

last: Huang

state: Beijing

address: Dong Da Jie No.8

institute: The Fifth Medical Center of Chinese PLA General Hospital

data_processing:
All raw sequencing reads were quality checked with FastQC (v0.11.9), and leading bases were trimmed from the reads with Trimmomatic (v0.39) as appropriate.
Quality-checked reads were mapped to the GRCm38/mm10 mouse reference genome with splice-aware aligner HISAT2 (v2.2.1).
featureCounts (Subread v2.0.3) was used to estimate the expression counts of the genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Retina

extract_protocol:
Total RNA was isolated using TRIzol® Reagent following the manufacturer's protocol. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Retina

tag: age

value: retinal ganglion cells

tag: facs type

value: Thy1.2 positive

value: GFP

value: optic nerve crush


title: mGCCtrl_HMD201207001_AK11

value: ovary

tag: developmental stage

value: granulosa cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Water deficit, Day 10, Mature, Rep 1

value: Single leaflet of mature leaf

value: WT (cv MoneyMaker)

value: Water deficit


title: RGCs of  UTX-AAV2-GFP mice (P42) 2


title: Mouse (WT-M-2) with NAc transduced with HSV-ZFP189WT, Morphine group, Day 7

value: Morphine + ZFP189WT


title: Mouse (WT-M-1) with NAc transduced with HSV-ZFP189WT, Morphine group, Day 7


title: mGCCtrl_HMD201207001_BC04

value: interstitial cells

tag: subpopulation gc


title: RGCs of  UTX-AAV2-GFP mice (P42) 1

tag: genotype


title: Control, Day 10, Mature, Rep 2

value: Control


title: mOCCtrl_HMD201207001_DF08

value: oocytes

tag: subpopulation oocyte


title: RGCs of UTX-AAV2-Cre mice (P42) 2

value: UTX knockout


title: Control, Day 10, Mature, Rep 3


title: mOCCtrl_HMD201207001_DH18

value: excluded by low quality

tag: marker expression_tdtomato


title: Mouse (WT-C-5) with NAc transduced with HSV-ZFP189WT, Cocaine group, Day 7

value: Microdissected Nucleus accumbens

value: Cocaine + ZFP189WT


title: Mouse (WT-C-4) with NAc transduced with HSV-ZFP189WT, Cocaine group, Day 7


title: mOCCtrl_HMD201207001_DH20

tag: marker expression_kit-apc


title: Water deficit, Day 8, Mature, Rep 1


title: RGCs of UTX-AAV2-Cre mice (P42) 1

value: Retina

value: retinal ganglion cells

value: Thy1.2 positive


title: Control, Day 8, Mature, Rep 2


title: MF61, ATAC

city: New York

first: Elena

last: Zaslavsky

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic single cell

data_processing:
Cell Ranger ARC 2.0.0 pipeline was run on the samples following 10x Genomics guidelines.
Assembly: mm10
Supplementary files format and content: Count matrices for cell barcodes in Hierarchical Data Format HDF5.  File includes both the Gene Expression UMI count matrix and the ATAC peaks fragment count matrix.
Supplementary files format and content: BED-like tabular file listing all unique fragments captured by the ATAC assay in tab-separated values (TSV) format.

source_name: frozen pituitary

extract_protocol:
Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. The pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei buffer for sn multiome (10X Genomics).
sn Multiome was performed as described (10x Genomics, Pleasanton, CA; (24)), following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guidelines. Nuclei were filtered and counted on a Countess instrument. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit J  PN-200264) was loaded to target 10,000 nuclei final. After transposition, linear amplification was performed in the emulsion and cDNA was amplified before the RNA and ATAC library constructions were performed following the Chromium multiome protocol. The library was tagged with an index for multiplexing (Chromium i7 Sample Index Plate N Set A for ATAC PN-3000427; Chromium i7 Sample Dual Index Plate TT Set A for ATAC PN-3000431). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using paired-end reads.

