title: Diesel_exhaust_sample_1

tag: tissue

tag: treatment

value: Diesel exhaust


title: Mta2GFP_2i_1_1

status: Public on Apr 17 2019

type: SRA

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

country: USA

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome (UCSC GRCm38/mm10) using bowtie (version 0.12.8) and the arguments -m 1 -v 1 allowing for uniquely mapping reads only.
Peaks were called using MACS2 version 2.1.0 with the default Q-value of < 0.05.
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Processed data files contain genome-wide ChIP-seq read counts (RPKM- normalized). Files were converted to UCSC genome browser bigWig format.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatin-coated plates in 2i/LIF conditions as described (Ying et al., 2008).

extract_protocol:
Chromatin immunoprecipitations were carried out as previously outlined (Reynolds et al., 2012).
ChIP-seq libraries were prepared using the NEXTflex Rapid DNA-seq kit (Illumina)

tag: cell type

value: embryonic stem cells

tag: culture conditions

tag: strain

tag: chip antibody

value: Anti-GFP

tag: genotype/variation

value: Mta2-GFP knocked in to the endogenous Mta2 locus


title: Tumor_8901

type: genomic

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

description: Genomic DNA extracted from breast tumors was genotyped using Infinium Omni2.5-8 v1.3 Genotyping BeadChips (Illumina)

hyb_protocol: Illumina protocol

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing:
GenomeStudio Software V2011.1
B allele frequency
Log R ratio

label: cy3 and cy5

organism: Homo sapiens

source_name: Human breast tumor

label_protocol: Illumina protocol

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status

value: pos

tag: pgr status

value: neg

tag: her2 status


title: OSCC_K45

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software (v2011.1; methylation modul 1.9.0; Illumina, Inc.). The GA_illumina_methylation_MatrixSignalIntensities.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: OSCC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen QIAmp Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction

tag: subject status

value: oral squamous cell carcinoma (OSCC)

tag: Sex

value: female

tag: age [years]

tag: smoking

value: yes

tag: alcohol


title: OSCC_K25


title: OSCC_K12

value: male


title: OSCC_K20

value: no


title: OSCC_K23


title: 1Kcell_input

city: Beijing

first: Wei

last: Zhu

address: No.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2 version 2.2 with default settings, uniquely mapped read pairs were kept and duplicates were removed by Picard tools
Peaks were called with MACS2 in broad peak mode
Genome_build: Zv9
Supplementary_files_format_and_content: bigwig files were generated with deeptools package. Peaks and bigwig files are available in tar archives on the series record.

organism: Danio rerio

source_name: whole embryo

extract_protocol:
ChIP DNA is extracted as following: chromatins were elutted from bead-antibody complex with 200 ul ChIP elution buffer(1% SDS, 100nm NaHCO3), and then reverse crosslinked at 60 degree, 1000 rpm at thermal shaker for 6 hours. then proteinase (qiagen)  were added to final concentration 2 ug/ml, incubated at 56 degree for 30 minutes. DNA were purified with Zymo ChIP DNA Clean & Concentrator Kits (cat. No. D5201)
standard illumina library prep procedure

value: TU

tag: genotype

value: WT

tag: tissue

value: whole embryo

tag: developmental stage

value: 1K cell

tag: antibody

value: none (input)


title: OSCC_K17


title: Mta1FLAG_2i_2_Input

tag: cell type

tag: culture conditions

tag: strain

tag: chip antibody

value: input

tag: genotype/variation

value: Mta1-FLAG knocked into endogenous Mta1 locus


title: Mta1FLAG_2i_2_3

value: embryonic stem cells

value: anti-FLAG


title: Tumor_8842

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status


title: 128cell_input

value: 128 cell


title: OSCC_K38

tag: subject status

tag: Sex

tag: age [years]


title: Mta1FLAG_2i_2_2


title: OSCC_K43

tag: smoking

tag: alcohol


title: OSCC_K10


title: Tumor_8828

value: neg

tag: pgr status

tag: her2 status

value: pos


title: 16cell_input

tag: genotype

tag: tissue

tag: developmental stage

value: 16 cell

tag: antibody


title: OLP_L12

source_name: OLP

value: oral lichen planus (OLP)

value: female

value: yes


title: Tumor_8860


title: Tumor_8652


title: Mta2GFP_2i_1_2

tag: cell type

tag: culture conditions

tag: strain

tag: chip antibody

value: Anti-GFP

tag: genotype/variation

value: Mta2-GFP knocked in to the endogenous Mta2 locus


title: Mta1FLAG_2i_1_3


title: Mta1FLAG_2i_2_1


title: OLP_L9

value: no


title: OLP_L14

value: male


title: 1Kcell_H3K27me3_rep2

value: TU

value: WT

value: whole embryo

value: 1K cell

value: H3K27me3 (Millipore 07-499


title: OSCC_K16

value: oral squamous cell carcinoma (OSCC)


title: sperm_input

source_name: gamete

value: gamete

value: mature sperm

value: none (input)


title: Mta1FLAG_2i_1_Input

value: embryonic stem cells

value: input

value: Mta1-FLAG knocked into endogenous Mta1 locus


title: Mta1FLAG_2i_1_2

value: anti-FLAG


title: oocyte_input

value: mature oocyte


title: Tumor_8629

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status

value: pos

value: neg


title: Tumor_8472


title: OLP_L1

tag: subject status

value: oral lichen planus (OLP)

tag: Sex

value: female

tag: age [years]

tag: smoking

value: no

tag: alcohol


title: OLP_L7

value: yes


title: 1Kcell_H3K27me3_rep1

value: TU

tag: genotype

value: WT

tag: tissue

value: whole embryo

tag: developmental stage

value: 1K cell

value: H3K27me3 (Millipore 07-499


title: Tumor_7631

tag: pgr status

tag: her2 status


title: Tumor_7325


title: OLP_L4


title: OLP_L2


title: Mta1FLAG_2i_1_1

tag: cell type

value: embryonic stem cells

tag: culture conditions

tag: strain

tag: chip antibody


title: Tumor_7253

tag: 8p11-p12 amplification

tag: age

tag: pt status


title: 128cell_H3K27me3_rep1

value: 128 cell

tag: antibody


title: Brain frontal cortex_MS+EA_C16

city: Guangzhou

first: Yongjun

last: Chen

state: Guangdong

address: 232 Wai Huan East Road, University Town,Panyu District

department: Medical College of Acu-Moxi and Rehabilitation

institute: Guangzhou University of Chinese Medicine

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Frontal cortex

growth_protocol: From PND1 to PND21, the maternal separation that kept the mothers from their filial generation of MS group into another cage for four hours (9:00-13:00) was conducted every day. While the mothers and litters in control group were under no disturbance until weaning. All pups were weaned at PND 21 and the males were housed by four or five per cage until adult age, and the females were eliminated.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats in acupuncture group were acupunctured at GV20 (Baihui) and GV29 (Yintang) from PND61 to PND81 every other day under anesthetized, including Control, MS.

value: Brain frontal cortex

tag: group

value: MS+EA

value: 14 weeks


title: 16cell_H3K27me3_rep1

value: 16 cell


title: 128cell_H3K27me3_rep2


title: Brain frontal cortex_MS+EA_C10


title: control_KO18

source_name: control

tag: subject status

value: normal control

tag: Sex

value: male

tag: age [years]


title: Brain frontal cortex_MS+EA_C3


title: control_KO17

tag: smoking

tag: alcohol


title: control_KO16


title: Brain frontal cortex_MS_B6

tag: tissue

value: MS


title: OLP_L10

value: oral lichen planus (OLP)


title: 2cell_input

tag: genotype

tag: developmental stage

value: 2 cell

value: none (input)


title: Brain frontal cortex_MS_B4


title: NoLigand_6h.3

type: RNA

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

description:
G4_012
gene expression after 6h without 20A compound

hyb_protocol: Samples were then analyzed on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

scan_protocol: Microarray were scanned using the Agilent DNA Micorarray scanner G2505C

data_processing: Raw data were normalized using limma R package version 3.30.13 functions backgroundCorrect with normexp method and normalizeBetweenArrays with quantile method.

growth_protocol: Hela cells were grown in RPMI 1640 and DMEM culture media respectively supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 µg/ml streptomycin and 2 mM glutamine (Gibco-Life technologies)

extract_protocol: otal RNA were extracted from cells with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures.  RNA were quantified using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: HeLa cells were left treated or treated  with 6mM 20A for either  6hours  or 16hours.

tag: cell line

value: Hela

tag: treated with

value: none (control)

tag: time point


title: 2cell_H3K27me3_rep2

tag: strain

value: TU

value: WT

value: whole embryo


title: control_KO14

value: yes

value: no


title: oocyte_H3K27me3_rep1

value: gamete

value: mature oocyte

value: H3K27me3 (Millipore 07-499


title: Brain frontal cortex_MS_B3

value: Brain frontal cortex

value: 14 weeks


title: sperm_H3K27me3_rep2

value: mature sperm


title: Brain frontal cortex_Control_A6

value: Control


title: 2cell_H3K27me3_rep1


title: control_KO15

value: normal control

value: female


title: sperm_H3K27me3_rep1


title: Brain frontal cortex_Control_A2


title: Tumor_8931

tag: 8p11-p12 amplification

value: Amplified

tag: lymph node status

tag: er status

value: pos

tag: pgr status

value: neg

tag: her2 status


title: 1Kcell_H3K4me3_rep2

value: TU

value: 1K cell

tag: antibody

value: H3K4me3 (Abcam 8580)


title: ligand_6h.3

description:
G4_010
gene expression after 6h with 20A compound

value: Hela

value: G4 ligand 20A


title: Brain frontal cortex_Control_A1

tag: group

tag: age


title: control_KO13

tag: subject status

tag: Sex

value: male

tag: age [years]

tag: smoking

value: yes


title: ligand_6h.2

description:
G4_009
gene expression after 6h with 20A compound


title: control_KO12

value: no

tag: alcohol


title: Opaque C. albicans colony RNA-seq

city: San Francisco

first: Leqian

last: Liu

state: CA

address: 1700 4th street

department: BTS

institute: UCSF

data_processing:
Base calls performed with bcl2fastq2.15.
Read 1 contains the barcode (bp 1-12) and UMI (bp 13-20).
Read 2 was aligned with Bowtie
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each colony; columns are colony, and rows are genes.
Genome_build: C. albicans SC5314; S. cerevisiae EF4
Supplementary_files_format_and_content: Digital expression matrices. Flat text files with tab delimiters.

