title: Sample 48

source_name: CN-AML blasts

value: CN-AML blasts

value: relapse


title: Endodermal cells treated with BMS 3 somites rep1 RNA-seq

status: Public on Mar 16 2021

type: SRA

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligment using STAR v2.5.4 : -outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 -- outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD -- outSAMstrandField intronMotif --quantMode GeneCounts
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample

molecule: polyA RNA

organism: Danio rerio

source_name: Endodermal cells (sox17:GFP +)

growth_protocol: Embryos were obtained by incrossing Tg(sox17:GFP) zebrafish adults. Embryos were collected and grow at 23 degrees in E3 media

extract_protocol:
Embryos were dechorionated and deyolked prior to cell isolation by pippeting up and down several times. Singles cells were FACS sorted and GFP+ and GPF- cells were collected. Cells were pelleted and lysed.
RNA was retrotranscribed using an Oligo dT primer to enriched in polyA RNA prior to library preparation using Nextera XT kit

treatment_protocol: Embryos were treated either with DMSO, RA or BMS493 from 2 cell stage until the 3 somites stage.

tag: developmental stage

value: 3 somites

tag: treatment

tag: cell type

value: Endodermal cells (sox17:GFP +)


title: Endodermal cells treated with RA 3 somites rep3 RNA-seq

value: RA


title: 8_N2_10uMDCVC_6hrs

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

country: USA

institute: San Diego State University

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh37 genes using featureCounts.
Genes with mean read counts-per-million less than four across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the edgeR package (version 3.1) for R statistical computing. Quasi-likelihood general linear modeling was used for differential gene expression testing.
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: placental extravillous trophblast cells

growth_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator. Cells were grown to 70–90% confluence at least 24 h after plating prior to use in any experiments. Cells were seeded at a density of 800,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 10 or 20 µM for 6 or 12 h.  Four independent biological replicate experiments were performed.

extract_protocol:
Cells were scraped and lysed with RLT lysis buffer containing beta-mercaptoethanol. Cell lysates were homogenized using QIA shredders (Qiagen), and mRNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacture’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: replicate

value: 10 uM DCVC

tag: treatment duration

value: 6 hours


title: Endodermal cells treated with RA 3 somites rep1 RNA-seq


title: Endodermal cells treated with DMSO 3 somites rep3 RNA-seq

value: DMSO (control)


title: 13_N3_NT_6hrs

treatment_protocol: Cells were seeded at a density of 800,000 cells per well in 6-well cell culture plates. Twenty-four hours later, cells were treated with RPMI 1640 complete medium alone (control) or complete medium plus DCVC diluted to a final concentration of 10 or 20 µM for 6 or 12 h.  Four independent biological replicate experiments were performed.

value: No Treatment


title: Endodermal cells treated with DMSO 3 somites rep2 RNA-seq


title: 4_N1_NT_12hrs

value: 12 hours


title: 5_N1_10uMDCVC_12hrs


title: 3_N1_20uMDCVC_6hrs

value: 20 uM DCVC


title: 2_N1_10uMDCVC_6hrs


title: Non endodermal cells 3 somites rep3 RNA-seq

source_name: Non endodermal cells (sox17:GFP -)

value: Non endodermal cells (sox17:GFP -)


title: 1_N1_NT_6hrs


title: CMP_rep3_3'READS

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Drive #0815

institute: UC San Diego Moores Cancer Center

description: CMP cells were isolated from healthy, human leukapheresis products. CD34-bead enrichment was followed by FACS.

data_processing:
CRISPR screening data were aligned and processed using the published MAGeCK-VISPR pipeline (Li et al. Genome Biology 2015).
For 3'READS data, reads were trimmed using Cutadapt then aligned to hg19 using bowtie2.
Following alignment, bigwig files were generated to visualize the peaks surrounding the gene-of-interest in the study. Reads from the four peaks in this single gene were quantified using multiBigwigSummary from DeepTools2.0
Genome_build: hg19
Supplementary_files_format_and_content: count' text file includes sgRNA counts per sample
Supplementary_files_format_and_content: summary' text file contains beta scores of enrichment in GFP high and low populations
Supplementary_files_format_and_content: countsummary' text file contains QC metrics
Supplementary_files_format_and_content: bigwig files show visualization of 3'READS peaks across the genome

growth_protocol: MDS-L cells were maintained in RPMI supplemented with 10% FBS and 10 ng/mL IL-3. CMPs were not cultured following enrichment from leukapheresis products prior to RNA extraction.

extract_protocol:
The protocol for 3'READS library preparation is described in detail in (Hoque et al. Nature Methods, 2016).
gDNA was extracted from MDS-L cells using the Qiagen DNeasy Blood and Tissue Kit. RNA was extracted from CMPs using Trizol reagent.

treatment_protocol: Cells were not treated.

value: Healthy, primary common myeloid progenitors (CD34+/CD38+/CD123+/CD45RA-)

tag: timepoint

tag: cell culture conditions


title: CMP_rep2_3'READS


title: CMP_rep1_3'READS


title: 10.5 hpf embryos - RARaa

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligment using bowtie2 v22.3.4.1 : --threads 3 --very- sensitive
peak calling with MACS2 : callpeak --gsize 1.4e9 -- nomodel --call-summits --qvalue 0.05
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file with peaks

molecule: genomic DNA

source_name: Zebrafish embryos

growth_protocol: Embryos were injected with myc-tagged RARaa mRNA and grow in E3 media until 10.5hpf

extract_protocol:
Embryos were dechorionated and deyolked prior to fixation with 1.85% PFA for 10 minutes.  Diagenode Bioruptor sonicator was used for chromatin shearing. Dynal Protein A magnetic beads (Diagenode) and ChIP-graded anti-myc antibody (ab9132, Abcam) were used for the immunoprecipitation, an aliquot of chromatin being taken before the immunoprecipitation step and used as negative control (input).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep kit

treatment_protocol: Embryos were treated either with RA for 1 hour before collection

tag: chip antibody

value: myc Tag


title: Non endodermal cells 3 somites rep1 RNA-seq


title: Sample 46

city: Columbus

first: Christopher

middle: J

last: Walker

state: Ohio

address: 1276 Eastwood Ave

institute: Ohio State

data_processing:
STAR alignment
FeatureCounts gene-leve quantification
DeSeq2 Normailzation
Genome_build: hg38
Supplementary_files_format_and_content: norm and raw counts

growth_protocol: Patient samples were thawed and directly used for RNA extraction. No cytokines or cell culture techniques were used to expand leukemic blasts.

extract_protocol: On average, 20 million leukemic blasts isolated from cryopreserved samples were thawed and subjected to total RNA extraction using the Trizol reagent and previously published protocols

tag: tissue

tag: group


title: Endodermal cells treated with BMS 3 somites rep3 ATAC-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligment using bowtie2 v22.3.4.1 : --threads 3 --very-sensitive --maxins 2000 --no-discordant
peak calling with MACS2 : --nomodel --shift 40 --extsize 80 -q 0.05 --gsize 1.4e9
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file with peaks for each sample

extract_protocol:
Embryos were dechorionated and deyolked prior to cell isolation by pippeting up and down several times. Singles cells were FACS sorted and GFP+ and GPF- cells were collected. Cells were pelleted and lysed.
Nuclei were purified and tagmented using the Nextera kit following Buenrostro protocol

tag: genotype/variation


title: T0_rep2_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
TO_2
MD7a-MLE.gene_summary.txt

data_processing:
Library strategy: Amplicon-seq
CRISPR screening data were aligned and processed using the published MAGeCK-VISPR pipeline (Li et al. Genome Biology 2015).
For 3'READS data, reads were trimmed using Cutadapt then aligned to hg19 using bowtie2.
Following alignment, bigwig files were generated to visualize the peaks surrounding the gene-of-interest in the study. Reads from the four peaks in this single gene were quantified using multiBigwigSummary from DeepTools2.0
Genome_build: hg19
Supplementary_files_format_and_content: count' text file includes sgRNA counts per sample
Supplementary_files_format_and_content: summary' text file contains beta scores of enrichment in GFP high and low populations
Supplementary_files_format_and_content: countsummary' text file contains QC metrics
Supplementary_files_format_and_content: bigwig files show visualization of 3'READS peaks across the genome

source_name: Amplicon-sequencing

extract_protocol:
Following gDNA extraction, integrated sgRNAs were PCR amplified using a primer set that flanks the sgRNA insert in the LentiCRISPR v2 backbone (Herculase II Fusion DNA polymerase). Illumina Nextera XT Indexes were then added to this PCR product by a second PCR step using NEB Taq DNA polymerase.
gDNA was extracted from MDS-L cells using the Qiagen DNeasy Blood and Tissue Kit. RNA was extracted from CMPs using Trizol reagent.