value: frozen pituitary

value: WT

value: 11 weeks

tag: Sex

value: Female


title: Water deficit, Day 8, Mature, Rep 2

tag: tissue

value: Single leaflet of mature leaf

value: WT (cv MoneyMaker)


title: Mouse (WT-C-2) with NAc transduced with HSV-ZFP189WT, Cocaine group, Day 7


title: MF60, ATAC


title: mGCCtrl_HMD201207001_BM12

value: ovary

value: pre-granulosa cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)

tag: cell size_(fsc1_area)


title: Mouse (WT-C-1) with NAc transduced with HSV-ZFP189WT, Cocaine group, Day 7

tag: strain


title: mGCCtrl_HMD201207001_BG06

tag: cell type

value: granulosa cells


title: mOCCtrl_HMD201207001_DJ24

value: oocytes

tag: intron ratio


title: Control, Day 8, Mature, Rep 1

tag: treatment

value: Control


title: Water deficit, Day 5, Mature, Rep 3

value: Water deficit


title: Mouse (WT-C-3) with NAc transduced with HSV-ZFP189WT, Cocaine group, Day 7

value: Microdissected Nucleus accumbens

value: Cocaine + ZFP189WT


title: MF57, ATAC


title: Mouse (VPR-S-5) with NAc transduced with HSV-ZFP189VPR, Saline group, Day 7

value: Saline + ZFP189VPR


title: Water deficit, Day 5, Mature, Rep 2


title: mGCCtrl_HMD201207001_AG13


title: Mouse (VPR-S-4) with NAc transduced with HSV-ZFP189VPR, Saline group, Day 7


title: mGCCtrl_HMD201207001_CJ01


title: MF56, ATAC


title: Water deficit, Day 5, Mature, Rep 1


title: MF64, ATAC


title: Mouse (VPR-S-3) with NAc transduced with HSV-ZFP189VPR, Saline group, Day 7


title: Control, Day 5, Mature, Rep 3


title: MF51, ATAC


title: Mouse (VPR-S-2) with NAc transduced with HSV-ZFP189VPR, Saline group, Day 7


title: mGCCtrl_HMD201207001_BE24


title: Control, Day 5, Mature, Rep 2


title: mGCCtrl_HMD201207001_BK10


title: Water deficit, Day 4, Mature, Rep 3


title: Mouse (VPR-M-4) with NAc transduced with HSV-ZFP189VPR, Morphine group, Day 7

value: Morphine + ZFP189VPR


title: Control, Day 5, Mature, Rep 1


title: mGCCtrl_HMD201207001_AM13


title: MF50, ATAC, bio rep 1

value: frozen pituitary


title: MF55, ATAC

value: WT


title: Water deficit, Day 4, Mature, Rep 2


title: MF45, ATAC

value: 11 weeks


title: mGCCtrl_HMD201207001_BG12

value: interstitial cells


title: MF44, ATAC, bio rep 2

value: Female


title: mGCCtrl_HMD201207001_AG07


title: Water deficit, Day 4, Mature, Rep 1

value: Single leaflet of mature leaf

value: WT (cv MoneyMaker)


title: Mouse (VPR-M-2) with NAc transduced with HSV-ZFP189VPR, Morphine group, Day 7


title: MF44, ATAC, bio rep 1


title: mOCCtrl_HMD201207001_DJ02

value: ovary


title: Mouse (VPR-M-1) with NAc transduced with HSV-ZFP189VPR, Morphine group, Day 7


title: MF42, ATAC


title: Control, Day 4, Mature, Rep 3


title: Mouse (VPR-S-1) with NAc transduced with HSV-ZFP189VPR, Saline group, Day 7


title: MF50, ATAC, bio rep 2


title: Mouse (VPR-M-5) with NAc transduced with HSV-ZFP189VPR, Morphine group, Day 7


title: Control, Day 4, Mature, Rep 2


title: mGCCtrl_HMD201207001_CB17

value: excluded by low quality

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mOCCtrl_HMD201207001_DN06

value: oocytes


title: MF41, ATAC


title: Control, Day 4, Mature, Rep 1

value: Control


title: Mouse (VPR-C-4) with NAc transduced with HSV-ZFP189VPR, Cocaine group, Day 7