molecule: polyA RNA

organism: Candida albicans

source_name: yeast colonies

growth_protocol: Yeast cells were single cell encapsulated in agarose hydrogel microdroplets followed by culture with standard yeast synthetic medium to form colonies

extract_protocol:
Colonies were lysed in droplet using a combination of enzyme and detergent. polyA RNA capature were performed based on Drop-seq protocol
Library construction were perfromed following Drop-seq protocol.

tag: growth stage

value: 18 hour culture


title: ligand_16h.2

description:
G4_007
gene expression after 16h with 20A compound

tag: cell line

tag: treated with


title: NoLigand_6h.2

description:
G4_008
gene expression after 6h without 20A compound

value: none (control)

tag: time point


title: alba_H3_2

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome using bowtie2.
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with binSize 1bp.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

extract_protocol:
For γH2AX ChIP-seq, native ChIP method were performed (Bernatavichute et al., 2008). Briefly, MMS treated seedlings were harvested and ground to a fine powder in liquid nitrogen. Nuclei was extracted and washed with Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES (pH 7.4), 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT and 1X protease inhibitor (Roche)). Resuspended nuclei in 500μl 1X MNase Buffer (50mM Tris-HCl pH 7.6, 5mM CaCl2, 0.1 mM PMSF, 1X protease inhibitor (Roche)) and incubated them with RNase A at 37°C for 30 min. Then total volume was made to 1ml with 1X MNase Buffer and added 4.5 μl Micrococcal Nuclease (NEB, M0247S) for incubation at 37°C for 30min. Stopped the fragmentation process by adding EDTA (final 10 mM). Released nucleosomes by adding 0.1% SDS and rotated at 4°C for 3 hours. Then centrifuged and diluted the supernatant with MNase dilution buffer (0.1% Triton X-100, 50 mM NaCl, 0.1mM PMSF and 1X protease inhibitor). In advance, protein Dynabeads G (Invitrogen) beads should be incubated with antibodies (γH2AX and H3 antibodies are from ABclonal) in ChIP Dilution Buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1X protease inhibitor) at 4°C overnight. Beads-antibody complex was washed twice with 1ml MNase dilution buffer and added into diluted chromatins. The immunoprecipitation step was performed at 4°C for 5 hours. Then beads were washed twice with low salt wash buffer (50mM Tris-HCl pH 7.6, 10mM EDTA, 50mM NaCl, 0.1mM PMSF, 1X protease inhibitor), washed twice with middle salt wash buffer (50mM Tris-HCl pH 7.6, 10 mM EDTA, 100mM NaCl, 0.1mM PMSF, 1X protease inhibitor), washed once with high salt wash buffer (50 mM Tris-HCl pH 7.6, 10 mM EDTA, 150 mM NaCl, 0.1mM PMSF, 1X protease inhibitor), finally washed once with TE buffer (1 mM EDTA, 10 mM Tris-HCl pH8.0). Immune complexes were eluted by adding 200 μl elution buffer (0.1%SDS, 0.1M NaHCO3) at 65°C for 10 min, twice. Then treated with 2μl Proteinase K (10 mg/ml) for 1h at 45°C. Final DNA was recovered by Phenol/Chloroform extraction and ethanol precipitation.
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

treatment_protocol: 5-day growth on normal 1/2 MS media then transferred to 1/2 MS containing 50 ppm MMS (methyl methanesulfonate) for 48h growth.

tag: genotype/variation

tag: background

value: Columbia

tag: development stage

value: seedlings

tag: ssdrip antibody

value: Histone H3 antibody (from ABclonal)


title: P.v Saimiri 2

city: Hamilton

first: Sarah

last: Anzick

state: MT

address: 903 South 4th Street

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
NGS19_normalized_counts.txt
processed data header: X11944

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Salvador I genome using hisat2, version 2.0.5
Reads mapping to genes were counted using htseq-count, version 0.9.1
Gene normalization and differential expression analysis were performed using Deseq2, version 1.16.1
Genome_build: ASM241v2
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

organism: Plasmodium vivax

source_name: Saimiri blood

growth_protocol: Blood was collected from two Aotus and two Saimiri monkeys infected with Plasmodium vivax, Salvador I strain, and centrifuged to remove plasma.  The blood/parasite pellet was resuspended in McCoy's medium and then passed through MACS LS magnetic columns.  Parasite trophozoites and schizonts were eluted from the MACS columns and blood films were made to determine the parasite stage.  Parasites in trophozoite stage were grown to schizont stage in complete McCoys media containing HEPES, hypoxanthine, human AB serum, and gentamicin at 37C for approximately 8-12 hours.

extract_protocol:
Total RNA was extracted from parasites using TRIzol reagent and purified using Qiagen AllPrep kit.
RNA libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

tag: Stage

value: schizont

tag: strain

value: Salvador I

tag: host

value: Saimiri


title: 128cell_H3K4me3_rep1

tag: genotype

value: WT

tag: tissue

value: whole embryo

tag: developmental stage

value: 128 cell

tag: antibody


title: 1Kcell_H3K4me3_rep1

value: TU

value: 1K cell

value: H3K4me3 (Abcam 8580)


title: 128cell_H3K4me3_rep2


title: P.v Saimiri 1

description:
NGS19_normalized_counts.txt
processed data header: X11943


title: ligand_16h.1

description:
G4_006
gene expression after 16h with 20A compound

value: Hela

value: G4 ligand 20A


title: ligand_16h

description:
G4_002
gene expression after 16h with 20A compound


title: control_KO9

tag: subject status

value: normal control

tag: Sex

value: female

tag: age [years]

tag: smoking

value: no


title: ligand_6h

description:
G4_001
gene expression after 6h with 20A compound

tag: cell line

tag: treated with


title: control_KO11

tag: alcohol


title: NoLigand_6h

description:
G4_003
gene expression after 6h without 20A compound

value: none (control)

tag: time point


title: alba_H3_1

tag: genotype/variation

tag: background

value: Columbia

tag: development stage

value: seedlings


title: 16cell_H3K4me3_rep2

tag: strain

value: 16 cell


title: control_KO10

value: male


title: input replicate 3

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

data_processing:
Paired end fastq datasets for each sample were aligned to the B37 human reference using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), sorted, and duplicates removed with Picard (https://broadinstitute.github.io/picard/)
Uniquely mapped, duplicate free, paired end alignments were merged and their center positions extracted using USeq (https://github.com/HuntsmanCancerInstitute/USeq).
Both replica specific and merged replica chIPSeq peak identification was perfomed using USeq following it's ChIPSeq protocol (http://bioserver.hci.utah.edu/USeq/Documentation/usage.html).
ChIPSeq peaks of moderate and high stringency were identified by setting both FDR - Log2Rto thresholds of 0.05 - 0.585  and 0.01 - 1 respectively. Peaks falling within satellite repeat regions were excluded.
Genome_build: B37
Supplementary_files_format_and_content: Excel ChIPSeq peak call spreadsheets, see description tab for a detailed explanation of column statistics. Relative read coverage tracks in bigwig format.

source_name: HCT116 cells

growth_protocol: Normal culture conditions. Subconfluent cells were grown in DMEM

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (Oct1: Bethyl A310-610A, H3K4me3: Cell Signaling #9727). Qiagen Qiaquick PCR cleanup kit (Cat # 28104). Elution in nuclease-free water.
NEBNext ChIP-Seq Library Prep Master Mix Set (Cat # E6240S) with Unique Dual Index Adapters

value: colorectal carcinoma

tag: chip antibody


title: P.v Aotus 2

description:
NGS19_normalized_counts.txt
processed data header: X11942

source_name: Aotus blood

tag: Stage

value: schizont

value: Salvador I

tag: host

value: Aotus


title: input replicate 2

tag: tissue


title: P.v Aotus 1

description:
NGS19_normalized_counts.txt
processed data header: X11941


title: WT_H3_2

value: wild type

tag: ssdrip antibody

value: Histone H3 antibody (from ABclonal)


title: control_KO7

tag: subject status


title: 2cell_H3K4me3_rep1

value: TU

tag: genotype

value: WT

value: whole embryo

tag: developmental stage

value: 2 cell

tag: antibody

value: H3K4me3 (Abcam 8580)


title: H3K4m3 replicate 3

value: histone H3K4me3


title: 2cell_H3K4me3_rep2


title: input replicate 1


title: 16cell_H3K4me3_rep1


title: H3K4m3 replicate 2


title: SGC_7901_normal

city: Dongguan

first: Libo

last: Li

address: No.3 Wan Road, Dongguan, Guangdong

department: Department of General Surgery

institute: Dongguan People's Hospital

data_processing:
Data Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads
Reads Mapping performed by Bowtie2 to map clean reads to reference gene and use HISAT to reference genome
Gene quantified by FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SGC7901 cell line

growth_protocol: Human gastric cancer cells SGC7901 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA for RNA sequencing (RNA-seq) was isolated from SGC7901 cells with different treatment. After extracting from cells, total RNA was quantified and integrity measured by BioAnalyzer 2100. Oligo (dT) magnetic beads were used to select mRNA with polyA tail and the target RNA was obtained after purification.
Fragmented the target RNA and reversed transcription to double-strand cDNA (dscDNA) by N6 random primer. Then End repair was performed. The dscDNA was ligated with adaptor and amplified by PCR. Denatured the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: SGC7901/DDP cells were continuously exposed to increasing concentrations of cisplatin

tag: cell type

value: gastric cancer cell

tag: transfection

value: Perform sequence after SGC7901/DDP cells were cultured in RPMI-1640 without cisplatin

tag: cell line

tag: gentoype

value: DDP sensitive


title: control_KO8

value: normal control

tag: Sex

value: female

tag: age [years]

tag: smoking

value: yes

tag: alcohol


title: oocyte_H3K4me3_rep2

tag: strain

value: gamete

value: mature oocyte


title: SGC_7901_DDP

value: Perform sequence after SGC7901/DDP cells were continuously exposed to increasing concentration of cisplatin

value: DDP resistant


title: IL-17A-treated Il17rd KO keratinocytes

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were aligned to mm10 by Hisat2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.01
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

source_name: mouse primary keratinocytes

growth_protocol: The primary epidermal keratinocytes were separated from neonatal C57BL/6 mice using dispase (25U/ml in PBS) digestion overnight at 4°C, followed 10 minutes 0.05% trypsin-EDTA digestion at 37°C. The primary keratinocytes were cultured with 154CF medium plus HKGS kit (Invitrogen) for 48h.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq  library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: Keratinocyte from neonatal WT, Il17rd KO, and Il17rc KO mice were stimulated with IL-17A (100 ng/mL, PeproTech) for 8h.