value: MDS-L Leukemia Cell Line

value: Day 0

value: RPMI + 10percentFBS + 10 ng/mL hIL-3


title: 6_N1_20uMDCVC_12hrs


title: 7_N2_NT_6hrs


title: Endodermal cells treated with RA 3 somites rep2 RNA-seq


title: T0_rep1_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
TO_1
MD7a-MLE.gene_summary.txt


title: T21_rep2_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
Tend_2
MD7a-MLE.gene_summary.txt

value: Day 21


title: GFP_Low_rep2_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
GFPl_2
MD7a-MLE.gene_summary.txt


title: Sample 43

value: CN-AML blasts

value: maintaincr


title: Endodermal cells treated with BMS 3 somites rep1 ATAC-seq

value: 3 somites

value: Endodermal cells (sox17:GFP +)


title: Endodermal cells treated with DMSO 3 somites rep1 RNA-seq


title: Endodermal cells treated with RA 3 somites rep1 ATAC-seq

value: RA


title: T21_rep1_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
Tend_1
MD7a-MLE.gene_summary.txt


title: Non endodermal cells 3 somites rep2 RNA-seq


title: Endodermal cells treated with RA 3 somites rep3 ATAC-seq


title: Endodermal cells treated with RA 3 somites rep2 ATAC-seq


title: GFP_High_rep2_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
GFPh_2
MD7a-MLE.gene_summary.txt


title: Endodermal cells treated with DMSO 3 somites rep3 ATAC-seq


title: Endodermal cells treated with BMS 3 somites rep2 ATAC-seq


title: GFP_High_rep1_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
GFPh_1
MD7a-MLE.gene_summary.txt


title: 10.5 hpf embryos - Input

value: input


title: 124_challenge

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Trimmomatic version 0.36
HISAT2 (version 2.1.0) mapping
HTSeq (version 0.6.1p1) counts
Genome_build: grch38
Supplementary_files_format_and_content: counts

source_name: alveolar macrophages

growth_protocol: not applicable

extract_protocol:
RNA was extracted using the Rneasy kit (Qiagen).
RNA-seq libraries were prepared using the KAPA RNA HyperPrep with RiboErase (Roche)

treatment_protocol: The alveolar macrophages (AM) were harvested from asthma patients.  These AM were exposed to either saline or house dust mite extract (50 biological units)combined with LPS (75 ng; from Escherichia coli) in vivo. After seven hours, a bilateral bronchoalveolar lavage (BAL) was performed. BAL fluid was pooled (per lung subsegment) and centrifuged at 4°C and 400g for 10 minutes. Cells were stained with CD45 phycoerythrin (PE)-CF594 and CD71 Brilliant Violet (BV)421 (both BD Biosciences, San Jose, CA, USA). AM, defined as cells expressing CD45 and CD71, were isolated by flow cytometry sorting using FACSAria III (BD Biosciences) with high purity (>95%). Sorted AM were stored in RNA later (Qiagen, Venlo, Netherlands) at -80 °C until analysis.

value: challenge


title: Endodermal cells treated with DMSO 3 somites rep2 ATAC-seq

value: DMSO (control)


title: Non endodermal cells 3 somites rep2 ATAC-seq


title: 124_saline

value: saline


title: 121_saline


title: Non endodermal cells 3 somites rep3 ATAC-seq


title: 121_challenge


title: Non endodermal cells 3 somites rep1 ATAC-seq


title: T_pDC_4

city: Changchun

first: Jing

last: Wu

state: Jilin

address: 519 Dongminzhu Ave

country: China

institute: 1st Hospital of Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
After reads filtering, we map clean reads to reference genome using HISAT.
After genome mapping, we use StringTie  to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC.
After genome mapping, we use GATK to call SNP and INDEL variant for each sample.
map clean reads to it using Bowtie2,then calculate gene expression level for each sample with RSEM.
Genome_build: use StringTie to reconstruct transcripts, and use Cuffcompare（Cufflinks tools） to compare reconstructed transcripts to reference annotation, after that, we select 'u','i','o','j' class code types as novel transcripts. And then, we use CPC  to predict coding potential of novel transcripts, then we merge coding novel transcripts with reference transcripts to get a complete reference, and downstream analysis will base on this reference.
Supplementary_files_format_and_content: xls files include FPKM values (calculated by RSEM software) for each Sample …

source_name: tumor region

extract_protocol:
Innate lymphoid cells 3 and plasmacytoid DCs were sorted,  RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon tumor region

value: plasmacytoid DCs


title: GFP_Low_rep1_CRISPR_RBP

description:
all.countsummary.txt
all.count.txt
GFPl_1
MD7a-MLE.gene_summary.txt


title: 120_saline


title: 119_challenge


title: 120_challenge


title: T_pDC_3


title: 119_saline


title: T_ILC3_4

value: Innate lymphoid cells 3


title: T_pDC_2


title: 111_challenge


title: 105_saline


title: 105_challenge


title: 104_saline


title: T_ILC3_2


title: 111_saline


title: T_ILC3_1


title: 104_challenge


title: N_pDC_4

source_name: tumor distal region

value: colon tumor distal region


title: Endodermal cells treated with DMSO 3 somites rep1 ATAC-seq


title: N_pDC_2


title: 103_challenge


title: N_pDC_3


title: 103_saline


title: N_ILC3_2


title: FB_H3

city: shanghai

first: XIAOTING

last: SUN

state: SHANGHAI

address: 1200 cailun Road

department: shuguang hospital

institute: shanghai university of TCM

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: primary fibroblast cells

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary fibroblast cells

tag: age

value: 6 weeks


title: N_ILC3_3


title: N_ILC3_1


title: FB_H1


title: FB_3

value: control


title: naïve mouse 4

city: PHILADELPHIA

first: Botond

middle: Z

last: Igyártó

state: PA

address: 233 South 10th Street, Bluemle Life Science Building, Suite 620

department: Microbiology and Immunology

institute: Thomas Jefferson University

data_processing:
RNAseq reads trimmed and aligned to mouse genome
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_count_table.csv

source_name: skin

extract_protocol:
Total RNA was isolated from tissue lysates using the RNeasy Mini Kit (Qiagen), including on-column DNase digestion. Total RNA was analyzed for quantity and quality using the RNA 6000 Pico Kit (Agilent)
Poly-A enriched NGS library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) using 50ng of input total RNA according to manufacturer’s protocol using 16 amplification cycles. Quality of the individual libraries was assessed using the High Sensitivity DNA Kit (Agilent). Individual libraries were quantitated via qPCR using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and equimolar pooled. Final pooled libraries were sequenced on an Illumina NextSeq 500 with paired-end 75 base read lengths

tag: gender

value: M

value: 8.3 weeks

value: PBS

value: skin


title: immunized mouse 4

value: LNP


title: FB_1


title: immunized mouse 3


title: FB_2


title: naïve mouse 2

value: F


title: peri-infarct cortex - Veh 2

city: Cincinnati

first: Lei

middle: Frank

last: Huang

address: 2600 Clifton Ave

institute: Uiversity of Cincinnati

data_processing:
Fastq reads were aligned to mouse genome by HiSat2
Read counts matrices were extracted from alignment by Htseq program
Differential expressed genes analyses were conducted by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read counts matrices (.csv)

source_name: peri-infarct cortex

extract_protocol:
Peri-infarct cortex was punched from frozen brain and total RNA extracted using RNeasy micro kit (Qiagen, Germany).
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA  is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: Mice were subjected to MCAo and received either vehicle (5% DMSO in saline) or ISP peptide (1μg/g/day) for 14 days before the brain was harvested.

value: Veh


title: immunized mouse 2


title: naïve mouse 3


title: peri-infarct cortex - Veh 6


title: peri-infarct cortex - Veh 8


title: peri-infarct cortex - ISP 18

value: ISP


title: immunized mouse 1


title: naïve mouse 1


title: FB_H2


title: MEF_BAHD1_W659G_2

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: mm10

source_name: MEF cells

growth_protocol: The MEF cells were grown in the DMEM base medium supplemented with 20% of FBS, 1% of antibiotics, 0.1mM of β-mercaptoethanol and 0.1mM of non-essential amino acids.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
RNA libraries were made with standard Illumina protocols.

treatment_protocol: Cells were grown in regular medium and collected.

value: mouse embryonic fibroblast (MEF)

tag: genotype

value: W659G homozygous mutation within Bahd1 BAH


title: peri-infarct cortex - ISP 12


title: MEF_BAHD1_WT_2

value: WT Bahd1


title: MEF_BAHD1_WT_1


title: w1118_Male_Ctrl_NIR_2

city: Detroit

first: Ekta

last: Shah

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

data_processing:
After de-multiplexing with Illumina’s CASAVA 1.8.2 software, the 50 bp reads were aligned to the Drosophila genome (Build dm3) with STAR_2.4 and tabulated for each gene region.
Differential gene expression analysis was used to compare transcriptome changes between conditions using edgeR v.3.22.3 and transcripts were defined  as significantly differentially expressed at absolute Log2 fold change >1, FDR <0.05
Genome_build: Dm3

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Direct-zol RNA MicroPrep kit
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (low-input protocol and 15 ng RNA input)

tag: strain


title: peri-infarct cortex - control 38


title: MEF_BAHD1_W659G_1


title: N_ILC3_4


title: peri-infarct cortex - control 21


title: peri-infarct cortex - control 36


title: peri-infarct cortex - control 19


title: peri-infarct cortex - Veh 10


title: MB6 - KO1 DM

city: Utrecht

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Bulk RNA sequencing of Pax6-KO mouse lacrimal gland organoids, in differentiation

data_processing:
Sequenced reads were mapped using the STAR mapping software version 2.7.0c and mapped to the genome. Genome build was done using the following settings: “STAR --runThreadN 4 --runMode genomeGenerate --genomeDir STAR_index_mouse --genomeFastaFiles reference/Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile reference/Mus_musculus.GRCm38.101.gtf”. mapping was performed using the following settings: STAR --runThreadN 4 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 ". Read counts were assigned from alignment files using the Featurecounts package using default settings using “featureCounts -a ", “reference/Mus_musculus.GRCm38.101.gtf”, " -T 4 -g gene_name ,”.
Genome_build: GRCm38
Supplementary_files_format_and_content: Files are in .csv format. They contain unnormalized transcript counts.

source_name: Mouse lacrimal gland organoids

growth_protocol: For expansion, organoids were grown in expansion medium (EM) for 7 days. For differentiation, organoids were grown for 2 days in EM then 5 days in differentiation medium (DM).

extract_protocol:
After a week, organoids were retrieved from BME and resuspended in 350 µL of RLT buffer (Qiagen). RNA was extracted using the RNeasy extraction kit (Qiagen).
Library was prepped using the Illumina Truseq RNA stranded polyA kit.

