title: nTreg_RNAseq_sgNT_Rep2

description:
RNA-seq in nTregs transduced with sgNT, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgFoxp3vssgNT_DiffExpOutput.txt
processed data: nTreg_sgBrd9vssgNT_DiffExpOutput.txt
processed data: nTreg_sgPbrmvssgNT_DiffExpOutput.txt


title: nTreg_RNAseq_DMSO_Rep2

status: Public on Jul 07 2020

type: SRA

city: San Diego

first: Diana

middle: C.

last: Hargreaves

state: CA

address: 10010 North Torrey Pines Road

country: USA

institute: The Salk Institute for Biological Studies

description:
RNA-seq in nTregs treated with DMSO, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_dBRD9vsDMSO_DiffExpOutput.txt

library_source: transcriptomic

data_processing:
Basecalls performed using RTA (Illumina).
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq, ChIP-seq and ATAC-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Foxp3, BRD9, BRG1 and PHF10 were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K27ac were called using the parameter "-style histone." ATAC-seq peaks were called using the parameter "-style dnase." For RNA-Seq, Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bed file Columns: (1) peak ID (2) chrom (3) chromStart (4) chromEnd (5) strand.
Supplementary_files_format_and_content: DiffExpOutput tab-delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value.

molecule: total RNA

organism: Mus musculus

source_name: nTregs isolated from Foxp3Thy1.1/Rosa-Cas9 mice

extract_protocol:
For ATAC-seq, 50k nTregs per replicate were washed with cold PBS and resuspension buffer (RB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) before lysis in RB with 0.1% NP40. Cells were then incubated in transposition mix containing Tn5 transposase for thirty minutes at 37degC. Purified DNA was ligated with adapters (NuGEN), amplified and size selected for sequencing.
For ChIP-Seq, 7.5e6 nTregs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Foxp3, BRG1, BRD9, PHF10 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.

tag: genotype/variation

tag: cell type

value: nTregs

tag: treatment

value: DMSO

tag: guide rna


title: nTreg_RNAseq_dBRD9_Rep1

description:
RNA-seq in nTregs treated with dBRD9, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_dBRD9vsDMSO_DiffExpOutput.txt

value: 2.5 uM dBRD9


title: nTreg_RNAseq_sgArid1a-2/1b-2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2/1b-2, replicate 1

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, transcript per milion (TPM) reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-58) TPM for each experiment

molecule: polyA RNA

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.
Strand-specific polyA+ RNA-seq

tag: sg-guide


title: nTreg_RNAseq_DMSO_Rep1

description:
RNA-seq in nTregs treated with DMSO, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_dBRD9vsDMSO_DiffExpOutput.txt


title: nTreg_ChIPseq_sgPbrm_Foxp3

description: ChIP-seq for Foxp3 in nTregs transduced with sgPbrm.

library_source: genomic

molecule: genomic DNA

value: sgPbrm

tag: chip antibody

value: In-house made Foxp3 antibody


title: nTreg_ChIPseq_sgBrd9_H3K27ac

description: ChIP-seq for H3K27ac in nTregs transduced with sgBrd9.

value: H3K27ac Abcam #ab4729


title: nTreg_ChIPseq_sgPbrm_Input

description: Input for ChIP-seq in nTregs transduced with sgPbrm.


title: nTreg_ChIPseq_sgBrd9_Foxp3

description: ChIP-seq for Foxp3 in nTregs transduced with sgBrd9.


title: nTreg_ChIPseq_sgBrd9_Input

description: Input for ChIP-seq in nTregs transduced with sgBrd9.


title: nTreg_ChIPseq_sgFoxp3_Foxp3

description: ChIP-seq for Foxp3 in nTregs transduced with sgFoxp3.


title: nTreg_ChIPseq_sgFoxp3_H3K27ac

description: ChIP-seq for H3K27ac in nTregs transduced with sgFoxp3.


title: nTreg_ChIPseq_sgNT_Foxp3

description: ChIP-seq for Foxp3 in nTregs transduced with sgNT.

value: sgNT


title: nTreg_ChIPseq_sgFoxp3_Input

description: Input for ChIP-seq in nTregs transduced with sgFoxp3.


title: nTreg_ChIPseq_sgNT_H3K27ac

description: ChIP-seq for H3K27ac in nTregs transduced with sgNT.


title: nTreg_ChIPseq_sgNT_Input

description: Input for ChIP-seq in nTregs transduced with sgNT.


title: nTreg_ChIPseq_dBRD9_Foxp3

description: ChIP-seq for Foxp3 in nTregs treated with dBRD9.


title: nTreg_ChIPseq_DMSO_Foxp3

description: ChIP-seq for Foxp3 in nTregs treated with DMSO.


title: nTreg_RNAseq_sgArid1a/1b_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a/1b, replicate 3


title: nTreg_ChIPseq_sgPbrm_H3K27ac

description: ChIP-seq for H3K27ac in nTregs transduced with sgPbrm.


title: nTreg_ChIPseq_BRG1

description: ChIP-seq for BRG1 in nTregs.

value: BRG1 Abcam #110641


title: nTreg_ChIPseq_Foxp3

description: ChIP-seq for Foxp3 in nTregs.


title: nTreg_ChIPseq_DMSO_Input

description: Input for ChIP-seq in nTregs treated with DMSO.


title: nTreg_ChIPseq_PHF10_Replicate2

description: ChIP-seq for PHF10 in Tregs Replicate 2

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq, ChIP-seq and ATAC-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Foxp3, BRD9, BRG1 and PHF10 were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K27ac were called using the parameter "-style histone." ATAC-seq peaks were called using the parameter "-style dnase." For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: Bed file Columns: (1) peak ID (2) chrom (3) chromStart (4) chromEnd (5) strand. DiffExpOutput tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq, 7.5e6 nTregs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Foxp3, BRG1, BRD9, PHF10 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, 50k nTregs per replicate were washed with cold PBS and resuspension buffer (RB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) before lysis in RB with 0.1% NP40. Cells were then incubated in transposition mix containing Tn5 transposase for thirty minutes at 37degC.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions. ATAC-seq -- purified DNA was ligated with adapters (NuGEN), amplified and size selected for sequencing.

tag: perturbation

tag: overexpression construct

tag: antibody source

value: PHF10 Thermo Fisher #PA5-30678


title: nTreg_ChIPseq_Input_Replicate2_forPHF10

description: Input for ChIP-seq in Tregs Replicate 2 for PHF10


title: nTreg_ATACseq_sgBrd9_Replicate2

description: ATAC-seq in sgBrd9 Tregs, Replicate 2


title: nTreg_ChIPseq_BRD9

description: ChIP-seq for BRD9 in nTregs.

value: BRD9 Active Motif #61537


title: nTreg_ATACseq_sgNT_Replicate2

description: ATAC-seq in sgNT Tregs, Replicate 2


title: nTreg_ATACseq_sgBrd9_Replicate1

description: ATAC-seq in sgBrd9 Tregs, Replicate 1


title: nTreg_ChIPseq_PHF10

description: ChIP-seq for PHF10 in nTregs.


title: nTreg_ChIPseq_Input

description: Input for ChIP-seq in nTregs.


title: NSTEMI_5

status: Public on May 27 2020

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples.
Using TopHat v2.0.11 with Bowtie 1 to handle colour space reads, we mapped all reads to the human genome version HG38/GRCh38.76 downloaded from the Ensembl database. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
We implemented the reference annotation based transcript (RABT) procedure, using Cufflinks suite v2.1.1 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 76) with those reads mapped in intergenic or intronic regions.
We estimated genes and transcripts expression levels by Cuffquant (using default parameters, apart from -multi-read-correct -frag-bias-correct 'reference.fasta' and -mux-bundle-frags 100000000) and then Cuffnorm (with default parameters, apart from -total-hits-norm).
For each feature we computed both reads counts and fragments per kilobase of transcript per million fragments mapped (FPKM) values. Genes with a FPKM value ≥ 0.046 in at least 60% of samples were considered expressed. This threshold was obtained correlating RNA-Seq data with those from a qPCR gene expression array in preliminary experiments.
Genome_build: HG38/GRCh38.76
Supplementary_files_format_and_content: Tab-delimited text files include raw counts or FPKM values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.
Supplementary_files_format_and_content: txt file containing raw expression measurements
Supplementary_files_format_and_content: txt file containing expression measurements expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) values
Supplementary_files_format_and_content: txt file containing expression measurements as filtered and normalized counts

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Blood samples were collected and mantained into Tempus Blood RNA tubes until processing following manufacturer's instructions.

extract_protocol:
Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.

tag: tissue

value: Whole blood

tag: Sex

value: Male

tag: age (years)

tag: country of origin

value: Italy


title: NSTEMI_3


title: STEMI_13


title: NSTEMI_6

value: Female


title: NSTEMI_2


title: STEMI_10


title: NSTEMI_1


title: NSTEMI_9


title: NSTEMI_14


title: NSTEMI_15


title: nTreg_ATACseq_sgNT_Replicate1

description: ATAC-seq in sgNT Tregs, Replicate 1


title: NSTEMI_13


title: NSTEMI_4


title: NSTEMI_7


title: STEMI_12


title: STEMI_8


title: STEMI_7


title: STEMI_5


title: STEMI_4


title: STEMI_3


title: STEMI_6


title: STEMI_2


title: GLAST_HS_IP_3

status: Public on May 05 2020

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description: Raw read counts

data_processing:
Map to mouse genome using STAR/2.5.2a
Command line parameters STAR --genomeDir /data/GCBCNIDCR/Refs/Stargenomes/MOUSE-GRCm38.vM11c/ --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesIn /data/GCBCNIDCR/RNASeqProjects/17_012Ribotag/input/Gfi1_Con_input_1_R1_all.fastq.gz /data/GCBCNIDCR/RNASeqProjects/17_012Ribotag/input/Gfi1_Con_input_1_R2_all.fastq.gz --readFilesCommand zcat --runThreadN 56 --outFileNamePrefix Gfi1_Con_input_1.star. --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:Gfi1_Con_input_1 LB:library PL:ILLUMINA PU:machine SM:Gfi1_Con_input_1 CN:NIDCD_GCBC --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts --sjdbGTFfile /data/GCBCNIDCR/Refs/Stargenomes/MOUSE-GRCm38.vM11c/GRCm38.vM11.annotation.erccTgSIRVs.gtf --outSAMunmapped Within --outWigType None --outWigStrand Stranded
ReadsPerGene.out.tab file generated by STAR:  Column1=geneID; Column2=counts unstranded RNA-seq; Column3=counts for 1st read strand aligned with RNA; Column4=counts for 2nd strand aligned with RNA
Raw gene counts were analyzed for differential gene expression using the RNA-Seq statistical method DESeq2 (Love et al., 2014).
Genes significantly enriched in the IP versus the matching input sample (log2>1 and adjP<0.05) were considered for further analysis in comparison of Control versus Heat Shock experiments.
For each Cre-driver experiment, expression values of the enriched genes (input versus IP) were compared between control and heat shocked samples. Significantly different genes could be either up or down-regulated and adjP-values <0.05.
Genome_build: GRCm38.vM11
Supplementary_files_format_and_content: raw read counts

source_name: Cultured utricles

growth_protocol: Mice were euthanized by CO2 asphyxiation followed by decapitation.  Utricles were immediately dissected in M199 media and the epithelial roof was gently dissected away, leaving the otoconia intact.  The utricles were incubated overnight at 37°C (95% air/5% CO2) in DMEM/F-12 media with 5% FBS , and 50 U/mL penicillin.