value: mouse primary keratinocytes

value: Il17rd KO


title: H3K4m3 replicate 1

value: colorectal carcinoma

tag: chip antibody


title: alba_gamma_1

tag: genotype/variation

tag: background

value: Columbia

tag: development stage

value: seedlings

value: [gamma]H2AX antibody (from ABclonal)


title: WT_H3_1

value: wild type

tag: ssdrip antibody

value: Histone H3 antibody (from ABclonal)


title: alba_gamma_2


title: control_KO6

tag: subject status


title: oocyte_H3K4me3_rep1

value: TU

tag: genotype

value: WT

tag: tissue

tag: developmental stage

value: H3K4me3 (Abcam 8580)


title: Oct1 replicate 3

value: Oct1 (Pou2f1)


title: WT_gamma_1


title: IL-17A-treated Il17rc KO keratinocytes

tag: cell type

value: Il17rc KO


title: sperm_H3K4me3_rep1

value: gamete

value: mature sperm

tag: antibody


title: WT

data_processing:
Library strategy: DRIP-seq
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome using bwa version 0.7.12.
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with binSize 5bp.

extract_protocol:
ssDRIP was performed as described previously (Xu et al., 2017) with some modifications. Briefly, 14-day-old seedlings (3g) were ground into fine powder in liquid N2 and resuspended in 30 ml pre-cooled Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextran T40, 20 mM HEPES KOH, pH 7.4, 10 mM MgCl2, 0.5% Triton X-100). After filtering through two layers of Miracloth and centrifuging at 2000 g for 15 min at 4°C, nuclei were washed 2–3 times with NRBT buffer (20 mM Tris-HCl pH 7.5, 25% Glycerol, 2.5 mM MgCl2, 0.2% Triton X-100). Pellet was resuspended in 2 ml TE buffer (1 mM EDTA pH8.0, 10 mM Tris‐HCl pH8.0) with 0.5 % SDS and 0.33 mg/ml Proteinase K and was incubated constant temperature shaker at 37°C, 400 rpm, overnight. DNA was recovered with phenol:chloroform extraction and purified genomic DNA was digested with MseI, MboI, DdeI and NlaIII (NEB) for fragmentation. For S9.6 immunoprecipitation, 4 μg fragmented DNA (DNA concentration was measured with Qubit dsDNA kit) was incubated with 10 μg S9.6 antibody in DRIP Binding Buffer (10 mM NaPO4 pH 7.0, 0.14 M NaCl, 0.05% Triton X-100) at 4°C overnight. DNA-antibody complexes were incubated with Protein G beads (Invitrogen) at 4°C for 4 hours with rotation then washed 4 times by DRIP Binding Buffer at room temperature. DNA was eluted with Elution Buffer (50 mM Tris pH 8.0, 10 mM EDTA), together with 200 μg Proteinase K incubation at 55°C for 1 hour, 1000 rpm. Finally, DRIPed DNA was recovered with phenol:chloroform extraction.
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.


title: Oct1 replicate 2


title: alba1-1/alba2-1


title: Oct1 replicate 1


title: sperm_H3K4me3_rep2


title: control_KO4

value: normal control

value: female

value: no


title: control_KO5

value: yes


title: control_KO3

value: male


title: 16cell_H3K27me3_rep2

value: whole embryo

value: 16 cell

value: H3K27me3 (Millipore 07-499


title: control_KO2


title: IL-17A-treated WT keratinocytes

value: mouse primary keratinocytes

value: wild type


title: untreated WT keratinocytes


title: control_KO1


title: brain_8beta_100uM_rep2

status: Public on Apr 16 2019

city: Tsu

first: Mikiko

last: Yamanaka

state: Mie

address: 2-174 edobashi

department: Department of Systems Pharmacology

country: Japan

institute: Mie University

description: Gene expression after 3hr in the brain of zebrafish

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,  55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Oligo DNA Microarrays ver.3.0 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 100uM, 3hr, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the One-Color Low Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The total RNA were extracted from ten brain samples using an RNeasy Micro kit (Quiagen, Hilden, Germany) according to manufacturer’s instructions. Preliminary RNA quantification was performed by a NanoDrop spectrophotometer (Wilmington, DE, USA).

treatment_protocol: Zebrafish at 8 dpf were placed individually into wells on a round 48-well plate (10 mm diameter, 300 μL of 0.3× Danieau’s solution). The 48-well plate was placed in an incubator at 28°C with constant light (255 lx) and 300 μL of sample solution were added to 48-well plate. After 3h, zebrafish were anesthetized with a ethylene glycol monophenyl ether (Nacalai Tesque, Kyoto, Japan). Brains were removed under a stereoscopic microscope (Nikon SMZ800) and immediately fixed in RNA-later (Applied Biosystems, Foster City, CA, USA)

tag: treatment

value: brain


title: brain_8beta_10uM_rep1

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 10uM, 3hr, replicate 1


title: brain_imipramine_rep1

source_name: brain, imipramine, 1uM, 3hr, replicate 1

value: imipramine, 1uM, 3hr


title: brain_suvorexant_rep1

source_name: brain, suvorexant, 1uM, 3hr, replicate 1

value: suvorexant, 1uM, 3hr


title: brain_8beta_10uM_rep3

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 10uM, 3hr, replicate 3


title: brain_imipramine_rep2

source_name: brain, imipramine, 1uM, 3hr, replicate 2


title: brain_8beta_100uM_rep1

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 100uM, 3hr, replicate 1


title: brain_8beta_10uM_rep2

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 10uM, 3hr, replicate 2


title: brain_8beta_100uM_rep3

source_name: brain, 8beta (4'-Hydroxytigloyloxy) costunolide, 100uM, 3hr, replicate 3


title: brain_imipramine_rep3

source_name: brain, imipramine, 1uM, 3hr, replicate 3


title: brain_suvorexant_rep3

source_name: brain, suvorexant, 1uM, 3hr, replicate 3


title: Lkb1_KO_Splenic_DC_rep1

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: CD11c+ splenic DCs

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Lymphocytes from spleen and peripheral lymph nodes were enriched using CD4 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions, and then stained and sorted for CD25+CD4+ Tregs. Mouse spleens were digested with Collagenase D (Worthington) and CD11c+ DCs were enriched using CD11c MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions. Enriched cells were stained and sorted for DCs (CD11c+MHC-II+TCRβ–CD19–CD49b–).

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: dendritic cell (DC)

value: spleen


title: brain_suvorexant_rep2

source_name: brain, suvorexant, 1uM, 3hr, replicate 2


title: WT_Splenic_DC_rep1

value: WT


title: brain_control_rep1

source_name: brain, DMSO, 3hr, replicate 1

value: DMSO, 3hr


title: brain_control_rep2

source_name: brain, DMSO, 3hr, replicate 2


title: brain_control_rep3

source_name: brain, DMSO, 3hr, replicate 3


title: WT_Treg_rep4

source_name: CD4+CD25+ Tregs

value: Treg

value: spleen and peripheral lymph nodes


title: WT_Treg_rep3


title: Lkb1_KO_Splenic_DC_rep2


title: Lkb1_KO_Treg_rep3


title: Lkb1_KO_Splenic_DC_rep3


title: WT_Splenic_DC_rep3


title: Lkb1_KO_Splenic_DC_rep4


title: WT_Treg_rep2


title: Lkb1_KO_Treg_rep2


title: WT_Splenic_DC_rep2


title: WT_Splenic_DC_rep4


title: HiChIP_Pax3_6day_rep2

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description:
processed data file:  6day_plusdox.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_02

data_processing:
library strategy: HiChIP
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. Peak analysis was performed using bedtools. For triplicate experiments, peaks called in 2 of the 3 replicates were further considered. For duplicate experiments, common peaks between the 2 replicates were further considered. In addition, the peak lists were filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
HiChIP analysis. Paired-end samples were processed using the HiC-Pro pipeline. Contact matrices were generated for 10Kb bin pairs using default parameters in HiC-Pro to map the reads to the mm10 genome, remove duplicate reads, assign reads to Mbol restriction fragments, and acquire valid interactions. Statistically significant bin pairs and number of contacts were determined using the Fit-Hi-C contact caller using default settings and interaction distance less than 2 Mb.   Generation of Contact Matrix Heat Maps. Raw contact matrices from the HiC-Pro pipeline were normalized by read depth. The resulting normalized matrices were used to generate heat maps. The matrix acquired for the condition with no addition of doxycycline (non-induced) was subtracted from the matrices for 1-day and 6-day in doxycycline conditions. This enhanced the visualization of the heat maps for contacts specific to the manipulated condition. Similarly, the matrix for the Ldb1 knockdown sample was subtracted from the shSCR matrix to emphasize loss of contacts with the knockdown of Ldb1. R Bioconductor package “HiTC” was used to assist the generation of the contact heat maps.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent author-curated list of peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input
Supplementary_files_format_and_content: HiChIP: processed files represent .hic matrix

growth_protocol: Mouse ES cell differentiation was achieved by diluting 40000 cells/ml in EB differentiation medium and incubation in an orbital shaker at 80 RPM. EB differentiation medium: IMDM supplemented with 15% FBS , 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol. Trangene induction was achieved by adding doxycycline (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml), and then maintained throughout the differentiation protocol by replacing the media (including dox) every two days. At day 5, EBs were disgregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences) and replated on gelatin coated dishes using serum- or serum-free EB differentiation media supplemented with 1µg/ml doxycycline and 10ng/ml mouse basic-FGF.

