title: RNA-seq_M14-D0-rep2

city: Guangzhou City

first: Shujuan

last: Xie

institute: The Third Affiliated Hospital,Sun Yat-Sen University

data_processing:
The raw data (raw reads)were filtered by removing the joints at both ends of the reads and removing the fragment length <17nt;
Clean reads were compared with the reference genome (mm10) to obtain the distribution map of whole-genome reads.
Clean reads were classified and annotated for mRNA and ncRNA classification, and differential expression was analyzed between samples
For the m6A modification, R package exomePeak was used to identify significant m6A peaks and differential peaks.IGV software and HOMER were used for de novo motif discovery based on top 1k most-enrichment peaks.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: bw
Supplementary_files_format_and_content: log2FoldChange

source_name: Mettl14-overexpressing C2C12

growth_protocol: C2C12 cells were cultured in growth medium (GM), which consisted of Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum , 100 U/ml penicillin, and 100 ug/ml streptomycin (1×penicillin–streptomycin).When  cells grow up to about 90% confluency, the GM was subsequently replaced with differentiation medium (DM), which was DMEM containing 2% horse serum.

extract_protocol:
Total RNA was extracted from C2C12 cellswith TRIzol reagent according to the manufacturer’s instruction.
The total RNA or m6A-specific antibody immunoprecipated RNA fragments of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection

tag: time point


title: mpkCCD dDAVP 3h replicate 3

status: Public on Jul 22 2021

type: SRA

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

country: USA

institute: Johns Hopkins University School of Medicine

library_source: transcriptomic

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 (M22) using salmon (0.14.10).
Genome_build: GRCm38.p6 (M22)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: mouse cortical collecting duct cell line

growth_protocol: mpkCCD cells were grown on a permeable filter membrane for 6 days in the complete medium and maintained in the minimum medium for 24 hours before dDAVP treatment.

extract_protocol:
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
cDNAs were synthesized from total RNA using SMART-Seq HT kit (Takara Bio). cDNA libraries were prepared for sequencing using a Nextera DNA library preparation protocol.

treatment_protocol: Vasopressin analog dDAVP (0.1 M) or vehicle was treated at the basolateral side (a bottom chamber) and then cells were incubated for appropriate time according to the time points.

tag: strain

tag: tissue

value: kidney

tag: age

value: passage 10-11

tag: genotype

value: wild type

tag: cell type

tag: treatment

value: dDAVP

tag: time


title: mpkCCD vehicle 6h replicate 1

value: mouse cortical collecting duct cell line

value: Vehicle


title: mpkCCD dDAVP 3h replicate 1


title: mpkCCD dDAVP 3h replicate 2


title: mpkCCD vehicle 3h replicate 3


title: RNA-seq_M3-D0-rep1

state: China

country: China

source_name: Mettl3-overexpressing C2C12

tag: cell line


title: RNA-seq_M14-D0-rep1


title: olaparib MDA-MB-468 rep1

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

institute: Wayne State University

data_processing:
Data were demultiplexed using Illumina's CASAVA 1.8.2 software.
After quality was assessed using FastQC, reads were aligned to the human reference genome using STAR before tabulation using htseq-count.
RNA-seq data were analyzed using the R/Bioconductor package edgeR.
Read counts within and between samples were normalized using the trimmed mean of M-values (TMM) method.
Genome_build: hg38
Supplementary_files_format_and_content: Parental_OlaR TNBC_.csv contains counts and differential expressions between isogenic parental and olaparib resistant MDA-MB-468 and SUM1315 cells treated with olaprib, cisplatin or combinations.

organism: Homo sapiens

source_name: TNBC BRCA1 wild type

growth_protocol: Parental MDA-MB-468 and SUM1315 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum. OlaR (OR) MDA-MB-468 and SUM1315 cells were maintained in same media supplemented with 15 or 25 mM olaparib, respectively.

extract_protocol:
Total RNA was isolated from cell lines using RNA later followed by purification with RNeasy mini kit (Qiagen) using the manufacturer’s recommended in-solution DNase digestion.
RNA-seq libraries were prepared using Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina) from 200 ng of DNAse I treated total RNA. Libraries were quantified using Qubit 2.0 dsDNA HS kit and the size distribution determined on a Fragment Analyzer.

treatment_protocol: Parental MDA-MB-468 cells were treated overnight with 3 mM olaparib, 1 or 2.5 mM cisplatin, or a combination of 3 mM olaparib and 1 or 2.5 mM cisplatin. Parental SUM1315 cells were treated overnight with 8  mM olaparib, 2 or 4 mM cisplatin, or a combination of 8  mM olaparib and 2 or 4 mM cisplatin. OlaR MDA-MB-468 cells maintained in 15 mM olaparib were treated with 1 or 2.5 mM cisplatin. OlaR SUM1315 cells were maintained in 25 mM olaparib were treated with 2 or 4 mM cisplatin.


title: SNU182-Combination

city: Amsterdam

first: Haojie

last: Jin

address: Plesmanlaan 121

department: The Netherlands Cancer Institute

country: Netherlands

institute: Division of Molecular Carcinogenesis

data_processing:
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38, using Tophat 2.1 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: nomalized counts

source_name: Liver cancer cells

growth_protocol: Liver cancer cell lines SNU449, JHH1, Huh6 and SNU182 were cultured in DMEM with 10% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2

extract_protocol:
RNA was  harvested using RLT lysis buffer and stored in a 2 mL Eppendorf tube at -80 degrees Celsius before analysis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Liver cancer cell lines SNU449, JHH1, Huh6 and SNU182 were treated with DMSO, 2.5 mM gefitinib, 5 mM lenvatinib, or two-drugs combination for 24 h, respectively

value: Liver cancer cells

value: treated with Gefitinib plus Lenvatinib for 24 hours


title: RNA-seq_GFP-D4-rep1

source_name: GFP-overexpressing C2C12


title: mpkCCD vehicle 3h replicate 2


title: RNA-seq_M3-D0-rep2


title: MZ.flox.4wk.5

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description: Tsc1-/- marginal zone B cell

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: Tsc1Flox.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Tsc1Flox.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Tsc1Flox.noIg.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts
Supplementary_files_format_and_content: Tsc1Flox.noIg.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts

source_name: Splenic B cell

growth_protocol: Tsc1F.hCD20-TamCre mice were bred and maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows:  follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech SMART-Seq HT kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: In-vivo samples are 4 weeks tamoxifen treated SPF mice.

value: Spleen

value: 12 weeks

value: 4 weeks tamoxifen


title: MZ.flox.4wk.4

description: Tsc1-/- marginal zone B cell


title: MZ.flox.4wk.6

description: Tsc1-/- marginal zone B cell


title: SNU182-Gefitinib

value: treated with Gefitinib for 24 hours


title: Huh6-Combination


title: SNU182-CT

value: untreated


title: MZ.flox.4wk.2

description: Tsc1-/- marginal zone B cell


title: RNA-seq_GFP-D4-rep2


title: MZ.flox.4wk.3

description: Tsc1-/- marginal zone B cell


title: RNA-seq_GFP-D0-rep2


title: MZ.flox.4wk.1

description: Tsc1-/- marginal zone B cell


title: SNU182-Lenvatinib

value: treated with Lenvatinib for 24 hours


title: RNA-seq_GFP-D0-rep1


title: MZ.het.4wk.6

description: Tsc1+/- marginal zone B cell


title: MZ.het.4wk.5

description: Tsc1+/- marginal zone B cell


title: Huh6-Lenvatinib


title: Huh6-Gefitinib


title: MZ.het.4wk.4

description: Tsc1+/- marginal zone B cell


title: JHH1-Combination


title: stress_3

city: Hamilton

first: Ryan

last: Shaler

state: Ontario

address: 1280 Main Street West

country: Canada

institute: McMaster University

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bsl2fastq v. 2.17 program.
Sequenced reads were trimmed for adaptor sequence using trimmatic and mapped to mm9 transcriptome using salmon v1.3.0 with parameters  -p 12 -o
quantified samples were imported into R and sumarized using trimeta and differential counts determined using DeSeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with relative gene expression for each sample .csv

source_name: stress_Ileal tissue

extract_protocol:
Ileal samples were removed and immediately placed intoTrizol reagent and transported on ice. RNA was extracted using a standard Trizol extraction. Ribosomal RNA depletion was performed on 16 samples using Ribo-Zero Gold Kit (Human/Mouse/Rat probe) (Illumina, San Diego, CA, USA).  The samples were sequenced using a 2x150 Paired End (PE)configuration.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: control mice were starved and water depleted, stress mice were restrained in a 50mL tube for 16h, stress mice treated with IL-22fc were given150ug IL-22fc 2h prior to being placed in a 50mL for 16h

value: Ileal tissue

value: 5 days post colonization NRG857c

value: IgG


title: stress_1


title: control_3

source_name: control_Ileal tissue


title: stress_IL22fc_3

source_name: stress_IL22fc_Ileal tissue


title: stress_2


title: stress_IL22fc_2


title: control_1


title: MZ.het.4wk.1

description: Tsc1+/- marginal zone B cell


title: control_2


title: JHH1-Lenvatinib


title: JHH1-Gefitinib


title: JHH1-CT


title: MZ.cre.4wk.6

description: Tsc1+/+ marginal zone B cell


title: MZ.cre.4wk.5

description: Tsc1+/+ marginal zone B cell


title: stress_IL22fc_1


title: MZ.het.4wk.3

description: Tsc1+/- marginal zone B cell


title: SNU449-Combination


title: MZ.cre.4wk.4

description: Tsc1+/+ marginal zone B cell


title: SNU449-Lenvatinib


title: MZ.het.4wk.2

description: Tsc1+/- marginal zone B cell


title: Huh6-CT


title: MZ.cre.4wk.3

description: Tsc1+/+ marginal zone B cell


title: MZ.cre.4wk.2

description: Tsc1+/+ marginal zone B cell


title: SNU449-Gefitinib


title: GB2_SD_12h

city: Minato-ku

first: Natsu

last: Nakajima

state: Tokyo

address: General Research Building 8th floor, 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

data_processing:
Data processing  were performed using Cell Ranger from the 10X Genomics pipeline (v2.1.0) with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated values files include raw count (UMI) values for each Sample.

molecule: polyA RNA

source_name: glioblastoma stem-like cells

growth_protocol: GSCs were cultured in DMEM/F12 (Invitrogen) containing B27 supplement minus vitamin A (Invitrogen), EGF and FGF2 (20 ng/ml each, Wako Pure Chemical Industries). For serum-induced differentiation, cells were cultured in DMEM/F12 containing 10% FBS.

extract_protocol: Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol

value: differentiated glioblastoma stem-like cells indeuced by serum for 12 hour.

tag: tumor stage

value: GBM


title: MZ.cre.4wk.1

description: Tsc1+/+ marginal zone B cell


title: Gingival tissue at 5M, Aged NHP 5

type: RNA

city: Lexington

first: kuey

middle: Chu

last: Chen

state: KENTUCKY

address: 800 Rose Street, UK Med Ctr

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

description: Gene expression data from gingival tissues of Aged NHPs 2 months after ligature removal (5M)

hyb_protocol: Following fragmentation, 5.5ug of cRNA were hybridized for 16-18 hrs at 45C on GeneChip RheGene-1_0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affy GeneChip scanner GC3000-7G.

data_processing: The data were analyzed with Partek GenomicsSuite 6.0 using GC-RMA and quantile normalization method.

label: biotin

organism: Macaca mulatta

source_name: Gingival tissue from Aged NHP-5M

label_protocol: Biotinylated cRNA were prepared from 250ng total RNA according to the protocol in Ambion WT Expression kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (user guide, 2011).

growth_protocol: Clinical characterization of each animal was done with a calibrated periodontal UNC probe including pocket depth and bleeding on probing at all time points.