value: Cocaine + ZFP189VPR


title: mGCCtrl_HMD201207001_AO23

value: ovarian surface epithelial cells


title: MF37, ATAC


title: MF38, ATAC


title: uninj_4, biol_rep_4_2

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description:
U4_fq2
uninj_4, biol_rep_4, fastq2
raw_counts_run2.txt

data_processing:
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Count matrices from both sequencing runs were summed in R, then differentially expressed transcripts were identified in EdgeR (edgeR_4.0.16) in R4.3.2. Transcripts with <1 cpm in 4/12 samples were removed. After recalcluation of library sizes, samples were normalized using the trimmed mean of M-values (TMM) method, and generalized linear model (GLM) common, trended, and tagwise dispersions were calculated. The negative binomial GLM was fitted with glmQLFit, followed by identification of differentially expressed transcripts with the GLM quasi-likelihood ratio test (glmQLFTest).
Assembly: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary files format and content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Change, logCPM, F-test, P value, and FDR-adjusted P value.

organism: Schmidtea mediterranea

source_name: tail (postpharyngeal region excluding ~10% of tail tip)

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in Montjuic water and fed with calf liver paste. Planarians were starved 7 days prior to injection experiments.

extract_protocol:
Total RNA was extracted from the tail (postpharyngeal region excluding ~10% of the posterior-most tail tip) of 5 planarian tail fragments per biological replicate using Trizol and Zymo RNA columns as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4 biological replicates per condition was used for library generation from ~750-1000 ng/sample using the IDT xGen RNA library prep kit with NEB poly-A selection, and RNA sequencing (150 bp PE reads on an Illumina NovaSeq X Plus) with standard Illumina adapters. Two sequencing runs were conducted per sample.

treatment_protocol: Extracellular vesicles were isolated from planarian tissue fragments 12 hours after amputation. 12 hpa fragments were dissociated in CMF-B/collagenase, and strained through a 70 um mesh. Supernatant was sequentially centrifuged at 200 x g, 3000 x g, and 10,000 x g, precipitated with 10% PEG 10,000, then EVs were enriched using SBI SmartSEC Mini EV size exclusion chromatography columns. EVs were eluted in 90 ul IB buffer, and mixed with 10 ul 546-Alexa-conjugated 10,000 kD dextrans (5 mg/ml), for a final concentration of ~1 animals' EVs per 1 ul. EVs (or buffer only + dextrans) were injected into planarian tails (~1 animal's EVs per planarian). Animals were allowed to recover for 1 hour, then animals with low dextran content were removed from the experiment.

tag: clonal line

value: wild type

value: none (control)


title: Mouse (VPR-M-3) with NAc transduced with HSV-ZFP189VPR, Morphine group, Day 7

value: Microdissected Nucleus accumbens

value: Morphine + ZFP189VPR


title: uninj_3, biol_rep_3_2

description:
U3_fq2
uninj_3, biol_rep_3, fastq2
raw_counts_run2.txt

value: tail (postpharyngeal region excluding ~10% of tail tip)


title: mGCCtrl_HMD201207001_BC06

value: granulosa cells


title: MF64, GEX

value: frozen pituitary

value: WT

value: 11 weeks


title: Mouse (VPR-C-3) with NAc transduced with HSV-ZFP189VPR, Cocaine group, Day 7


title: mOCCtrl_HMD201207001_DL08


title: uninj_2, biol_rep_2_2

description:
U2_fq2
uninj_2, biol_rep_2, fastq2
raw_counts_run2.txt


title: Mouse (VPR-C-1) with NAc transduced with HSV-ZFP189VPR, Cocaine group, Day 7


title: uninj_1, biol_rep_1_2

description:
U1_fq2
uninj_1, biol_rep_1, fastq2
raw_counts_run2.txt


title: Mouse (VPR-C-2) with NAc transduced with HSV-ZFP189VPR, Cocaine group, Day 7