value: Pax6 KO clone 1

value: Differentiation (DM)


title: MB8 - KO2 DM

value: Pax6 KO clone 2


title: MB5 - KO1 EM

description: Bulk RNA sequencing of Pax6-KO mouse lacrimal gland organoids, in expansion

value: Expansion (EM)


title: MB3 - WT2 EM

description: Bulk RNA sequencing of WT mouse lacrimal gland organoids, in expansion

value: Wildtype clone 2


title: WT infected and OI treated Rep2

first: Ashok

last: Kumar

state: MI

address: 4717 St. Antoine

department: Department of Ophthalmology, Visual, and Anatomical Sciences

institute: Wayne State University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned based on STAR aligner and mapped against mm9 reference
Reads Per Kilobase of exon per Megabase of library size (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Mouse Bone marrow-derived macrophages

growth_protocol: Briefly, BMDMs were plated in 65 mm Petri-dishes (4x106) for in-vitro experiments and placed in a 5% CO2 37°C incubator overnight.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions for the paired-end RNA sequencing using Illumina platform.
As per manufacturer’s instructions for the paired-end RNA sequencing using Illumina platform

treatment_protocol: BMDMs were either untreated or pre-treated (2 h) with 4-Octyl itaconate (125 µM) and left uninfected or infected with S. aureus RN6390 strain (multiplicity of infection (MOI) 10:1), for 8 h.

value: S. aureus infected and OI treated

value: BMDMs


title: WT infected and OI treated Rep1


title: MB2 - WT1 DM

description: Bulk RNA sequencing of WT mouse lacrimal gland organoids, in differentiation

value: Wildtype clone 1


title: WT infected and OI treated Rep3


title: MB4 - WT2 DM


title: MB1 - WT1 EM


title: WT Infected Rep3

value: S. aureus infected


title: WT Infected Rep1


title: YP12 - LG8 differentiation

value: Wildtype bulk 8


title: WT Infected Rep2


title: YP11 - LG7 differentiation

value: Wildtype bulk 7


title: MB7 - KO2 EM


title: YP10 - LG6 differentiation

value: Wildtype bulk 6


title: WT Control Rep2

value: Uninfected control


title: WT Control Rep3


title: YP9 - LG8 expansion


title: YP8 - LG7 expansion


title: IVA262A1A

city: London

first: Kenzo

last: Ivanovitch

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, which deconvolved reads to their cell of origin using the UMI tags, aligned these to a custom transcriptome built from the Ensembl mouse GRCm38 release 86 with the addition of the sequence from tdtomato Ai9 plasmid (Madisen et al., 2010)  and reported cell-specific gene expression count estimates.
All subsequent analyses were performed in R v.3.6.1 using the Seurat (v3) package. Primary filtering was performed by removing from consideration: cells expressing unique feature counts fewer than 500, number of UMIs fewer than 1000 and cells for which mitocondrial genes made up greater than 3 times the standard deviation value of all expressed genes.
Genome_build: Custom transcriptome built from the Ensembl mouse GRCm38 release 86 with the addition of the sequence from tdtomato Ai9 plasmid (Madisen et al., 2010)
Supplementary_files_format_and_content: tab delimited text containing raw counts

source_name: EHF E7+14h mouse embyro

extract_protocol:
The embryos were isloted and  incubated separately in a solution of papain  for 11 min at 37ºC in presence of 10ug/ml of both DNAse  and Rock Inhibitor. The papain solution was then removed, and mechanical dissociation was performed through pipetting medium.
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina).

treatment_protocol: Tamoxifen administration by oral gavage (0.08mg/bw)

value: embryo


title: YP7 - LG6 expansion


title: YP3 - LG8 tissue

description: Bulk RNA sequencing of WT mouse lacrimal gland tissue

source_name: Mouse lacrimal gland tissue


title: pancreatic islets, FACS-sorted for mTomato and mGFP fluorescence

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

data_processing:
The 10X Genomics core computational software Cellranger v.2.1 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.4.5.post2, anndata v.0.7rc1 and scrublet v.0.1 were used.
Genome_build: mm10 + custom genes (mTomato and mGFP)
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

source_name: pancreas

growth_protocol: G-Solution: HBSS (Lonza) supplemented with 1x P/S (Gibco) and 1% BSA;  Islet culture medium: RPMI1640 (Lonza) supplemented with 1X P/S and 10% FCS (PAA)

extract_protocol: Islets of Langerhans were isolated from mice. Mice were sacrificed by cervical dislocation. The abdominal cavity was  opened and pancreas, common bile duct and gallbladder exposed. The ampulla was sealed with a bulldog clamp and Collagenase P (Roche) (1 mg/mL in G-solution) injected in the bile duct with a syringe and a 30G needle. Once the organ was perfused with 3ml of the abovementioned solution, pancreats was dissected and incubated in 3ml of Collagenase P solution and placed on ice. Afterwards, the pancreas was digested at 37°C for 12 minutes and shaken vigorously at least once at half the time of incubation. The digestion was stopped on ice by adding 10ml G-solution plus 10% FBS. The mixture was centrifugated (1620rpm, 3 min, 4°C) in order to pellet the digested tissue and remove the solution containing the collagenase. The pellet was then resuspended in 5.5ml of gradient solution (40%Optiprep). This was then centrifugated (1700rpm, 10 min, RT, acceleration 3 and deceleration 0). Islets were sedimented at the interface between the first and second phase. They were collected and washed on a 70µm cell strainer with G-solution, then placed in a 10cm dish in islets medium. Considering that the obtained solution is still rich in exocrine cells, islets were handpicked and placed in a new dish with fresh medium. Islets are cultured at 37°C and 5%CO2. Islets were then picked in an 1.5 mL Eppendorf tube, pelleted (800 rpm, 2 min) washed with PBS (-Mg/Ca) and digested with TrypLE™ Express Enzyme (1X) (Thermo Fisher Scientific) at 37 °C for 10 min, gently pipetting every 2 minutes. After this, the tube was placed in ice and FACS buffer was added to the cells and finally centrifuged at 900rpm for 5 min. The supernatant was discarded and an appropriate amount of FACS buffer was added to resuspend the single cells. Finally cells were sorted in the FACS Aria III into 3 sepaerate tubes.

value: pancreas

value: FltpiCre;mTmG

value: postnatal day 16


title: pancreatic islets, FACS-sorted for mTomato fluorescence


title: YP2 - LG7 tissue


title: YP1 - LG6 tissue


title: ko-2

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description: polyA mRNA

data_processing:
Basecalling and demultiplexing: standard Illumina software to generate fastq files
Alignments (Samples 1-6): STAR --runThreadN 16 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 500000 --alignMatesGapMax 500000 -- --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Counts (Samples 1-6): htseq-count -f bam -r pos -s yes
Mapping (Samples 7-12): Salmon --libType SR --threads 8 --fldMean 250 --fldSD 50 –validateMappings
Count normalization and DEGs: DESeq2
Genome_build: STAR: mm10. Salmon: Ensembl Grcm38.v79
Mapping (Sample 13): Alevin –chromiumV3 -p 12 –dumpMtx
Cell Filtering, Clustering, Differential expression: Seurat R package
Genome_build: Gencode GRCm38.vM24
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Text file with barcodes and genes for Sample 14

source_name: embryonic fetal liver

extract_protocol:
Trizol
At Embryonic Day E13.5 fetal livers were dissected out of mouse embryos and homogenized by gentle pipetting in 1X PBS + 2% FBS. Cells were strained through a 70μm nylon cell strainer (Thermo Fisher) into 1X PBS + 2% FBS. After staining for appropriate antibodies, cells were sorted by FACS and collected in Trizol solution immediately for RNA-Seq, or purified by EZ-Sep (Cell Signaling technologies #17656) and processed for single cell sequencing using the Chromium V3 single cell kit (10X Genomics). RNA was extracted using ethanol precipitation, except for samples 7, 8, and 9 where we used the Agilent Absolutely RNA Nanoprep kit (#400753)
Libraries were constructed using Illumina Truseq stranded RNA kit
Single-end second strand RNA-Seq
Paired-end single cell sequencing

value: EKLF-/- (null)


title: wt-2

description: polyA mRNA

value: wild type


title: Esrrb_Sorted_Bottom_R1

city: Berlin

first: Oriana

last: Genolet

address: Ihnestrasse 63

department: OWL Schulz

institute: Max Planck Institute for Molecular Genetics

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the lowest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 1.
Esrrb_Screen_counts.txt

data_processing:
Tab delimited text files with normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015)
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Tab delimited text files include normalized counts for each sample
Supplementary_files_format_and_content: Alignment: GeCKOx/GeCKOxs sgRNA library (tab delimited text files provided)

source_name: mESCs

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily. For stable expression of the Cas9 endonuclease, cells were transduced with virus carrying Cas9 and selected for cells with stable integration. Cells were then transduced with the respective sgRNA library with a MOI (multiplicity of infection) of 0.3 and selected for stable sgRNA cassette integration. Cells were then grown for seven days prior to sorting.

extract_protocol:
For the primary screen, genomic DNA was isolated from the frozen cell pellets by using the DNeasy Blood and Tissue kit (Qiagen) following the manufacturer's instructions. For the secondary screens, genomic DNA from frozen cell pellets was isolated via Phenol/Chloroform extraction due to higher yields. Briefly, cell pellets were thawed and resuspended in 250µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2M NaCl and 5mM DTT (Roth) in TE Buffer) and incubated over night at 65°C. 200µg of RNAse A (Thermo Fisher Scientific) was added to the sample and incubated at 37°C for 1h. 100µg of Proteinase K (Sigma) were subsequently added followed by a 1h incubation at 50°C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at RT for 1 min and subsequently centrifuged at 16000 xg for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 hr. DNA was pelleted by centrifugation for 13000 rpm for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50µl H2O.
The PCR amplification of the sgRNA cassette was performed in two PCR steps as described previously with minor modifications (Shalem et al. 2014).

treatment_protocol: No treatment was carried out.