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

treatment_protocol: Interproximal gingival tissue samples (papillae) from the same animal at different time points were obtained through a standard gingivectomy technique. Gingival tissues were preserved in RNAlater for further processing and RNA extraction.

tag: gender

value: Female

tag: age group

value: 5 months


title: Gingival tissue at 5M, Aged NHP 8

value: Male


title: Gingival tissue at 5M, Aged NHP 4


title: Gingival tissue at 5M, Aged NHP 9


title: GB2_S_P10

value: patient derived glioblastoma stem-like cells (GSCs) cultured in serum free condition.

tag: passage


title: Gingival tissue at 5M, Aged NHP 7


title: Gingival tissue at 5M, Aged NHP 1


title: FO.flox.4wk.5

description: Tsc1-/- follicular B cell


title: Gingival tissue at 5M, Aged NHP 2


title: SNU449-CT

value: Liver cancer cells


title: Gingival tissue at 3M, Aged NHP 6

description: Gene expression data from gingival tissues of Agedt NHPs 3M post-ligation

source_name: Gingival tissue from Aged NHP-3M

value: 3 months


title: Gingival tissue at 5M, Aged NHP 3


title: Gingival tissue at 3M, Aged NHP 8


title: Gingival tissue at 3M, Aged NHP 9


title: Gingival tissue at 3M, Aged NHP 3


title: Gingival tissue at 5M, Aged NHP 6


title: FO.flox.4wk.4

description: Tsc1-/- follicular B cell

value: Spleen


title: Gingival tissue at 3M, Aged NHP 5


title: Gingival tissue at 3M, Aged NHP 7


title: FO.flox.4wk.6

description: Tsc1-/- follicular B cell

value: 12 weeks


title: Gingival tissue at 3M, Aged NHP 2


title: HYPO50

city: Orange

first: Patricia

middle: C

last: Lopes

state: CA

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
Normalized abundance counts were generated using the DESeq2 R package
Genome_build: GCA_001577835.1 Coturnix_japonica_2.0
Supplementary_files_format_and_content: tab-delimited text file includes raw (not normalized) readcount values for each sample

organism: Coturnix japonica

extract_protocol:
Brains were removed and flash frozen on dry ice; brain regions were later punched out on a cryostat, placed in Qiazol lysis reagent and homogeneized; Total RNA was extracted from the aqueous layer formed after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

tag: Sex

value: M

value: exposed (I) to a parental sensitization treatment

tag: behavioral response

tag: brain region

value: hypothalamus


title: Gingival tissue at 3M, Aged NHP 1


title: FO.flox.4wk.3

description: Tsc1-/- follicular B cell

value: 4 weeks tamoxifen


title: FO.flox.4wk.2

description: Tsc1-/- follicular B cell


title: HYPO49

value: R


title: MLN-1

city: Beijing

first: Changying

last: Li

address: Panjiayuan Street 17, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

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

source_name: Hepatic double negative T cells

extract_protocol:
7-AAD-CD45+CD3+NK1.1-CD4-CD8- cells were sorted using FACS Aria II in mouse liver, then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult

tag: diet

value: normal diet


title: Gingival tissue at 3M, Aged NHP 4

tag: time point


title: Gingival tissue at 1M, Aged NHP 8

description: Gene expression data from gingival tissues of Aged NHPs 1M post-ligation

source_name: Gingival tissue from Aged NHP-1M

value: 1 month


title: FO.het.4wk.6

description: Tsc1+/- follicular B cell

tag: strain

tag: tissue


title: Gingival tissue at 1M, Aged NHP 6

tag: age


title: HYPO48


title: MLM-2

value: methionine-choline deficient diet


title: HYPO47

value: NR


title: MLM-1


title: Gingival tissue at 1M, Aged NHP 5

value: Female


title: HYPO46


title: FO.het.4wk.3

description: Tsc1+/- follicular B cell

tag: genotype


title: FO.het.4wk.2

description: Tsc1+/- follicular B cell

tag: treatment


title: FO.het.4wk.4

description: Tsc1+/- follicular B cell


title: HYPO31

value: not exposed (C) to a parental sensitization treatment

value: NS


title: FO.het.4wk.1

description: Tsc1+/- follicular B cell


title: MLN-2


title: MED4_degron_6h_nascent_RNAseq_Rep2

city: Los Angeles

first: Fei

last: Sun

state: California

address: 615 Charles E Young Drive South

department: Biological Chemistry

institute: UCLA

data_processing:
Base-calling was performed with RTA.
Sequence reads were mapped to mm9 using TopHat2 with option –g 1 –N 2. For Spike-ins, sequence reads were mapped to hg19 using TopHat2 with option –g 1 –N 2.
Reads within the entire gene body (including all exons and introns) were counted with a custom script. An RPK (reads per kilobase) value was calculated for each gene by dividing the read counts by the gene body size. RPK values were normalized to the spike-ins when comparing between different samples.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files containing normalized RPK values

growth_protocol: Degron or V6.5 cells were cultured on a MEF feeder layer (Invitrogen) in media containing DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/ml LIF, 100 M nonessential amino acids, 2 mM L-gultamine and 8 nL/ml of 2-mercaptoethanol at 37oC in a humidified 5% CO2/95% air incubator.

extract_protocol:
Mouse ESCs were harvested at ~80% confluency and washed with DPBS. Cells were counted and 10 million cells were collected for subsequent steps. Half a million human BEAS-2B cells were mixed into the 10 million mouse ESCs as the spike-in. Cells were lysed in 200 μL of ice-cold lysis buffer (10 mM Tris-HCl pH 7.5, 0.1% NP40, 150 mM NaCl). The cell lysate was gently layered over 500 μL of a chilled sucrose cushion (24% RNase-free sucrose in lysis buffer) in a new Eppendorf tube and centrifuged for 10 min at 4°C at 10,000xg. The supernatant (cytoplasmic fraction) was removed and the pellet (nuclei) was washed once with 200 μL of ice-cold 1×PBS/1 mM EDTA. The nuclear pellet was resuspended in 100 μL of pre-chilled glycerol buffer (20 mM Tris-HCl pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) by gentle flicking of the tube. An equal volume (100 μl) of cold nuclear lysis buffer (10 mM HEPES pH 7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added. The mix was vortexed vigorously for 2 s. The sample was incubated for 2 min on ice, and then centrifuged for 2 min at 4°C at 10,000xg. The supernatant (nuclear fraction/nucleoplasm) was removed and the pellet (chromatin) was gently rinsed with ice-cold 1×PBS/1 mM EDTA. 1 mL of Trizol reagent was added to the chromatin and incubated for 30 min at 50°C to dissolve it. Nascent RNA was extracted following the manufacturer’s instructions.
Libraries were constructed using KAPA Stranded RNA-Seq Kit with RiboErase (HMR).

treatment_protocol: Degron cells were treated with auxin for 6 hours. For the degron controls and V6.5 cells, no treatment was performed.

tag: cell type

value: embryonic stem cell

value: treated with auxin for 6 hours

tag: molecule subtype

value: nascent RNA


title: MED4_degron_0h_nascent_RNAseq_Rep2

value: untreated


title: MED4_degron_6h_nascent_RNAseq_Rep1


title: V65_nascent_RNAseq_Rep2

source_name: V6.5 cells


title: V65_nascent_RNAseq_Rep1


title: FO.cre.4wk.6

description: Tsc1+/+ follicular B cell

value: Spleen

value: 12 weeks


title: MED4_degron_0h_nascent_RNAseq_Rep1


title: HYPO29

value: M

value: hypothalamus


title: Gingival tissue at 1M, Aged NHP 3

value: Male


title: FO.cre.4wk.5

description: Tsc1+/+ follicular B cell

value: 4 weeks tamoxifen


title: TAF12_degron_6h_nascent_RNAseq_Rep2


title: HYPO21


title: HYPO20

value: exposed (I) to a parental sensitization treatment


title: HYPO30


title: HYPO18

value: R


title: HYPO16


title: Gingival tissue at 1M, Aged NHP 7

value: 1 month


title: HYPO19


title: HYPO17


title: HYPO15

value: NR


title: FO_B.48h.4

description: 48 hr anti-Notch2 treated mouse: follicular B cell

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: NotchBlockade.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: NotchBlockade.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol

growth_protocol: C57BL6 mice purchased from Jackson Labs and were maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows:  follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD1d-.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD1dhigh.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech SMART-Seq HT kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: In-vivo samples are from anti-Notch2 or isotype control treated SPF mice.

value: wild type

value: anti-Notch2 Ab 48h


title: FO.cre.4wk.4

description: Tsc1+/+ follicular B cell


title: FO.cre.4wk.3

description: Tsc1+/+ follicular B cell


title: V65_mRNAseq_shControl_for_Med1_and_Med14_Rep2

data_processing:
Base-calling was performed with
Sequence reads were mapped to mm9 using TopHat2 with option –g 1 –N 2.
Gene transcription levels were normalized to RPKM using SAMMate with the mode of Read Assignment Expectation Maximization (RAEM).
Genome_build: mm9
Supplementary_files_format_and_content: Excel files containing RPKM of all transcripts

growth_protocol: V6.5 cells were cultured on a MEF feeder layer (Invitrogen) in media containing DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/ml LIF, 100 M nonessential amino acids, 2 mM L-gultamine and 8 nL/ml of 2-mercaptoethanol at 37oC in a humidified 5% CO2/95% air incubator.

extract_protocol:
Total RNA was extracted with TRIzol Reagent following manufacturer’s instructions.
mRNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kits following manufacturer’s instructions.

treatment_protocol: MEF-depleted V6.5 cells were grown to ~50% confluency in 12-well plates before being transfected with 1.8 microgram shRNA plasmids using Lipofectamine 2000 following manufacturer’s instructions. 24 h post transfection, 1 ug/ml puromycin was added and cells were selected for 72 h before downstream analysis.

value: transfected with shRNA plasmid


title: TAF12_degron_0h_nascent_RNAseq_Rep1

value: embryonic stem cell


title: FO_B.48h.3


title: V65_mRNAseq_shControl_for_Gcn5_Usp22_and_all_Mediator_subunits_EXCEPT_Med15_16_23_24_25_Rep2


title: TAF12_degron_6h_nascent_RNAseq_Rep1

value: treated with auxin for 6 hours


title: TAF12_degron_0h_nascent_RNAseq_Rep2

value: nascent RNA


title: Gingival tissue at 1M, Aged NHP 2

value: Female


title: V65_mRNAseq_shControl_for_Med1_and_Med14_Rep1


title: Gingival tissue at 1M, Aged NHP 1


title: FO_B.48h.1

value: Spleen


title: FO.cre.4wk.1

description: Tsc1+/+ follicular B cell

value: 12 weeks


title: FO_B.48h.2


title: Gingival tissue at 2W, Aged NHP 5

description: Gene expression data from gingival tissues of Aged NHPs 2W post-ligation

source_name: Gingival tissue from Aged NHP-2W

value: 2 weeks


title: HYPO14

value: M

value: hypothalamus


title: Gingival tissue at 1M, Aged NHP 4

value: Male


title: V65_mRNAseq_shControl_for_Gcn5_Usp22_and_all_Mediator_subunits_EXCEPT_Med15_16_23_24_25_Rep1


title: Gingival tissue at 2W, Aged NHP 3


title: HYPO13

value: exposed (I) to a parental sensitization treatment


title: V65_mRNAseq_shControl_for_all_TFIID_subunits_and_Med15_16_23_24_25_Rep2


title: FO_B.24h.3

description: 24 hr anti-Notch2 treated mouse: follicular B cell

value: anti-Notch2 Ab 24h


title: HYPO12

value: not exposed (C) to a parental sensitization treatment

value: NS


title: FO_B.24h.4

value: wild type


title: HYPO11

value: S


title: V65_mRNAseq_shUsp22_Rep2

value: transfected with shRNA plasmid


title: V65_mRNAseq_shControl_for_all_TFIID_subunits_and_Med15_16_23_24_25_Rep1

value: embryonic stem cell


title: V65_mRNAseq_shUsp22_Rep1


title: Gingival tissue at 2W, Aged NHP 7


title: FO_B.12h.4

description: 12 hr anti-Notch2 treated mouse: follicular B cell

value: anti-Notch2 Ab 12h


title: FO_B.24h.2


title: FO_B.12h.3


title: HYPO10


title: V65_mRNAseq_shTbp_Rep2


title: HYPO9


title: FO_B.12h.2


title: Gingival tissue at 2W, Aged NHP 2


title: Gingival tissue at 2W, Aged NHP 9


title: Gingival tissue at 2W, Aged NHP 8


title: Gingival tissue at 2W, Aged NHP 4


title: Gingival tissue at 2W, Aged NHP 6


title: Gingival tissue at BL, Aged NHP 8

description: Gene expression data from gingival tissues of Aged NHPs before ligation