extract_protocol:
RNA was extracted using the RNeasy Micro Plus kit (Qiagen) including the genomic DNA removal spin column step.
Sequencing libraries were prepared using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA).  Dual indexed libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina).

treatment_protocol: Cultured utricles were then either exposed to heat shock in microcentrifuge tubes placed in a 43°C in a water bath for 30 minutes and allowed to recover for 2 hours, or they remained at 37°C under control culture conditions.

value: Cultured utricles

tag: genotype

value: GLAST-CreER; Rpl22tm1.1Psam/J

tag: condition

value: Heat-shock; 37 degrees C culture + 30 min @ 43degrees C

tag: sample type

value: ribotag immunoprecipitated


title: STEMI_11


title: GLAST_HS_IP_2

description: Raw read counts


title: STEMI_9


title: GLAST_HS_input_2

description: Raw read counts

value: input


title: GLAST_HS_input_3

description: Raw read counts


title: STEMI_1


title: GLAST_Con_input_3

description: Raw read counts

value: Control; 37 degrees C culture


title: GLAST_HS_input_1

description: Raw read counts


title: GLAST_Con_input_4

description: Raw read counts


title: GLAST_Con_input_1

description: Raw read counts


title: GLAST_HS_IP_4

description: Raw read counts


title: Gfi1_stroma-free_Con_IP_2

description:
underlying stroma removed
Raw read counts

value: Gfi1-Cre; Rpl22tm1.1Psam/J


title: Gfi1_stroma-free_Con_IP_1


title: GLAST_HS_IP_1

description: Raw read counts


title: Gfi1_HS_IP_4

description: Raw read counts


title: Gfi1_stroma-free_Con_input_1


title: GLAST_Con_input_2

description: Raw read counts


title: Gfi1_HS_IP_1

description: Raw read counts


title: Gfi1_HS_IP_3

description: Raw read counts


title: ONT_REH

status: Public on May 19 2020

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

description: Lymphoblast morphology

data_processing:
For basecalling guppy version 3.2.2 was used
The reads were aligned using minimap2 version 2.17-r941
We used FLAIR (v1.4) to correct the reads and define high-confidence isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file summarizes high-confidence isoforms identified by FLAIR.

source_name: Leukemia cells

growth_protocol: Reh cell line was passaged in RPMI + 10% FBS + 1%GlutaMax + 1%pencillin/streptomycin

extract_protocol:
Total RNA was extracted from 20 x 10^6 Reh cells using TRIzol reagent.NucleoTrap Mini kit (Cat# 740655) from Takara was used to enrich for polyA mRNA from 100 ug of total RNA.
The library was prepared following manufacturer's protocol using Direct RNA sequencing kit (SQK-RNA002) from ONT. The library was loaded on R9.4 flow cell and sequenced using FLO-MIN106D MinION device for 48 hrs.

tag: disease state

value: Acute lymphocytic leukemia

value: Suspension cell line

tag: passage

value: passages 10-15


title: Gfi1_HS_input_3

description: Raw read counts


title: Gfi1_Con_IP_4

description: Raw read counts


title: Gfi1_Con_IP_3

description: Raw read counts


title: GLAST_HS_input_4

description: Raw read counts


title: GLAST_Con_IP_2

description: Raw read counts


title: Gfi1_stroma-free_HS_IP_2


title: GLAST_Con_IP_1

description: Raw read counts


title: Gfi1_stroma-free_HS_IP_1


title: Gfi1_stroma-free_HS_input_1


title: GLAST_Con_IP_4

description: Raw read counts


title: Gfi1_stroma-free_HS_input_2


title: Gfi1_stroma-free_Con_input_2


title: Gfi1_Con_input_3

description: Raw read counts


title: Gfi1_Con_input_4

description: Raw read counts


title: Gfi1_Con_input_1

description: Raw read counts


title: Gfi1_Con_IP_1

description: Raw read counts


title: H2B120Ub ChIP-seq in sgRnf20 Rep3

status: Public on Apr 29 2020

description: H2BK120Ub ChIP-seq in sgRnf20 Rep3

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5). Only reads that mapped to unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for USP22 and RNF20 were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H2BK120Ub1 were called using the parameter "-style histone."
Genome_build: mm10
Supplementary_files_format_and_content: Bed file Columns: (1) peak ID (2) chrom (3) chromStart (4) chromEnd (5) strand.

source_name: Primary Tregs from Foxp3-GFP-Cre/Rosa26-RFP/Cas9 mice

growth_protocol: Cells from Usp22fl/fl/Foxp3-YFPCre and WT (Foxp3-YFPCre) mice were not grown in culture. YFP+ Tregs were FACS sorted and immediately fixed for ChIP. For cells with acute loss of Usp22 or Rnf20 by Cas9 RNP editing, FACS sorted GFP+ Tregs were cultured in DMEM, 10% FBS, 1% pen/strep + 2000U hIL-2 in 24 well plates at 1 million cells/mL. Tregs were stimulated using CD3/CD28 Mouse T-Activator Dynabeads (Thermo Fisher, Cat# 11456D) at a ratio of 3:1 beads to cells for 48 hours. Cells were split and media was refreshed every 2-3 days.

extract_protocol:
For chromatin modifier ChIP-Seq, 4 e6 nTregs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. For histone modification ChIP-seq, 0.5-1 e6 nTregs were cross-linked in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against USP22, RNF20, H2AK119Ub, or H2BK120Ub then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed, eluted, and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.

treatment_protocol: After 48h of TCR stimulation, Tregs were edited by nucleofection with Cas9 RNPs. RNPs were produced by complexing a two-component gRNA to Cas9, as previously described (Roth et al, 2018). Tregs were collected from their culture vessels and centrifuged for 8 min at 200g, aspirated, and resuspended in the Lonza electroporation buffer P3 using 20μl buffer per condition. 2-5e5 cells Tregs were electroporated per well using a Lonza 4D 96-well electroporation system with pulse code EO148. Immediately after electroporation, 80μL of pre-warmed media was added to each well and the cells were incubated at 37°C for 15 minutes. The cells were then transferred to a round-bottom 96-well tissue culture plate and cultured in complete DMEM, 10% FBS, 1% pen/strep + 2000U hIL-2 at 1-2.5e5cells/well in 200μl of media for 5 days.

value: primary regulatory T cells (Tregs)

tag: genotype/variation

tag: antibody

value: H2BK120Ub Cell Signaling Technology 5546S Lot # 5


title: H2AK119Ub ChIP-seq in sgUsp22 Rep2

description: H2AK119Ub ChIP-seq in sgUsp22 Rep2

value: H2AK119Ub Cell Signaling Technology 8240S Lot # 6


title: Input for histone ChIP-seq in sgRnf20 Rep3


title: H2B120Ub ChIP-seq in sgNT Rep3

description: H2BK120Ub ChIP-seq in sgNT Rep3

value: sgNT (non-targeting control)


title: Input for histone ChIP-seq in sgNT Rep3

description: Input for histone ChIP-seq in sgNT Rep3


title: Input for histone ChIP-seq in sgUsp22 Rep2


title: Input for histone ChIP-seq in sgNT Rep2

description: Input for histone ChIP-seq in sgNT Rep2


title: H2B120Ub ChIP-seq in sgUsp22 Rep2

description: H2BK120Ub ChIP-seq in sgUsp22 Rep2


title: H2B120Ub ChIP-seq in sgNT Rep2

description: H2BK120Ub ChIP-seq in sgNT Rep2


title: H2AK119Ub ChIP-seq in sgNT Rep2

description: H2AK119Ub ChIP-seq in sgNT Rep2


title: Gfi1_HS_input_4

description: Raw read counts


title: H2AK119Ub ChIP-seq in sgUsp22 Rep1

description: H2AK119Ub ChIP-seq in sgUsp22 Rep1


title: H2AK119Ub ChIP-seq in sgRnf20 Rep1

description: H2AK119Ub ChIP-seq in sgRnf20 Rep1


title: Input for histone ChIP-seq in sgUsp22 Rep1


title: H2AK119Ub ChIP-seq in sgNT Rep1

description: H2AK119Ub ChIP-seq in sgNT Rep1


title: H2B120Ub ChIP-seq in sgUsp22 Rep1

description: H2BK120Ub ChIP-seq in sgUsp22 Rep1


title: Input for H2BK120Ub ChIP-seq in Usp22KO mice Replicate 2b

source_name: Primary Tregs from Usp22fl/fl/Foxp3-YFPCre

value: Usp22 KO


title: H2B120Ub ChIP-seq in sgRnf20 Rep1

description: H2BK120Ub ChIP-seq in sgRnf20 Rep1


title: Input for histone ChIP-seq in sgRnf20 Rep1


title: H2B120Ub ChIP-seq in sgNT Rep1

description: H2BK120Ub ChIP-seq in sgNT Rep1


title: Input for H2BK120Ub ChIP-seq in WT mice Replicate 2

source_name: Primary Tregs from WT (Foxp3-YFPCre) mice

value: Usp22 WT


title: Input for H2BK120Ub ChIP-seq in WT mice Replicate 1


title: Input for H2BK120Ub ChIP-seq in Usp22KO mice Replicate 1


title: Input for H2BK120Ub ChIP-seq in Usp22KO mice Replicate 2a


title: H2BK120Ub ChIP-seq in Usp22KO mice Replicate 1


title: H2BK120Ub ChIP-seq in WT mice Replicate 1


title: H2BK120Ub ChIP-seq in Usp22KO mice Replicate 2a


title: H2BK120Ub ChIP-seq in Usp22KO mice Replicate 2b


title: H2BK120Ub ChIP-seq in WT mice Replicate 2


title: RNF20 ChIP-seq Replicate 1

description: RNF20 ChIP-seq Replicate 1

value: RNF20 Novus NB100-2242, Lot # A2


title: Input for USP22 ChIP-seq Replicate 1

description: Input for USP22 ChIP-seq Replicate 1


title: Input for USP22 ChIP-seq Replicate 2

description: Input for USP22 ChIP-seq Replicate 2


title: Input for histone ChIP-seq in sgNT Rep1

description: Input for histone ChIP-seq in sgNT Rep1


title: Patient2-CD4-IL-17A+

status: Public on Apr 17 2020

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

country: United Kingdom

institute: King's College London

data_processing:
Illumina Casavax software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-quality sequence
Mapped to hg38 whole genome using RNASTAR using gencode v27 annotation with genecounts option enabled focused on "gene" feature
Genome_build: Hg38
Supplementary_files_format_and_content: Tab delimited count matrix including non normalised counts for each gene

source_name: Synovial fluid

extract_protocol:
Mononuclear cells were extracted from the synovial fluid of PSA patients using a Ficoll density centrifugation. CD8+ and CD4+ T cells were enriched using a CD3 magnetic isolation kit, cells were then activated with PMA and ionomycin for 90 minutes before being stained with a Mylteni IFNy and IL-17A cytokine secretion assay. Cells were then sorted based on Live>CD3+ cells and further sorted based on markers detailed in sample section. Cells were then washed with steril PBS and lysed in Trizol.
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA). Illumina Nextera XT library was then used for sequencing library preparation.