title: mGCCtrl_HMD201207001_BO14


title: Mouse (NFD-S-5) with NAc transduced with HSV-ZFP189NFD, Saline group, Day 7

value: Saline + ZFP189NFD


title: MF60, GEX

value: Female


title: mGCCtrl_HMD201207001_BI12

value: ovary

value: pre-granulosa cells


title: EV_inj_4, 24_hpi, biol_rep_4_2

description:
E4_fq2
EV_inj_4, 24_hpi, biol_rep_4, fastq2
raw_counts_run2.txt

value: EV injection, 24 hpi


title: MF57, GEX


title: mGCCtrl_HMD201207001_AA23

value: early theca cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: MF61, GEX


title: Mouse (VPR-C-5) with NAc transduced with HSV-ZFP189VPR, Cocaine group, Day 7

value: Cocaine + ZFP189VPR


title: Mouse (NFD-S-3) with NAc transduced with HSV-ZFP189NFD, Saline group, Day 7


title: Mouse (NFD-S-4) with NAc transduced with HSV-ZFP189NFD, Saline group, Day 7


title: EV_inj_3, 24_hpi, biol_rep_3_2

description:
E3_fq2
EV_inj_3, 24_hpi, biol_rep_3, fastq2
raw_counts_run2.txt

value: wild type


title: EV_inj_2, 24_hpi, biol_rep_2_2

description:
E2_fq2
EV_inj_2, 24_hpi, biol_rep_2, fastq2
raw_counts_run2.txt


title: MF56, GEX


title: mOCCtrl_HMD201207001_DH10

value: oocytes


title: mGCCtrl_HMD201207001_CD11


title: Mouse (NFD-S-2) with NAc transduced with HSV-ZFP189NFD, Saline group, Day 7

value: Microdissected Nucleus accumbens


title: MF55, GEX


title: Mouse (NFD-S-1) with NAc transduced with HSV-ZFP189NFD, Saline group, Day 7


title: EV_inj_1, 24_hpi, biol_rep_1_2

description:
E1_fq2
EV_inj_1, 24_hpi, biol_rep_1, fastq2
raw_counts_run2.txt


title: mOCCtrl_HMD201207001_DH24


title: ctrl_inj_4, 24_hpi, biol_rep_4_2

description:
C4_fq2
ctrl_inj_4, 24_hpi, biol_rep_4, fastq2
raw_counts_run2.txt

value: buffer injection, 24 hpi


title: MF51, GEX


title: Mouse (NFD-M-5) with NAc transduced with HSV-ZFP189NFD, Morphine group, Day 7

value: Morphine + ZFP189NFD


title: ctrl_inj_3, 24_hpi, biol_rep_3_2

description:
C3_fq2
ctrl_inj_3, 24_hpi, biol_rep_3, fastq2
raw_counts_run2.txt

value: tail (postpharyngeal region excluding ~10% of tail tip)


title: MF50, GEX, bio rep 2

value: frozen pituitary


title: MF50, GEX, bio rep 1

value: WT


title: Mouse (NFD-M-4) with NAc transduced with HSV-ZFP189NFD, Morphine group, Day 7


title: MF45, GEX

value: 11 weeks


title: MF44, GEX, bio rep 2


title: Mouse (NFD-M-3) with NAc transduced with HSV-ZFP189NFD, Morphine group, Day 7


title: Mouse (NFD-M-2) with NAc transduced with HSV-ZFP189NFD, Morphine group, Day 7


title: ctrl_inj_2, 24_hpi, biol_rep_2_2

description:
C2_fq2
ctrl_inj_2, 24_hpi, biol_rep_2, fastq2
raw_counts_run2.txt


title: mGCCtrl_HMD201207001_AM09

value: granulosa cells


title: Mouse (NFD-M-1) with NAc transduced with HSV-ZFP189NFD, Morphine group, Day 7