tag: gdna isolation

value: Phenol/Chloroform


title: Esrrb_Sorted_Bottom_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the lowest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 2.
Esrrb_Screen_counts.txt


title: Esrrb_Sorted_Bottom_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the lowest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 3.
Esrrb_Screen_counts.txt


title: wt-1

description: polyA mRNA


title: Esrrb_Sorted_Top_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the highest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 1.
Esrrb_Screen_counts.txt


title: Esrrb_Sorted_Top_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the highest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 3.
Esrrb_Screen_counts.txt


title: IVA262A1: EHF E7+14h mouse embyro


title: WT Control Rep1


title: ko-1

description: polyA mRNA


title: peri-infarct cortex - ISP 16

value: ISP


title: pancreatic islets, FACS-sorted for mGFP fluorescence


title: IVA262A2: OB/EB-E+3h mouse embryo

source_name: OB/EB-E+3h mouse embryo


title: Esrrb_Sorted_Top_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
10% of cells with the highest Esrrb expression (based on mCherry fluorescence levels of a C-terminally tagged Esrrb locus) were FACS-sorted. Replicate 2.
Esrrb_Screen_counts.txt


title: IVA262A3: MS/LS -E6+21h mouse embryo

source_name: MS/LS -E6+21h mouse embryo


title: peri-infarct cortex - ISP 14


title: Nanog_DoubleSorted_Top_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the highest Nanog expression (based on mCherry fluorescence levels of a C-terminally tagged Nanog locus) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the highest fluorescence. Replicate 2.
Nanog_Screen_counts.txt


title: Nanog_DoubleSorted_Top_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the highest Nanog expression (based on mCherry fluorescence levels of a C-terminally tagged Nanog locus) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the highest fluorescence. Replicate 1.
Nanog_Screen_counts.txt


title: S198_WT4

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

institute: Amsterdam UMC, location AMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of raw reads

source_name: CD4+ T cells

extract_protocol:
Splenic CD4+ T cells were negatively selected for using antibody-conjugated magnetic beads Total RNA was isolated from the CD4+ T cells using the Qiagen RNeasy Mini Kit
100 ng of total RNA was used to constructed strand-specific libraries using the NuGen Ovation RNA-Seq System

value: spleen

value: ApoE-/-

value: CD4+ T cells

value: WT


title: S198_WT6


title: S198_TG7


title: wt-3

description: polyA mRNA


title: ko-3

description: polyA mRNA


title: Esrrb_Unsorted_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells have a C-terminally mCherry tagged Esrrb locus. Replicate 2.
mpimg_L11128_Sample-46_S22
processed data file: Esrrb_Screen_counts.txt

data_processing:
Tab delimited text files with normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015)
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: normalized counts for each sample
Supplementary_files_format_and_content: GeCKOx/GeCKOxs sgRNA library; sgRNA name, sgRNA sequence and Gene for read alignment

tag: strain/cell line background

value: mouse embryonic stem cells (mESCs)


title: Esrrb_Unsorted_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells have a C-terminally mCherry tagged Esrrb locus. Replicate 3.
mpimg_L11134_Sample-52_S28
processed data file: Esrrb_Screen_counts.txt


title: S198_TG5


title: Esrrb_Unsorted_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells have a C-terminally mCherry tagged Esrrb locus. Replicate 1.
mpimg_L11122_Sample-40_S16
processed data file: Esrrb_Screen_counts.txt


title: S198_TG6


title: Nanog_Unsorted_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells have a C-terminally mCherry tagged Nanog locus. Replicate 2.
mpimg_L11114_Sample-32_S8
processed data file: Nanog_Screen_counts.txt


title: S198_WT5


title: Nanog_Unsorted_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells have a C-terminally mCherry tagged Nanog locus. Replicate 1.
mpimg_L11107_Sample-25_S1
processed data file: Nanog_Screen_counts.txt


title: Nanog_DoubleSorted_Bottom_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the lowest Nanog expression (based on mCherry fluorescence levels of a C-terminally tagged Nanog locus) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the lowest fluorescence. Replicate 1.
Nanog_Screen_counts.txt


title: C2_D9K13HET_R3

data_processing:
The tab delimited text files containing raw counts for each sample were generated with the FWD-UMI Mouse (GRCm38) Lexogen QuantSeq 2.6.1 pipeline from the BlueBee NGS data analysis platform (https://www.bluebee.com/) by inputing their respective fastq files. Cpm normalized counts were generated using the EdgeR package.
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: raw counts or cpm normalized counts for each sample

source_name: Dusp9 +/- & Klhl13 +/-_mESCs

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily.

extract_protocol:
For gene expression profiling, ~ 2*106 cells were washed with ice-cold PBS and lysed by directly adding 500µl of Trizol (Invitrogen). RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions.
The QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen) was used with 800ng starting material.


title: C1_D9K13HET_R3


title: P35_HIP_HET_mouse_5 [P35_27_HIP]

first: Lilia

middle: M

last: Iakoucheva

state: California

address: 9500 Gilman Drive, MC0603

department: Psychiatry

institute: University of California San Diego

data_processing:
Illumina RTA version 2.7.6 software used for base calling
All fastqs were trimmed for adapter sequence and low base call quality (Phred score < 30 at ends) using Cutadapt (v1.14).
Trimmed reads were then aligned to the GRCm38.p5 (mm10) reference genome via STAR (2.5.3a) using comprehensive gene annotations from Gencode (v16).
Gene-level quantifications were calculated using RSEM (v1.3).
Genome_build: Human GRCm38.p5 (mm10) reference genome
Supplementary_files_format_and_content: count matrix with rows as genes (EnsembIDs) and columns as samples

extract_protocol:
Total RNA was extracted at three developmental time periods (Embryonic E17.5, postnatal day-7 (P7) and adult (P35) from different brain regions (cerebral cortex (CX), hippocampus (HIP), and cerebellum (CB)) of WT and Cul3+/- mice. The total RNA was extracted using the QIAGEN RNAeasy isolation kit (QIAGEN) following manufacturer’s instructions. RNA sequencing was performed using the same input amount of total RNA for each sample. RNA samples were ribodepleted using Ribo-Zero rRNA Removal Kit (Illumina) and library preparation was performed using the TrueSeq Stranded Total RNA kit for Illumina Sequencing according to the manufacturer’s instructions. Paired-end RNA sequencing (2x100bp) was performed on an Illumina HiSeq4000 to an average depth of 40M reads per sample.
RNA-seq libraries were prepared using standard Illumina protocols

tag: strain background

value: adult

value: Hippocampus


title: P35_HIP_HET_mouse_6 [P35_32_HIP]


title: C2_D9K13HET_R1

tag: cell type


title: C1_D9K13HET_R2


title: C2_D9K13HET_R2


title: P35_HIP_HET_mouse_4 [P35_22_HIP]


title: P35_HIP_HET_mouse_2 [P35_14_HIP]


title: C1_D9K13HET_R1


title: C2_K13HOM_R3

source_name: Klhl13 -/-_mESCs


title: P35_HIP_WT_mouse_5 [P35_26_HIP]

source_name: Wild Type_P35_Hippocampus


title: C2_K13HOM_R2


title: P35_HIP_WT_mouse_4 [P35_23_HIP]


title: P35_HIP_WT_mouse_3 [P35_17_HIP]


title: C2_K13HOM_R1


title: C1_K13HOM_R3


title: P35_HIP_WT_mouse_2 [P35_15_HIP]


title: P35_HIP_HET_mouse_3 [P35_16_HIP]


title: C1_K13HOM_R1


title: C2_K13HET_R3

source_name: Klhl13 +/-_mESCs


title: P35_HIP_WT_mouse_1 [P35_11_HIP]


title: P35_CB_HET_mouse_5 [P35_27_CB]

value: Cerebellum


title: C1_K13HOM_R2


title: P35_HIP_HET_mouse_1 [P35_12_HIP]


title: P35_CB_HET_mouse_4 [P35_22_CB]


title: C2_K13HET_R1


title: C2_K13HET_R2


title: P35_HIP_WT_mouse_6 [P35_31_HIP]


title: P35_CB_HET_mouse_3 [P35_16_CB]


title: P35_CB_HET_mouse_1 [P35_12_CB]


title: T_ILC3_3

source_name: tumor region

value: colon tumor region

value: Innate lymphoid cells 3


title: C1_K13HET_R2


title: C1_K13HET_R1


title: C2_D9HOM_R2

source_name: Dusp9 -/-_mESCs

value: Dusp9 -/-


title: P35_CB_WT_mouse_5 [P35_26_CB]

source_name: Wild Type_P35_Cerebellum


title: C2_D9HOM_R1


title: C2_D9HOM_R3


title: P35_CB_WT_mouse_3 [P35_17_CB]


title: P35_CB_WT_mouse_2 [P35_15_CB]


title: P35_CB_WT_mouse_4 [P35_23_CB]


title: P35_CB_HET_mouse_6 [P35_32_CB]


title: C1_D9HOM_R2


title: P35_CX_HET_mouse_6 [P35_32_CX]

value: Cortex


title: C2_D9HET_R3

source_name: Dusp9 +/-_mESCs

value: Dusp9 +/-


title: P35_CB_WT_mouse_1 [P35_11_CB]


title: C1_K13HET_R3


title: C2_D9HET_R2


title: P35_CX_HET_mouse_5 [P35_22_CX]


title: C1_D9HOM_R1


title: P35_CX_HET_mouse_4 [P35_27_CX]


title: P35_CB_HET_mouse_2 [P35_14_CB]


title: P35_CX_HET_mouse_3 [P35_16_CX]


title: C2_D9HET_R1


title: P35_CX_HET_mouse_2 [P35_14_CX]


title: C1_D9HET_R2


title: P35_CX_HET_mouse_1 [P35_12_CX]


title: P35_CB_WT_mouse_6 [P35_31_CB]


title: C1_D9HET_R3


title: P35_CX_WT_mouse_6 [P35_31_CX]

source_name: Wild Type_P35_Cortex


title: C3_XO_R3

source_name: Wildtype XO subclone_mESCs

value: Wildtype XO subclone


title: C3_XO_R2


title: P35_CX_WT_mouse_4 [P35_26_CX]