tag: cell type

value: CD4+ T cell

tag: cytokine secretion


title: Patient2-CD8-IFNy+

value: CD8+  T cell


title: Input for RNF20 ChIP-seq Replicate 2

description: Input for RNF20 ChIP-seq Replicate 2


title: USP22 ChIP-seq Replicate 2 (technical)

description: USP22 ChIP-seq Replicate 2 (technical)


title: RNF20 ChIP-seq Replicate 2

description: RNF20 ChIP-seq Replicate 2


title: Patient1-CD8-IFNy+


title: Patient2-CD8-IL-17A+


title: Patient3-CD8-IL-17A+


title: Patient3-CD4-IL-17A+


title: Patient1-CD4-IL-17A+


title: Patient3-CD8-IFNy+


title: Patient1-CD8-IL-17A+


title: P1se_3

status: Public on Apr 09 2020

description: Post-partum day 1 cochlear sensory epithelium

data_processing:
Cell Ranger version 2.1.1 was used to align the 10x sequence reads onto the mm10 genome assembly and generate feature-barcode matrices.
Expression counts were log2 normalized and converted to Transcripts Per Million of library size (TPM) with Seurat v2.0.
Normalized expression values were scaled and stress/mitochondrial gene expression was accounted for with Seurat before downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include log2 normalized TPM expression values for pooled timepoint samples.

source_name: Cochlear Sensory Epithelium Cells

extract_protocol:
Inner ear was dissected with Thermolysin and DNAase to isolate cochlear epithelium. Cells were dissociated with Papain and 20% Ovomucoid. 10x Genomics Chromium System was used to capture single-cells captured in oil droplets and prepare cDNA and sequencing library.
RNA libraries were constructed in accordance with the standard Illumina sequencing protocols

tag: strain

value: Inner Ear

value: Wildtype

tag: age

value: Cochlear Sensory Epithelium Cells


title: P1se_1


title: P7se_5

description: Post-partum day 7 cochlear sensory epithelium


title: E16se_3

description: Embryonic day 16 cochlear sensory epithelium


title: P7se_4


title: P1se_2


title: E16se_1


title: E14se_2

description: Embryonic day 14 cochlear sensory epithelium


title: E14se_1


title: KI-3066_S5

status: Public on Mar 25 2020

data_processing:
The reads were mapped to the mouse genome (GRCm38.vM11) using STAR (v2.5.2 )(Dobin et al., 2013).
Differentially expressed (DE) genes were determined by DeSeq2 (Love et al., 2014).
Genome_build: GRCm38.vM11

source_name: cochlea

extract_protocol:
KI and WT littermate mice at 5-27 weeks of age were euthanized via CO2 asphyxiation, and dissections of the cochlea, lung, and kidney were immediately frozen in liquid nitrogen. Tissue was pulverized with a Covaris CPO2 CryoPrep Automated Dry Pulverizer (Covaris, Woburn, MA) and RNA was extracted with Trizol (Invitrogen).
For RNA-seq, total RNA from cochleae was reverse transcribed with random primers after ribo-depletion using a TruSeq library kit (15031048 Rev. C, Illumina, San Diego, CA), and 2x93bp sequenced on an Illumina HiSeq1500 instrument.

value: cochlea


title: wt-1063_S3

value: Hgf+/+


title: wt-3051_S2


title: wt-2044_S1


title: KI-3069_S6


title: KI-3065_S4


title: P1se_4


title: E16se_2


title: ssy1_aa_2

status: Public on Feb 20 2020

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

description: PolyA RNA

data_processing:
Base calling was performed using CASAVA v1.8.
Raw sequence reads were mapped to reference ORF sequences using alignment free abundance estimation with Salmon v0.8.2, with default settings for an unstranded, single-end library.
Genome_build: C. albicans SC5314 version A22-s07-m01-r56 - ORF coding sequences (available from Candida Genome Database).
Supplementary_files_format_and_content: Salmon output files (.quant.sf). These contain gene name, length, and effective length (modeled based on factors affecting the probability of sampling fragments from this transcript), TPM (transcripts per million, a normalized measure of abundance) and estimated number of mapped reads. For more information, see https://salmon.readthedocs.io/en/latest/file_formats.html.

organism: Candida albicans SC5314

source_name: Whole cell

growth_protocol: Cells were grown overnight in YEPD medium (1% yeast extract, 2% peptone, 2% dextrose) at 30 °C in a shaking incubator at 180 rpm.

extract_protocol:
RNA was isolated from cell pellets by bead beating followed by use of the RNeasy Mini kit (Qiagen).
TruSeq unstranded libraries were constructed at the University of Texas Medical Branch Nex-Gen Core for sequencing on the NextSeq 550 platform.

treatment_protocol: Cells were diluted to an OD 600 of 0.2 in YNBA medium (0.17% yeast nitrogen base w/o amino acids and ammonium sulfate, 0.25% allantoin), supplemented with either 2% glucose, 1% casamino acids, or 1% peptone; samples were incubated at 37 °C in a shaking incubator at 180 rpm for 1 hr prior to harvesting by centrifugation.

value: Whole cell

tag: carbon source

value: Casamino acids


title: ssy1_aa_3

description: PolyA RNA


title: ssy1_glc_2

description: PolyA RNA

value: Glucose


title: stp2_aa_3

description: PolyA RNA


title: stp2_aa_2

description: PolyA RNA


title: ssy1_aa_1

description: PolyA RNA


title: stp2_glc_3

description: PolyA RNA


title: ssy1_glc_3

description: PolyA RNA


title: ssy1_glc_1

description: PolyA RNA


title: stp2_aa_1

description: PolyA RNA


title: stp2_glc_2

description: PolyA RNA


title: stp1_glc_2

description: PolyA RNA


title: stp1_aa_1

description: PolyA RNA


title: stp1_aa_3

description: PolyA RNA


title: stp1_aa_2

description: PolyA RNA


title: stp2_glc_1

description: PolyA RNA


title: WT_pept_3

description: PolyA RNA

value: Wild type

value: Peptone


title: WT_aa_3

description: PolyA RNA


title: stp1_glc_3

description: PolyA RNA


title: stp1_glc_1

description: PolyA RNA


title: WT_aa_2

description: PolyA RNA


title: WT_glc_3

description: PolyA RNA


title: WT_glc_1

description: PolyA RNA


title: CER_3b (10x)

status: Public on Jan 30 2020

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description:
10x Genomics Single Cell Expression Experiment
CER_H_barcodes.tsv
CER_H_genes.tsv
CER_H_matrix.mtx
CER_C_barcodes.tsv
CER_C_genes.tsv
CER_C_matrix.mtx
CER_B_barcodes.tsv
CER_B_genes.tsv
CER_B_matrix.mtx
CER_M_barcodes.tsv
CER_M_genes.tsv
CER_M_matrix.mtx
CER_species.txt

data_processing:
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-26bp.
The Cell Ranger v2.2.0 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a custom reference genome (genome.fa). The custom reference genome was created using Cell Ranger pipeline by concatenating the sequences of hg38, panTro5, panPan2 and rheMac8 genomes.
To assign each cell to species, we used custom scripts. First, the table was normalized for the total number of UMIs per species, to balance the mappability differences arising due to the evolutionary differences between the primate species. Then, a cell was assigned to a particular species if >50% of its UMIs were mapped to this species. The threshold of 50% was chosen based on the distribution of maximal proportions of UMI mapped to one species per cell. Cells, which could not be assigned to species unambiguously, were discarded.
Genome_build: hg38; panTro5; panPan2; rheMac8
Supplementary_files_format_and_content: 10x Digital Gene Expression matrix, gene list, barcode list and the list of filtered cells

molecule: nuclear RNA

organism:
Macaca mulatta
Pan paniscus
Pan troglodytes
Homo sapiens

source_name: Cerebellar Grey Matter (a mixture from all four organisms)

extract_protocol:
Nuclear RNA from frozen tissue samples was extracted according to Nuc-Seq protocol
Library was constructed according to manufacturers protocol (10x Genomics, Chomium single-cell)

value: brain

tag: tissue region

value: Cerebellar Grey Matter


title: CER_3a (10x)

tag: tissue


title: WT_pept_2

description: PolyA RNA


title: WT_aa_1

description: PolyA RNA


title: WT_pept_1

description: PolyA RNA


title: CN_1a (10x)

description:
10x Genomics Single Cell Expression Experiment
CN_H_barcodes.tsv
CN_H_genes.tsv
CN_H_matrix.mtx
CN_C_barcodes.tsv
CN_C_genes.tsv
CN_C_matrix.mtx
CN_B_barcodes.tsv
CN_B_genes.tsv
CN_B_matrix.mtx
CN_M_barcodes.tsv
CN_M_genes.tsv
CN_M_matrix.mtx
CN_species.txt

source_name: Caudate (a mixture from all four organisms)

value: Caudate


title: CN_1b (10x)


title: ACC_3b (10x)

description:
10x Genomics Single Cell Expression Experiment
ACC_H_barcodes.tsv
ACC_H_genes.tsv
ACC_H_matrix.mtx
ACC_C_barcodes.tsv
ACC_C_genes.tsv
ACC_C_matrix.mtx
ACC_B_barcodes.tsv
ACC_B_genes.tsv
ACC_B_matrix.mtx
ACC_M_barcodes.tsv
ACC_M_genes.tsv
ACC_M_matrix.mtx
ACC_species.txt

source_name: Cingulate Anterior (BA24) (a mixture from all four organisms)

value: Cingulate Anterior (BA24)


title: CN_3b (10x)


title: CER_1b (10x)


title: CER_2b (10x)


title: WT_glc_2

description: PolyA RNA


title: CN_3a (10x)


title: CN_2b (10x)


title: CN_2a (10x)


title: CER_1a (10x)


title: ACC_3a (10x)


title: ACC_2b (10x)


title: ACC_2a (10x)


title: ACC_1 (10x)


title: DEHP male_140 3 ppm

status: Public on Jan 08 2020

type: RNA

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

description:
3
DEHP male_140

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID:028639_D_F_20100525). Normalized signal intensity provided here is quantile Normalization.