source_name: Gingival tissue from Aged NHP-BL

value: base line


title: HYPO44

value: F

value: NR


title: V65_mRNAseq_shTaf9_Rep1


title: Gingival tissue at 2W, Aged NHP 1

value: Female


title: Gingival tissue at BL, Aged NHP 5


title: V65_mRNAseq_shTaf9_Rep2


title: HYPO43

value: R


title: Gingival tissue at BL, Aged NHP 7


title: HYPO45


title: Gingival tissue at BL, Aged NHP 9


title: FO_B.IC.3

description: Isotype control treated mouse: follicular B cell

value: Spleen

value: 12 weeks

value: Isotype control Ab 48h


title: Gingival tissue at BL, Aged NHP 4

value: Male


title: HYPO42

value: exposed (I) to a parental sensitization treatment

value: hypothalamus


title: FO_B.IC.4


title: V65_mRNAseq_shTaf8_Rep2


title: V65_mRNAseq_shTaf8_Rep1


title: FO_B.IC.2


title: V65_mRNAseq_shTbp_Rep1


title: Gingival tissue at BL, Aged NHP 6


title: Gingival tissue at BL, Aged NHP 3


title: Gingival tissue at BL, Aged NHP 2


title: Gingival tissue at 5M, Adult NHP 9

description: Gene expression data from gingival tissues of Adult NHPs 2 months after ligature removal (5M)

source_name: Gingival tissue from Adult NHP-5M

value: 5 months


title: Gingival tissue at BL, Aged NHP 1


title: FO_B.IC.1

value: wild type


title: HYPO40

value: not exposed (C) to a parental sensitization treatment

value: NS


title: Gingival tissue at 5M, Adult NHP 8


title: FO_B.12h.1


title: V65_mRNAseq_shTaf7_Rep2

value: embryonic stem cell

value: transfected with shRNA plasmid


title: HYPO39


title: HYPO37


title: V65_mRNAseq_shTaf7_Rep1


title: V65_mRNAseq_shTaf6_Rep2


title: V65_mRNAseq_shTaf6_Rep1


title: MZ_B.48h.4

description: 48 hr anti-Notch2 treated mouse: marginal zone B cell

value: anti-Notch2 Ab 48h


title: MZ_B.48h.2


title: V65_mRNAseq_shTaf5_Rep2


title: HYPO36

value: F


title: MZ_B.48h.1


title: MZ_B.48h.3


title: HYPO35

value: S


title: MZ_B.24h.4

description: 24 hr anti-Notch2 treated mouse: marginal zone B cell

value: anti-Notch2 Ab 24h


title: V65_mRNAseq_shTaf5_Rep1


title: HYPO34


title: MZ_B.24h.3


title: Gingival tissue at 5M, Adult NHP 6

value: Female


title: HYPO38


title: V65_mRNAseq_shTaf4_Rep2


title: MZ_B.24h.2

value: Spleen


title: Gingival tissue at 5M, Adult NHP 7


title: V65_mRNAseq_shTaf4_Rep1


title: HYPO32


title: HYPO33


title: Gingival tissue at 5M, Adult NHP 4


title: Gingival tissue at 5M, Adult NHP 5


title: MZ_B.12h.4

description: 12 hr anti-Notch2 treated mouse: marginal zone B cell

value: 12 weeks

value: anti-Notch2 Ab 12h


title: MZ_B.12h.3


title: V65_mRNAseq_shTaf4b_Rep2


title: HYPO28

value: NR


title: Gingival tissue at 5M, Adult NHP 3

value: Male


title: Gingival tissue at 5M, Adult NHP 2


title: V65_mRNAseq_shTaf4b_Rep1


title: HYPO26

value: exposed (I) to a parental sensitization treatment

value: R

value: hypothalamus


title: V65_mRNAseq_shTaf3_Rep2


title: HYPO27


title: V65_mRNAseq_shTaf3_Rep1


title: Gingival tissue at 5M, Adult NHP 1

value: 5 months


title: Gingival tissue at 3M, Adult NHP 9

description: Gene expression data from gingival tissues of Adult NHPs 3M post-ligation

source_name: Gingival tissue from Adult NHP-3M

value: 3 months


title: HYPO25


title: MZ_B.IC.4

description: Isotype control treated mouse: marginal zone B cell

value: wild type

value: Isotype control Ab 48h


title: MZ_B.12h.1


title: HYPO24

value: not exposed (C) to a parental sensitization treatment

value: NS


title: MZ_B.IC.3


title: V65_mRNAseq_shTaf2_Rep2

value: embryonic stem cell

value: transfected with shRNA plasmid


title: Gingival tissue at 3M, Adult NHP 6

value: Female


title: HYPO23

value: F


title: V65_mRNAseq_shTaf2_Rep1


title: MZ_B.IC.2

value: Spleen

value: 12 weeks


title: Gingival tissue at 3M, Adult NHP 5


title: MZ_B.12h.2

value: anti-Notch2 Ab 12h


title: HYPO22


title: V65_mRNAseq_shTaf1_Rep2


title: Gingival tissue at 3M, Adult NHP 7


title: V65_mRNAseq_shTaf1_Rep1


title: HYPO7


title: wt.sham.12w.rep2

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

institute: Hubrecht Institute

data_processing:
aligment - STAR 2.7.3a
readcount analysis - featurecounts (SubRead 2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: PLN_featureCounts_raw.txt (raw readcounts)

source_name: Sham 3 days post surgery  left ventricle

extract_protocol:
Standard Trizol total RNA extraction
TruSeq mRNA stranded (illumina)

treatment_protocol: For ischemic heart disease models, 12-week-old male C57Bl6/J mice were randomized to temporary (ischemia-reperfusion; I/R) or permanent (myocardial infarction; MI) ligation of the left anterior descending (LAD) coronary artery or sham surgery. Three days post-I/R or 8 weeks post-MI, left ventricular (LV) tissues were collected from the area remote of the infarcted myocardium.

value: wt

tag: surgery

value: sham

value: left ventricle


title: HYPO6

value: exposed (I) to a parental sensitization treatment

value: R

value: hypothalamus


title: wt.sham.20w.rep2

source_name: Sham 8 weeks post surgery left ventricle


title: Gingival tissue at 3M, Adult NHP 8

tag: gender

value: 3 months


title: Gingival tissue at 3M, Adult NHP 3

value: Male

tag: age group


title: HYPO5


title: V65_mRNAseq_shTaf13_Rep1


title: wt.sham.20w.rep1


title: HYPO4

value: not exposed (C) to a parental sensitization treatment


title: V65_mRNAseq_shTaf13_Rep2


title: Gingival tissue at 3M, Adult NHP 1


title: Gingival tissue at 3M, Adult NHP 2


title: V65_mRNAseq_shTaf12_Rep2


title: Gingival tissue at 3M, Adult NHP 4


title: Gingival tissue at 1M, Adult NHP 8

description: Gene expression data from gingival tissues of Adult NHPs 1M post-ligation

source_name: Gingival tissue from Adult NHP-1M

value: 1 month


title: Gingival tissue at 1M, Adult NHP 9


title: wt.sham.12w.rep1


title: MZ_B.IC.1

source_name: Splenic B cell

value: wild type

value: Isotype control Ab 48h


title: V65_mRNAseq_shTaf12_Rep1

value: embryonic stem cell

value: transfected with shRNA plasmid


title: HYPO3

value: F


title: HYPO2

value: S


title: V65_mRNAseq_shTaf11_Rep2


title: wt.MI.rep4

source_name: Myocardial infarction 8 weeks post injury left ventricle


title: V65_mRNAseq_shTaf11_Rep1


title: HYPO1


title: Gingival tissue at 1M, Adult NHP 7

value: Female


title: wt.MI.rep2

value: wt


title: wt.MI.rep3


title: Gingival tissue at 1M, Adult NHP 6


title: V65_mRNAseq_shTaf10_Rep2


title: NST45

value: bed nucleus of the stria terminalis (BNST)


title: wt.MI.rep1

value: left ventricle


title: NST44

value: exposed (I) to a parental sensitization treatment

value: NR


title: V65_mRNAseq_shTaf10_Rep1


title: NST43

value: R


title: wt.IR.rep3

source_name: Ischemia-reperfusion 3 days post injury left ventricle


title: wt.IR.rep4


title: V65_mRNAseq_shMed9_Rep2


title: NST42


title: V65_mRNAseq_shMed9_Rep1


title: V65_mRNAseq_shMed8_Rep2


title: wt.IR.rep2


title: NST40

value: NS


title: Gingival tissue at 1M, Adult NHP 3

value: Male


title: V65_mRNAseq_shMed8_Rep1


title: wt.IR.rep1


title: NST39

value: not exposed (C) to a parental sensitization treatment


title: Pln.mut.8w.rep4

source_name: PLN R14del homozygous mutant left ventricle 8w

value: Pln R14del/R14del


title: V65_mRNAseq_shMed7_Rep2


title: Gingival tissue at 1M, Adult NHP 5

value: 1 month


title: Pln.mut.8w.rep3


title: V65_mRNAseq_shMed7_Rep1


title: Gingival tissue at 1M, Adult NHP 1


title: Gingival tissue at 1M, Adult NHP 2


title: NST38


title: NST37


title: Pln.mut.8w.rep2


title: Gingival tissue at 2W, Adult NHP 8

description: Gene expression data from gingival tissues of Adult NHPs 2W post-ligation

source_name: Gingival tissue from Adult NHP-2W

value: 2 weeks


title: Gingival tissue at 2W, Adult NHP 9


title: Pln.mut.8w.rep1


title: NST36


title: V65_mRNAseq_shMed6_Rep2

value: embryonic stem cell


title: V65_mRNAseq_shMed6_Rep1

value: transfected with shRNA plasmid


title: Gingival tissue at 2W, Adult NHP 7


title: Gingival tissue at 1M, Adult NHP 4


title: Pln.het.8w.rep4

source_name: PLN R14del heterozygous mutant left ventricle 8w

value: Pln wt/R14del


title: NST35

value: F

value: S


title: Gingival tissue at 2W, Adult NHP 6

value: Female


title: NST34

value: bed nucleus of the stria terminalis (BNST)


title: Pln.het.8w.rep3

value: left ventricle


title: Gingival tissue at 2W, Adult NHP 5


title: NST33


title: V65_mRNAseq_shMed4_Rep1


title: Gingival tissue at 2W, Adult NHP 3


title: Pln.het.8w.rep2


title: Gingival tissue at 2W, Adult NHP 4


title: V65_mRNAseq_shMed4_Rep2


title: NST32


title: NST28

value: exposed (I) to a parental sensitization treatment


title: wt.8w.rep3

source_name: WT left ventricle 8w

value: wt


title: Gingival tissue at 2W, Adult NHP 2


title: Gingival tissue at 2W, Adult NHP 1


title: NST27

value: R


title: wt.8w.rep2


title: V65_mRNAseq_shMed30_Rep1


title: Gingival tissue at BL, Adult NHP 9

description: Gene expression data from gingival tissues of Adult NHPs before ligation