extract_protocol:
ChIP-seq: D4 EBs (1-day induced and control Pax3 mouse cells) were trypsin-treated at 37°C for 1 minute with gentle shacking and reaction was inhibited by adding 10%FBS/PBS. 1-day induced Pax3 NIH3T3 cells and 6-day induced Pax3 mouse cells growing in monolayer were harvested by incubation with trypsin for 1-2 minutes. Single cells were washed once with PBS, resuspended in 10%FBS/PBS and supplemented with formaldehyde (final concentration 1%) for crosslinking of protein-DNA complexes (10 minutes at RT) followed by quenching with glycine and staining with PDGFRα-PE antibody. PDGFRα+ cells were sorted using FACSAriaII, snap-frozen in liquid nitrogen and stored at -80°C if not processed immediately. Cell pellets were incubated in lysis buffer LB1 supplemented with protease inhibitors (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 + Complete-mini - Roche) for 10 minutes at +4°C followed by incubation in buffer LB2 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA + Complete-mini - Roche) for 10 minutes at +4°C. Cell pellet was then resuspended in LB3 supplemented with protease inhibitors (10mM TRIS HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine + Complete-mini - Roche) and then sonicated. Cells were sonicated with a Branson sonicator at 18% power for 1 minute with intervals of 10 sec ON-10 sec OFF to achieve an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 minutes at 16000g and snap frozen in liquid nitrogen if not processed immediately. 10-15µg (histone mark) or 25-40µg (Ldb1, Smc1, Ctcf) of chromatin were diluted to 250µl and 500µl, respectivley, and then precleared for 4h at 4°C with 20µl of BSA-blocked Protein A (or Protein G)-conjugated sepharose beads (GE healthcare). Samples were supplemented with 1/10 volume of 10% Triton X-100 and incubated overnight with the indicated antibody. Immune complexes were recovered by incubation with 20µl of BSA-blocked Protein G-conjugated sepharose beads for 4h at 4°C and then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 20 minutes at 65°C. Chromatin from IP and Input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Followed 30 minutes centrifuge at 16000g, pellet were washed with 75% ethanol, air dried and dissolved in 45µl H2O.
ChIP-seq libraries were generated following a gel-free protocol using AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were end repaired using End-it DNA end repair (Epicentre), then A-tailed using Klenow Fragment (3'→5' exo-  NEB) followed by adapter-barcode ligation using T4 DNA ligase (Enzymatics). Illumina compatible adapter-barcodes were purchased from BIOO scientific. After ligation, DNAs were negatively size selected using 0.5x Ampure XP beads and unbound DNAs were positively size selected by adding 0.4x Ampure XP beads (this step allows for retention of DNA fragments ranging 200-500bp). Libraries were amplified using Phusion High Fidelity PCR master mix 2x (NEB) with a 16 cycles program. Libraries from Ldb1, histone marks in 6-day induced cells and H3K4me1 in dTAD and dTAD-Ldb1 immunoprecipitations were generated using the NEBNext DNA library prep kit (NEB).
HiChIP libraries. Long range interactions involving Pax3 binding sites were analyzed following the detailed protocol described by the Chang group. Briefly, non-induced, 1-day and 6-day Pax3-induced cells (respectively mesoderm, paraxial mesoderm precursors and myogenic progenitors) and 6-day+shSCR and 6-day+shLdb1 cells were harvested using trypsin for 1-2 min followed by inactivation with PBS/10%FBS, centrifuged 5 min at 400g, washed with PBS twice and then counted. 13 million cells, diluted to 1million/ml in PBS, were crosslinked for 15 min using methanol-free formaldehyde (Pierce – Thermoscientific). In situ contact generation was performed by digesting chromatin with MboI (NEB) followed by blunting with dNTP mix containing biotin-dATP (Thermo Fisher, 19524016) and ligation using T4 DNA ligase (NEB). After centrifugation, nuclei were resuspended in 880μL in Nuclear Lysis Buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, Complete Protease inhibitor - Roche), transferred in a Millitube and sonicated using a Covaris S220 (parameters: fill level = 10, duty cycle = 5, PIP = 140, cycles/burst = 200, time = 4 min). Chromatin was cleared by centrifugation, diluted 1:2 in ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 7.5, 167 mM NaCl), precleared for 4h at +4°C with 75µl of Protein G-conjugated magnetic beads and then incubated with 30µg of anti-Pax3 and anti-Ldb1 antibodies overnight at +4°C. Immune complexes were recovered by incubation with 60µl of BSA-blocked Protein G-conjugated sepharose beads for 5h at +4°C, then washed 5 times with RIPA wash buffer (50mM HEPES KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP40, 0.25% Triton X-100, 0.7% Sodium Deoxycholate) and one time with TEN buffer (10mM TRIS HCl pH 8, 1mM EDTA, 50mM NaCl). Due to the sample volume during the Pax3 IP, Protein-G:Pax3-chromatin bound beads were splitted in two 1.5ml tubes during the previous procedure. Immunoprecipitated chromatin was recovered by incubating beads with 200µl/tube of Elution buffer (50mM TRIS HCl pH 8, 10mM EDTA, 1% Sodium Dodecyl Sulfate) for 30 minutes at 65°C. ChIP samples and Input (equivalent to 1% of starting material) were reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM TRIS HCl pH 8, 1mM EDTA) supplemented with 4µl of RNaseA 20mg/ml and incubated for 2 hours at 37°C followed by Proteinase K treatment (4µl of 20mg/ml stock for each sample) for 30 minutes at 55°C. DNA was purified by Phenol-chloroform-isoamyl alcol extraction (twice) followed by chloroform extraction, then supplemented with 1/10 of volume of 3M Sodium Acetate pH 5 and 1.5µl of Glycogen and precipitated with 2 volumes of 100% Ethanol at -80°C for >1 hour. Following 30 minutes centrifuge at 16000g, pellets were washed with 75% ethanol, air dried and the combined DNA pellet were dissolved in 40µl H2O. Before proceeding with the biotin capture and transposase mediated library generation, ChIP samples were analyzed by qPCR to ensure enrichment at Pax3 sites vs control region. Samples were quantified using Pico-green (Invitrogen), resuspended in binding buffer and then incubated with 20µl of Streptavidin T1-conjugated magnetic beads (Invitrogen). After washing, DNA-bound streptavidin beads were incubated with 1.5µl of Tn5 transposase in a final volume of 50µl for 10 minutes at 55°C. This amount of transposase was selected based on the picogreen results of the ChIP, which yielded 25ng of DNA. Following quenching and washing, transposed DNA was incubated 5 minutes at 65°C with activated NEBNext UltraII QS Taq (+Illumina adaptor/barcodes) to allow primer extension and then amplified for 5 cycles (15 seconds 98°C followed by 1.5 minutes at 65°C). Additional cycles for library amplification were determined by qPCR using T5-T7 primer

value: differentiating mES cells

tag: time

value: day9 of differentiation

tag: purification

value: PDGFRα+FLK1- sorted

tag: doxycycline-treatment


title: HiChIP_Pax3_6day_rep1

description:
processed data file:  6day_plusdox.allValidPairs.hic
Pax3_HiChIP_6day_dox_iPax3_01


title: Lkb1_KO_Treg_rep1


title: ChIPseq_Smc1_nodox_rep3

description:
processed data file:  Smc1_d4_nodox_noBl.bed
Smc1_ChIP_nodox_iPax3_03

data_processing:
ChIP-seq analysis. Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. Similar results were obtained by performing peak calling using QESEQ with the following parameters: -s 100 -c 15 -p 0.01. Peak analysis was performed using bedtools. For triplicate experiments, peaks called in 2 of the 3 replicates were further considered. For duplicate experiments, common peaks between the 2 replicates were further considered. In addition, the peak lists were filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and in the mouse ChIP-seq black-list. Density maps were generated with SeqMiner using the enrichment file enr.sgr produced by QESEQ. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS  using the Kent tool Wig-to-BigWig.
HiChIP analysis. Paired-end samples were processed using the HiC-Pro pipeline. Contact matrices were generated for 10Kb bin pairs using default parameters in HiC-Pro to map the reads to the mm10 genome, remove duplicate reads, assign reads to Mbol restriction fragments, and acquire valid interactions. Statistically significant bin pairs and number of contacts were determined using the Fit-Hi-C contact caller using default settings and interaction distance less than 2 Mb.   Generation of Contact Matrix Heat Maps. Raw contact matrices from the HiC-Pro pipeline were normalized by read depth. The resulting normalized matrices were used to generate heat maps. The matrix acquired for the condition with no addition of doxycycline (non-induced) was subtracted from the matrices for 1-day and 6-day in doxycycline conditions. This enhanced the visualization of the heat maps for contacts specific to the manipulated condition. Similarly, the matrix for the Ldb1 knockdown sample was subtracted from the shSCR matrix to emphasize loss of contacts with the knockdown of Ldb1. R Bioconductor package “HiTC” was used to assist the generation of the contact heat maps.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: processed files represent author-curated list of peaks obtained by removing Encode blacklist and peaks detected in non-induced samples or input
Supplementary_files_format_and_content: HiChIP: processed files represent .hic matrix

value: day4 of differentiation

value: not treated


title: ChIPseq_Smc1_1day_rep3

description:
processed data file:  Smc1_d4_plusdox_noBl.bed
Smc1_ChIP_1day_dox_iPax3_03


title: HiChIP_Pax3_1day_rep1

description:
processed data file:  1day_plusdox.allValidPairs.hic
Pax3_HiChIP_1day_dox_iPax3_01


title: ChIPseq_Smc1_1day_rep2

description:
processed data file:  Smc1_d4_plusdox_noBl.bed
Smc1_ChIP_1day_dox_iPax3_02


title: ChIPseq_Smc1_nodox_rep2

description:
processed data file:  Smc1_d4_nodox_noBl.bed
Smc1_ChIP_nodox_iPax3_02