organism: Danio rerio

source_name: adult zebrafish 8 months old

label_protocol: Agilent one color protocol for Cy3 following manufacturer's protocol

extract_protocol: Trizol protocol for total RNA following manufacturer's protocol

treatment_protocol: One dose of DEHP: control males (n=5), control females (n=6), DEHP males (n=5), DEHP females (n=7)

tag: age tissue

value: 8 months old


title: DEHP female_131 3 ppm

description:
3
DEHP female_131


title: DEHP male_122 3 ppm

description:
3
DEHP male_122


title: DEHP male_111 3 ppm

description:
3
DEHP male_111


title: DEHP female_114 3 ppm

description:
3
DEHP female_114


title: control male_77 0 ppm

description:
0
control male_77


title: DEHP female_145 3 ppm

description:
3
DEHP female_145


title: DEHP female_107 3 ppm

description:
3
DEHP female_107


title: DEHP male_130 3 ppm

description:
3
DEHP male_130


title: VilCreER APCfl/fl [DVR18151217_155_S2]

status: Public on Dec 31 2019

city: GLASGOW

first: Karen

last: Pickering

state: Scotland

address: Garscube Estate, Switchback Road, Bearsden

institute: CRUK Beatson institute

description: 20 Apc [DVR18151217_155_S2]

data_processing:
Quality checks on the raw RNASeq data files were done using fastqc version 0.10.1 [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc] and fastq_screen version 0.4.2 [http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/]. RNASeq reads were aligned to the GRCm38[Church et al 2011 PLoS Biol] version of the mouse genome using tophat2 version 2.1.0 [Kim et al  2013 Genome Biol] with Bowtie version 2.2.6.0[Langmead et al 2012 Nat Methods ]. Expression levels were determined and statistically analised by a combination of HTSeq version 0.5.4p3 [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html], the R version 3.4.1 environment, utilizing packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2 to normalise for the library size using GLMs to hypothesis test for differential expression [Love et al Genome Biology 2014]. Multiple test corrections were performed for all calculated p values (using the DESeq2 package). Finally, the fold change values were considered in ranking genes of interest.
Genome_build: GRCm38
Supplementary_files_format_and_content: Read counts normalised for library size

source_name: Apc

extract_protocol:
1cm of proximal intestine was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer.  RNA was extracted using Qiagen RNA extreatcion kit following manufacturers instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

tag: strain background

value: VilCreER APCfl/fl

value: Whole intestine


title: VilCreER APCfl/fl [DVR18151217_156_S3]

description: 21 Apc [DVR18151217_156_S3]


title: control male_70 0 ppm

description:
0
control male_70


title: VilCreER APCfl/fl Kras G12D [DVR18151211_171_S12]

description: 12 ApcKras [DVR18151211_171_S12]

source_name: ApcKras

value: VilCreER APCfl/fl Kras G12D


title: DEHP female_119 3 ppm

description:
3
DEHP female_119


title: control male_82 0 ppm

description:
0
control male_82


title: DEHP female_138 3 ppm

description:
3
DEHP female_138


title: control female_91 0 ppm

description:
0
control female_91


title: DEHP female_136 3 ppm

description:
3
DEHP female_136


title: control female_71 0 ppm

description:
0
control female_71


title: CER_2a (10x)


title: VilCreER APCfl/fl Kras G12D [DVR18151211_170_S11]

description: 11 ApcKras [DVR18151211_170_S11]


title: control male_84 0 ppm

description:
0
control male_84


title: control female_76 0 ppm

description:
0
control female_76


title: VilCreER APCfl/fl Kras G12D [DVR18151211_169_S10]

description: 10 ApcKras [DVR18151211_169_S10]


title: control male_92 0 ppm

description:
0
control male_92


title: VilCreEr APCfl/fl Vav2-/-, Vav3-/-, Tiam1-/- - 2 [KPR18170807_S8]

data_processing:
Quality checks on the raw RNASeq data files were done using fastqc version 0.10.1 [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc] and fastq_screen version 0.4.2 [http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/]. RNASeq reads were aligned to the GRCm38[Church et al 2011 PLoS Biol] version of the mouse genome using tophat2 version 2.1.0 [Kim et al  2013 Genome Biol] with Bowtie version 2.2.6.0[Langmead et al 2012 Nat Methods ]. Expression levels were determined and statistically analised by a combination of HTSeq version 0.5.4p3 [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html], the R version 3.4.2 environment, utilizing packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2 [Love et al Genome Biology 2014]. Cell files were normalized and analyzed in Partek Genomics Suite Software. RMA normalization and log2 transformation of the data was followed by the differential gene expression analysis using ANOVA and post hoc linear contrasts between all pairs of experimental conditions. Multiple test corrections were performed for all calculated p values. Finally, the fold change values were considered in ranking genes of interest.
Genome_build: GRCm38

source_name: VilCreEr APCfl/fl Vav2-/-, Vav3-/-, Tiam1-/-_Intestinal organoids

growth_protocol: Intestinal organoids were grown in matrigel with ADM/L-glutamine-Pen-strep with EGF and Nanog added

extract_protocol:
Lysates were obtained by incubating organoids with b-ME in RLT buffer according to QIAGEN's RNA extraction protocol.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

value: Mouse derived intestinal organoids

tag: passages


title: control female_95 0 ppm

description:
0
control female_95


title: VilCreER APCfl/fl [DVR18151217_154_S1]

description: 19 Apc [DVR18151217_154_S1]


title: VilCreEr APCfl/fl Vav2-/-, Vav3-/-, Tiam1-/- - 1 [KPR18170807_S7]


title: VilCreEr APCfl/fl - 1 [KPR18170807_S4]

source_name: VilCreEr APCfl/fl _Intestinal organoids

value: VilCreEr APCfl/fl


title: VilCreEr APCfl/fl - 2 [KPR18170807_S5]


title: DEHP male_137 3 ppm

description:
3
DEHP male_137


title: VilCreEr APCfl/fl Vav2-/-, Vav3-/-, Tiam1-/- - 3 [KPR18170807_S9]


title: control female_80 0 ppm

description:
0
control female_80


title: VilCreEr APCfl/fl - 3 [KPR18170807_S6]


title: brainless no infection, rep 2

status: Public on Sep 30 2019

data_processing:
The quality of the RNA-Seq sequence data was first evaluated using FastQC prior to further downstream analysis. Low quality sequences were trimmed and poor quality reads were removed using Trimmomatic.
Alignments were conducted by Genotypic (India). Eight samples were aligned to the reference based transcriptome Xenopus_laevis_v2, downloaded from NCBI [https://www.ncbi.nlm.nih.gov/genome/?term=xenopus+laevis]. There were two biological replicates per treatment (brain intact, not infected; brain intact infected; brainless, not infected; brainless, infected). The raw data from Illumina was checked for quality using FastQC1 and pre- processed, which included removing the adapter sequences and removing the low quality bases (<q30). Pre-processing of data was done with Cutadapt2. Mapping was performed with HISAT2 to align the high quality data to the reference genome with the default parameters.
Cufflinks was used to estimate and calculate transcript abundance. It results in normalized read count in the form of FPKM values. FPKM is a unit of measuring gene/transcript expression Four comparisons were conducted (1) brain intact NI vs. brain intact UTI, (2) brainless NI vs. brainless UTI (3) brain NI. Cufflinks includes a script called “Cuffmerge” that can be used to merge several Cufflinks assemblies together. The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff. "Cuffdiff" was used to identify significant changes in transcript expression. Merged GTF files produced by Cuffmerge were used as input in Cuffdiff.
Cuffdiff was used to calculate the differentially expressed transcripts and generated p-values, FDR corrected p-values (Q-value) and the log2fold change values.
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: Excel sheet with normalized counts for each sample, log2 fold change, p-value, gene identifier.

organism: Xenopus laevis

source_name: embryo

extract_protocol:
Total RNA for each sample was isolated by using TRIzolTM Reagent (Ambion, Invitrogen #15596018) –chloroform, following standard manufacturer’s protocol.
NGS analyses were performed by The MIT BioMicro Center (Boston, MA). Samples were quality controlled on a Fragment Analyzer (Advanced Analytical) to determine DV200 scores. The mRNA from 1 μg of total RNA was isolated using Illumina human/mouse/rat RiboZero Gold and prepared into Illumina libraries using the Kapa RNA HyperPrep kit and 10 cycles of amplification. Final libraries were pooled and quality controlled using qPCR (Roche LC480II) as well as the Fragment Analyzer and sequenced on HiSeq2000 for 40 nucleotides.
Following sequencing, data processing was performed using the standard Illumina pipeline. Fastq files were generated for data processing and assembly.

value: no brain

tag: infection

value: no


title: brainless with infection, rep 1

value: yes


title: brainless no infection, rep 1


title: Intact brain no infection, rep 1

value: intact brain


title: Q. Norm. of _8 [testis]

status: Public on Dec 20 2019

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided was done by data standardization of the median.

organism: Micropterus salmoides

source_name: testis

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

value: testis

value: toxaphene


title: Q. Norm. of _2 [testis]


title: Q. Norm. of _1 [testis]

value: control


title: brainless with infection, rep 2


title: Q. Norm. of _7 [testis]


title: Q. Norm. of _6 [testis]


title: Q. Norm. of _3 [testis]


title: Q. Norm. of _2 [liver]

source_name: liver

value: liver


title: Q. Norm. of _4 [testis]


title: control female_101 0 ppm

description:
0
control female_101


title: Q. Norm. of _3 [liver]


title: Q. Norm. of _4 [liver]


title: Q. Norm. of _6 [liver]


title: Intact brain with infection, rep 2


title: Q. Norm. of _5 [testis]


title: Q. Norm. of _5 [liver]


title: USP22 ChIP-seq Replicate 1 (technical)

description: USP22 ChIP-seq Replicate 1 (technical)

source_name: Primary Tregs from Foxp3-GFP-Cre/Rosa26-RFP/Cas9 mice

value: primary regulatory T cells (Tregs)

value: sgNT (non-targeting control)


title: Intact brain with infection, rep 1


title: Intact brain no infection, rep 2


title: Q. Norm. of _1 [liver]


title: Q. Norm. of _7 [liver]


title: Q. Norm. of Fip_Cntl6

status: Public on Aug 22 2019

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. There was 600 ng of Cy3-labeled cRNA used.