source_name: Gingival tissue from Adult NHP-BL

value: base line


title: V65_mRNAseq_shMed30_Rep2


title: V65_mRNAseq_shMed31_Rep1


title: NST26


title: wt.8w.rep1


title: Pln.mut.5w.rep4

source_name: PLN R14del homozygous mutant left ventricle 5w


title: NST25


title: Gingival tissue at BL, Adult NHP 7


title: Gingival tissue at BL, Adult NHP 6


title: Gingival tissue at BL, Adult NHP 8


title: V65_mRNAseq_shMed31_Rep2


title: Pln.mut.5w.rep3


title: V65_mRNAseq_shMed29_Rep1


title: Pln.het.8w.rep1


title: NST23

value: NS


title: NST24

value: not exposed (C) to a parental sensitization treatment


title: Pln.mut.5w.rep2

value: Pln R14del/R14del


title: Gingival tissue at BL, Adult NHP 4


title: V65_mRNAseq_shMed28_Rep1


title: Gingival tissue at BL, Adult NHP 5


title: Pln.mut.5w.rep1


title: V65_mRNAseq_shMed27_Rep2


title: Gingival tissue at BL, Adult NHP 2

value: Male


title: V65_mRNAseq_shMed27_Rep1


title: wt.5w.rep4

source_name: WT left ventricle 5w


title: V65_mRNAseq_shMed29_Rep2


title: NST6


title: wt.5w.rep3


title: V65_mRNAseq_shMed28_Rep2


title: NST5


title: V65_mRNAseq_shMed26_Rep2


title: wt.5w.rep2


title: V65_mRNAseq_shMed26_Rep1


title: NST3


title: Pln.mut.3w.rep4

source_name: PLN R14del homozygous mutant left ventricle 3w


title: NST4


title: NST7


title: NST22


title: V65_mRNAseq_shMed25_Rep1


title: NST2


title: Pln.mut.3w.rep3


title: V65_mRNAseq_shMed24_Rep2


title: Gingival tissue at 5M, Adolescent NHP 8

description: Gene expression data from gingival tissues of Adolescent NHPs 2 months after ligature removal (5M)

source_name: Gingival tissue from Adolescent NHP-5M

value: 5 months


title: wt.5w.rep1


title: Pln.mut.3w.rep2


title: Gingival tissue at BL, Adult NHP 1


title: TN45

value: nucleus taena


title: V65_mRNAseq_shMed25_Rep2

value: embryonic stem cell

value: transfected with shRNA plasmid


title: V65_mRNAseq_shMed24_Rep1


title: Gingival tissue at 5M, Adolescent NHP 9


title: wt.3w.rep4

source_name: WT left ventricle 3w


title: Gingival tissue at 5M, Adolescent NHP 7


title: Pln.mut.3w.rep1


title: Gingival tissue at 5M, Adolescent NHP 5


title: V65_mRNAseq_shMed23_Rep2


title: Gingival tissue at BL, Adult NHP 3


title: V65_mRNAseq_shMed23_Rep1


title: TN44

value: F

value: NR


title: wt.3w.rep3


title: TN43


title: TN42


title: Gingival tissue at 5M, Adolescent NHP 6

value: Female


title: wt.3w.rep2


title: wt.3w.rep1


title: TN40


title: TN38


title: WT_OB_1B

city: London

first: Keat-Eng

last: Ng

state: England

address: William Harvey Heart Centre

country: United Kingdom

institute: Queen Mary University of London

data_processing:
In Galaxy v19.05, FASTQ files were mapped to GRCm38.97 mouse Ensembl genome using RNAstar v2.6
Gene and transcript counts were made with StringTie v1.3.4
Genome_build: GRCm38.97 mouse Ensembl genome
Supplementary_files_format_and_content: tab-delimited text (txt) files include FPKM values for each sample

extract_protocol:
Samples were collected from 2 or 10 week mouse hearts. Heart samples were stored in RNALater. RNA was extracted with RNeasy Fibrous Tissue Mini Kit 74704
Libraries were constructed with KAPA Stranded RNA-Seq Kit with RiboErase

value: heart

value: Wild-type

value: 2 Weeks


title: TN39


title: V65_mRNAseq_shMed21_Rep1


title: WT_OB_1L


title: V65_mRNAseq_shMed20_Rep2


title: WT_OA_1B


title: V65_mRNAseq_shMed21_Rep2


title: TN36


title: TN35

value: S


title: WT_OA_1R


title: V65_mRNAseq_shMed1_Rep2


title: V65_mRNAseq_shMed22_Rep1


title: Gingival tissue at 5M, Adolescent NHP 2


title: TN34


title: Gingival tissue at 3M, Adolescent NHP 9

description: Gene expression data from gingival tissues of Adolescent NHPs 3M post-ligation

source_name: Gingival tissue from Adolescent NHP-3M

value: 3 months


title: KO_OB_2L


title: V65_mRNAseq_shMed1_Rep1


title: TN37


title: Gingival tissue at 5M, Adolescent NHP 4


title: Gingival tissue at 3M, Adolescent NHP 7


title: Gingival tissue at 5M, Adolescent NHP 3


title: Gingival tissue at 3M, Adolescent NHP 5


title: Gingival tissue at 3M, Adolescent NHP 3


title: Gingival tissue at 3M, Adolescent NHP 4


title: Gingival tissue at 3M, Adolescent NHP 8


title: Gingival tissue at 3M, Adolescent NHP 2


title: Gingival tissue at 5M, Adolescent NHP 1


title: Gingival tissue at 3M, Adolescent NHP 6


title: V65_mRNAseq_shMed19_Rep2


title: KO_OA_1L


title: V65_mRNAseq_shMed18_Rep2


title: KO_OB_1R


title: KO_OA_2R


title: TN28

value: exposed (I) to a parental sensitization treatment


title: TN33

value: NS


title: WT_MPa_2L

value: 10 weeks


title: V65_mRNAseq_shMed19_Rep1


title: Gingival tissue at 3M, Adolescent NHP 1


title: Gingival tissue at 1M, Adolescent NHP 8

description: Gene expression data from gingival tissues of Adolescent NHPs 1M post-ligation

source_name: Gingival tissue from Adolescent NHP-1M

value: 1 month


title: TN27

value: R


title: WT_MPa_2R

value: Male


title: V65_mRNAseq_shMed18_Rep1


title: V65_mRNAseq_shMed17_Rep2


title: TN26

value: nucleus taena


title: WT_MN_2R


title: TN25


title: WT_ML_1B


title: V65_mRNAseq_shMed16_Rep2

value: embryonic stem cell


title: Gingival tissue at 1M, Adolescent NHP 7


title: V65_mRNAseq_shMed16_Rep1

value: transfected with shRNA plasmid


title: KO_MM_2R


title: NST1

value: F

value: not exposed (C) to a parental sensitization treatment

value: bed nucleus of the stria terminalis (BNST)


title: TN23


title: V65_mRNAseq_shMed15_Rep2


title: TN22


title: KO_ML_1L

value: heart

value: Female


title: TN32


title: Gingival tissue at 1M, Adolescent NHP 6


title: KO_MI_1B


title: V65_mRNAseq_shMed15_Rep1


title: TN7


title: KO_MQb_1B


title: TN6


title: TN24


title: TN5


title: V65_mRNAseq_shMed17_Rep1


title: Gingival tissue at 1M, Adolescent NHP 9


title: V65_mRNAseq_shMed14_Rep2


title: V65_mRNAseq_shMed14_Rep1


title: V65_mRNAseq_shMed13_Rep2


title: H3K4me2-LSCs rep1

city: Bengbu

first: Mingsen

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

library_source: genomic

data_processing:
STAR software was used to align the RNA-Seq reads to the human hg19 reference genome. For ATAC-Seq and ChIP-Seq, BWA software was used to map trimmed reads to the human hg19 reference genome and the uniquely mapped reads were selected using the Picard MarkDuplicates tools.
For RNA-Seq data, the RSEM tool was used to calculate the TPM values. For ATAC-Seq and ChIP-Seq data, we used MACS2 to call peaks.
Differentially expressed genes were identified using the DESeq2 R package, with a log2 fold-change value of ≥ 1 and a false-discovery rate of < 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.xlsx: Excel files; Gene expression matrices include TMM values.
Supplementary_files_format_and_content: *.bed: Peak files.

molecule: genomic DNA

source_name: limbal stem cells

growth_protocol: LSCs and dCECs were grown in 1:1 DMEM/F-12 medium containing 1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol:
The RNeasy Mini Kit (Qiagen) was used to isolate total RNA from cells. For ChIP-seq, chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer. Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen). For ATAC-seq, in total, 50,000 cells were digested, collected, and lysed in ice-cold lysis buffer for 5 min. Then, Tn5 transposase reactions (Vazyme Biotech, TD501) were performed using the TruePrep DNA Library Prep Kit (Vazyme Biotech).
RNA libraries were prepared for sequencing using NEBNext RNA first and second Strand Synthesis Module (NEB, USA) and KAPA Library Preparation Kit (KAPA Biosystem). The KAPA Hyper Prep Kit (Kapa Biosystems, KK8502) was used to construct ChIP-seq libraries for Illumina PE150 sequencing. For ATAC-seq library, the transposed DNA fragments were amplified and collected using the TruePrep DNA Library Prep Kit (Vazyme Biotech).

treatment_protocol: Limbus was isolated from postmortem human eyeballs and cut into small pieces, followed by digestion with 0.2% collagenase IV (Gibco) at 37℃ for 2h and further digestion by 0.25% trypsin-EDTA (Gibco) at 37℃ for 15 min. Then, cells were seeded and cultured on polystyrene plates (Corning) coated with 2% Matrigel (BD Biosciences). LSCs were plated in transwell culture inserts (Corning), and the medium was added to the upper and lower compartments. The cells were cultured for approximately 3–6 days until they reached confluency, after which the medium was removed from the inserts. LSCs were induced to differentiate for another 5–14 days to form dCESs through contact with the medium in the lower chamber.

value: primary limbal stem cells

value: WT

tag: shRNA

tag: chip antibody

value: H3K4me2 (Millipore, 07-030)


title: V65_mRNAseq_shMed12_Rep1


title: FOXC1-LSCs rep2

value: FOXC1 (Bethyl Laboratories, A303-519A)


title: TN4

tag: Sex

tag: behavioral response


title: V65_mRNAseq_shMed13_Rep1


title: TN3

tag: brain region


title: Gingival tissue at 2W, Adolescent NHP 9

description: Gene expression data from gingival tissues of Adolescent NHPs 2W post-ligation

source_name: Gingival tissue from Adolescent NHP-2W

value: 2 weeks


title: Gingival tissue at 1M, Adolescent NHP 3


title: H3K4me2-LSCs rep2


title: Gingival tissue at 2W, Adolescent NHP 7


title: Gingival tissue at 1M, Adolescent NHP 5


title: V65_mRNAseq_shMed12_Rep2


title: ATAC-LSCs rep2


title: TN1

value: S


title: ATAC-LSCs rep1


title: TN2


title: Gingival tissue at 1M, Adolescent NHP 4

value: 1 month


title: V65_mRNAseq_shMed11_Rep2


title: TN49

value: M

value: exposed (I) to a parental sensitization treatment

value: R


title: shFOXC1-dCECs-RNAseq rep2

description:
DIFF_shFOXC1_2
dCEC_scramble_and_shFOXC1_TPM_values.xlsx

source_name: dCECs

value: 3D-differentiated corneal epithelial cells


title: V65_mRNAseq_shMed10_Rep2

value: embryonic stem cell

value: transfected with shRNA plasmid


title: TN48

value: nucleus taena


title: Gingival tissue at 2W, Adolescent NHP 3


title: scramble-dCECs-RNAseq rep2

description:
DIFF_SCR_2
dCEC_scramble_and_shFOXC1_TPM_values.xlsx

value: scramble


title: V65_mRNAseq_shMed11_Rep1


title: shFOXC1-dCECs-RNAseq rep1

description:
DIFF_shFOXC1_1
dCEC_scramble_and_shFOXC1_TPM_values.xlsx


title: V65_mRNAseq_shMed10_Rep1


title: scramble-dCECs-RNAseq rep1

description:
DIFF_SCR_1
dCEC_scramble_and_shFOXC1_TPM_values.xlsx


title: Gingival tissue at 1M, Adolescent NHP 2

value: Male


title: V65_mRNAseq_shMed22_Rep2


title: V65_mRNAseq_shGcn5_Rep2


title: TN46


title: Gingival tissue at 2W, Adolescent NHP 8


title: V65_mRNAseq_shGcn5_Rep1


title: Gingival tissue at 2W, Adolescent NHP 6

value: Female


title: shFOXC1-LSCs-RNAseq rep2

description:
shFOXC1_LSC_2
LSC_scramble_and_shFOXC1_TPM_values.xlsx

value: primary limbal stem cells


title: V65_mRNAseq_shCdk8_Rep2


title: TN30

value: not exposed (C) to a parental sensitization treatment

value: NS


title: TN31


title: scramble-LSCs-RNAseq rep2

description:
scr_LSC_2
LSC_scramble_and_shFOXC1_TPM_values.xlsx


title: TN47

value: NR


title: shFOXC1-LSCs-RNAseq rep1

description:
shFOXC1_LSC_1
LSC_scramble_and_shFOXC1_TPM_values.xlsx


title: Gingival tissue at 2W, Adolescent NHP 5

value: 2 weeks


title: V65_mRNAseq_shCdk8_Rep1


title: TN29


title: Gingival tissue at 2W, Adolescent NHP 4


title: dCECs-RNAseq rep2

description:
CEC_2
LSC_and_dCEC_TPM_values.xlsx

value: WT


title: Gingival tissue at 1M, Adolescent NHP 1

value: 1 month


title: TN21

value: M


title: V65_mRNAseq_shCcnc_Rep2


title: dCECs-RNAseq rep1

description:
CEC_1
LSC_and_dCEC_TPM_values.xlsx


title: Gingival tissue at BL, Adolescent NHP 9

description: Gene expression data from gingival tissues of Adolescent NHPs before ligation