value: wild type


title: C3_XO_R1


title: P35_CX_WT_mouse_5 [P35_23_CX]


title: P35_CX_WT_mouse_3 [P35_17_CX]


title: C2_XO_R3


title: P35_CX_WT_mouse_2 [P35_15_CX]


title: P35_CX_WT_mouse_1 [P35_11_CX]


title: C2_XO_R2


title: P7_HIP_HET_mouse_5 [P7_C2_9_HIP]

value: postnatal


title: P7_HIP_HET_mouse_6 [P7_C4_3_HIP]


title: P7_HIP_HET_mouse_4 [P7_C2_6_HIP]


title: C1_XO_R1


title: C1_D9HET_R1


title: C1_XO_R3


title: C2_XX_R3

source_name: Female wildtype_mESCs

value: Female wildtype


title: C2_XX_R1


title: P7_HIP_HET_mouse_2 [P7_C1_7_HIP]


title: P7_HIP_WT_mouse_6 [P7_C4_5_HIP]

source_name: Wild Type_P7_Hippocampus


title: P7_HIP_HET_mouse_1 [P7_C1_3_HIP]


title: P7_HIP_WT_mouse_5 [P7_C2_4_HIP]


title: C1_XX_R3


title: P7_HIP_HET_mouse_3 [P7_C2_5_HIP]


title: C2_XX_R2


title: C1_XX_R2


title: C1_XX_R1


title: P7_HIP_WT_mouse_4 [P7_C2_2_HIP]


title: P7_HIP_WT_mouse_2 [P7_C1_8_HIP]


title: P7_HIP_WT_mouse_1 [P7_C1_5_HIP]


title: P7_CB_HET_mouse_6 [P7_C2_9_CB]


title: C2_XO_R1


title: HUB-MA-s007

description: Cells were sorted into a 384-well plate and processed for single-cell sequencing

data_processing:
Fastq files were trimmed with TrimGalore-0.4.3 and mapped with STAR-2.5.3a to the human reference genome (GRCh38). Introns and exons were extracted from the corresponding annotation files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Files are in .csv format. They contain unnormalized transcript counts.

source_name: Organoids

extract_protocol:
Live cells  were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described SORT-seq technique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired-end sequencing.

treatment_protocol: Tissue cells were stained for EpCAM, NGFR or nothing, before being sorted.

value: Human lacrimal gland organoids

tag: patient number

tag: antibody sort

tag: passage number

tag: treatment

value: Differentiation (DM)

tag: treatment length

value: 9 days


title: HUB-MA-s008

source_name: Tissue

value: EPCAM+ or EPCAM+/NGFR+


title: HEK293_siBAHD1_FLAG_mut#1_W667G_cell_PE_CR2

data_processing:
Library strategy: CUT&RUN
CUT&RUN reads were aligned to human genome build GRCh37/hg19 using Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of CUT&RUN read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
Genome_build: hg19

source_name: HEK293 cells

growth_protocol: HEK293 cells with stable expression of exogenous Flag-BAHD1 (resistant to siRNA used for endogenous BAHD1 KD) or empty vector (EV) control were grown in the DMEM base medium plus 10% of FBS and 1% of antibiotics. The BAHD1-targeting siRNA was transfected into cells and cells collected 48 hours later.

extract_protocol:
Cells were trypsinized with 0.05% trypsin and pellets were collected for CUT&RUN. CUT&RUN was performed according to manufacturer’s instructions (CUTANA™ pAG-MNase for ChIC/CUT&RUN, EpiCypher, Cat# 15-1116) with the antibodies against FLAG (Sigma cat#F1804). WT-BAHD1-expressing cells labeled as WT#1_SE were processed in parallel with samples labeled as EV (which is a negative control with empty vector) and mut#1_W667G_SE (which expressed a BAHD1 W677G mutant), followed by the single-end (SE) sequencing; the rest of libraries for WT and the two BAH mutants of BAHD1 (WT#2_PE, mut#1_W667G_PE and mut#2_Y669A_PE) were processed in a separate experiment and subjected to paired-end (PE) sequencing later on.
10 ng of the purified CUT&RUN-enriched DNA was used for preparation of multiplexed sequencing libraries with the NEB Ultra II DNA Library Prep Kit per manufacturer's instructions (NEB #E7103).

tag: antibody used

value: FLAG (Sigma; F1804)

tag: treatment condition

value: Stable expression of W667G mutant BAHD1 (siRNA-resistant), followed by KD of endogenous BAHD1


title: C1_XO_R2

value: mouse embryonic stem cells (mESCs)


title: HUB-MA-005

tag: tissue

value: Expansion (EM)

value: 7 days


title: P7_CB_HET_mouse_5 [P7_C4_3_CB]

tag: genotype/variation

value: Cerebellum


title: HUB-JP-051

value: Human lacrimal gland tissue


title: P7_CB_HET_mouse_4 [P7_C2_6_CB]

tag: age


title: P7_CB_HET_mouse_2 [P7_C1_3_CB]


title: HUB-JP-050


title: P7_CB_HET_mouse_3 [P7_C2_5_CB]


title: P7_CB_HET_mouse_1 [P7_C1_7_CB]


title: HUB-MA-006


title: HUB-JP-049


title: HEK293_siBAHD1_FLAG_mutnum2_Y669A_cell_PE_CR2_R1

data_processing:
CUT&RUN reads were aligned to human genome build GRCh37/hg19 using Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of CUT&RUN read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
Genome_build: hg19

growth_protocol: HEK293 cells with stable expression of exogenous Flag-BAHD1 or vector control were grown in the DMEM base medium plus 10% of FBS and 1% of antibiotics. The BAHD1-targeting RNAi was transfected into cells and cells collected 48 hours later.

extract_protocol:
Cells were trypsinized with 0.05% trypsin and pellets were collected for CUT&RUN. WT-BAHD1-expressing cells labeled as WTnum1 and WTnum2 were processed in parallel with cells labeled as mutnum1 (W667G) and mutnum2 (Y669A), respectively. CUT&RUN was performed according to manufacturer’s instructions (CUTANA™ pAG-MNase for ChIC/CUT&RUN, EpiCypher, Catnum 15-1116) with the antibodies against FLAG (Sigma catnumF1804).
10 ng of the purified CUT&RUN-enriched DNA was used for preparation of multiplexed sequencing libraries with the NEB Ultra II DNA Library Prep Kit per manufacturer's instructions (NEB numE7103).

value: Stable expression of Y669A mutant BAHD1, followed by knockdown (KD) of endogenous BAHD1


title: P7_CB_WT_mouse_5 [P7_C4_5_CB]

source_name: Wild Type_P7_Cerebellum


title: P7_CB_WT_mouse_4 [P7_C2_2_CB]


title: P7_CB_WT_mouse_6 [P7_C2_10_CB]


title: P7_HIP_WT_mouse_3 [P7_C2_10_HIP]

value: Hippocampus


title: HEK293_siBAHD1_FLAG_WTnum1_cell_PE_CR_R1

value: Stable expression of wildtype BAHD1, followed by knockdown (KD) of endogenous BAHD1


title: HEK293_siBAHD1_FLAG_WTnum2_cell_PE_CR2_R1


title: HUB-MA-s010

value: Expansion (EM) & Differentiation (DM)


title: P7_CB_WT_mouse_3 [P7_C2_4_CB]

value: wild type

value: postnatal


title: HEK293_siBAHD1_FLAG_mutnum1_W667G_cell_SE_CR1

value: Stable expression of W667G mutant BAHD1, followed by knockdown (KD) of endogenous BAHD1


title: P7_CB_WT_mouse_1 [P7_C1_5_CB]


title: P7_CB_WT_mouse_2 [P7_C1_8_CB]


title: HEK293_siBAHD1_FLAG_WTnum1_cell_SE_CR1


title: HEK293_siBAHD1_EV_cell_SE_CR1

value: Stable expression of EV, followed by knockdown (KD) of endogenous BAHD1


title: JQ1_BRD4

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
Alignment was performed using bowtie v1.2.2
Peak calling was performed using MACS2 v2.1.0
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Genome_build: hg38

source_name: NK cells

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

value: NK cells

tag: donor


title: C1_D9HOM_R3

value: Dusp9 -/-


title: JQ1_BRD2


title: P7_CX_HET_mouse_4 [P7_C2_6_CX]

value: Cortex


title: input_JQ1_S11


title: P7_CX_HET_mouse_2 [P7_C1_3_CX]


title: input_DMSO_S2

value: DMSO


title: input_DMSO2


title: P7_CX_HET_mouse_3 [P7_C2_5_CX]


title: input_DMSO1


title: DMSO_BRD2


title: BRD4_JQ1_S14


title: P7_CX_HET_mouse_1 [P7_C1_7_CX]


title: DMSO_BRD4


title: P7_CX_WT_mouse_3 [P7_C2_4_CX]

source_name: Wild Type_P7_Cortex


title: BRD4_DMSO_S15


title: BRD2_JQ1_S13


title: P7_CX_WT_mouse_4 [P7_C2_2_CX]


title: P7_CX_WT_mouse_5 [P7_C4_5_CX]


title: P7_CX_WT_mouse_2 [P7_C1_8_CX]


title: BRD2_DMSO_S6


title: E17.5_HIP_HET_mouse_6 [E17_5_S4_6_HIP]

value: embryonic


title: DEG-N704 (scRNA-seq)