title: mGCCtrl_HMD201207001_CL19


title: uninj_4, biol_rep_4_1

description:
U4_fq1
uninj_4, biol_rep_4, fastq1
raw_counts_run1.txt

value: none (control)


title: mOCCtrl_HMD201207001_DF22

value: ovary


title: ctrl_inj_1, 24_hpi, biol_rep_1_2

description:
C1_fq2
ctrl_inj_1, 24_hpi, biol_rep_1, fastq2
raw_counts_run2.txt


title: mGCCtrl_HMD201207001_AK15

value: interstitial cells


title: MF42, GEX

value: Female


title: uninj_2, biol_rep_2_1

description:
U2_fq1
uninj_2, biol_rep_2, fastq1
raw_counts_run1.txt


title: mGCCtrl_HMD201207001_CN01

value: ovarian surface epithelial cells


title: Mouse (NFD-C-5) with NAc transduced with HSV-ZFP189NFD, Cocaine group, Day 7

value: Cocaine + ZFP189NFD


title: MF38, GEX


title: mGCCtrl_HMD201207001_CD13

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: uninj_1, biol_rep_1_1

description:
U1_fq1
uninj_1, biol_rep_1, fastq1
raw_counts_run1.txt

value: wild type


title: mGCCtrl_HMD201207001_BM16


title: Mouse (NFD-C-4) with NAc transduced with HSV-ZFP189NFD, Cocaine group, Day 7


title: mGCCtrl_HMD201207001_CL15


title: Mouse (NFD-C-2) with NAc transduced with HSV-ZFP189NFD, Cocaine group, Day 7


title: MF37, GEX


title: Mouse (NFD-C-1) with NAc transduced with HSV-ZFP189NFD, Cocaine group, Day 7


title: mGCCtrl_HMD201207001_AA19

value: excluded by low quality


title: MF44, GEX, bio rep 1


title: uninj_3, biol_rep_3_1

description:
U3_fq1
uninj_3, biol_rep_3, fastq1
raw_counts_run1.txt


title: gd IEL, UC7-13D5, PBS, biol rep 3

first: Matthew

last: Fischer

address: 1470 Madison Ave

department: Pathology

data_processing:
Partek Flow pipline (v11.0.23.1004), PGS7.21.1119
Sequence reads were aligned to mm39 using STAR (2.7.8a)
Aligned reads were filtered with a maximum <=100 reads and quantified to PartekE/M annotation model (Ensembl Transcripts release 104)
Read count normalization was performed with Median ratio followed by DESeq2 using Partek Flow
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes Median ratio (for DESeq2 only) normalized counts for all samples

source_name: small intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq HT kit following the manufacturer's protocols

treatment_protocol:
Mice were i.p. injected with either 200 ug UC7-13D5 or Armenian Hamster IgG Antibody 48 and 24 hours prior to IEL isolation.
Mice from both antibody treatment groups were treated with PBS or 1 ug IFNa i.v. 5 hours prior to IEL isolation

value: small intestine

value: gd intraepithelial lymphocyte

value: PBS


title: EV_inj_2, 24_hpi, biol_rep_2_1

description:
E2_fq1
EV_inj_2, 24_hpi, biol_rep_2, fastq1
raw_counts_run1.txt

value: tail (postpharyngeal region excluding ~10% of tail tip)