source_name: Gingival tissue from Adolescent NHP-BL

value: baseline


title: limbal stem cells-RNAseq rep2

description:
LSC_2
LSC_and_dCEC_TPM_values.xlsx


title: Gingival tissue at 2W, Adolescent NHP 1


title: Gingival tissue at 2W, Adolescent NHP 2


title: V65_input_Rep2

data_processing:
Base-calling was performed with RTA.
Sequence reads were mapped to mm9 using Bowtie2 with the --very-sensitive option.
Clonal reads were removed with a custom script.
Peakcalling was carried out using a custom script. To call peaks, the mouse genome was segmented into 50-bp windows. A Poisson p value was calculated for each window based on the IP and normalized input counts in this window. A significant peak was retained only when p values of its own window and the 2 neighboring windows were all below 0.001.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing normalized counts

extract_protocol:
Cells were harvested at 70%–80% confluency by trypsinization. After washing with DPBS, cells were formaldehyde-crosslinked to a final concentration of 1% for 10 min at room temperature, followed by 5 min quenching with 125 mM glycine. Cells were washed twice with cold DPBS. If not used immediately, the cell pellet was flash frozen in liquid nitrogen and stored at −80°C. Crosslinked cells were resuspended in swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, and 1×cOmplete protease inhibitor cocktail) and incubated for 10 min on ice. Cells were centrifuged and the cell pellet was resuspended in Buffer A (50 mM HEPES-KOH pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS) plus 1×cOmplete protease inhibitor cocktail. Cell sonication was performed on a Qsonica Q800R2 sonicator with 20% amplitude for 20 cycles at 10 s each with 30 s between cycles at 4°C. Sonicated lysate was pre-cleared by incubating with Dynabeads Protein A/G. Part of the pre-cleared lysate was used as input and the remainder was incubated overnight at 4°C with 2-10 μg of antibody. DNA/Protein-antibody conjugates were precipitated using Dynabeads Protein A/G. Beads were washed twice each with Buffer A, Buffer B (50 mM HEPES-KOH pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Na-deoxycholate, 0.5% NP-40) and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). DNA was eluted in elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS). Cross-links were reversed overnight at 65°C. RNA and protein were digested using RNase A and Proteinase K, respectively, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP-seq libraries were constructed using KAPA HyperPrep Kit.

value: untreated


title: Gingival tissue at BL, Adolescent NHP 8


title: Gingival tissue at BL, Adolescent NHP 6


title: V65_mRNAseq_shMed20_Rep1


title: TN20

value: exposed (I) to a parental sensitization treatment


title: V65_mRNAseq_shCcnc_Rep1

value: embryonic stem cell


title: Gingival tissue at BL, Adolescent NHP 5


title: Gingival tissue at BL, Adolescent NHP 7


title: TN17

value: R


title: TN19

value: nucleus taena


title: Gingival tissue at BL, Adolescent NHP 4


title: TN16


title: V65_input_Rep1


title: TN18


title: Gingival tissue at BL, Adolescent NHP 3


title: limbal stem cells-RNAseq rep1

description:
LSC_1
LSC_and_dCEC_TPM_values.xlsx


title: scramble-LSCs-RNAseq rep1

description:
scr_LSC_1
LSC_scramble_and_shFOXC1_TPM_values.xlsx

value: scramble


title: TN15


title: V65_TAF12_ChIP_Rep2

value: Proteintech 12353-1-AP


title: TN14


title: MJ-11

city: Cambridge

first: Joon Sang

last: Lee

state: MA

address: 270 Albany Street

institute: Sanofi

description:
MC38-resistant - cultured cells
untreated, cultured MC38-resistant cells

data_processing:
STAR aligner
Cufflink
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: cultured cells

growth_protocol: Cells were injected subcutaneously into C57BL6/J mice.

extract_protocol:
Qiagen total RNA extraction with DNase treatment
RNA libraries were prepared for sequencing using KAPA RNA Hyperprep Kits

treatment_protocol: Tumors were grown in untreated mice and tumor tissue collected for RNA extraction.

value: Colon adenocarcinoma cell line

tag: cell line


title: MJ-12


title: V65_TAF12_ChIP_Rep1


title: V65_MED4_ChIP_Rep2

value: Invitrogen PA5-79659


title: V65_MED4_ChIP_Rep1


title: TN13


title: MJ-10


title: MJ-6


title: MJ-3


title: MED4_degron_6h_input_Rep2

value: treated with auxin for 6 hours


title: TN12

value: not exposed (C) to a parental sensitization treatment

value: NS


title: MJ-14

description:
MC38 parental - cultured cells
untreated, cultured MC38 cells

value: MC38 parental


title: TN11

value: S


title: MJ-1


title: MED4_degron_0h_input_Rep2


title: MED4_degron_6h_input_Rep1


title: Gingival tissue at 5M, Young NHP 9

description: Gene expression data from gingival tissues of young NHPs 2 months after ligature removal (5M)

source_name: Gingival tissue from Young NHP-5M

value: Female

tag: time point

value: 5 months


title: Gingival tissue at BL, Adolescent NHP 2

value: Male

value: baseline


title: TN10

value: M


title: Gingival tissue at BL, Adolescent NHP 1


title: Gingival tissue at 5M, Young NHP 7


title: GPN-12212_43

description:
MC38-resistant - subcutaneous tumor
untreated MC38-resistant tumor

source_name: subcutaneous tumor


title: Gingival tissue at 5M, Young NHP 6


title: Gingival tissue at 5M, Young NHP 5


title: TN9


title: Gingival tissue at 5M, Young NHP 8


title: Gingival tissue at 5M, Young NHP 4


title: MED4_degron_6h_XPB_ChIP_Rep2

value: embryonic stem cell


title: GPN-12212_56


title: NST50

value: exposed (I) to a parental sensitization treatment

value: bed nucleus of the stria terminalis (BNST)


title: Gingival tissue at 5M, Young NHP 2


title: GPN-12212_59


title: Gingival tissue at 5M, Young NHP 3


title: MED4_degron_0h_input_Rep1

value: untreated


title: GPN-12212_41


title: MED4_degron_0h_XPB_ChIP_Rep1


title: Gingival tissue at 5M, Young NHP 1


title: NST47

value: NR


title: MED4_degron_0h_XPB_ChIP_Rep2


title: NST48

value: R


title: GPN-12212_44

value: Colon adenocarcinoma cell line


title: GPN-12212_53


title: Gingival tissue at 3M, Young NHP 8

description: Gene expression data from gingival tissues of young NHPs 3M post-ligation

source_name: Gingival tissue from Young NHP-3M

value: 3 months


title: MED4_degron_6h_TFIIB_ChIP_Rep2

value: treated with auxin for 6 hours

value: stock of Carey Lab


title: MED4_degron_6h_XPB_ChIP_Rep1


title: Gingival tissue at 3M, Young NHP 9


title: MED4_degron_6h_TFIIB_ChIP_Rep1


title: Gingival tissue at 3M, Young NHP 6


title: NST30

value: not exposed (C) to a parental sensitization treatment

value: NS


title: NST46


title: GPN-12212_52


title: NST49


title: NST31


title: GPN-12212_42


title: MED4_degron_0h_TFIIB_ChIP_Rep1


title: GPN-12212_45


title: TN50

value: nucleus taena


title: GPN-12212_60


title: MED4_degron_0h_TFIIB_ChIP_Rep2


title: Gingival tissue at 3M, Young NHP 7

value: Female


title: FOXC1-LSCs rep1

value: primary limbal stem cells

value: WT

value: FOXC1 (Bethyl Laboratories, A303-519A)


title: MED4_degron_6h_TFIIA_ChIP_Rep2

value: embryonic stem cell

value: Abcam ab196770


title: NST29

value: M

value: bed nucleus of the stria terminalis (BNST)


title: MED4_degron_6h_TFIIA_ChIP_Rep1


title: GPN-12212_51


title: Gingival tissue at 3M, Young NHP 4


title: NST21


title: MED4_degron_0h_TFIIA_ChIP_Rep2

value: untreated


title: Gingival tissue at 3M, Young NHP 5


title: GPN-12212_57


title: Gingival tissue at 3M, Young NHP 3

value: Male


title: NST20

value: exposed (I) to a parental sensitization treatment

value: NR


title: MED4_degron_0h_TFIIA_ChIP_Rep1


title: NST19

value: R


title: GPN-12212_3

description:
MC38 parental - subcutaneous tumor
untreated MC38 parental tumor

value: Colon adenocarcinoma cell line

value: MC38 parental


title: MED4_degron_6h_TAF1_ChIP_Rep2

value: treated with auxin for 6 hours

value: Bethyl A303-505A


title: GPN-12212_13


title: NST18


title: MED4_degron_0h_TAF1_ChIP_Rep2


title: Gingival tissue at 3M, Young NHP 2

value: 3 months


title: NST17


title: MED4_degron_6h_TAF1_ChIP_Rep1


title: NST16


title: GPN-12212_12


title: Gingival tissue at 1M, Young NHP 9

description: Gene expression data from gingival tissues of young NHPs 1M post-ligation

source_name: Gingival tissue from Young NHP-1M

value: Female

value: 1 month


title: Gingival tissue at 1M, Young NHP 8


title: Gingival tissue at 1M, Young NHP 7


title: Gingival tissue at 3M, Young NHP 1


title: MED4_degron_0h_TAF1_ChIP_Rep1


title: NST15


title: NST13


title: GPN-12212_1


title: MED4_degron_6h_PolII_ChIP_Rep2

value: QED Bioscience 70101


title: GPN-12212_7


title: Gingival tissue at 1M, Young NHP 6


title: GPN-12212_20


title: NST12

value: not exposed (C) to a parental sensitization treatment

value: NS


title: MED4_degron_0h_PolII_ChIP_Rep2

value: embryonic stem cell


title: Gingival tissue at 1M, Young NHP 5


title: Gingival tissue at 1M, Young NHP 1


title: NST10

value: M

value: bed nucleus of the stria terminalis (BNST)


title: NST11

value: S


title: MED4_degron_6h_PolII_ChIP_Rep1


title: GPN-12212_5


title: MED4_degron_6h_MED6_ChIP_Rep1

value: Proteintech 15338-1-AP


title: MED4_degron_0h_PolII_ChIP_Rep1

value: untreated


title: Gingival tissue at 1M, Young NHP 3

value: Male


title: GPN-12212_9

value: Colon adenocarcinoma cell line


title: MED4_degron_6h_MED6_ChIP_Rep2


title: MED4_degron_0h_MED6_ChIP_Rep2


title: NST9


title: Gingival tissue at 1M, Young NHP 2


title: GPN-12212_6

value: MC38 parental


title: GPN-12212_11


title: Gingival tissue at 2W, Young NHP 9

description: Gene expression data from gingival tissues of young NHPs 2W post-ligation

source_name: Gingival tissue from Young NHP-2W

value: 2 weeks


title: Gingival tissue at 2W, Young NHP 7


title: Gingival tissue at 2W, Young NHP 8


title: Root tip, DI-2

city: Daqing

first: jili

last: zhang

address: 5 Xinfeng Road

institute: heilongjiang bayi agricultural university

description: DW-root2 representing drip irrigation repeat 3 sample

data_processing:
Data quality control application software FastQC version 0.10.1; RNAseq quality control application software RSeQC version 2.6.4; Genome comparison application software Hisat version 2.0; Transcript splicing and merging application software StringTie version 1.3.4; Transcript quantification and difference comparison And the visualization application software edgeR;
The expression level of genes mainly adopts FPKM (Fragments Per Kilobase of exon model per Million mapped reads)
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/zea_mays/dna/, GO: http://geneontology.org, KEGG: http://www.kegg.jp/kegg
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: Maize root system