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/Acribbs/scflow)
Sequenced reads were demultiplexed and then aligned to the hg38 genome using salmon alevin v1.3.0. Downstream analysis was performed using a Seurat based workflow
Genome_build: Hg38
Supplementary_files_format_and_content: A tarball containing files with a list of barcodes and gene names and a market matrix file format of counts for each cell

extract_protocol:
Single-cell RNA sequencing libraries were performed using droplet based sequencing (Drop-seq)
Single-cell libraries were contructed using the Macoscko et al 2015 protocol
Single-cell RNA-seq

value: DEG

value: NK


title: P7_CX_HET_mouse_5 [P7_C4_3_CX]


title: JQ1-N702 (scRNA-seq)


title: DMSO-N701 (scRNA-seq)


title: E17.5_HIP_HET_mouse_3 [E17_5_S3_7_HIP]


title: AZD5153-N703 (scRNA-seq)


title: P7_CX_WT_mouse_6 [P7_C2_10_CX]


title: Nanog_DoubleSorted_Bottom_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the lowest Nanog expression (based on mCherry fluorescence levels of a C-terminally tagged Nanog locus) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the lowest fluorescence. Replicate 2.
Nanog_Screen_counts.txt

source_name: mESCs

value: Phenol/Chloroform


title: E17.5_HIP_WT_mouse_4 [E17_5_S3_8_HIP]

source_name: Wild Type_E17.5_Hippocampus


title: i9-CD8-D1-iBRD9_S12

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text files of read counts for each sample

source_name: PBMCs

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols


title: E17.5_HIP_WT_mouse_5 [E17_5_S4_4_HIP]


title: E17.5_HIP_WT_mouse_6 [E17_5_S4_7_HIP]


title: i6-NK-D1-BRD9162_S18


title: E17.5_HIP_WT_mouse_3 [E17_5_S3_6_HIP]


title: E17.5_HIP_HET_mouse_5 [E17_5_S4_3_HIP]


title: E17.5_HIP_WT_mouse_1 [E17_5_S2_6_HIP]


title: E17.5_HIP_WT_mouse_2 [E17_5_S2_11_HIP]


title: i4-NK-D1-JQ1_S14


title: E17.5_CB_HET_mouse_6 [E17_5_S4_6_CB]

value: Cerebellum


title: E17.5_HIP_HET_mouse_4 [E17_5_S3_9_HIP]


title: i6-CD4-D3-BRD9162_S8


title: P7_CX_HET_mouse_6 [P7_C2_9_CX]


title: E17.5_CB_HET_mouse_5 [E17_5_S4_3_CB]


title: E17.5_HIP_HET_mouse_2 [E17_5_S2_10_HIP]


title: i48-CD4-D2-BRD9162_S20


title: E17.5_CB_HET_mouse_4 [E17_5_S3_9_CB]


title: i46-CD4-D2-JQ1_S9


title: i8-CD8-D1-VS_S23

value: No treatment


title: E17.5_CB_HET_mouse_3 [E17_5_S3_7_CB]


title: i7-CD8-D1-V_S13


title: E17.5_HIP_HET_mouse_1 [E17_5_S2_7_HIP]

value: Hippocampus


title: i45-CD4-D2-iBRD9_S11


title: i44-CD4-D2-VS_S4


title: i5-NK-D1-AZ5153_S10


title: i43-CD4-D2-V_S12


title: i41-CD4-D1-AZ5153_S2


title: E17.5_CB_WT_mouse_6 [E17_5_S4_7_CB]

source_name: Wild Type_E17.5_Cerebellum


title: E17.5_CB_HET_mouse_2 [E17_5_S2_10_CB]


title: E17.5_CB_WT_mouse_3 [E17_5_S3_6_CB]


title: i42-CD4-D1-BRD9162_S24


title: E17.5_CB_WT_mouse_5 [E17_5_S4_4_CB]


title: i4-CD4-D3-JQ1_S18


title: E17.5_CB_HET_mouse_1 [E17_5_S2_7_CB]


title: E17.5_CB_WT_mouse_4 [E17_5_S3_8_CB]


title: E17.5_CB_WT_mouse_1 [E17_5_S2_6_CB]


title: i40-CD4-D1-JQ1_S3


title: i3-CD4-D3-iBRD9_S13


title: i3-NK-D1-iBRD9_S5


title: E17.5_CB_WT_mouse_2 [E17_5_S2_11_CB]


title: i37-CD4-D1-V_S5


title: i39-CD4-D1-iBRD9_S14


title: E17.5_CX_HET_mouse_6 [E17_5_S4_6_CX]


title: E17.5_CX_HET_mouse_3 [E17_5_S3_7_CX]


title: E17.5_CX_HET_mouse_5 [E17_5_S4_3_CX]


title: i2-NK-D1-VS_S8


title: i2-CD4-D3-VS_S19


title: E17.5_CX_HET_mouse_4 [E17_5_S3_9_CX]


title: i38-CD4-D1-VS_S10


title: E17.5_CX_HET_mouse_1 [E17_5_S2_7_CX]


title: E17.5_CX_HET_mouse_2 [E17_5_S2_10_CX]


title: i247-CD4-D2-AZ5153_S15


title: i23-CD8-D3-AZ5153_S4


title: E17.5_CX_WT_mouse_5 [E17_5_S4_4_CX]

source_name: Wild Type_E17.5_Cortex


title: i22-CD8-D3-JQ1_S15


title: E17.5_CX_WT_mouse_6 [E17_5_S4_7_CX]


title: E17.5_CX_WT_mouse_4 [E17_5_S3_8_CX]


title: E17.5_CX_WT_mouse_1 [E17_5_S2_6_CX]


title: i1-CD4-D3-V_S23


title: i21-CD8-D3-iBRD9_S11


title: E17.5_CX_WT_mouse_2 [E17_5_S2_11_CX]


title: E17.5_CX_WT_mouse_3 [E17_5_S3_6_CX]


title: i1-NK-D1-V_S24


title: kdm5-shRNA_R71C09_dam-polII_3

city: Bronx

first: Hayden

middle: A. M.

last: Hatch

state: New York

address: 1300 Morris Park Avenue, Ullmann 809

department: Dominick P. Purpura Department of Neuroscience; Department of Genetics

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: Targeted DamID
Libraries were sequenced on a BGISEQ-500 platform with 50 bp read length and 20 M clean reads.
For Targeted DamID analyses, sequencing data were aligned to release 6 of the Drosophila melanogaster genome and processed using damidseq_pipeline as previously described (Marshall et al., 2016; Marshall & Brand, 2017).
RNA Pol II occupancy over gene bodies was calculated via polii.gene.call (Marshall et al., 2016).
Differentially expressed genes were called via the NOIseq R package (Tarazona et al., 2011); briefly, RNA pol II gene occupancy scores were scaled, and inverse log values used as input to NOIseq with parameters  of upper quantile normalization and biological replicates. DEGs were called with a q value of 0.95.
Genome_build: dm6 (BDGP6, Ensembl release 98)
Supplementary_files_format_and_content: xlsx spreadsheets including log2foldchange for DEGs in kdm5-140 TaDa and kdm5-shRNA TaDa

source_name: NPCs/immature neurons

growth_protocol: To profile Pol II occupancy in GMCs and immature neurons of kdm5140 pupae, kdm5140/CyO:gfp; UAS-LT3-dam or kdm5140/CyO:gfp; UAS-LT3-dam-pol II flies were crossed with kdm5140/CyO:gfp; R71C09-Gal4 flies and were allowed to lay eggs for 24-hrs at 25 ºC. Embryos were then moved to 18 ºC for a period of 16 days, and GFP negative wandering 3rd instar larvae were transferred to a restrictive temperature of 29 ºC for 3 days to induce the expression of the UAS-dam and UAS-dam-pol II transgenes. As a parallel control, kdm5 wild-type animals carrying UAS-LT3-dam or UAS-LT3-dam-pol II were crossed with R71C09-Gal4 and were also allowed to lay eggs for 24-hrs at 25 ºC. Embryos were then moved to 18 ºC for 9 days and subsequently transferred to 29 ºC for 3 days. For kdm5 knockdown experiments, flies carrying either UAS-LT3-dam; UAS-kdm5_shRNA or UAS-LT3-dam-pol II; UAS-kdm5_shRNA were crossed with flies carrying UAS-tubulin-Gal80ts; R71C09-Gal4. Parallel crosses were also performed with flies bearing a scrambled shRNA sequence in place of kdm5 shRNA. All flies were allowed to lay eggs for 24-hrs at 25 ºC. Embryos were then transferred to 18 ºC for 4 days and then subsequently transferred to 29 ºC for 6 days.

extract_protocol:
Tissue processing for all TaDa experiments was performed as previously described in Marshall et al., 2016 with the following modifications. A total of 40 pupae of each genotype were homogenized in 500 mM EDTA followed by DNA extraction using the Zymo Quick-DNA Miniprep Plus Kit. DpnI digestion, PCR adaptor ligation, DpnII digestion, and PCR amplification were performed as described. DNA was sonicated using a Diagenode Bioruptor for 8-10 cycles (5-min at high power, 30-s on/30-s off) and analyzed using an Agilent Bioanalyzer. DamID adaptor removal and DNA cleanup were performed as described and samples were submitted to BGI Genomics for library construction and sequencing.
Libraries were prepared at BGI Genomics following a ChIP-seq workflow. DNA fragments were first end-repaired and dA-tailed using End Repair and A-Tailing (ERAT) enzyme. Adaptors were then ligated for sequencing and ligated DNA purified using AMPure beads. DNA was then PCR amplified with BGI primers for 8 cycles and PCR purified with AMPure beads. DNA was then homogenized, circularized, digested, and again purified. DNA was then prepared into proprietary DNA nanoballs (DNB™) for sequencing.