value: EV injection, 24 hpi


title: eWAT, IR 4A, replicate 4

first: Eunhee

last: Choi

address: 630 West 168th Street

institute: Columbia University

data_processing:
Raw sequencing reads were quantified with Salmon v1.8.0 to obtain transcript abundance counts by mapping to mouse genome GRCm39 GENCODE v.M31. The resulting counts were summarized to the gene level using tximport v1.20.0.
Differential expression was analyzed using DESeq2 v1.32.0. Differentially expressed (DE) genes were defined by an absolute fold change > 1.5 and false discovery rate (FDR)-adjusted P value < 0.05 and visualized using Volcano plots.
The output of DESeq2 were scored and ranked by apeglm v1.14.0 using ranking metrics “−log10 P value multiplied by the sign of shrunken log2 fold-change”. The ranked gene list was then subjected to Gene Set Enrichment Analysis (GSEA) to identify the gene sets overrepresented at the top or bottom of the ranked list using pathway definition file “Mouse_GOBP_AllPathways_no_GO_iea_November_17_2022_symbol.gmt” downloaded from http://baderlab.org/GeneSets. Only ontologies with more than 15 genes and less than 200 genes were considered.
The top ranked pathways were manually curated to remove the repetitive pathways and visualized using dot plots.
The leading-edge genes enriched in the identified pathways were visualized using pheatmap v1.0.12.
Assembly: mouse genome GRCm39 GENCODE v.M31
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld
Supplementary files format and content: Differential expression analysis results by DESeq2

source_name: eWAT

extract_protocol:
Total RNA was extracted from liver and adipose tissues using TRIzol (Invitrogen) RNeasy mini kit (Qiagen).
All samples were prepared simultaneously to avoid bias related to batched library preparation. Library preparation and RNA sequencing were performed by the Columbia Genome Center. In brief, mRNA was isolated using poly-A tail pulldown and cDNA libraries constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).
RNA-seq, Libraries were sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. Samples were multiplexed in each lane, yielding approximately 20 million 100 bp paired-end reads for each sample.

value: eWAT

value: male

value: 2 months

value: IR 4A


title: MF41, GEX

value: frozen pituitary

value: WT

value: 11 weeks


title: gd IEL, UC7-13D5, PBS, biol rep 2


title: Mouse (NFD-C-3) with NAc transduced with HSV-ZFP189NFD, Cocaine group, Day 7

value: Microdissected Nucleus accumbens


title: mGCCtrl_HMD201207001_AM17

value: ovary

value: ovarian surface epithelial cells


title: gd IEL, UC7-13D5, PBS, biol rep 1


title: EV_inj_4, 24_hpi, biol_rep_4_1

description:
E4_fq1
EV_inj_4, 24_hpi, biol_rep_4, fastq1
raw_counts_run1.txt

value: wild type


title: eWAT, IR 4A, replicate 2


title: gd IEL, UC7-13D5, IFNa, biol rep 3

value: IFNa


title: mGCCtrl_HMD201207001_CP19

value: granulosa cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: ctrl_inj_4, 24_hpi, biol_rep_4_1

description:
C4_fq1
ctrl_inj_4, 24_hpi, biol_rep_4, fastq1
raw_counts_run1.txt

value: buffer injection, 24 hpi


title: eWAT, IR 4A, replicate 1


title: mGCCtrl_HMD201207001_AI13

value: interstitial cells


title: ctrl_inj_2, 24_hpi, biol_rep_2_1

description:
C2_fq1
ctrl_inj_2, 24_hpi, biol_rep_2, fastq1
raw_counts_run1.txt

value: tail (postpharyngeal region excluding ~10% of tail tip)


title: mGCCtrl_HMD201207001_BM08


title: EV_inj_3, 24_hpi, biol_rep_3_1

description:
E3_fq1
EV_inj_3, 24_hpi, biol_rep_3, fastq1
raw_counts_run1.txt

value: EV injection, 24 hpi


title: eWAT, IR 4A, replicate 5

value: eWAT

value: male


title: gd IEL, UC7-13D5, IFNa, biol rep 2

value: small intestine

value: gd intraepithelial lymphocyte


title: mGCCtrl_HMD201207001_BK14

value: pre-granulosa cells


title: mOCCtrl_HMD201207001_DN24

value: oocytes


title: ctrl_inj_1, 24_hpi, biol_rep_1_1

description:
C1_fq1
ctrl_inj_1, 24_hpi, biol_rep_1, fastq1
raw_counts_run1.txt


title: gd IEL, UC7-13D5, IFNa, biol rep 1

value: WT


title: eWAT, WT, replicate 4

value: 2 months


title: mOCCtrl_HMD201207001_DD08

value: ovary