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root tip

value: deficit irrigation (DI)


title: GPN-12212_18


title: Root tip, DI-3

description: DW-root3 representing drip irrigation repeat 3 sample


title: Gingival tissue at 1M, Young NHP 4

value: Female


title: MED4_degron_6h_MED4_ChIP_Rep2

value: treated with auxin for 6 hours

value: Invitrogen PA5-79659


title: Root tip, DI-1

description: DW-root1 representing drip irrigation repeat 1 sample


title: MED4_degron_6h_MED4_ChIP_Rep1


title: MED4_degron_0h_MED6_ChIP_Rep1


title: rapamycin.MZ_B.pos.4

description: rapamycin-treated undivided (Blimp) GFP+ CpG+IL-4,5-stimulated from marginal zone B cell

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: CCinhib_PC_stim.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: CCinhib_PC_stim.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: CCinhib_PC_stim.noIg.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts
Supplementary_files_format_and_content: CCinhib_PC_stim.noIg.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts

source_name: in-vitro cultured primary B cell

growth_protocol: B6.Blimp1GFP/+ mice were maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows:  follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high.  In-vitro cultured were FACS sorted by live, singlet, CTV dilution GFP (Blimp1) expression.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech SMART-Seq HT kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: In-vivo samples are untreated from SPF mice.  In-vitro cultures from these mice were prepared from follicular and marginal zone B cells stimulated for  72 and 48 hours, respectively,  with CpG DNA (ODN1826) with and without IL-4 and IL-5 and indicated inhibitors.

tag: strain

value: Spleen

value: 12 weeks


title: MED4_degron_0h_MED4_ChIP_Rep2

value: embryonic stem cell


title: rapamycin.MZ_B.pos.3

tag: tissue


title: rapamycin.MZ_B.pos.2

tag: age


title: GPN-12212_2


title: MED4_degron_0h_MED4_ChIP_Rep1


title: MED4_degron_6h_MED1_ChIP_Rep2

value: Santa Cruz sc-5334


title: rapamycin.MZ_B.pos.1

tag: genotype


title: Root tip, NPI-2

description: SW-root2 representing negative pressure irrigation repeat 2 sample

tag: treatment

value: negative pressure irrigation (NPI)


title: Root tip,  NPI-1

description: SW-root1 representing negative pressure irrigation repeat 1 sample


title: PD0332991.MZ_B.pos.3

description: PD0332991-treated undivided (Blimp) GFP+ CpG+IL-4,5-stimulated from marginal zone B cell


title: PD0332991.MZ_B.pos.4


title: w1118_whole_fly_wgs

first: Martin

middle: Heinrich

last: Fabry

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: Cancer Research UK, Cambridge Institute

institute: University of Cambridge

description: w1118_whole_fly_wgs WGS

data_processing: Raw fastq files contained 50bp reads. The first and the last two bases of all reads were trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). Reads from small RNA-Seq libraries were adapter clipped using fastx_clipper with settings -Q33 -l 15 -a AGATCGGAAGAGCACACGTCT. The first and last 4 bases of adapter clipped reads were trimmed using seqtk trimfq (https://github.com/lh3/seqtk). Reads were first aligned to the consensus sequence for all Drosophila melanogaster transposons using STAR (Dobin et al., 2013) allowing random allocation of multimappers. Unmapped reads were further uniquely aligned to Drosophila melanogaster genome release 6 (dm6). Generated bam files for RNA-Seq were split in reads originating from sense and antisense genomic strands using samtools view options -f 0x10 and -F 0x10 for sense and antisense reads respectively (Li et al., 2009). Indexes were generated using samtools index function. Coverage files were generated using bamCoverage with normalisation mode --normalizeUsing CPM (Ramirez et al., 2014) and applying a scaling factor (-- ScaleFactor). Scaling factors for individual files were calculated by dividing the sum of mapped reads contained in the file by the sum of all transposon and dm6 mapping reads of the corresponding library. Reads mapping to protein-coding genes were counted with htseq (Anders et al., 2015) using a feature file downloaded from Ensembl (https://www.ensembl.org/Drosophila_melanogaster/Info/Index). Reads mapping to individual transposons were counted with a custom script using samtools idxstats function to extract reads mapping to individual sequences of the reference genome/transposon consensus sequence. Count files generated as described above were normalised to reads per million (RPM) and plotted using ggplot2 (Wickham, 2016). Bar graphs displaying transposon expression profiles and heatmap during embryogenesis were calculated from collapsed replicates. Bar graphs and heatmaps were plotted using ggplot2 in R. Differential expression analysis was performed using DeSeq2 (Love et al., 2014). Metaplots flanking euchromatic transposon insertion sites were calculated using deepTools2?s computeMatrix scale-region function with bin size 10.

organism: Drosophila melanogaster

growth_protocol: Flies were grown at 25°C

extract_protocol:
Whole Genome Sequencing (WGS): 100 flies were collected in a 1.5ml tube and frozen at -80°C for at least 1h. High molecular weight genomic DNA (HMW gDNA) was isolated using the Blood and Cell Culture DNA Mini kit (Qiagen). Flies were homogenised using a rotating pestle on ice for 1min. 700µl G2 and 50µl Proteinase K (800U/ml, NEB) was added to each tube and incubated at 50°C for 2h with occasional tube inversions. Tubes were spun at 5,000g for 10min at 4°C and supernatant transferred to new tube avoiding debris. A Qiagen Genomic-tip 20/G was equilibrated with 1ml QBT buffer and allowed to empty by gravity flow. The supernatant containing digested proteins and genomic DNA was added to the column and allowed to flow through. The column was washed 3 times with 1ml QC buffer. Elution was carried out with 1ml QF elution buffer and repeated once. Flow through was transferred to two new tubes (1ml each) and 700µl isopropanol added. Tubes were inverted 10 times and centrifuged at full speed for 15min at 4°C. The pellet was washed with 70% ethanol twice and air-dried for 5min. 25µl RNase-free water was added and DNA resuspended by flicking tube gently several times while incubating at 37°C for 2h. DNA was stored at 4°C. DNA was sheered using a Covaris S220 (Covaris). 3µg of genomic DNA was diluted in RNase-Free water and transferred to a AFA Fiber Crimp-Cap (PN520052, Covaris) microtube. Sonication was carried out with the following settings: Peak incident Power (W) 105, Duty Factor 5%, Cycles per Burst 200, Treatment time 80sec. This resulted in sheared DNA fragments peaking at 500bp. DNA was recovered using the QIAquick PCR Purification Kit (Qiagen).
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
Whole genome sequencing

tag: replicate number

tag: experiment

value: WGS


title: degron_whole_fly_wgs

description: degron_whole_fly_wgs WGS


title: Gingival tissue at 2W, Young NHP 4


title: Gingival tissue at 2W, Young NHP 6


title: Gingival tissue at 2W, Young NHP 2


title: Gingival tissue at 2W, Young NHP 3


title: Gingival tissue at 2W, Young NHP 5


title: Gingival tissue at 2W, Young NHP 1


title: Root tip, NPI-3

description: SW-root3 representing negative pressure irrigation repeat 3 sample


title: MED4_degron_6h_MED1_ChIP_Rep1

tag: cell type


description: gap90_embryo_2_2.5h_auxin_treat_rna_rep3 mRNA-Seq

source_name: embryo

growth_protocol: Flies were kept and grown at 25°C

extract_protocol:
RNA for mRNA-Seq and qRT-PCR experiments was isolated using the RNeasy Mini kit (Qiagen) with on-column DNA digestion (RNase-free DNase Set, Qiagen) according to the manufacturer’s recommendations.
NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)

treatment_protocol: Treatment of embryos for auxin-induced degradation:Embryos were collected for 1h and dechorionated. Control embryos were transferred into a fine mesh strainer placed in a plastic dish and submerged in PBS. 1M auxin solution was generated by diluting Indole-3-acetic acid (IAA) in water and stored at -20°C protected from light. Auxin-treated embryos were submerged in PBS with indicated auxin concentrations. Embryos were placed at 25°C for appropriate times and harvested for RNA experiments by transferring into 1ml Trizol followed by RNA extraction. Embryos used for ChIP-Seq were processed as described above.

value: GFP-AID-Piwi

value: embryo

value: 5mM Auxin (IAA)

tag: time after egg laying

value: mRNA-Seq


title: PD0332991.MZ_B.pos.1


title: PD0332991.MZ_B.pos.2


title: TAF12_degron_6h_input_Rep2


title: Gingival tissue at BL, Young NHP 7

description: Gene expression data from gingival tissues of young NHPs before ligation

source_name: Gingival tissue from Young NHP-BL

tag: gender

tag: age group

value: baseline


title: TAF12_degron_6h_input_Rep1

tag: chip antibody


description: gap90_embryo_2_2.5h_auxin_treat_rna_rep1 mRNA-Seq


title: CpG_IL45.MZ_B.pos.4

description: 3+ divided (Blimp1) GFP+ CpG+IL-4,5-stimulated from marginal zone B cell


title: Gingival tissue at BL, Young NHP 8

value: Male


title: MED4_degron_0h_MED1_ChIP_Rep2

value: untreated


title: Gingival tissue at BL, Young NHP 9


title: Gingival tissue at BL, Young NHP 6


title: CpG_IL45.MZ_B.pos.3


title: TAF12_degron_0h_input_Rep2


title: gap90_embryo_2_2.5h_pbs_treat_rna_rep3

description: gap90_embryo_2_2.5h_pbs_treat_rna_rep3 mRNA-Seq

value: PBS


title: CpG_IL45.MZ_B.pos.1


title: gap90_embryo_2_2.5h_pbs_treat_rna_rep2

description: gap90_embryo_2_2.5h_pbs_treat_rna_rep2 mRNA-Seq


title: TAF12_degron_0h_input_Rep1


title: Gingival tissue at BL, Young NHP 5

value: Female


description: gap90_embryo_2_2.5h_auxin_treat_rna_rep2 mRNA-Seq


title: CpG_IL45.MZ_B.pos.2


title: gap90_embryo_2_2.5h_pbs_treat_rna_rep1

description: gap90_embryo_2_2.5h_pbs_treat_rna_rep1 mRNA-Seq


title: TAF12_degron_6h_H3K9ac_ChIP_Rep2

value: treated with auxin for 6 hours

value: stock of Carey Lab


title: MED4_degron_0h_MED1_ChIP_Rep1


description: degron_embryo_6.5_7h_auxin_treat_h3k9me3_chip_rep3 ChIP-Seq

extract_protocol:
Samples were crosslinked in formaldehyde and lysed, followed by sonication.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: anti-H3K9me3 (Active Motif #39161)

value: ChIP-Seq


title: UTX.MZ_B.neg.5

description: marginal zone B cell

source_name: Splenic B cell

value: Spleen

value: 12 weeks


title: TAF12_degron_6h_H3K9ac_ChIP_Rep1

value: embryonic stem cell


description: degron_embryo_6.5_7h_auxin_treat_h3k9me3_chip_rep2 ChIP-Seq


title: Gingival tissue at BL, Young NHP 3


title: UTX.MZ_B.neg.4

description: marginal zone B cell


title: HeLa control DMSO replicate 2

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Illumina RTA software was usd for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
Reads where pseudoaligned to a Kallisto index  created from Ensembl version 92 transcriptome using Kallisto version 0.44.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each Sample

source_name: HeLa

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Thermo Fisher Scientific, #41965039) supplemented with 10% Fetal Bovine Serum (FBS, Thermo Fisher Scientific, #10270106), 1% Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 1% GlutaMAX (Thermo Fisher Scientific, #35050038).