data_processing: Agilent Feature Extraction Software (v10.7) was used. Normalized signal intensity provided here is Quantile Normalization. Data was filtered prior to ANOVA to 1.5 as limit of detection

organism: Rattus norvegicus

source_name: N27 rat dopaminergic neural cell line

treatment_protocol: Cells treated with 25 uM fipronil

tag: treatment

value: Cntl

tag: cell line

value: dopaminergic neuron


title: Q. Norm. of Fip_High2

value: Fip


title: Q. Norm. of Fip_High1


title: Q. Norm. of Fip_Cntl7


title: Q. Norm. of VDAC_KO4

status: Public on Jul 31 2019

data_processing: Agilent Feature Extraction Software (v10.7) was used. Normalized signal intensity provided here is Quantile Normalization.  Data was filtered prior to ANOVA to 1.5 as limit of detection.

treatment_protocol: Wild type cells, and cells with the voltage dependant anion channel removed via CRISPR

tag: genotype

value: VDAC1 KO


title: Q. Norm. of Fip_Cntl5


title: Q. Norm. of Fip_Cntl8


title: Q. Norm. of Fip_High4


title: Q. Norm. of Fip_Cntl3


title: R1159Q-rep2-ATACseq

status: Public on Jul 30 2019

description: ATAC-seq of H9 derived R1159Q/+ hNPCs replicate 2

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the human genome (hg38) using STAR alignment tool (v2.5) for RNA-seq, ChIP-seq and ATAC-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.10) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq). For ChIP-seq, peaks for H3K4me, H3K4me3, H3K27me3 and H3K27ac were called by using the findPeaks program in HOMER with the default parameters for option "-style histones"   using the appropriate ChIP input experiments as background and peaks were stitch together into regions. ChIP-seq peaks for SMARCA2 and SMARCA4 were called by using the findPeaks program in HOMER with the default parameters using the appropriate ChIP input experiments as background. For ATAC-seq, peaks were called by using the findPeaks program in HOMER with the default parameters for option "-style dnase" using paired end 42 bp reads.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

source_name: R1159Q/+ hNPCs

growth_protocol: WT and K755R/+, R1159Q/+ hNPCs were culture in DMEM/F12 (Thermo Fisher Sci #10565018) supplemented with 1x N2 (Thermo Fisher Sci #17502048), 1x B27 without Vitamin A (Thermo Fisher Sci # 12587010), 20ng/ml FGF2 (Joint protein central). hNPCs were maintained on poly-l-ornithine and laminin coated plates initially and amplified on matrigel coated plates, at 37°C, 5% CO2 with media changes every other day.

extract_protocol:
For RNA-seq, RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq of Histone modificatons, ~1.5E6 hNPCs were collected and cross-linked in 1% formaldehyde. For ChIP-Seq of SMARCA2 and SMARCA4, ~6E6 hNPCs were first collected and cross-linked in 2mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E220 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against H3K4me, H3K4me3, H3K27me3, H3K27ac, SMARCA2 and SMARCA4 bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, ~50000 hNPCs were collected and washed with cold PBS. Cells were resuspended in resuspension buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) and then lysed in lysis buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei was collected and incubated in transposition mix containing Tn5 transposase(Illumina). Purified DNA was then ligated with adapters to prepare library for sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.


title: Q. Norm. of Fip_High7


title: Q. Norm. of Fip_High3


title: K755R-siCT-rep1-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs tranfected with non-targeting siRNA replicate 1

source_name: K755R/+ hNPCs

extract_protocol:
For RNA-seq, RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq of Histone modificatons, ~1.5E6 hNPCs were collected and cross-linked in 1% formaldehyde. For ChIP-Seq of SMARCA2,  SMARCA4 and FOSL2, ~6E6 hNPCs were first collected and cross-linked in 2mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E220 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against H3K4me, H3K4me3, H3K27me3, H3K27ac, SMARCA2 and SMARCA4 bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, ~50000 hNPCs were collected and washed with cold PBS. Cells were resuspended in resuspension buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) and then lysed in lysis buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei was collected and incubated in transposition mix containing Tn5 transposase(Illumina). Purified DNA was then ligated with adapters to prepare library for sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.

treatment_protocol: For ChIP-seq of hNPCs with lentiviral expression , R1159Q/+ hNPCs were infected on plate with lentivirus that expresses WT-SMARCA2-AM or R1159Q-SMARCA2-AM for overnight. Infected cells were selected with puromycin(1ug/ml) for 2 days and amplified for 1 passage before collecting for ChIP-seq. For ChIP-seq and ATAC-seq of hNPCs with siRNA knock down, WT or K755R/+ hNPCs were transfected with non-targeting, siSOX or siAP siRNA(20nM for each siRNA and same amount of CT siRNA were used) using Lipofectamine™ RNAiMAX. 72 hours post transfection, cells were collected for ChIP-seq and ATAC-seq.

tag: sirna

value: non-targeting siRNA for 72 hours

tag: lentiviral expression

tag: antibody source


title: K755R-siAP-rep1-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs tranfected with FOSL1, FOSL2 and JUNB siRNA replicate 1

tag: genotype/variation

value: FOSL1, FOSL2 and JUNB siRNA for 72 hours


title: K755R-siAP-rep2-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs tranfected with FOSL1, FOSL2 and JUNB siRNA replicate 2


title: Q. Norm. of VDAC_WT7

value: WT

tag: cell type


title: K755R-siCT-rep2-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs tranfected with non-targeting siRNA replicate 2


title: Q. Norm. of Fip_High8


title: Q. Norm. of VDAC_WT3


title: Q. Norm. of VDAC_WT5


title: Q. Norm. of Fip_Cntl2


title: Q. Norm. of VDAC_KO3


title: Q. Norm. of VDAC_KO1


title: Q. Norm. of VDAC_WT8


title: Q. Norm. of VDAC_KO5


title: Q. Norm. of VDAC_KO6


title: R1159Q-rep1-ATACseq

description: ATAC-seq of H9 derived R1159Q/+ hNPCs replicate 1


title: WT-rep2-ATACseq

description: ATAC-seq of H9 derived WT hNPCs replicate 2

source_name: hNPCs

value: wild type


title: K755R-rep2-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs replicate 2


title: K755R-rep1-ATACseq

description: ATAC-seq of H9 derived K755R/+ hNPCs replicate 1


title: WT-rep1-ATACseq

description: ATAC-seq of H9 derived WT hNPCs replicate 1


title: SMARCA2-K755R-siCT-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived K755R/+ hNPCs tranfected with non-targeting siRNA

value: Bethyl A301-015A


title: SMARCA2-K755R-siAP-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived K755R/+ hNPCs tranfected with FOSL1, FOSL2 and JUNB siRNA


title: SMARCA4-K755R-siCT-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived K755R/+ hNPCs tranfected with non-targeting siRNA

value: Abcam ab110641


title: Input_SMARCA-K755R-siAP-ChIPseq

description: Input for ChIP-seq of SMARCA from H9 derived K755R/+ hNPCs tranfected with FOSL1, FOSL2 and JUNB siRNA


title: Input_SMARCA4-WT-siCT-ChIPseq

description: Input for ChIP-seq of SMARCA4 from H9 derived hNPCs tranfected with non-targeting siRNA


title: SMARCA4-WT-siSOX-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived hNPCs tranfected with SOX2 and SOX3 siRNA

value: SOX2 and SOX3 siRNA for 72 hours


title: AM-SMARCA2-R1159Q-ChIPseq

description: ChIP-seq of AM from H9 derived R1159Q hNPCs expressing R1159Q-SMARCA2-AM

value: Lenriviral expressed R1159Q SMARCA2-AM

value: Active Motif 91111


title: Input_SMARCA-K755R-siCT-ChIPseq

description: Input for ChIP-seq of SMARCA from H9 derived K755R/+ hNPCs tranfected with non-targeting siRNA


title: SMARCA4-WT-siCT-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived hNPCs tranfected with non-targeting siRNA


title: Input_SMARCA4-WT-siSOX-ChIPseq

description: Input for ChIP-seq of SMARCA4 from H9 derived hNPCs tranfected with SOX2 and SOX3 siRNA


title: SMARCA4-K755R-siAP-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived K755R/+ hNPCs tranfected with FOSL1, FOSL2 and JUNB siRNA


title: Q. Norm. of VDAC_KO7


title: AM-SMARCA2-WT-ChIPseq

description: ChIP-seq of AM from H9 derived R1159Q hNPCs expressing WT-SMARCA2-AM

value: Lenriviral expressed WT SMARCA2-AM


title: SOX2-WT-ChIPseq

description: ChIP-seq of SOX2 from H9 derived WT hNPCs

value: Cell signaling Technology 5024S


title: Q. Norm. of VDAC_KO2


title: Input_AM-SMARCA2-WT-ChIPseq

description: Input for ChIP-seq of AM from H9 derived R1159Q hNPCs expressing WT-SMARCA2-AM


title: SOX3-K755R-ChIPseq

description: ChIP-seq of SOX3 from H9 derived K755R/+ hNPCs

value: Novus biology AF2569


title: Input_SOX-K755R-ChIPseq

description: Input for ChIP-seq of SOX from H9 derived K755R/+ hNPCs


title: Input_SOX-WT-ChIPseq

description: Input for ChIP-seq of SOX from H9 derived WT hNPCs


title: SOX3-R1159Q-ChIPseq

description: ChIP-seq of SOX3 from H9 derived R1159Q/+ hNPCs


title: SOX2-R1159Q-ChIPseq

description: ChIP-seq of SOX2 from H9 derived R1159Q/+ hNPCs


title: SOX3-WT-ChIPseq

description: ChIP-seq of SOX3 from H9 derived WT hNPCs


title: Input_SOX-R1159Q-ChIPseq

description: Input for ChIP-seq of SOX from H9 derived R1159Q/+ hNPCs


title: SOX2-K755R-ChIPseq

description: ChIP-seq of SOX2 from H9 derived K755R/+ hNPCs


title: Input_SMARCA2-R1159Q-rep2-ChIPseq

description: Input for ChIP-seq of SMARCA2 from H9 derived R1159Q/+ hNPCs replicate 2