title: WT_Treg_rep1


title: ChIPseq_Smc1_nodox_rep1

description:
processed data file:  Smc1_d4_nodox_noBl.bed
Smc1_ChIP_nodox_iPax3_01


title: ChIPseq_Ctcf_1day_rep2

description:
processed data file:  Ctcf_d4_plusdox_noBl.bed
Ctcf_ChIP_1day_dox_iPax3_02

value: 07-729 (EMD Millipore)


title: ChIPseq_Ctcf_nodox_rep2

description:
processed data file:  Ctcf_d4_nodox_noBl.bed
Ctcf_ChIP_nodox_iPax3_02


title: ChIPseq_Smc1_1day_rep1

description:
processed data file:  Smc1_d4_plusdox_noBl.bed
Smc1_ChIP_1day_dox_iPax3_01


title: ChIPseq_Ctcf_nodox_rep1

description:
processed data file:  Ctcf_d4_nodox_noBl.bed
Ctcf_ChIP_nodox_iPax3_01


title: ChIPseq_Ctcf_1day_rep1

description:
processed data file:  Ctcf_d4_plusdox_noBl.bed
Ctcf_ChIP_1day_dox_iPax3_01


title: ChIPseq_Ldb1_1day_rep1

description:
processed data file:  Ldb1_d4_plusdox_noBl.bed
Ldb1_ChIP_1day_dox_iPax3_01


title: ChIPseq_Ldb1_nodox_rep2

description:
processed data file:  Ldb1_d4_nodox_noBl.bed
Ldb1_ChIP_nodox_iPax3_02


title: ChIPseq_Ldb1_1day_rep2

description:
processed data file:  Ldb1_d4_plusdox_noBl.bed
Ldb1_ChIP_1day_dox_iPax3_02


title: ChIPseq_Ldb1_1day_rep3

description:
processed data file:  Ldb1_d4_plusdox_noBl.bed
Ldb1_ChIP_1day_dox_iPax3_03


title: Input_plusdox_rep4

description:
processed data file:  Ctcf_d4_plusdox_noBl.bed
Input_plusdox_04

value: not applicable


title: ChIPseq_Ldb1_nodox_rep1

description:
processed data file:  Ldb1_d4_nodox_noBl.bed
Ldb1_ChIP_nodox_iPax3_01


title: ChIPseq_Ldb1_nodox_rep3

description:
processed data file:  Ldb1_d4_nodox_noBl.bed
Ldb1_ChIP_nodox_iPax3_03


title: Input_nodox rep4

description:
processed data file:  Ctcf_d4_nodox_noBl.bed
Input_nodox_04


title: Input_plusdox rep3

description:
processed data file:  Ldb1_d4_plusdox_noBl.bed
Input_plusdox_03


title: Input_nodox rep3

description:
processed data file:  Ldb1_d4_nodox_noBl.bed
Input_nodox_03


title: Input_plusdox rep2

description:
processed data file:  H3K4me1_plus_A7_filt_peaks.bed
Input_plusdox_02


title: Input_plusdox rep1

description:
processed data file:  H3K4me1_plus_B7_filt_peaks.bed
Input_plusdox_01


title: Input_nodox rep2

description:
processed data file:  H3K4me1_no_A2_filt_peaks.bed
Input_nodox_02


title: Input_nodox rep1

description:
processed data file:  H3K4me1_no_B2_filt_peaks.bed
Input_nodox_01


title: ChIPseq_H3K4me3_1day_rep1

value: ab8580 (Abcam)


title: ChIPseq_H3K4me3_1day_rep2


title: ChIPseq_H3K4me1_1day_rep1

description:
processed data file:  H3K4me1_plus_B7_filt_peaks.bed
H3K4me1_ChIP_1day_dox_iPax3_01

value: ab8895 (Abcam)


title: ChIPseq_H3K4me3_nodox_rep1


title: ChIPseq_H3K4me1_1day_rep2

description:
processed data file:  H3K4me1_plus_A7_filt_peaks.bed
H3K4me1_ChIP_1day_dox_iPax3_02


title: ChIPseq_H3K4me3_nodox_rep2


title: ChIPseq_H3K4me1_nodox_rep2

description:
processed data file:  H3K4me1_no_A2_filt_peaks.bed
H3K4me1_ChIP_nodox_iPax3_02


title: ChIPseq_H3K4me1_nodox_rep1

description:
processed data file:  H3K4me1_no_B2_filt_peaks.bed
H3K4me1_ChIP_nodox_iPax3_01


title: ChIPseq_H3K27me3_1day_rep2

value: 07-449 (EMD Millipore)


title: ChIPseq_H3K27me3_1day_rep1


title: ChIPseq_H3K27me3_nodox_rep2


title: ChIPseq_H3K27me3_nodox_rep1


title: ChIPseq_H3K27Ac_1day_rep1

value: ab4729 (Abcam)


title: ChIPseq_H3K27Ac_1day_rep2


title: NF31-1960KO-PIC0h-5

first: Fei

last: Ning

address: Tsinghua Yuan Street

institute: Institute for Immunology

data_processing:
Basecalls performed using Real Time Analysis.
Tophat (v2.1.0) was used for pair-end reads alignment with the following parameters:  -i 70 -g 1 --no-novel-indels
Gene expression level were quantified by using Cufflinks (v2.2.1), and Cufflinks was also used for further differential expression analysis
Genome_build: Mus Musculus (mm10)
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM and adjusted p-value for differentail expression analysis.

source_name: Bone marrow derived macrophages

growth_protocol: Murine Bone marrow cells maintained in DMEM supplemented with 10% FBS (Gibco) and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor for 5 days,then the BMDMs were replated in 12-wells plate for stimulation.

extract_protocol:
Cells in each condition were then harvested for total RNA extraction with a total RNA purification Kit (GeneMark).
RNA were converted into RNA-Seq quantification library (Low-input library (200ng)

treatment_protocol: 1ug/ml Poly(I:C) was added to cells for 1 or 3 hours post 12 hours replate.

value: 1 ug/ml Poly(I:C)

value: Hes1fl/fl Cre-ERT2

tag: time point


title: NF31-1960KO-PIC1h-6

tag: strain


title: ChIPseq_H3K27Ac_nodox_rep1


title: NF31-1935WT-PIC3h-3

value: Hes1+/+ Cre-ERT2


title: NF31-1960KO-PIC3h-7


title: NF31-1935WT-PIC1h-2


title: NF31-1935WT-PIC0h-1


title: WT_gamma_2

source_name: Arabidopsis thaliana

value: wild type

value: Columbia

value: seedlings

value: [gamma]H2AX antibody (from ABclonal)


title: ChIPseq_H3K27Ac_nodox_rep2

value: differentiating mES cells


title: PBMC_Rep3

city: Pleasanton

first: Preyas

last: Shah

address: 7068 Koll Center Pkwy #401

institute: 10x Genomics

data_processing:
The Cell Ranger ATAC Software Suite (version 1.0.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified along the genome
Barcodes likely associated with whole cells were identified by analyzing the number of fragments mapped near TSS regions and a peak-barcode matrix is defined
Genome_build: hg19

source_name: Healthy donor

growth_protocol: Human (GM12878) and Mouse A20 (ATCC TIB-208) B Lymphocytes were acquired and cultured according to guidelines from Coriell and ATCC, respectively. Fresh PBMCs, GM12878, and A20 cells were frozen according to the instructions outlined here: https://assets.ctfassets.net/an68im79xiti/18T8YsKiwKcGUakQmc8U22/086d0daa06444314fb757e35828f3c08/CG000169_DemonstratedProtocol_NucleiIsolation_ATAC_Sequencing_RevA.pdf. Healthy volunteer PBMC and BM samples were obtained from AllCells or the Stanford Blood Center (SBC).

extract_protocol:
All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are  available here: https://support.10xgenomics.com/single-cell-atac. The isolation, washing, and counting of nuclei suspensions were performed according to the Demonstrated Protocol: Nuclei Isolation for Single Cell ATAC Sequencing (10x Genomics). Briefly, anywhere from 100,000 to 1,000,000 cells were added to a 2 ml microcentrifuge tube and centrifuged (300 rcf for 5 min at 4°C). The supernatant was removed without disrupting the cell pallet and 100 µl chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) was added then pipette mixed 10 times. The microcentrifuge tube was then incubated on ice, with the length of time optimized for each cell type: GM12878 and A20 cell lines were 5 min; PB and BM cells were 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and the resulting solution and pipette mixed 5 times. Nuclei were centrifuged (500 rcf for 5 min at 4°C) and the supernatant removed without disrupting the nuclei pellet. Based on the starting number of cells and desired final nuclei concentration, an appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics; 2000153) was used to resuspend nuclei. The resulting nuclei concentration was determined using a Countess II FL Automated Cell Counter. Nuclei were then immediately used to generate single cell ATAC-seq libraries as described below.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev A). Briefly, the desired number of nuclei were combined with ATAC Buffer (10x Genomics; 2000122) and ATAC Enzyme (10x Genomics; 2000123/2000138), to form a Transposition Mix which was then incubated for 60 min at 37°C. A Master Mix comprising of Barcoding Reagent (10x Genomics; 2000124), Reducing Agent B (10x Genomics; 2000087) and Barcoding Enzyme (10x Genomics; 2000125/2000139) was then added to the same tube as Transposed Nuclei. The resulting solution was loaded onto a Chromium Chip E (10x Genomics; 2000121) in a Chip Holder (10x Genomics; 330019). Vortexed Chromium Single Cell ATAC Gel Beads (10x Genomics; 2000132) then Partitioning Oil (10x Genomics; 220088) were also loaded onto the same Chromium Chip E before attaching a 10x Gasket (10x Genomics; 370017/3000072) and placing into on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA). Resulting single-cell GEMs were collected at the completion of the run (~7 min) and linear amplification was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; 1851197): 72°C for 5 min, 98°C for 30 s, cycled 12 x: 98°C for 10 s, 59°C for 30 s and 72°C for 1 min. Emulsions were coalesced using tje Recovery Agent (10x Genomics; 220016) then subjected to Dynabeads (2000048) and SPRIselect reagent (Beckman Coulter; B23318) bead clean-ups. Indexed sequencing libraries were constructed by combining the barcoded linear amplification product with a Sample Index PCR Mix comprising of SI-PCR Primer B (10x Genomics; 2000128), Amp Mix (10x Genomics; 2000047/2000103) and Chromium i7 Sample Index (10x Genomics; 3000262). Amplification was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98°C for 45 s, cycled variable amounts depending on cell load: 98°C for 20 s, 67°C for 30 s, 72°C for 20 s with a final extension of 72°C for 1 min. The barcode sequencing libraries were subjected to a final bead clean-up SPRIselect reagent and quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms; KK4824).
Sequencing libraries were loaded on an Illumina sequencer with 2 × 50 paired-end kits using the following read length: 50 bp Read 1N, 8 bp i7 Index, 16 bp i5 Index and 50 bp Read 2N.