value: Third instar larvae/pupae

value: NPCs/immature neurons

tag: genotype


title: kdm5-shRNA_R71C09_dam-polII_2


title: i20-CD8-D3-VS_S16


title: i24-CD8-D3-BRD9162_S9


title: kdm5-shRNA_R71C09_dam-polII_1


title: i19-CD8-D3-V_S6


title: kdm5-shRNA_R71C09_dam_3


title: i17-NK-D3-AZ5153_S22


title: kdm5-shRNA_R71C09_dam_1


title: i18-NK-D3-BRD9162_S21


title: i17-CD8-D2-AZ5153_S7


title: kdm5-shRNA_R71C09_dam_2


title: scram-shRNA_R71C09_dam-polII_2


title: i16-CD8-D2-JQ1_S1


title: i15-NK-D3-iBRD9_S16


title: i16-NK-D3-JQ1_S6


title: i15-CD8-D2-iBRD9_S17


title: scram-shRNA_R71C09_dam-polII_3


title: scram-shRNA_R71C09_dam_3


title: i14-NK-D3-VS_S7


title: scram-shRNA_R71C09_dam-polII_1


title: i14-CD8-D2-VS_S19


title: scram-shRNA_R71C09_dam_1


title: i18-CD8-D2-BRD9162_S3


title: i11-CD8-D1-AZ5153_S22


title: i13-CD8-D2-V_S20


title: kdm5-140_R71C09_dam-polII_5

value: kdm5[140]; R71C09-Gal4/UAS-dam:polII


title: i13-NK-D3-V_S17


title: kdm5-140_R71C09_dam-polII_2


title: i10-CD8-D1-JQ1_S2


title: kdm5-140_R71C09_dam_5


title: i12-CD8-D1-BRD9162_S21


title: kdm5-140_R71C09_dam_4


title: kdm5-140_R71C09_dam-polII_3


title: kdm5-140_R71C09_dam-polII_1


title: kdm5-140_R71C09_dam_3


title: kdm5-140_R71C09_dam_1


title: kdm5-wt_R71C09_dam-polII_4


title: kdm5-wt_R71C09_dam-polII_5


title: kdm5-140_R71C09_dam_2


title: scram-shRNA_R71C09_dam_2


title: RNASeq_Arid1a_Het_3

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: RNA-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/+ mouse

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method.
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing the gene expression matrix

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
The corpus regions of the stomach that have tumors (or analogous region in normal stomachs) were dissected and incubated in 20 mM EDTA for 30 minutes. The glands were then extracted by gently scraping the surface using a glass slide. The glands were washed thoroughly in PBS before downstream application. Isolated epithelial cells were immediately frozen and RNA isolation was conducted using an RNA isolation kit (Qiagen, Cat No. 74104).
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

treatment_protocol: No treatment

value: stomach gland

value: Atp4bCre; Rosa26NICD; Arid1aflox/+


title: WT rep2

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

institute: University of Liverpool

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 hg19 whole genome using tophat v2.0.9 with parameters -p 8  -q 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) and differential expression were calculated against ensemble gene annotations using cuffdiff program with default options and masking repeats.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and differential expression calculation

extract_protocol:
At harvesting time, total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen, Germany), treated with Amplification Grade DNase I (sigma) to remove genomic DNA and quantified by NanoDrop. The quality of RNA was checked using Agilent's Tapestation.
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq®  Stranded mRNA Library Prep Kit for NeoPrep™

tag: ccdc26 status

value: WT

value: wild type


title: P7_CX_WT_mouse_1 [P7_C1_5_CX]

city: La Jolla

value: postnatal


title: KO.2 rep1


title: kdm5-140_R71C09_dam-polII_4


title: KO.2 rep2


title: kdm5-wt_R71C09_dam-polII_1


title: KO.1 rep1


title: KO.1 rep2


title: ChIP-Seq_H3K27ac_Arid1a_Homo_Deletion_2

description: H3K27ac ChIP-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse

data_processing:
For ChIP-Seq, the filtered single-end reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with default parameters. ChIP-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig and .txt files containing ChIP-Seq peak regions generated by MACS2.

extract_protocol:
Fresh epithelial pellets were fixed in 1% PFA for 10 minutes at room temperature, quenched with 1/20th volume of 2.5 M glycine for 5 minutes, washed twice with cold 1x PBS and flash frozen. When enough sample was acquired (approximately 0.1g of tissue per region), fixed pellets were pooled, dounced in cold PBS with protease inhibitor, and filtered through a 70 µm mesh. Samples were then incubated in cold cell membrane and nuclear lysis buffers containing non-denaturating detergents for 30 mins each on a shaker at 4˚C. Washed samples were pelleted and resuspend in 300µl of sonication buffer containing 0.1% SDS. Sonication was conducted using the Diagenode bioruptor (Diagenode, B01020001) at high power for 30 cycles, 30 seconds ON/OFF. Sonicated samples were cleared with 1:10 dilution of 30% Triton-X and added to antibody bound beads (rabbit anti-H3K27ac: abcam, ab4729). The next day, beads were washed with high and low salt buffers and treated with Proteinase K overnight at 65˚C. DNA was isolated using phenol/chloroform extraction and 10ng of immunoprecipitated DNA was used for cDNA library construction using the Rubicon DNA-seq Thruplex 48S kit. Libraries were size selected and submitted to be sequenced at 50 base pair read length, single end reads with 15-20 million reads per library.
ThruPLEX DNA-Seq kit

value: Atp4bCre; Rosa26NICD; Arid1aflox/flox

tag: antibody


title: CHIP-1484801_iTr-STAT5 Replicate 2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
ChIP-seq data analysis: Single-end reads of 50bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data, details and codes can be found in our previously publications(Yang, X. et al. Nat Neurosci. 2019).
After confirmed the quality were good, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks(normalized to 15M uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”).
Paired-end reads of 50bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5M fragments as suggested by Cut&Run protocols paper. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

source_name: Male mice

growth_protocol: Tn, Te, Treg cells were sorted from the lymphocytes isolated from male Foxp3gfp mice by CD4+GFP- CD25-CD44loCD62Lhi, CD4+GFP-CD44hiCD62Llo, and CD4+GFP+,respectively.  iTreg cells were induced from CD4 Tn isolated from male Foxp3gfp mice with TCR agonists, IL-2, TGF-beta for 4 days in the presence or absence of 0.25mM ascorbic acid 2-phosphate.  At the end of induction, live GFP+ cells were FACS sorted.

extract_protocol:
A two-step protocol was used to fix the cells for Stat5 ChIP-seq as we previously described (PMID: 25126783).  Cut&Run was performed according to a method recently described (PMID: 28079019).
Libraries were constructed according to standard protocols for ChIP or Cut&Run sequencing.

treatment_protocol: Natural Treg (nTreg) cells from Foxp3gfp male mice were FACS sorted and expanded in vitro for 5 days with Dynabeads® Mouse T-Activator CD3/CD28 in the presence of 500-1000 U/ml recombinant IL-2.  To perform Stat5 ChIP, iTreg or nTreg cells were starved for 4 hours in complete RPMI 1640 without cytokines.  Cells were then restimulated with 100-500 U/ml IL-2 for 30 min before being fixed for ChIP experiments.

tag: strain

tag: Sex

value: male

value: In vitro induced wild-type regulatory T cells (control)

tag: chip antibody


title: CHIP-1484802_iTr-AA2P-STAT5 Replicate 2

tag: cell type

value: In vitro induced wild-type regulatory T cells (ascorbic acid treated)


title: CHIP-1484800_iTr-AA2P-STAT5 Replicate 1


title: kdm5-wt_R71C09_dam-polII_3


title: ChIP-Seq_H3K27ac_Arid1a_Homo_Deletion_1

source_name: stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: WT rep1


title: kdm5-wt_R71C09_dam-polII_2


title: kdm5-wt_R71C09_dam_5


title: kdm5-wt_R71C09_dam_3


title: pMek_Sorted_Bottom_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the lowest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 3.
pMek_Screen_counts.txt

tag: gdna isolation


title: GeCKOx sgRNA library

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Cloned GeCKOx sgRNA library
GeCKOx_Library_counts.txt


title: kdm5-wt_R71C09_dam_2


title: pMek_Sorted_Bottom_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the lowest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 1.
pMek_Screen_counts.txt


title: kdm5-wt_R71C09_dam_1


title: pMek_Sorted_Top_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the highest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 1.
pMek_Screen_counts.txt


title: pMek_Sorted_Bottom_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the lowest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 2.
pMek_Screen_counts.txt


title: GeCKOxs sgRNA library

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Cloned GeCKOxs sgRNA library
GeCKOxs_Library_counts.txt


title: kdm5-wt_R71C09_dam_4


title: pMek_Sorted_Top_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the highest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 2.
pMek_Screen_counts.txt


title: scRNA-Seq #8

data_processing:
Raw reads were processed using the 10X CellRanger pipeline to align these to the reference transcriptome (mm10) and to generate gene cell count matrices. Initial QC and clustering was performed with R package Seurat version 2.3.0. To remove falsely identified cells, cells having a UMI count less than 1000, or genes expressed less than 10% of cells were excluded from further analysis. For imputating missing expression values, we used MAGIC (Markov Affinity-based Graph Imputation of Cells) program with optimal diffusion constant t =2. Data normalization and scaling to remove unwanted sources of variation principal component analysis (PCA) was conducted using genes with highly variable expression. Identified clusters were represented using t-SNE plot. Differential gene expression (DGE) analysis was then used to identify significantly differentially expressed genes within each cluster using the t-test for significance.
Genome_build: mm10
Supplementary_files_format_and_content: ".txt" file of filtered single cell reads count matrix

source_name: stomach gland # 8 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse

growth_protocol: The stomach glands of a Atp4bCre;Rosa26NICD;Arid1aflox/flox mouse at 23 weeks is isolated.

extract_protocol:
Isolated glands are digested into single cell suspension using collagenase and dispase and stained using EPCAM (Ab95641) and Sytox Blue (Thermo Fisher Scientific S34857).
EPCAM high, Sytox low Cells are sorted using the Moflo Astrios, and submitted for scRNA-seq using the 10x platform.
single cell RNA-Seq


title: CHIP-1484799_iTr-STAT5 Replicate 1


title: scRNA-Seq #6

source_name: stomach gland # 6 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: scRNA-Seq #7

source_name: stomach gland # 7 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: scRNA-Seq #3

source_name: stomach gland # 3 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: SY60R1

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

description: Whole fruits of accession Piquin Sonora Yellow at 60 Days After Anthesis. Biological replicate R1.