extract_protocol:
For RNA-seq, RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq of Histone modificatons, ~1.5E6 hNPCs were collected and cross-linked in 1% formaldehyde. For ChIP-Seq of SMARCA2,  SMARCA4 and FOSL2, ~6E6 hNPCs were first collected and cross-linked in 2mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E220 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against H3K4me, H3K4me3, H3K27me3, H3K27ac, SMARCA2 and SMARCA4 bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, ~50000 hNPCs were collected and washed with cold PBS. Cells were resuspended in resuspension buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) and then lysed in lysis buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei was collected and incubated in transposition mix containing Tn5 transposase(Illumina). Purified DNA was then ligated with adapters to prepare library for sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.
Strand-specific polyA+ RNA-seq, ChIP-seq, ATAC-seq

tag: shRNA


title: SMARCA2-K755R-rep2-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived K755R/+ hNPCs replicate 2

value: Abcam ab15597


title: SMARCA2-WT-rep2-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived WT hNPCs replicate 2


title: SMARCA2-R1159Q-rep2-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived R1159Q/+ hNPCs replicate 2


title: Q. Norm. of VDAC_WT6


title: Input_AM-SMARCA2-R1159Q-ChIPseq

description: Input for ChIP-seq of AM from H9 derived R1159Q hNPCs expressing R1159Q-SMARCA2-AM


title: SMARCA4-WT-rep2-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived WT hNPCs replicate 2


title: SMARCA4-R1159Q-rep2-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived R1159Q/+ hNPCs replicate 2


title: Input_SMARCA2-WT-rep2-ChIPseq

description: Input for ChIP-seq of SMARCA2 from H9 derived WT hNPCs replicate 2


title: Input_SMARCA2-K755R-rep2-ChIPseq

description: Input for ChIP-seq of SMARCA2 from H9 derived K755R/+ hNPCs replicate 2


title: SMARCA4-K755R-rep2-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived K755R/+ hNPCs replicate 2


title: Input_SMARCA4-K755R-ChIPseq

description: Input for ChIP-seq of SMARCA4 from H9 derived K755R/+ hNPCs


title: SMARCA4-K755R-rep1-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived K755R/+ hNPCs replicate 1


title: SMARCA4-R1159Q-rep1-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived R1159Q/+ hNPCs replicate 1


title: Input_SMARCA4-WT-ChIPseq

description: Input for ChIP-seq of SMARCA4 from H9 derived WT hNPCs


title: Input_SMARCA4-R1159Q-ChIPseq

description: Input for ChIP-seq of SMARCA4 from H9 derived R1159Q/+ hNPCs


title: Input_SMARCA2-K755R-ChIPseq

description: Input ChIP-seq for SMARCA4/SMARCA2 from H9 derived K755R/+ hNPCs

extract_protocol:
For RNA-seq, RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq of Histone modificatons, ~1.5E6 hNPCs were collected and cross-linked in 1% formaldehyde. For ChIP-Seq of SMARCA2 and SMARCA4, ~6E6 hNPCs were first collected and cross-linked in 2mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E220 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against H3K4me, H3K4me3, H3K27me3, H3K27ac, SMARCA2 and SMARCA4 bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, ~50000 hNSCs were collected and washed with cold PBS. Cells were resuspended in resuspension buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) and then lysed in lysis buffer (10mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei was collected and incubated in transposition mix containing Tn5 transposase(Illumina). Purified DNA was then ligated with adapters to prepare library for sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.

tag: antibody


title: Input_SMARCA2-R1159Q-rep1-ChIPseq

description: Input ChIP-seq for SMARCA4/SMARCA2 from H9 derived R1159Q/+ hNPCs replicate1


title: SMARCA2-R1159Q-rep1-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived R1159Q/+ hNPCs replicate1

value: SMARCA2 (Bethyl A301-015A)


title: Input_SMARCA2-WT-rep1-ChIPseq

description: Input ChIP-seq for SMARCA2 from H9 derived WT hNPCs replicate1


title: SMARCA2-K755R-rep1-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived K755R/+ hNPCs replicate1


title: SMARCA2-WT-rep1-ChIPseq

description: ChIP-seq of SMARCA2 from H9 derived WT hNPCs replicate1


title: H3K27ac-R1159Q-ChIPseq

description: ChIP-seq of H3K27ac from H9 derived R1159Q/+ hNPCs

value: H3K27ac (Abcam ab4729)


title: Input_FOSL2-WT-ChIPseq

description: Input ChIP-seq for FOSL2 from H9 derived WT hNPCs


title: Input_FOSL2-R1159Q-ChIPseq

description: Input ChIP-seq for FOSL2 from H9 derived R1159Q/+ hNPCs


title: Input_FOSL2-K755R-ChIPseq

description: Input ChIP-seq for FOSL2 from H9 derived K755R/+ hNPCs


title: FOSL2-WT-ChIPseq

description: ChIP-seq of FOSL2 from H9 derived WT hNPCs

value: FOSL2 (Cell signaling Technology 19967)


title: FOSL2-R1159Q-ChIPseq

description: ChIP-seq of FOSL2 from H9 derived R1159Q/+ hNPCs


title: FOSL2-K755R-ChIPseq

description: ChIP-seq of FOSL2 from H9 derived K755R/+ hNPCs


title: H3K4me-R1159Q-ChIPseq

description: ChIP-seq of H3K4me from H9 derived R1159Q/+ hNPCs

value: H3K4me (Abcam  ab8895)


title: SMARCA4-WT-rep1-ChIPseq

description: ChIP-seq of SMARCA4 from H9 derived WT hNPCs replicate 1


title: H3K27me3-R1159Q-ChIPseq

description: ChIP-seq of H3K27me3 from H9 derived R1159Q/+ hNPCs

value: H3K27me3 (Active Motif 39155)


title: H3K27me3-K755R-ChIPseq

description: ChIP-seq of H3K27me3 from H9 derived K755R/+ hNPCs


title: Input_Histone-R1159Q-ChIPseq

description: Input ChIP-seq for histone modifications from H9 derived R1159Q/+ hNPCs


title: H3K27ac-K755R-ChIPseq

description: ChIP-seq of H3K27ac from H9 derived K755R/+ hNPCs


title: H3K4me3-R1159Q-ChIPseq

description: ChIP-seq of H3K4me3 from H9 derived R1159Q/+ hNPCs

value: H3K4me3 (Millipore 05-745)


title: H3K4me-K755R-ChIPseq

description: ChIP-seq of H3K4me from H9 derived K755R/+ hNPCs


title: Input_Histone-K755R-ChIPseq

description: Input ChIP-seq for histone modifications from H9 derived K755R/+ hNPCs


title: H3K4me3-WT-ChIPseq

description: ChIP-seq of H3K4me3 from H9 derived WT hNPCs


title: H3K4me3-K755R-ChIPseq

description: ChIP-seq of H3K4me3 from H9 derived K755R/+ hNPCs


title: H3K27me3-WT-ChIPseq

description: ChIP-seq of H3K27me3 from H9 derived WT hNPCs


title: H3K4me-WT-ChIPseq

description: ChIP-seq of H3K4me from H9 derived WT hNPCs


title: R1159Q-rep2-RNAseq

description:
RNA-seq of H9 derived R1159Q/+ hNPCs replicate 2
hNPCfpkm.txt.gz


title: R1159Q-rep1-RNAseq

description:
RNA-seq of H9 derived R1159Q/+ hNPCs replicate 1
hNPCfpkm.txt.gz


title: Input_Histone-WT-ChIPseq

description: Input ChIP-seq for histone modifications from H9 derived WT hNPCs


title: K755R-rep1-RNAseq

description:
RNA-seq of H9 derived K755R/+ hNPCs replicate 1
hNPCfpkm.txt.gz


title: WT-rep1-RNAseq

description:
RNA-seq of H9 derived WT hNPCs replicate 1
hNPCfpkm.txt.gz


title: WT-rep2-RNAseq

description:
RNA-seq of H9 derived WT hNPCs replicate 2
hNPCfpkm.txt.gz


title: Input_ChIPSeq 1

status: Public on May 02 2019

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

data_processing:
The ChIP-seq data were mapped with BWA-ALN and BWA-SAMSE mapper. The RNA-seq data were mapped using Bowtie mapper against human transcriptome version GRCh37.72 and MMseq to calculate FPKM value. To generate bigWig file for RNA-seq, BWA-MEM mapper was used.
The PCR duplicates were removed from the ChIP-seq data using PICARD tools. For both ChIP-seq and RNA-seq data, we used the reads with minimal mapping quality score of 15.
For the ChIP-seq data, peaks were called with a q-value cutoff of 0.01, and bigWig files were generated using bam2bw script.
For generating bigWig files of RNA-seq,  we mapped FASTQ file using BWA-MEM against hg19, and bigWig files were generated using bam2bw script.
Genome_build: hg19, GRCh37.72
Supplementary_files_format_and_content: The mapped reads of ChIP-seq (mapping quality score>=15) were used to generate bigWig files. The reads were extended 200 bp.

source_name: U937 cells

growth_protocol: U937, were cultured in RPMI 1640 (Euroclone, Italy) supplemented with 10% heat-inactivated FBS (Sigma-Aldrich, Italy), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 μg/mL streptomycin and 250 ng/mL amphotericin-B). HeLa-S3 cells were grown in DMEM (Euroclone) supplemented with 10% FBS, 100 U/mL penicillin/streptomycin (Euroclone), and 2 mM glutamine (Euroclone).