treatment_protocol: Fresh BCC biopsies were digested in 5 mL DMEM/F12 media + 250 ug/mL Liberase TL and 200 U/mL DNAse I with the gentleMACS Octo system at 37C for 3 hours at 20 rpm. After tissue pieces were fully digested, 50 uL of 500 mM EDTA was added and samples were collected by centrifugation at 300xg for 5 minutes. Single-cell suspensions were filtered through 70 um mesh and pelleted by centrifugation at 300xg at 4C for 10 minutes. Finally, cells were then resuspended in 1 mL of RPMI media and cryopreserved in FBS supplemented with 10% DMSO.Cells were gently thawed at 37C for 5 min and resuspended in media prior to FACS. Cells were stained with anti-CD45 V500 (clone HI30, cat. no. 560779, BD Biosciences), anti- CD3 FITC (clone OKT3, cat. no. 11-0037-41, Invitrogen), anti-CD8 Pacific Blue (clone 3B5, cat. no. MHCD0828, Invitrogen), anti-PD-1 APC/Cy7 (clone EH12.2H7, cat. no. 329921, BioLegend), and anti-HLA-DR eVolve 605 (clone LN3, cat. no. 83-9956-41, Affymetrix-Ebioscience). All antibodies were used at a 1:200 dilution, with the exception of anti-CD45 and anti-HLA-DR antibodies, which were used at a 1:100 dilution. Propidium iodine (cat. no. P3566, Invitrogen) was used for live/dead staining at a final concentration of 2.5 g/mL. PI-negative live cells were sorted as T cells (CD45+CD3+), non-T immune cells (CD45+CD3-), or tumor/stromal cells (CD45-CD3-). Cells were processed following 10x  Demonstrated Protocol (https://assets.ctfassets.net/an68im79xiti/18T8YsKiwKcGUakQmc8U22/086d0daa06444314fb757e35828f3c08/CG000169_DemonstratedProtocol_NucleiIsolation_ATAC_Sequencing_RevA.pdf) for PBMCs and Low Cell Input Nuclei Isolation protocol was followed for samples with cell count < 100,000. Isolated nuclei were further processed for scATAC-seq.

value: PBMCs


title: PBMC_Rep4


title: Memory_CD4_T_Cells_Rep2

value: Memory CD4 T cells


title: Naive_CD4_T_Cells_Rep2

value: Naive CD4 T cells


title: PBMC_Rep2


title: Bone_Marrow_Rep1

value: Bone Marrow Cells


title: HeLa_NaCl_SB_replicate1 (Cy3) / HeLa_NaCl_replicate1 (Cy5)

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios. Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s Medium supplemented with 10% fetal calf serum (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 U/ml Penicillin and 100 μg/ml Streptomycin (GibCO) and were cultured in a 5% CO2 humidified incubator at 37ºC.

extract_protocol: Total RNA was isolated using the RNAspin Mini Kit (GE Healthcare). An additional treatment with DNAse was performed using the TURBO DNA-free Kit  (Ambion inc).    Quality assessment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: HeLa cells were incubated with 100 mM NaCl for 2h or pre-treated with 10 uM SB for 30 min and treated with 100 mM NaCl for 2 h

tag: cell line

value: HeLa cells

tag: sample type

value: HeLa_NaCl_replicate1 (Cy5)


title: Liver cells, Mock (vehicle) treated

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetric Expression Console using default analysis settings

label: Biotin

source_name: Huh7 human hepatoma cultured cells treated 24 hours with vehicle (0.1% DMSO)

label_protocol: Biotinylated cRNA were prepared using the Affimetrix GeneChip™ WT PLUS Reagent Kit with Biotin Allonamide Triphosphate from 5.5 ug total RNA

growth_protocol: Human hepatoma (Huh7) cells  were grown at 37°C in DMEM (Gibco, Life Technologies) with 10% FBS (Wisent) and 10 mM non-essential amino acids.

extract_protocol: RNA isolation was performed using the RNeasy (Qiagen) isolation kit as per manufacturer’s protocol

treatment_protocol: One day prior to treatment, cells were seeded at 2.75x10^5 cells per well in a 6-well plate. The following day, Schizocommunin or its analogue were added to final concentrations of 10 μM or 0.5 μM respectively and 0.1% final DMSO. Mock treatment consisted of DMSO only. Cells were incubated with the compounds for 24 hours.

value: Mock (DMSO only)


title: Liver cells, Schizocommunin analogue treated

source_name: Huh7 human hepatoma cultured cells treated 24 hours with Analogue (0.1% DMSO)

value: Analogue


title: HeLa_NaCl_SB_replicate2 (Cy3) / HeLa_NaCl_replicate2 (Cy5)

value: HeLa_NaCl_replicate2 (Cy5)


title: Liver cells, Schizocommunin treated

source_name: Huh7 human hepatoma cultured cells treated 24 hours with Schizocommunin (0.1% DMSO)

value: Schizocommunin


title: HeLa_NaCl_replicate3 (Cy3) / HeLa_O_replicate3 (Cy5)

value: HeLa_O_replicate3 (Cy5)


title: HeLa_NaCl_SB_replicate3 (Cy3) / HeLa_NaCl_replicate3 (Cy5)

value: HeLa_NaCl_replicate3 (Cy5)


title: HeLa_NaCl_SB_replicate3 (Cy5) / HeLa_NaCl_replicate3 (Cy3)

value: HeLa_NaCl_SB_replicate3 (Cy5)


title: HeLa_NaCl_SB_replicate1 (Cy5) / HeLa_NaCl_replicate1 (Cy3)

value: HeLa_NaCl_SB_replicate1 (Cy5)


title: SU009_Tcell_Pre

source_name: Donor

value: T cells

value: before immunotherapy


title: SU009_Tumor_Immune_Post

value: Tumor and immune cells

value: post immunotherapy


title: SU009_Tcell_Post


title: HeLa_NaCl_replicate1 (Cy3) / HeLa_O_replicate1 (Cy5)

value: HeLa_O_replicate1 (Cy5)


title: HeLa_NaCl_replicate2 (Cy3) / HeLa_O_replicate2 (Cy5)

value: HeLa_O_replicate2 (Cy5)


title: HeLa_NaCl_replicate1 (Cy5) / HeLa_O_replicate1 (Cy3)


title: HeLa_NaCl_replicate3 (Cy5) / HeLa_O_replicate3 (Cy3)


title: CD34_Progenitors_Rep2

value: CD34 Progenitor cells


title: SU009_Tumor_Immune_Pre


title: SU010_Total_Post

value: cells from the BCC biopsy


title: HeLa_NaCl_replicate2 (Cy5) / HeLa_O_replicate2 (Cy3)

value: HeLa cells


title: SU008_Tumor_Pre


title: HeLa_NaCl_SB_replicate2 (Cy5) / HeLa_NaCl_replicate2 (Cy3)

value: HeLa_NaCl_SB_replicate2 (Cy5)


title: SU008_Tumor_Post


title: SU010_Total_Pre

value: mixture of tumor and normal immune cells


title: SU008_Tcell_Pre


title: SU007_Total_Post


title: SU008_Immune_Post

value: Immune cells


title: SU008_Tcell_Post


title: SU006_Tumor_Pre

value: Tumor cells


title: SU005_Total_Post


title: SU001_Tumor_Immune_Post


title: SU006_Immune_Pre


title: SU006_Tcell_Pre


title: SU001_Total_Pre


title: Frozen_sorted_pbmc_5k

source_name: All Cells

value: PBMCs


title: Dendritic_all_cells

value: Dendritic cells


title: Fresh_pbmc_5k


title: SU001_Total_Post2


title: Memory_CD8_T_Cells

value: Memory CD8 T cells


title: SU001_Tcell_Post


title: Frozen_unsorted_pbmc_5k


title: CD4_Naive

value: CD4 Naive T cells


title: Naive_CD8_T_Cells

value: Naive CD8 T cells


title: NK_Cells

value: CD56 NK cells


title: Regulatory_T_Cells

value: Regulatory T cells


title: CD4_Memory

value: CD4 Memory T cells


title: Naive_CD4_T_Cells_Rep1

value: Naive CD4 T cells


title: Memory_CD4_T_Cells_Rep1

value: Memory CD4 T cells


title: CD34_Progenitors_Rep1

value: CD34 Progenitor cells


title: CD4_HelperT

value: CD4 Helper T cells


title: SU008_Immune_Pre

value: before immunotherapy


title: SU006_Total_Post

value: cells from the BCC biopsy

value: post immunotherapy


title: SU001_Tcell_Post2

value: T cells


title: Monocytes

value: Monocytes


title: B_Cells

value: B cells


title: SU001_Immune_Post2

value: Immune cells


title: Dendritic_Cells

value: Dendritic cells


title: 99p9_0p1_CD4Mem_CD8Naive

value: Mixture of CD4 Memory and CD8 Naive T cells


title: 99p5_0p5_CD4Mem_CD8Naive


title: 99p5_0p5_MonoT

value: Mixture of Monocytes and T cells


title: 99_1_MonoT


title: 99_1_CD4Mem_CD8Naive


title: 1_99_CD4Mem_CD8Naive


title: PBMC_Rep1

value: PBMCs


title: 50_50_CD4Mem_CD8Naive


title: 50_50_Mono_T


title: 1_99_Mono_T


title: 0p5_99p5_Mono_T


title: 0p5_99p5_CD4Mem_CD8Naive


title: 0p1_99p9_Mono_T


title: 60_4_ACDMPV_lung

city: Houston

first: Neil

middle: A.