data_processing:
Total RNA Sample QC. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280). (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination. (3) Agilent 2100: checks RNA integrity.
Library Construction. After the QC procedures, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
Library QC and sequencing. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina NovaSeq 6000 machines for sequencing.
Raw data and quality control. The original raw data from Illumina were transformed to Sequenced Reads by base calling. Raw data were recorded in a FASTQ files. GC content distribution was evaluated. Raw reads were filtered to remove reads containing adapters or reads of low quality.
Mapping to the Capsicum annuum reference genome. For mapping TopHat (v2.0.12) was employed with mismatch parameter set to 2 and other parameters set to defaults. Only filtered reads were used to analyze the mapping status of RNA-seq data to the reference genome. RAW FILES  were created in the binary alignment/map format (".bam").
Genome_build: Capsicum_annuum.Annuum.v.2.0.genome.fa
Supplementary_files_format_and_content: Processed data files are in the cvs format with three columns, 1 - "id" (a unique numeric identifier of each feature), 2 - "Gene.id" (the identifier of the gene or gene feature) and 3 - A column with the same name than the sample which contains the read count for the corresponding feature.

organism: Capsicum annuum

source_name: Piquin Sonora Yellow

growth_protocol: Seeds of 10 Capsicum annuum accessions were surface sterilized with a 70% ethanol solution for 10 s before treatment with a 10% hypochlorite solution for 10 s and six rinses with distilled water. Wild accession seeds were similarly treated, after an initial treatment with 50% sulfuric acid solution to break seed dormancy. All accession seeds were germinated in plastic trays containing a mixture of three parts peat moss, one part perlite, one part vermiculite, one part sludge and two parts forest soil in a growth chamber, with 16 h light (photon flux of 70 μmol m-2 s-1) at 28 °C and 66% relative humidity. Three-week-old chili pepper plants were transplanted individually into plastic 5 L pots containing the same soil mixture described above. During transplantation, 15 g of a mycorrhizae fungal and beneficial bacteria mixture were added to optimize root growth and development. Plants were fertilized with Long Ashton solution every two weeks. Flowers and fruits at 0, 10, 20, 30, 40, 50 and 60 DAA were collected and immediately frozen in liquid nitrogen, and stored at -80 °C.

extract_protocol:
Total RNA was extracted from flowers and whole chili pepper fruits at different developmental stages using a NucleoSpin™ RNA Plant kit (MACHEREY-NAGEL) according to the manufacturer’s instructions. RNA was extracted from two biological samples comprising either flowers (time 0 DAA) fruits or seedlings from 2-6 different plants. RNA quality was verified by determining the RNA Integrity Number (RIN) for each sample.
Samples of total RNA were shipped to Novogene (https://en.novogene.com/) for library construction, sequencing and mapping to a reference genome. At Novogene, libraries were prepared and sequenced using the Illumina NovaSeq platform to obtain at least 20 million raw paired-end reads of 150 bp per sample.

treatment_protocol: No treatments were employed. Samples of fruits and seedlings were collected at the times indicated in the "characteristics: collection time" of the "SAMPLES" section.

tag: sample type

value: Wild accession (C. a. var. glabriusculum)

value: Whole fruit

tag: collection time

value: 60 Days After Anthesis (DAA)


title: SY60R2

description: Whole fruits of accession Piquin Sonora Yellow at 60 Days After Anthesis. Biological replicate R2.


title: scRNA-Seq #5

source_name: stomach gland # 5 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: scRNA-Seq #4

source_name: stomach gland # 4 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: LF 2

city: Nanning

first: Yu

last: Pan

state: Guangxi

address: No. 100, Daxuedong Road, Xixiangtang District, Nanning, Guangxi

department: College of Animal Science and Technology

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM)  calculated using a protocol from Li, et al. 2015 . 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: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bubalus bubalis

source_name: granulosa cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: late atretic follicle


title: EF 2

value: early atretic follicle


title: HF 3

value: healthy follicle


title: HF 1


title: EF 3


title: LF 1


title: LF 3


title: SY50R2

description: Whole fruits of accession Piquin Sonora Yellow at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: HF 2


title: EF 1


title: GlcAC_2

type: RNA

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with Affymetrix RJpGene-1_1-st-v1 (Affymetrix) and scanned at GreenGene biotech.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We extracted a probeset as present with default options  apt-probeset-summarize with options: -p RJpGene-1_1-st.pgf -b RJpGene-1_1-st.bgp --qc-probesets RJpGene-1_1-st.qcc -m RJpGene-1_1-st.mps -a rma-sketch

label: biotin

organism: Oryza sativa

source_name: rice embryo

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Rice embryos were harvested from whole rice seeds (Oryza sativa L. cv. Dongjin),

extract_protocol: Rice embryos were ground to a fine powder with liquid nitrogen using a mortar and pestle, and extracted with TLE (0.2 M Tris, 0.1 M LiCl, and 5 mM EDTA; pH 8.2) and phenol-chloroform-isoamylalcohol solution. Total RNA was extracted with TRIZOL® reagent (Invitrogen, UK) and RNeasy plant mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. The quantity and purity of the extracted RNA were assessed by measuring the OD260/280 using a NanoDrop spectrophotometer. For microarray experiments, total RNA was re-purified using low-elution Qiagen RNeasy columns (Qiagen), according to the manufacturer’s instructions. Total RNA was also used for the synthesis of the first strand cDNA for real-time quantitative reverse transcriptase PCR (qRT-PCR).

treatment_protocol: Approximately 150~200 surface-sterilized embryos were placed on a single layer of 3 mm Whatman paper soaked in 10 mM calcium chloride (CaCl2) solution containing 60 mM of either glucose or mannitol and incubated for 24 h at 28°C in the dark for aerobic germination. For anaerobic germination, 150~200 surface-sterilized rice embryos were submerged in orange conical tubes containing 50 mL of the aforementioned incubation media and flushed with N2 gas and incubated under the same conditions as aerobic germination. To induce energy starvation in cells, rice embryos were germinated aerobically as described above, except that 0.08 mM of the uncoupler 2,4-dinitrophenol (DNP; Sigma Aldrich, St. Louis, MO, USA) was added to the incubation media.

value: embryo

tag: condition

value: Glc/AC


title: scRNA-Seq #2

source_name: stomach gland # 2 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse

value: stomach gland


title: GlcAC_1


title: MtlDNP_2

value: Mtl/DNP


title: scRNA-Seq #1

source_name: stomach gland # 1 of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse


title: MtlAC_1

value: Mtl/AC


title: SY50R1

description: Whole fruits of accession Piquin Sonora Yellow at 50 Days After Anthesis. Biological replicate R1.


title: pMek_Sorted_Top_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% cells with the highest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted. Replicate 3.
pMek_Screen_counts.txt

data_processing:
Tab delimited text files with normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015)
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Tab delimited text files include normalized counts for each sample
Supplementary_files_format_and_content: Alignment: GeCKOx/GeCKOxs sgRNA library (tab delimited text files provided)

source_name: mESCs

extract_protocol:
For the primary screen, genomic DNA was isolated from the frozen cell pellets by using the DNeasy Blood and Tissue kit (Qiagen) following the manufacturer's instructions. For the secondary screens, genomic DNA from frozen cell pellets was isolated via Phenol/Chloroform extraction due to higher yields. Briefly, cell pellets were thawed and resuspended in 250µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2M NaCl and 5mM DTT (Roth) in TE Buffer) and incubated over night at 65°C. 200µg of RNAse A (Thermo Fisher Scientific) was added to the sample and incubated at 37°C for 1h. 100µg of Proteinase K (Sigma) were subsequently added followed by a 1h incubation at 50°C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at RT for 1 min and subsequently centrifuged at 16000 xg for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 hr. DNA was pelleted by centrifugation for 13000 rpm for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50µl H2O.
The PCR amplification of the sgRNA cassette was performed in two PCR steps as described previously with minor modifications (Shalem et al. 2014).

value: Phenol/Chloroform


title: i5-CD4-D3-AZ5153_S1

source_name: PBMCs

tag: treatment


title: SY40R2

description: Whole fruits of accession Piquin Sonora Yellow at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: MtlAC_2


title: GlcDNP_1

value: Glc/DNP


title: SY40R1

description: Whole fruits of accession Piquin Sonora Yellow at 40 Days After Anthesis. Biological replicate R1.


title: AF3

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
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample …

source_name: ovarian granulosa cell

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation.
The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048)  by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: group

value: Atresia follicle

value: ovarian


title: GlcDNP_2

tag: tissue


title: SY30R2

description: Whole fruits of accession Piquin Sonora Yellow at 30 Days After Anthesis. Biological replicate R2.

value: Wild accession (C. a. var. glabriusculum)

value: Whole fruit

value: 30 Days After Anthesis (DAA)


title: SY30R1

description: Whole fruits of accession Piquin Sonora Yellow at 30 Days After Anthesis. Biological replicate R1.


title: AF2


title: Glc_2

value: Glc


title: HF3


title: RNASeq_Ctrl_3

description: RNA-Seq in stomach gland of a Atp4bCre; Rosa26NICD mouse

value: Atp4bCre; Rosa26NICD


title: RNASeq_WT_2

description: RNA-Seq in stomach gland of a wild type mouse

source_name: stomach gland of a wild type mouse

value: wild type


title: RNASeq_WT_3


title: Mtl_1

value: Mtl


title: SY20R1

description: Whole fruits of accession Piquin Sonora Yellow at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: HF1

value: healthy follicle


title: HF2


title: SY20R2

description: Whole fruits of accession Piquin Sonora Yellow at 20 Days After Anthesis. Biological replicate R2.


title: RNASeq_Ctrl_1

source_name: stomach gland of a Atp4bCre; Rosa26NICD mouse

value: stomach gland


title: AF1


title: Glc_1

value: embryo


title: MtlDNP_1

value: Mtl/DNP


title: RNASeq_Arid1a_Het_2

description: RNA-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/+ mouse

value: Atp4bCre; Rosa26NICD; Arid1aflox/+