extract_protocol:
ChIP-seq: Chromatin preparation was essentially performed as previously described 36 with some modifications. Briefly, U937 and HeLa cells were protein cross-linked using 2 mM DSG for 45 min at RT. Cells were then washed twice with PBS, and DNA cross-linking was performed with 1% formaldehyde for 15 min (U937) or 10 min (HeLa) at RT with gentle shaking. Cross-linking reaction was quenched using 1.25 M glycine. Cells were then washed with PBS twice and harvested in Buffer B (20 mM HEPES, 0.25% Triton X-100, 10 mM EDTA, and 0.5 mM EGTA). Cells were pelleted by centrifuge at 2000 RPM for 5 min at 4 °C and resuspended in Buffer C (150 mM NaCl, 50 mM HEPES, 1 mM EDTA, and 0.5 mM EGTA). After that, cells were pelleted and resuspended in 1x incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1mM EDTA, 0.5mM EGTA, and 20mM HEPES) at 15 million cells/mL. Cells were sheared in a Bioruptor Pico sonicator (Diagenode) at 4 °C using 6 (U937) or 7 cycles (HeLa) of 30 sec ON, 30 sec OFF. Sonicated material was centrifuged at 13000 RPM for 15 min at 4 °C, then stored at  80°C.
RNA-seq: The total RNA of cells was extracted using Trizol (Life Technologies) according to manufacturer’s instructions. After DNase treatment, 5 μg of extracted RNA was depleted from ribosomal RNA using Ribo-Zero Gold Kit (Epicenter Madison, Winsconsin, USA). After fragmentation of the rRNA-depleted RNA, 500ng was reverse-transcribed using Super Script III Reverse Transcriptase (Invitrogen) and random primers (Invitrogen) following the manufacturer’s instructions.
ChIP-seq: Ten million cells were used as input for library preparation, and 5x106 cells were used as input for ChIP-qPCR experiments. Chromatin was pre-cleaned by incubating with Protein A/G Dynabeads (Invitrogen) for 90 min at 4 °C in 1x incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) supplemented with protease inhibitors and 0.1% BSA. Chromatin was then incubated with 5 μg of antibody (anti-BRD9, Active  Motifs, catalog number: 61538) overnight at 4 °C in 1x incubation buffer supplemented with protease inhibitors and 0.1% BSA. Protein A/G Dynabeads were added the day after followed by a 90 min incubation. The beads were washed twice with Wash Buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), once with Wash Buffer 2 (Wash Buffer 1 with 500 mM NaCl), once with Wash Buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-50, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), and twice with Wash Buffer 4 (1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES). After washing, beads were rotated for 30 min at RT in Elution Buffer (1% SDS, 0.1 M NaHCO3). The supernatant was decross-linked with 200 mM NaCl and 100 μg/mL Proteinase K over night at 65 °C. Decross-linked DNA was purified by MinElute PCR Purification columns (Qiagen). DNA amount was quantified using Qubit fluorometric quantitation (Thermo Fisher Scientific).  ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit for Illumina sequencing (Kapa Biosystems) according to the manufacturer’s protocol with the following modifications. 5 ng ChIP DNA was used as input, with NEXTflex adapters (Bioo Scientific) and 10 cycles of PCR amplification. Post-amplification clean-up was performed with QIAquick MinElute columns (Qiagen) and size selection was done with an E-gel (300 bp fragments) (Thermo Fisher Scientific). Size-selected samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Samples were sequenced on an Illumina HiSeq2000 or NextSeq500. The 43 or 75 bp tags were mapped to the reference mouse genome mm9 (NCBI build 37) or Drosophila genome dm3 (for spike-in) using the Burrows-Wheeler Alignment tool (BWA) allowing one mismatch38. Only uniquely mapped reads were used for data analysis and visualization. Mapped reads were filtered for quality and duplicates were removed. Peak-calling was performed with the MACS 2.0 tool against a reference input sample from the same cell line39.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were indexed using NEXTflex adapters (Bioo- Scientific Corporation, Austin, TX, USA), and the quality was assessed by qPCR and Bioanalyzer (BioRad). Single-end 43bp deep sequencing was performed on Illumina instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.

treatment_protocol: U937 were diluted to 200000 cells/ml, HeLa-S3 were diluted at 50% of confluence; To generate stable BRD9 knockdown cells, lentiviral shRNAs targeting BRD9 (TRC0000131081, TRC0000127634) and scrambled control  339 (TRC000035) plasmids were purchased from Sigma MISSION human shRNA library (Sigma-Aldrich), and the knockdown was performed using a standard lentiviral transduction protocol.

value: Human monocytes

tag: passenage


title: shBRD9_RNAseq 2

source_name: HeLa-S3 cells

value: Human cervix epithelial cells

tag: lentivirus

value: scrambled control


title: Scramble_RNAseq 1

value: shRNAs targeting BRD9


title: Input_ChIPSeq 2


title: BRD9_ChIPSeq 2

value: anti-BRD9, Active Motifs, catalog number:61538


title: H3K27ac-WT-ChIPseq

description: ChIP-seq of H3K27ac from H9 derived WT hNPCs

value: wild type


title: gingival tissues: 33LT

status: Public on Dec 31 2018

data_processing:
Alignment with STAR/2.5.2
Differential gene expression analysis with DeSeq2
Differential gene expression analysis with EdgeR
Differential gene expression analysis with Limma-Voom
Genome_build: MOUSE-GRCm38.vM11

source_name: gingival tissues, induced, GSK805 treated

growth_protocol: Total RNA from gingival tissues from mice undergoing experimental periodontitis .

extract_protocol:
Trizol extraction
Illumina TruSeq Stranded cDNA with ribodepletion

treatment_protocol: Each mouse has a ligated (induction site) side and a control side and mice are treated with an inhibitor of TH17 inflammation or vehicle control.

tag: transgenic genotype

tag: tissue

value: gingival tissues

tag: age

value: 11 weeks

tag: Sex

value: female

tag: classification

value: induced, GSK805 treated


title: gingival tissues: 35LT


title: gingival tissues: 23LV

source_name: gingival tissues, induced, vehicle treated

value: induced, vehicle treated


title: gingival tissues: 34UT

source_name: gingival tissues, control, GSK805 treated

value: control, GSK805 treated


title: gingival tissues: 38UT


title: gingival tissues: 30UT


title: gingival tissues: 37LT


title: gingival tissues: 32UT


title: gingival tissues: 24UV

source_name: gingival tissues, control, vehicle treated

value: control, vehicle treated


title: gingival tissues: 28UT


title: K755R-rep2-RNAseq

description:
RNA-seq of H9 derived K755R/+ hNPCs replicate 2
hNPCfpkm.txt.gz


title: gingival tissues: 39LT


title: gingival tissues: 17LV


title: gingival tissues: 16UV


title: gingival tissues: 15LV


title: BRD9_ChIPSeq 1


title: gingival tissues: 14UV


title: gingival tissues: 27LT


title: gingival tissues: 22UV


title: gingival tissues: 25LV


title: Heat Shock 3

description:
Whole Tissue
HS-3_S7

data_processing:
FastQC and Trimmomatic
STAR Alignment to GRCm38
featureCounts (subread) to generate raw gene counts
Differential gene expression using DESeq2, EdgeR, Limma Voom
Genome_build: GRCm38.p3 Release M4

source_name: Adult mouse utricle explant

growth_protocol: Adult CBA/J mice (male and female) were anesthetized, decapitated, and temporal bones were dissected out into M199 media (Life Technologies).  Utricles were dissected using sterile forceps in a tissue culture hood, and were transferred into sterile 24-well plates (Life Technologies).  The utricles were cultured overnight at 37C and 95% air/5% CO2.

extract_protocol:
Disruption and homogenization of tissues was performed by triturating tissue in lysis buffer with a sterile 27G syringe, and extraction of RNA was accomplished using the RNAqueous micro kit protocol (Ambion).
SMARTer Ultra Low RNA kit (Clontech) was used to prepare double-stranded cDNA.  Nextera XT (Illumina) was used for library preparation
Double-stranded cDNA library, paired end sequencing, multiplexed libraries

treatment_protocol: Following overnight culture, utricles were transferred into a sterile microcentrifuge tube using a sterile glass pipette.  The centrifuge tube was transferred into a water bath held at 43C for 30 minutes to induce a heat shock response.  Following this induction, utricles were returned to 37C and recovered for 2 hours to up-regulate the transcriptional heat shock response

tag: strain

value: CBA/J

value: Vestibular system tissue (Utricle)

value: Adult (P30-P60)

tag: treatment

value: Heat Shock

value: Cultured


title: Control 3

description:
Whole Tissue
Con-3_S3

value: Control (no heat shock)


title: Control 4

description:
Whole Tissue
Con-4_S4


title: Control 2

description:
Whole Tissue
Con-2_S2


title: Control 1

description:
Whole Tissue
Con-1_S1


title: gingival tissues: 26UV


title: gingival tissues: 21LV


title: Heat Shock 4

description:
Whole Tissue
HS-4_S8


title: Heat Shock 1

description:
Whole Tissue
HS-1_S5


title: Heat Shock 2

description:
Whole Tissue
HS-2_S6


title: Ute_P1_tdTom_59

status: Public on Nov 21 2018

description:
GSM1849086
1_A9-CS4_5u
Single Cell

data_processing:
STAR Alignment to GRCm38
RSEM v1.2.19 was used to generate TPM
Genome_build: GRCm38.p4 Release M3
Supplementary_files_format_and_content: text file with normalized TPM as described in the paper Burns et al 2015; PMID: 26469390

source_name: Utricle

growth_protocol: Procedure for capture of P1 cells was reported in a previous publication (Burns et al., 2015).  P12 and P100 cell were captured following primary dissociation of utricles from LfngEGFP; R26RCAG-tdTomato; Gfi1Cre mice

extract_protocol:
Lysis of cells and extraction of RNA was accomplished using the manufactuere's protocol (100-7168 I1 )
SMARTer Ultra Low RNA kit (Clontech) according to the volumes indicated in the Fluidigm protocol

treatment_protocol: Following dissociation, cells were captured using a Fluidigm C1 Platform

value: LfngEGFP; R26RCAG-tdTomato; Gfi1Cre

value: Utricle

value: Postnatal day 1

value: Immature


title: Ute_P1_tdTom_61

description:
GSM1849088
1_E10-CS78_5u
Single Cell


title: Ute_P1_tdTom_54

description:
GSM1849081
1_H5-CS92_5u
Single Cell

value: Type I


title: Ute_P1_tdTom_5

description:
GSM1848968
1_D5-CS68_2u
Single Cell


title: Ute_P1_tdTom_53

description:
GSM1849080
1_E4-CS75_5u
Single Cell


title: S2-3

status: Public on Nov 29 2018

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. There was 825 ng of Cy3-labeled cRNA used.

scan_protocol: Microarrays were scanned using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.