last: Hanchard

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Samples were demultiplexed using Casava (v1.8, Illumina).
Bismark (v0.12.3, default parameters) was used to (1) align FASTQ files to the hg19 reference genome, (2) remove duplicate reads, (3) trim five bases off the 5’ ends of all reads and one base off the 3’ end of “read 2” paired reads in order to eliminate known methylation biases, and (4) extract counts of methylated and unmethylated cytosines found on the forward and reverse strand in a CpG dinucleotide context.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file containing percent methylation values based on the number of sequencing reads in support of methylation/non-methylation at locus

source_name: lung

growth_protocol: Fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
DNA was extracted from blood using Gentra Puregene Kit (Qiagen, Germantown, CA, USA). Fibroblast DNA was extracted using a Gentra Puregene Kit (Qiagen). DNA was extracted from frozen lung tissues using DNeasy Blood and Tissue Kit (Qiagen).
Sample libraries were prepared using the KAPA Library Preparation Kit for Illumina Platforms (Kapa Biosystems, Boston, MA, USA), according to manufacturer’s protocol v2.14.
Custom SeqCap Epi Enrichment Kit (Roche NimbleGen, Madison, WI, USA)

tag: condition

value: ACDMPV


title: 0p1_99p9_CD4Mem_CD8Naive


title: 115_3_ACDMPV_lung


title: 215_control_lung

value: control


title: BAB_8048_UPD16mat_fibroblast

source_name: skin fibroblast culture


title: 99p9_0p1_Mono_T


title: M_control_blood

source_name: peripheral blood


title: 2_0204_UPD16pat_blood


title: PS_control_blood


title: 2_0300_UPD16mat_blood


title: 2_0225_UPD16pat_blood


title: R2_MHCII-AKI-1

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Trimmed reads were then aligned with TopHat version 2.0.12 (Bowtie2 version 2.2.3) to UCSC hg19 reference genome with parameters: -r 150, --library-type fr-firststrand, --keep-fasta-order, --transcriptome-index, --rg-id, --rg-sample, --rg-library, --rg-platform-unit, --rg-platform, -o
Cufflinks version 2.2.1 estimated transcript abundances with parameters: --library-type fr-firststrand, -o, -g, -L, -b, -u
Cuffmerge, Cuffquant, Cuffdiff, and Cuffquant were then run to get to final differential expression results
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx format for differential gene expression between MHCII-positive_AKI relative to Quiescent kidney resident macrophages.

source_name: kidney resident macrophages

extract_protocol:
Tissue resident macrophages and infiltrative mononuclear phagocytes were isolated via electronic cell sorting and total RNA was isolated using the miRNEasy Micro Kit (Qiagen, 217084) following the manufacturer protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and only samples with a RIN score > 8.0 were used for qPCR or RNAseq. RNA was sequenced on NextSeq500 system (San Diego, CA) and the library was prepared with the Agilent SureSelect Stranded mRNA kit.
RNA libraries was prepared with the Agilent SureSelect Stranded mRNA kit.

value: NEG

tag: macrophage origin

value: KRM

value: AKI


title: R2_MHCII-AKI-2


title: R2_MHCII_P7-3


title: R2_MHCII_P7-2


title: AC_UPD16mat_blood


title: R2_MHCII-AKI-3


title: R2_MHCII_P7-1


title: R2_MHCII_AKI-5

value: POS


title: R2_MHCII_AKI-4


title: R2_MHCII_AKI-6


title: 98_R2_Qui

value: QUI


title: 96_R2_Qui


title: 95_R2_Qui


title: genomic DNA from cord blood 109

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

description: cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Raw Illumina IDAT data were imported and preprocessed using the R package methylumi

source_name: cord blood 109

extract_protocol: DNA was extracted and purified from neonatal cord blood using an Autopure LS Automated DNA Purification System with Autopure reagents (Autogen, Inc., Holliston, MA).

tag: gender

value: male

tag: leptin

tag: birth weight

tag: fat mass

tag: percent fat


title: genomic DNA from cord blood 111

description: cord blood sample

source_name: cord blood 111

value: female


title: 73_R1c_MHCII

source_name: infiltrative mononuclear phagocytes

value: MONO


title: genomic DNA from cord blood 105

description: cord blood sample

source_name: cord blood 105


title: genomic DNA from cord blood 107

description: cord blood sample

source_name: cord blood 107


title: 70_R1c_MHCII


title: genomic DNA from cord blood 110

description: cord blood sample

source_name: cord blood 110


title: genomic DNA from cord blood 106

description: cord blood sample

source_name: cord blood 106


title: genomic DNA from cord blood 98

description: cord blood sample

source_name: cord blood 98


title: 69_R1c_MHCII


title: genomic DNA from cord blood 93

description: cord blood sample

source_name: cord blood 93


title: genomic DNA from cord blood 114

description: cord blood sample

source_name: cord blood 114


title: genomic DNA from cord blood 100

description: cord blood sample

source_name: cord blood 100


title: genomic DNA from cord blood 113

description: cord blood sample

source_name: cord blood 113


title: genomic DNA from cord blood 101

description: cord blood sample

source_name: cord blood 101


title: Input-Fast-DKO-H3K27ac-ChIP-seq

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

description: male whole-body Ppara knockout and heptocyte Bcl6 double knockout overnight fasted liver input for Samples 56-58

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using Bowtie
Filtering: Aligned reads were filtered in HOMER to limit to count only one read per position per length of the read
Peak calling: Peaks were called in HOMER using "getDifferentialPeaksReplicates.pl" which uses DESeq2 to call peaks that pass 2-fold enrichment over input and FDR < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Peak files (.txt)

source_name: liver

extract_protocol:
Crosslinked nuclei were sonicated and cleared. Protein-DNA complexes were isolated with antbody against BCL6, PPARa, PPARd, or H3K27ac and then IgG paramagnetic beads. After decrosslinking, DNA was isolated with MinElute columns (Qiagen).
Kapa Hyper Prep Kit

tag: tissue

value: liver

tag: genotype

value: Ppara-/-;Bcl6 fl/fl Albumin-cre


title: genomic DNA from cord blood 102

description: cord blood sample

source_name: cord blood 102


title: H3K27ac-Fast-DKO-Rep3-ChIP-seq

description: male whole-body Ppara knockout and heptocyte Bcl6 double knockout overnight fasted liver ChIP DNA w/H3K27ac


title: genomic DNA from cord blood 108

description: cord blood sample

source_name: cord blood 108


title: H3K27ac-Fast-DKO-Rep2-ChIP-seq


title: genomic DNA from cord blood 96

description: cord blood sample

source_name: cord blood 96


title: genomic DNA from cord blood 104

description: cord blood sample

source_name: cord blood 104


title: genomic DNA from cord blood 97

description: cord blood sample

source_name: cord blood 97


title: genomic DNA from cord blood 103

description: cord blood sample

source_name: cord blood 103


title: genomic DNA from cord blood 99

description: cord blood sample

source_name: cord blood 99


title: genomic DNA from cord blood 94

description: cord blood sample

source_name: cord blood 94


title: genomic DNA from cord blood 112

description: cord blood sample

source_name: cord blood 112


title: genomic DNA from cord blood 92

description: cord blood sample

source_name: cord blood 92


title: Input-Fast-PparaKO-H3K27ac-ChIP-seq

description: male whole-body Ppara knockout overnight fasted liver input for Samples 52-54

value: Ppara-/-


title: genomic DNA from cord blood 90

description: cord blood sample

source_name: cord blood 90


title: genomic DNA from cord blood 89

description: cord blood sample

source_name: cord blood 89


title: genomic DNA from cord blood 91

description: cord blood sample

source_name: cord blood 91


title: H3K27ac-Fast-DKO-Rep1-ChIP-seq


title: H3K27ac-Fast-PparaKO-Rep3-ChIP-seq

description: male whole-body Ppara knockout overnight fasted liver ChIP DNA w/H3K27ac


title: H3K27ac-Fast-PparaKO-Rep2-ChIP-seq


title: H3K27ac-Fast-PparaKO-Rep1-ChIP-seq


title: Input-Fast-WT-H3K27ac-ChIP-seq

description: male wild type overnight fasted liver input for Samles 48-50

value: Bcl6 fl/fl


title: genomic DNA from cord blood 95

description: cord blood sample

source_name: cord blood 95


title: H3K27ac-Fast-WT-Rep3-ChIP-seq

description: male wild type overnight fasted liver ChIP DNA w/H3K27ac


title: genomic DNA from cord blood 87

description: cord blood sample

source_name: cord blood 87


title: H3K27ac-Fast-WT-Rep1-ChIP-seq


title: H3K27ac-Fast-WT-Rep2-ChIP-seq


title: PPARd-Fast-C57-Rep3-ChIP-seq

description: male wild type overnight fasted liver ChIP DNA w/PPARd

value: WT


title: PPARd-Fast-C57-Rep2-ChIP-seq


title: PPARd-Fast-C57-Rep1-ChIP-seq


title: Input-Fed-C57-PPARd-ChIP-seq

description: male wild type ad lib fed liver input for Samples 40-42


title: PPARd-Fed-C57-Rep3-ChIP-seq

description: male wild type ad lib fed liver ChIP DNA w/PPARd


title: Input-Fast-C57-PPARd-ChIP-seq

description: male wild type overnight fasted liver input for Samles 44-46


title: PPARd-Fed-C57-Rep2-ChIP-seq


title: PPARd-Fed-C57-Rep1-ChIP-seq


title: genomic DNA from cord blood 83

description: cord blood sample

source_name: cord blood 83


title: genomic DNA from cord blood 82

description: cord blood sample

source_name: cord blood 82


title: Input-Fed-LKO-PPARa-ChIP-seq

description: male hepatocyte Bcl6 knockout ad lib fed liver input for Samples 36-38