extract_protocol:
RNA extraction was performed with RNeasy Mini Kit (QIAGEN) under manufacturer's instructions with DNAse digestion treatment
Ribosomal depletion was used to remove rRNAs from total RNA samples before proceeding with library construction using Illumina TruSeq chemistry.

treatment_protocol: Cells were treated with DMSO 1:1000 (control, mock treatment) for 5h.

value: HeLa

value: DMSO


title: Gingival tissue at BL, Young NHP 4

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


title: TAF12_degron_0h_H3K9ac_ChIP_Rep2


title: HeLa control DMSO replicate 1


title: UTX.MZ_B.neg.3

description: marginal zone B cell


title: Gingival tissue at BL, Young NHP 2


title: Gingival tissue at BL, Young NHP 1


description: degron_embryo_6.5_7h_auxin_treat_h3k9me3_chip_rep1 ChIP-Seq

value: embryo


description: degron_embryo_6.5_7h_pbs_treat_h3k9me3_chip_rep2 ChIP-Seq


title: UTX.MZ_B.neg.2

description: marginal zone B cell


description: degron_embryo_6.5_7h_pbs_treat_h3k9me3_chip_rep1 ChIP-Seq


title: UTX.MZ_B.neg.1

description: marginal zone B cell


description: degron_embryo_2_2.5h_auxin_treat_rna_rep3 mRNA-Seq

value: 5mM Auxin (IAA)


title: HeLa control DMSO replicate 3


title: TAF12_degron_6h_ESRRB_ChIP_Rep1

value: Perseus Proteomics PP-H6705-00


title: rapamycin.FO_B.neg.7

description: rapamycin-treated undivided GFP- CpG+IL-4,5-stimulated from follicular B cell


title: rapamycin.FO_B.neg.8


title: rapamycin.FO_B.neg.5


description: degron_embryo_6.5_7h_pbs_treat_h3k9me3_chip_rep3 ChIP-Seq


description: degron_embryo_2_2.5h_auxin_treat_rna_rep2 mRNA-Seq

value: mRNA-Seq


title: TAF12_degron_6h_MED1_ChIP_Rep1

value: Santa Cruz sc-5334


title: TAF12_degron_6h_MED1_ChIP_Rep2


title: PD0332991.FO_B.neg.7

description: PD0332991-treated undivided GFP- CpG+IL-4,5-stimulated from follicular B cell


title: degron_embryo_2_2.5h_pbs_treat_rna_rep2

description: degron_embryo_2_2.5h_pbs_treat_rna_rep2 mRNA-Seq


title: degron_embryo_2_2.5h_pbs_treat_rna_rep3

description: degron_embryo_2_2.5h_pbs_treat_rna_rep3 mRNA-Seq


title: GPN-12212_16

description:
MC38 parental - subcutaneous tumor
untreated MC38 parental tumor

value: Colon adenocarcinoma cell line

value: MC38 parental


title: degron_embryo_2_2.5h_pbs_treat_rna_rep1

description: degron_embryo_2_2.5h_pbs_treat_rna_rep1 mRNA-Seq

value: PBS


title: TAF12_degron_0h_ESRRB_ChIP_Rep1

value: untreated


title: TAF12_degron_0h_MED1_ChIP_Rep2


title: TAF12_degron_6h_TFIIB_ChIP_Rep2

value: treated with auxin for 6 hours

value: stock of Carey Lab


title: TAF12_degron_0h_MED1_ChIP_Rep1


title: w1118_head_na_h3k9me3_chip_rep2

description: w1118_head_na_h3k9me3_chip_rep2 ChIP-Seq

source_name: head

value: head

value: anti-H3K9me3 (Active Motif #39161)

value: ChIP-Seq


title: rapamycin.FO_B.neg.6

value: Spleen

value: 12 weeks


title: PD0332991.FO_B.neg.6


description: degron_embryo_2_2.5h_auxin_treat_rna_rep1 mRNA-Seq


title: NST14

extract_protocol:
Brains were removed and flash frozen on dry ice; brain regions were later punched out on a cryostat, placed in Qiazol lysis reagent and homogeneized; Total RNA was extracted from the aqueous layer formed after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

tag: Sex

value: M

value: exposed (I) to a parental sensitization treatment

value: R

value: bed nucleus of the stria terminalis (BNST)


title: w1118_head_na_h3k9me3_chip_rep1

description: w1118_head_na_h3k9me3_chip_rep1 ChIP-Seq


title: PD0332991.FO_B.neg.5


title: PD0332991.FO_B.neg.8


title: TAF12_degron_0h_H3K9ac_ChIP_Rep1

value: embryonic stem cell


title: CpG_IL45.FO_B.pos.8

description: 4+ divided (Blimp1) GFP+ CpG+IL-4,5-stimulated from follicular B cell


title: TAF12_degron_6h_TFIIB_ChIP_Rep1


title: TAF12_degron_0h_TFIIB_ChIP_Rep2


title: CpG_IL45.FO_B.pos.7


title: w1118_ovary_na_h3k9me3_chip_rep2

description: w1118_ovary_na_h3k9me3_chip_rep2 ChIP-Seq

source_name: ovary

value: ovary


title: TAF12_degron_6h_TFIIA_ChIP_Rep2

value: Abcam ab196770


title: CpG_IL45.FO_B.pos.6


title: w1118_ovary_na_h3k9me3_chip_rep1

description: w1118_ovary_na_h3k9me3_chip_rep1 ChIP-Seq


title: CpG_IL45.FO_B.pos.5


title: w1118_embryo_16_18h_h3k9me3_chip_rep2

description: w1118_embryo_16_18h_h3k9me3_chip_rep2 ChIP-Seq

value: embryo


title: TAF12_degron_0h_TFIIA_ChIP_Rep2


title: w1118_embryo_8_10h_h3k9me3_chip_rep2

description: w1118_embryo_8_10h_h3k9me3_chip_rep2 ChIP-Seq


title: UTX.FO_B.neg.4

description: follicular B cell


title: TAF12_degron_0h_TFIIB_ChIP_Rep1


title: w1118_embryo_16_18h_h3k9me3_chip_rep1

description: w1118_embryo_16_18h_h3k9me3_chip_rep1 ChIP-Seq


title: w1118_embryo_8_10h_h3k9me3_chip_rep1

description: w1118_embryo_8_10h_h3k9me3_chip_rep1 ChIP-Seq


title: TAF12_degron_6h_TFIIA_ChIP_Rep1


title: TAF12_degron_6h_TBP_ChIP_Rep2

value: Proteintech 22006-1-AP


title: UTX.FO_B.neg.5

description: follicular B cell


title: w1118_embryo_6_8h_h3k9me3_chip_rep2

description: w1118_embryo_6_8h_h3k9me3_chip_rep2 ChIP-Seq


title: UTX.FO_B.neg.3

description: follicular B cell


title: w1118_embryo_4_6h_h3k9me3_chip_rep2

description: w1118_embryo_4_6h_h3k9me3_chip_rep2 ChIP-Seq


title: WUE_8

type: genomic

city: Frankfurt am Main

first: Patrick

middle: Nikolaus

last: Harter

address: Heinrich-Hoffmann Strasse 7

department: Edinger Institute

country: Germany

institute: Goethe University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using RnBeads software package, Methylation data was normalized using the “dasen” method from the wateRmelon R-package, deconvolution was performed using MeDeCom and MethylCIBERSORT

label: Cy5 and Cy3

source_name: melanoma skin metastasis

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell FFPE DNA Purification Kit according to the manufacturer’s instructions.

value: melanoma

value: female

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: pre-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: PD


title: UTX.FO_B.neg.2

description: follicular B cell

tag: strain

tag: tissue

tag: age


title: TAF12_degron_0h_TBP_ChIP_Rep1

tag: treatment

value: untreated


title: WUE_10


title: TAF12_degron_0h_ESRRB_ChIP_Rep2

value: Perseus Proteomics PP-H6705-00


title: WUE_11


title: TAF12_degron_6h_ESRRB_ChIP_Rep2

value: treated with auxin for 6 hours


title: WUE_6

value: DC


title: WUE_5

value: male

value: UNK


title: WUE_12


title: TAF12_degron_6h_TBP_ChIP_Rep1


title: UTX.FO_B.neg.1

description: follicular B cell

value: Spleen

value: 12 weeks

tag: genotype


title: E17.5_STAU2_INPUT_rep3

city: Rensselaer

first: Rebecca

last: Chowdhury

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

description:
E17.3
Total RNA (input)
Table_S1_masterpeaks.csv

data_processing:
RIP-seq reads were aligned to the mm10 genome using STARmapper (version 2.5).
Peaks were called using Homer (version 4.10).
findPeaks and getDifferentialPeaksReplicates programs from HOMER were used to identify peaks statistically enriched across replicates, and fold enrichment over input was determined.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MasterPeaks.cts.csv

source_name: mouse brain cortex

extract_protocol:
RNA immunoprecipitation with Stau2 antibody (Abcam ab60724). RNA isolation and purification with acid phenol/chloroform extraction (also as described in Baroni, T.E., Chittur, S.V., George, A.D., and Tenenbaum, S.A. (2008)).
The libraries were prepared using ‘ScriptSeq™ Complete Kit (Human/Mouse/Rat)-Low Input (Cat. No. SCL24H) from Epicentre/Illumina using manufacturer’s instructions. A maximum of 800 ng of DNA-free RNA was used for ribosomal RNA removal using Ribo-Zero rRNA removal kit. rRNA free samples were purified and proceeded with ScriptSeq v2 RNA-Seq Library Preparation reaction which included RNA fragmentation, cDNA synthesis and terminal tagging of cDNA at both ends. Purified cDNAs were PCR amplified using primers against the adapters at both ends. The reverse primers for PCR amplification were used from ScriptSeq™ Index PCR Primers (Set 1, Cat. No. RSBC10948) using manufacturer’s instructions to barcode the libraries for multiplexing.