data_processing: Agilent Feature Extraction Software was used. Normalized signal intensity provided here is Quantile Normalization.  Data filtered at cut-off 2.5 for final analysis

organism: Xenopus tropicalis

source_name: whole embryo

extract_protocol: Qiagen minikit protocol for total RNA following manufacturer's protocol

value: whole embryo

value: 3 days post fertilization


title: Ute_P1_tdTom_44

description:
GSM1849044
1_B12-CS60_4u
Single Cell


title: Ute_P1_tdTom_48

description:
GSM1849075
1_B2-CS8_5u
Single Cell


title: C-4

value: C


title: S1-2


title: C-3


title: S2-4


title: S2-2


title: C-1


title: Ute_P1_tdTom_51

description:
GSM1849078
1_C3-CS13_5u
Single Cell


title: S1-3


title: C-2


title: Ute_P1_tdTom_43

description:
GSM1849043
1_G11-CS89_4u
Single Cell


title: Ute_P1_tdTom_41

description:
GSM1849041
1_C10-CS64_4u
Single Cell


title: Ute_P1_tdTom_4

description:
GSM1848967
1_C5-CS62_2u
Single Cell


title: S2-1


title: Ute_P1_tdTom_68

description:
GSM1849095
1_H12-CS94_5u
Single Cell


title: S1-1


title: Ute_P1_tdTom_8

description:
GSM1848971
1_D7-CS24_2u
Single Cell


title: Ute_P1_tdTom_56

description:
GSM1849083
1_D6-CS69_5u
Single Cell

value: immature


title: Ute_P1_tdTom_39

description:
GSM1849039
1_D9-CS22_4u
Single Cell


title: Ute_P1_tdTom_36

description:
GSM1849036
1_A9-CS4_4u
Single Cell


title: Ute_P1_tdTom_34

description:
GSM1849034
1_B8-CS11_4u
Single Cell


title: Ute_P1_tdTom_40

description:
GSM1849040
1_E9-CS30_4u
Single Cell


title: Ute_P1_tdTom_38

description:
GSM1849038
1_C9-CS16_4u
Single Cell


title: Ute_P1_tdTom_35

description:
GSM1849035
1_C8-CS17_4u
Single Cell


title: Ute_P1_tdTom_33

description:
GSM1849033
1_G7-CS40_4u
Single Cell


title: Ute_P1_tdTom_31

description:
GSM1849031
1_C7-CS18_4u
Single Cell


title: Ute_P1_tdTom_30

description:
GSM1849030
1_D6-CS69_4u
Single Cell


title: Ute_P1_tdTom_26

description:
GSM1849026
1_B5-CS56_4u
Single Cell


title: Ute_P1_tdTom_28

description:
GSM1849028
1_G5-CS86_4u
Single Cell


title: Ute_P1_tdTom_24

description:
GSM1849024
1_F4-CS81_4u
Single Cell


title: Ute_P1_tdTom_23

description:
GSM1849023
1_G3-CS39_4u
Single Cell


title: Ute_P1_tdTom_11

description:
GSM1848962
1_B9-CS10_2u
Single Cell


title: Ute_P1_tdTom_2

description:
GSM1848965
1_G2-CS38_2u
Single Cell


title: Ute_P1_tdTom_12

description:
GSM1848963
1_F9-CS36_2u
Single Cell


title: Ute_P1_tdTom_14

description:
GSM1848995
1_A1-CS3_3u
Single Cell


title: Ute_P1_tdTom_21

description:
GSM1849021
1_C3-CS13_4u
Single Cell


title: Ute_P1_tdTom_22

description:
GSM1849022
1_F3-CS33_4u
Single Cell


title: Ute_P1_tdTom_13

description:
GSM1848964
1_B12-CS60_2u
Single Cell


title: Ute_P100_tdTom_9

description:
1_A8-CS5_8u
Single Cell

value: Postnatal day 100

value: Type II


title: Ute_P100_tdTom_6

description:
1_B6-CS57_8u
Single Cell


title: Ute_P100_tdTom_32

description:
1_A8-CS5_11u
Single Cell


title: Ute_P1_tdTom_1

description:
GSM1848960
1_E1-CS25_2u
Single Cell


title: Ute_P100_tdTom_31

description:
1_E4-CS75_11u
Single Cell


title: Ute_P100_tdTom_5

description:
1_C5-CS62_8u
Single Cell


title: Ute_P1_tdTom_10

description:
GSM1848961
1_A8-CS5_2u
Single Cell


title: Ute_P100_tdTom_29

description:
1_G11-CS89_11u
Single Cell


title: Ute_P100_tdTom_3

description:
1_A3-CS1_8u
Single Cell


title: Ute_P100_tdTom_30

description:
1_F11-CS83_10u
Single Cell


title: Ute_P100_tdTom_28

description:
1_F7-CS34_11u
Single Cell


title: S1-4


title: Ute_P100_tdTom_27

description:
1_B11-CS59_10u
Single Cell


title: Ute_P100_tdTom_4

description:
1_A4-CS49_8u
Single Cell


title: Ute_P100_tdTom_25

description:
1_A3-CS1_11u
Single Cell


title: Ute_P1_tdTom_29

description:
GSM1849029
1_C6-CS63_4u
Single Cell


title: Ute_P100_tdTom_21

description:
1_H1-CS43_11u
Single Cell


title: Ute_P100_tdTom_19

description:
1_B6-CS57_10u
Single Cell


title: Ute_P100_tdTom_23

description:
1_G9-CS42_11u
Single Cell


title: Ute_P100_tdTom_17

description:
1_H4-CS93_10u
Single Cell


title: Ute_P100_tdTom_16

description:
1_H2-CS44_10u
Single Cell


title: Ute_P100_tdTom_18

description:
1_A5-CS50_10u
Single Cell


title: Ute_P100_tdTom_15

description:
1_D4-CS67_10u
Single Cell


title: Ute_P100_tdTom_13

description:
1_H1-CS43_10u
Single Cell


title: Ute_P100_tdTom_10

description:
1_B8-CS11_8u
Single Cell


title: Ute_P100_tdTom_11

description:
1_E12-CS76_8u
Single Cell


title: Ute_P100_tdTom_12

description:
1_G12-CS88_8u
Single Cell


title: Ute_P12_tdTom_54

description:
1_D12-CS72_9u
Single Cell

value: Postnatal day 12


title: Ute_P100_tdTom_1

description:
1_E1-CS25_8u
Single Cell


title: Ute_P12_tdTom_53

description:
1_H11-CS95_9u
Single Cell


title: Ute_P12_tdTom_6

description:
1_F4-CS81_6u
Single Cell


title: Ute_P12_tdTom_50

description:
1_C11-CS65_9u
Single Cell


title: Ute_P100_tdTom_0

description:
1_D1-CS21_8u
Single Cell


title: Ute_P12_tdTom_51

description:
1_F11-CS83_9u
Single Cell


title: Ute_P12_tdTom_52

description:
1_G11-CS89_9u
Single Cell


title: Ute_P12_tdTom_48

description:
1_H10-CS96_9u
Single Cell


title: Ute_P12_tdTom_8

description:
1_D5-CS68_6u
Single Cell


title: Ute_P12_tdTom_9

description:
1_C6-CS63_6u
Single Cell


title: Ute_P12_tdTom_7

description:
1_G4-CS87_6u
Single Cell


title: Ute_P12_tdTom_56

description:
1_G12-CS88_9u
Single Cell


title: Ute_P12_tdTom_55

description:
1_E12-CS76_9u
Single Cell


title: Ute_P12_tdTom_46

description:
1_C10-CS64_9u
Single Cell


title: Ute_P12_tdTom_44

description:
1_C9-CS16_9u
Single Cell


title: Ute_P12_tdTom_5

description:
1_C4-CS61_6u
Single Cell


title: Ute_P12_tdTom_43

description:
1_H8-CS47_9u
Single Cell


title: Ute_P12_tdTom_42

description:
1_G8-CS41_9u
Single Cell


title: Ute_P12_tdTom_41

description:
1_B8-CS11_9u
Single Cell


title: Ute_P12_tdTom_47

description:
1_E10-CS78_9u
Single Cell


title: Ute_P12_tdTom_4

description:
1_B3-CS7_6u
Single Cell


title: Ute_P12_tdTom_37

description:
1_F6-CS79_9u
Single Cell


title: Ute_P12_tdTom_39

description:
1_E7-CS28_9u
Single Cell


title: Ute_P12_tdTom_36

description:
1_B6-CS57_9u
Single Cell


title: Ute_P12_tdTom_35

description:
1_H5-CS92_9u
Single Cell


title: Ute_P12_tdTom_31

description:
1_G4-CS87_9u
Single Cell


title: Ute_P12_tdTom_34

description:
1_F5-CS80_9u
Single Cell


title: Ute_P12_tdTom_49

description:
1_A11-CS53_9u
Single Cell


title: Ute_P12_tdTom_30

description:
1_F4-CS81_9u
Single Cell


title: Ute_P12_tdTom_27

description:
1_B4-CS55_9u
Single Cell


title: Ute_P12_tdTom_29

description:
1_D4-CS67_9u
Single Cell


title: Ute_P12_tdTom_28

description:
1_C4-CS61_9u
Single Cell


title: Ute_P12_tdTom_23

description:
1_D3-CS19_9u
Single Cell


title: Ute_P12_tdTom_21

description:
1_B2-CS8_9u
Single Cell


title: Ute_P12_tdTom_22

description:
1_D2-CS20_9u
Single Cell


title: Ute_P12_tdTom_25

description:
1_F3-CS33_9u
Single Cell


title: Ute_P12_tdTom_18

description:
1_B11-CS59_6u
Single Cell


title: Ute_P12_tdTom_26

description:
1_A4-CS49_9u
Single Cell


title: Ute_P12_tdTom_16

description:
1_D10-CS70_6u
Single Cell


title: Ute_P12_tdTom_2

description:
1_F2-CS32_6u
Single Cell


title: Ute_P12_tdTom_20

description:
1_A2-CS2_9u
Single Cell


title: Ute_P12_tdTom_13

description:
1_H7-CS46_6u
Single Cell


title: Ute_P12_tdTom_19

description:
1_H1-CS43_9u
Single Cell

value: type II


title: Ute_P12_tdTom_15

description:
1_G9-CS42_6u
Single Cell


title: Ute_P12_tdTom_11

description:
1_E6-CS73_6u
Single Cell


title: Ute_P12_tdTom_14

description:
1_D9-CS22_6u
Single Cell


title: Ute_P12_tdTom_17

description:
1_G10-CS90_6u
Single Cell


title: Ute_P12_tdTom_12

description:
1_F7-CS34_6u
Single Cell


title: Ute_P12_tdTom_1

description:
1_B2-CS8_6u
Single Cell


title: Ute_P12_tdTom_0

description:
1_H1-CS43_6u
Single Cell


title: Ute_P12_tdTom_10

description:
1_D6-CS69_6u
Single Cell


title: DC.8an103n.PP.3

status: Public on Nov 03 2018

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: CD8- Dendritic Cell

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Peyer's Patch

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

value: 7 weeks old

tag: sorting markers

value: Dendritic Cell


title: DC.8an103n11bn.MLN.2

description: CD8- Dendritic Cell

source_name: Lymph Node (Mesenteric)


title: DC.8an103n11bn.PP.1

description: CD8- Dendritic Cell


title: DC.8an103n.PP.1

description: CD8- Dendritic Cell


title: DC.8an103n11bn.PP.3

description: CD8- Dendritic Cell


title: DC.8an103n11bn.MLN.1

description: CD8- Dendritic Cell


title: DC.8an103n.MLN.3

description: CD8- Dendritic Cell


title: DC.8an103n11bn.PP.4

description: CD8- Dendritic Cell


title: DC.8an103n.MLN.2

description: CD8- Dendritic Cell


title: DC.8an103n.MLN.1

description: CD8- Dendritic Cell