value: brain cortex

tag: developmental stage

tag: rip antibody


title: TAF12_degron_0h_TBP_ChIP_Rep2

tag: cell type

value: embryonic stem cell


title: WUE_7

tag: gender


title: WUE_9


title: WUE_4


title: E17.5_STAU2_INPUT_rep2

description:
E17.2
Total RNA (input)
Table_S1_masterpeaks.csv


title: TAF12_degron_0h_TFIIA_ChIP_Rep1

tag: chip antibody

value: Abcam ab196770


title: w1118_embryo_4_6h_h3k9me3_chip_rep1

description: w1118_embryo_4_6h_h3k9me3_chip_rep1 ChIP-Seq

value: embryo

value: anti-H3K9me3 (Active Motif #39161)

tag: time after egg laying

tag: replicate number

tag: experiment

value: ChIP-Seq


title: E17.5_STAU2_RIP_rep3

description:
E17.3
STAU2-bound RNA
Table_S1_masterpeaks.csv

value: anti-STAU2 (Abcam ab60724)


title: w1118_embryo_2_4h_h3k9me3_chip_rep1

description: w1118_embryo_2_4h_h3k9me3_chip_rep1 ChIP-Seq


title: TAF12_degron_0h_TAF3_ChIP_Rep2

value: Abcam ab188332


title: TAF12_degron_6h_TAF3_ChIP_Rep2


title: w1118_embryo_2_4h_h3k9me3_chip_rep2

description: w1118_embryo_2_4h_h3k9me3_chip_rep2 ChIP-Seq


title: E17.5_STAU2_INPUT_rep1

description:
E17.1
Total RNA (input)
Table_S1_masterpeaks.csv


title: TAF12_degron_6h_TAF3_ChIP_Rep1


title: WUE_3

value: melanoma

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

value: pre-ICI

value: PD


title: E17.5_STAU2_RIP_rep2

description:
E17.2
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: w1118_embryo_0_2h_h3k9me3_chip_rep2

description: w1118_embryo_0_2h_h3k9me3_chip_rep2 ChIP-Seq


title: WUE_2

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: WUE_1

tag: tissue

tag: age

value: DC


title: B_10

value: male


title: w1118_embryo_0_2h_h3k9me3_chip_rep1

description: w1118_embryo_0_2h_h3k9me3_chip_rep1 ChIP-Seq

tag: strain


title: TAF12_degron_6h_TAF1_ChIP_Rep2

tag: treatment

value: treated with auxin for 6 hours

value: Bethyl A303-505A


title: E17.5_STAU2_RIP_rep1

description:
E17.1
STAU2-bound RNA
Table_S1_masterpeaks.csv

tag: developmental stage

tag: rip antibody


title: TAF12_degron_0h_TAF3_ChIP_Rep1

tag: cell type

value: untreated


title: E15.5_STAU2_INPUT_rep3

description:
E15.3
Total RNA (input)
Table_S1_masterpeaks.csv

value: brain cortex


title: w1118_embryo_0_8h_rep_1

description: w1118_embryo_0_8h_rep_1 IP-smallRNA-Seq

extract_protocol:
Piwi-piRNA complexes were isolated from ovaries or 0-8h w1118 embryos as previously reported (Hayashi et al., 2016; Mohn et al., 2015)
Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.
smallRNA-seq

value: IP-smallRNA-Seq


title: w1118_ovary_0_8h_rep_1

description: w1118_ovary_0_8h_rep_1 IP-smallRNA-Seq

value: ovary


title: B_11

tag: gender

value: female


title: w1118_embryo_6_8h_h3k9me3_chip_rep1

description: w1118_embryo_6_8h_h3k9me3_chip_rep1 ChIP-Seq

value: embryo

tag: chip antibody

value: anti-H3K9me3 (Active Motif #39161)

tag: time after egg laying


title: TAF12_degron_6h_TAF1_ChIP_Rep1

value: embryonic stem cell


title: TAF12_degron_0h_TAF1_ChIP_Rep2


title: E15.5_STAU2_INPUT_rep2

description:
E15.2
Total RNA (input)
Table_S1_masterpeaks.csv


title: w1118_embryo_17_18h_rep_2

description: w1118_embryo_17_18h_rep_2 mRNA-Seq

tag: replicate number

tag: experiment

value: mRNA-Seq


title: B_14

value: melanoma

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

value: post-ICI


title: TAF12_degron_0h_TAF1_ChIP_Rep1


title: TAF12_degron_6h_TAF12_ChIP_Rep2

value: Proteintech 12353-1-AP


title: B_13

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)


title: w1118_embryo_17_18h_rep_1

description: w1118_embryo_17_18h_rep_1 mRNA-Seq


title: w1118_embryo_12_13h_rep_2

description: w1118_embryo_12_13h_rep_2 mRNA-Seq


title: B_8

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: PD


title: E15.5_STAU2_INPUT_rep1

description:
E15.1
Total RNA (input)
Table_S1_masterpeaks.csv

tag: tissue


title: E15.5_STAU2_RIP_rep1

description:
E15.1
STAU2-bound RNA
Table_S1_masterpeaks.csv

tag: strain

value: anti-STAU2 (Abcam ab60724)


title: E15.5_STAU2_RIP_rep2

description:
E15.2
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: TAF12_degron_6h_TAF12_ChIP_Rep1

tag: treatment

value: treated with auxin for 6 hours


title: w1118_embryo_12_13h_rep_1

description: w1118_embryo_12_13h_rep_1 mRNA-Seq


title: TAF12_degron_0h_TAF12_ChIP_Rep2


title: E13.5_STAU2_INPUT_rep3

description:
E13.3
Total RNA (input)
Table_S1_masterpeaks.csv

tag: developmental stage


title: w1118_embryo_9_10h_rep_2

description: w1118_embryo_9_10h_rep_2 mRNA-Seq


title: B_12

value: male

tag: age


title: TAF12_degron_0h_TAF12_ChIP_Rep1

tag: cell type

value: untreated


title: E13.5_STAU2_RIP_rep3

description:
E13.3
STAU2-bound RNA
Table_S1_masterpeaks.csv

value: brain cortex

tag: rip antibody


title: B_9

tag: gender

value: pre-ICI


title: w1118_embryo_9_10h_rep_1

description: w1118_embryo_9_10h_rep_1 mRNA-Seq

tag: time after egg laying


title: B_7


title: TAF12_degron_6h_PolII_ChIP_Rep1

tag: chip antibody

value: QED Bioscience 70101


title: E13.5_STAU2_INPUT_rep2

description:
E13.2
Total RNA (input)
Table_S1_masterpeaks.csv


title: E13.5_STAU2_RIP_rep2

description:
E13.2
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: w1118_embryo_8_9h_rep_1

description: w1118_embryo_8_9h_rep_1 mRNA-Seq

tag: replicate number

tag: experiment


title: TAF12_degron_6h_PolII_ChIP_Rep2


title: TAF12_degron_0h_PolII_ChIP_Rep2


title: E13.5_STAU2_INPUT_rep1

description:
E13.1
Total RNA (input)
Table_S1_masterpeaks.csv


title: E15.5_STAU2_RIP_rep3

description:
E15.3
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: TAF12_degron_0h_PolII_ChIP_Rep1


title: E13.5_STAU2_RIP_rep1

description:
E13.1
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: w1118_embryo_7_8h_rep_1

description: w1118_embryo_7_8h_rep_1 mRNA-Seq


title: w1118_embryo_6_7h_rep_2

description: w1118_embryo_6_7h_rep_2 mRNA-Seq


title: ATAC-seq_ILC2P_rep2

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 924 E. 57th Street BSLC

department: Pathology

institute: University of Chicago

data_processing:
ATAC-seq reads were aligned to the mouse genome (mm10) with Bowtie and duplicate reads were removed using Picard Tools.
Bam files were filtered through a custom blacklist, prior to bedGraph conversion, to remove reads with an unknown sequencing read/alignment anomaly at the following positions: chr2:9857245-9859423, chr3:94396436-94400555, and chr9:44046598-44046961.
BedGraph files were generated from bam files using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Generation of bigWig files was performed using the UCSC bedGraphToBigWig program.

source_name: Bone Marrow

extract_protocol:
Bone marrow was collected from the femur, tibia, and ilium (6 bones in total), crushed with the syringe plunger flange, passed through a 70um cell strainer, and resuspended in FACS Buffer (1X HBSS (Gibco), 0.25% BSA (Millipore-Sigma), 50 ng/mL DNase, and 5 mM sodium azide (Millipore-Sigma)). Bone marrow was lineage depleted using an autoMACS, stained for surface markers and viability, and individual bone marrow precursors were sorted into FACS Buffer.
Library construction was performed as described in the published Omni-ATAC protocol: Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Meth. 14, 959-962 (2017).

value: Bone Marrow

value: 6 - 8 weeks

tag: genotype


title: w1118_embryo_8_9h_rep_2

description: w1118_embryo_8_9h_rep_2 mRNA-Seq

value: embryo


title: E11.5_STAU2_INPUT_rep3

description:
E11.3
Total RNA (input)
Table_S1_masterpeaks.csv


title: ATAC-seq_ILC2P_rep1


title: E11.5_STAU2_RIP_rep3

description:
E11.3
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: w1118_embryo_6_7h_rep_1

description: w1118_embryo_6_7h_rep_1 mRNA-Seq


title: E11.5_STAU2_INPUT_rep2

description:
E11.2
Total RNA (input)
Table_S1_masterpeaks.csv


title: ATAC-seq_ILCP_rep1


title: w1118_embryo_5_6h_rep_2

description: w1118_embryo_5_6h_rep_2 mRNA-Seq


title: w1118_embryo_5_6h_rep_1

description: w1118_embryo_5_6h_rep_1 mRNA-Seq


title: ATAC-seq_ILCP_rep2


title: E11.5_STAU2_RIP_rep2

description:
E11.2
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: B_4

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: DC


title: ATAC-seq_iILCP_rep2


title: E11.5_STAU2_INPUT_rep1

description:
E11.1
Total RNA (input)
Table_S1_masterpeaks.csv


title: ATAC-seq_iILCP_rep1


title: w1118_embryo_4_5h_rep_1

description: w1118_embryo_4_5h_rep_1 mRNA-Seq

value: mRNA-Seq


title: E11.5_STAU2_RIP_rep1

description:
E11.1
STAU2-bound RNA
Table_S1_masterpeaks.csv


title: ATAC-seq_rEILP_rep2


title: B_1

value: melanoma

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: B_6

tag: tissue

value: female


title: w1118_embryo_7_8h_rep_2

description: w1118_embryo_7_8h_rep_2 mRNA-Seq

tag: strain


title: B_5

tag: age


title: FFM_39

value: post-ICI


title: w1118_embryo_3_4h_rep_2

description: w1118_embryo_3_4h_rep_2 mRNA-Seq


title: FFM_38

value: Skin metastasis


title: B_3

value: PD


title: B_2


title: ATAC-seq_rEILP_rep1


title: siHAND2_4

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
For day 20 ventricular iRFP670+ subpopulations ex3 samples, two files after STAR mapping were combined to obtain enough reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: siRNA transfected cardiomyotes derived from hiPSC

growth_protocol: For the standard ventricular protocol, on day 0, hiPSCs were aggregated and made into embryonic bodies (EBs) with 10 µM Y-27632 and 2 ng/ml BMP4 in each well of a 96-well plate coated with HEMA (Poly(2-hydroxyethyl methacrylate)) (2 × 10^4 cells/well). On day 1, cardiac mesoderm cells were induced by treatment with 18 ng/ml BMP4, 12 ng/ml Activin A and 10 ng/ml bFGF for 48 hours. On day 3, the EBs were dissociated and re-aggregated with day 3 medium: 10 ng/ml VEGF and 1 µM IWP-3 (8 × 10^4 cells/well). After day 7, the EBs were cultured with maintenance medium including 5 ng/ml VEGF in each well of a 6-well plate coated with HEMA until day 19. The EBs were incubated at 37℃ in a CO2 incubator (5% O2) from day 0 to day 12.   For the atrial differentiation, a standard protocol was followed except 0.5 µM all trans retinoic acid was appended to day 3 medium.

extract_protocol:
RNeasy Mini Kit / RNeasy micro kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

tag: subpopulation

value: isolated iRFP670+

tag: differentiation protocol

value: Ventricular protocol, siRNA transfected

tag: day

value: Day 20


title: FFM_36

tag: gender

value: male


title: ATAC-seq_Flt3p_aLP_rep2


title: w1118_embryo_2.5_3h_rep_2

description: w1118_embryo_2.5_3h_rep_2 mRNA-Seq

tag: time after egg laying


title: ATAC-seq_Flt3p_aLP_rep1


title: w1118_embryo_2.5_3h_rep_1

description: w1118_embryo_2.5_3h_rep_1 mRNA-Seq

tag: replicate number


title: siNC_4


title: FFM_37


title: ATAC-seq_CLP_rep2


title: siLEF1_4


title: FFM_34


title: w1118_embryo_2_2.5h_rep_2

description: w1118_embryo_2_2.5h_rep_2 mRNA-Seq

tag: experiment


title: FFM_32


title: FFM_33


title: ATAC-seq_CLP_rep1

tag: genotype