source_name: liver

value: Bcl6 fl/fl; Albumin-cre


title: genomic DNA from cord blood 84

description: cord blood sample

source_name: cord blood 84


title: PPARa-Fed-LKO-Rep3-ChIP-seq

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/PPARa


title: PPARa-Fed-LKO-Rep2-ChIP-seq


title: genomic DNA from cord blood 88

description: cord blood sample

source_name: cord blood 88


title: genomic DNA from cord blood 81

description: cord blood sample

source_name: cord blood 81


title: PPARa-Fed-LKO-Rep1-ChIP-seq


title: PPARa-Fed-WT-Rep3-ChIP-seq

description: male wild type ad lib fed liver ChIP DNA w/PPARa


title: Input-Fed-WT-PPARa-ChIP-seq

description: male wild type ad lib fed liver input for Samples 32-34


title: PPARa-Fed-WT-Rep2-ChIP-seq


title: genomic DNA from cord blood 86

description: cord blood sample

source_name: cord blood 86


title: genomic DNA from cord blood 79

description: cord blood sample

source_name: cord blood 79


title: PPARa-Fed-WT-Rep1-ChIP-seq


title: Input-Fast-C57-PPARa-ChIP-seq

description: male wild type overnight fasted liver input for Samples 28-30


title: PPARa-Fast-C57-Rep3-ChIP-seq

description: male wild type overnight fasted liver ChIP DNA w/PPARa


title: genomic DNA from cord blood 74

description: cord blood sample

source_name: cord blood 74


title: PPARa-Fast-C57-Rep2-ChIP-seq


title: genomic DNA from cord blood 77

description: cord blood sample

source_name: cord blood 77


title: genomic DNA from cord blood 69

description: cord blood sample

source_name: cord blood 69


title: PPARa-Fast-C57-Rep1-ChIP-seq


title: genomic DNA from cord blood 73

description: cord blood sample

source_name: cord blood 73


title: genomic DNA from cord blood 76

description: cord blood sample

source_name: cord blood 76


title: Input-Fed-C57-PPARa-ChIP-seq

description: male wild type ad lib fed liver input for Samples 24-26


title: genomic DNA from cord blood 67

description: cord blood sample

source_name: cord blood 67


title: genomic DNA from cord blood 71

description: cord blood sample

source_name: cord blood 71


title: genomic DNA from cord blood 72

description: cord blood sample

source_name: cord blood 72


title: genomic DNA from cord blood 75

description: cord blood sample

source_name: cord blood 75


title: genomic DNA from cord blood 78

description: cord blood sample

source_name: cord blood 78


title: genomic DNA from cord blood 66

description: cord blood sample

source_name: cord blood 66


title: genomic DNA from cord blood 70

description: cord blood sample

source_name: cord blood 70


title: PPARa-Fed-C57-Rep3-ChIP-seq

source_name: liver


title: PPARa-Fed-C57-Rep1-ChIP-seq


title: PPARa-Fed-C57-Rep2-ChIP-seq


title: Input-PpardKO-BCL6-ChIP-seq

description: male hepatocyte Ppard knockout ad lib fed liver input for Samples 21-22

value: Ppard fl/fl; Albumin-cre


title: genomic DNA from cord blood 60

description: cord blood sample

source_name: cord blood 60


title: genomic DNA from cord blood 59

description: cord blood sample

source_name: cord blood 59


title: genomic DNA from cord blood 61

description: cord blood sample

source_name: cord blood 61


title: genomic DNA from cord blood 64

description: cord blood sample

source_name: cord blood 64


title: genomic DNA from cord blood 63

description: cord blood sample

source_name: cord blood 63


title: genomic DNA from cord blood 68

description: cord blood sample

source_name: cord blood 68


title: BCL6-PpardKO-Rep1-ChIP-seq

description: male hepatocyte Ppard knockout ad lib fed liver ChIP DNA w/BCL6


title: genomic DNA from cord blood 65

description: cord blood sample

source_name: cord blood 65


title: Input-Control-BCL6-ChIP-seq

description: male wild type ad lib fed liver input for Samles 18-19

value: Ppard fl/wt


title: BCL6-Control-Rep2-ChIP-seq

description: male wild type ad lib fed liver ChIP DNA w/BCL6


title: genomic DNA from cord blood 62

description: cord blood sample

source_name: cord blood 62


title: genomic DNA from cord blood 56

description: cord blood sample

source_name: cord blood 56


title: BCL6-Fed-PparaKO-Rep2-ChIP-seq

description: male whole-body Ppara knockout ad lib fed liver ChIP DNA w/BCL6


title: BCL6-PpardKO-Rep2-ChIP-seq


title: BCL6-Fed-PparaKO-Rep3-ChIP-seq


title: genomic DNA from cord blood 55

description: cord blood sample

source_name: cord blood 55


title: BCL6-Fed-PparaKO-Rep1-ChIP-seq


title: genomic DNA from cord blood 54

description: cord blood sample

source_name: cord blood 54


title: genomic DNA from cord blood 57

description: cord blood sample

source_name: cord blood 57


title: Input-Fast-C57-BCL6-ChIP-seq

description: male wild type overnight fasted liver input for Samples 10-12


title: Input-Fed-PparaKO-BCL6-ChIP-seq

description: male whole-body Ppara knockout ad lib fed liver input for Samples 14-16


title: genomic DNA from cord blood 80

description: cord blood sample

source_name: cord blood 80


title: genomic DNA from cord blood 58

description: cord blood sample

source_name: cord blood 58


title: BCL6-Fast-C57-Rep3-ChIP-seq

description: male wild type overnight fasted liver ChIP DNA w/BCL6


title: BCL6-Fast-C57-Rep2-ChIP-seq


title: BCL6-Fast-C57-Rep1-ChIP-seq


title: Input-Fed-C57-BCL6-ChIP-seq

description: male wild type ad lib fed liver input for Samples 6-8


title: BCL6-Fed-C57-Rep2-ChIP-seq


title: genomic DNA from cord blood 49

description: cord blood sample

source_name: cord blood 49


title: genomic DNA from cord blood 50

description: cord blood sample

source_name: cord blood 50


title: BCL6-Fed-C57-Rep1-ChIP-seq

source_name: liver


title: genomic DNA from cord blood 53

description: cord blood sample

source_name: cord blood 53


title: BCL6-Control-Rep1-ChIP-seq


title: genomic DNA from cord blood 51

description: cord blood sample

source_name: cord blood 51


title: BCL6-Fed-LKO-ChIP-seq

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/BCL6


title: Input-Fed-WT-BCL6-ChIP-seq

description: male wild type ad lib fed liver input for Samples1-4


title: BCL6-Fed-C57-Rep3-ChIP-seq


title: genomic DNA from cord blood 48

description: cord blood sample

source_name: cord blood 48


title: BCL6-Fed-WT-Rep3-ChIP-seq


title: genomic DNA from cord blood 85

description: cord blood sample

source_name: cord blood 85


title: genomic DNA from cord blood 39

description: cord blood sample

source_name: cord blood 39


title: genomic DNA from cord blood 47

description: cord blood sample

source_name: cord blood 47


title: genomic DNA from cord blood 46

description: cord blood sample

source_name: cord blood 46


title: BCL6-Fed-WT-Rep1-ChIP-seq


title: DKO-Fasted-Rep4-RNA-seq

description: male whole-body Ppara and hepatocyte Bcl6 double knockout overnight fasted liver total RNA

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Quantification of gene expression: gene expression at exons was quantified as integer counts using HOMER
Differenial expression analysis: differentially expressed exonic RNAs were identified using DESeq2 (FDR-adjusted p-value <0.05 and |LFC| > 1).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differential expression and individual replicate normalized rlog values

extract_protocol:
Total RNA was isolated from mouse liver tissue using RLT Buffer (Qiagen) and RNeasy columns (Qiagen).  RNA quality was assessed using a Bioanalyzer (Agilent).
Stranded RNA-seq Kit with RiboErase (HMR) (Kapa)

value: Ppara-/-;Bcl6 fl/fl; Alb-cre


title: DKO-Fasted-Rep3-RNA-seq


title: genomic DNA from cord blood 45

description: cord blood sample

source_name: cord blood 45


title: genomic DNA from cord blood 40

description: cord blood sample

source_name: cord blood 40


title: genomic DNA from cord blood 41

description: cord blood sample

source_name: cord blood 41


title: DKO-Fasted-Rep2-RNA-seq


title: DKO-Fasted-Rep1-RNA-seq


title: BCL6-Fed-WT-Rep2-ChIP-seq


title: genomic DNA from cord blood 35

description: cord blood sample

source_name: cord blood 35


title: genomic DNA from cord blood 44

description: cord blood sample

source_name: cord blood 44


title: PparaKO-Fasted-Rep4-RNA-seq

description: male whole-body Ppara knockout overnight fasted liver total RNA


title: genomic DNA from cord blood 37

description: cord blood sample

source_name: cord blood 37


title: PparaKO-Fasted-Rep2-RNA-seq


title: PparaKO-Fasted-Rep3-RNA-seq


title: genomic DNA from cord blood 43

description: cord blood sample

source_name: cord blood 43


title: genomic DNA from cord blood 52

description: cord blood sample

source_name: cord blood 52


title: PparaKO-Fasted-Rep1-RNA-seq


title: genomic DNA from cord blood 33

description: cord blood sample

source_name: cord blood 33


title: genomic DNA from cord blood 34

description: cord blood sample

source_name: cord blood 34


title: LKO-Fasted-Rep4-RNA-seq

description: male hepatocyte Bcl6 knockout overnight fasted liver total RNA

source_name: liver

value: Bcl6 fl/fl; Alb-Cre


title: LKO-Fasted-Rep3-RNA-seq


title: genomic DNA from cord blood 36

description: cord blood sample

source_name: cord blood 36


title: genomic DNA from cord blood 30

description: cord blood sample

source_name: cord blood 30


title: genomic DNA from cord blood 38

description: cord blood sample

source_name: cord blood 38


title: LKO-Fasted-Rep1-RNA-seq


title: genomic DNA from cord blood 32

description: cord blood sample

source_name: cord blood 32


title: LKO-Fasted-Rep2-RNA-seq


title: LKO-Fed-Rep3-RNA-seq

description: male hepatocyte Bcl6 knockout ad lib fed liver total RNA


title: genomic DNA from cord blood 29

description: cord blood sample

source_name: cord blood 29


title: genomic DNA from cord blood 28

description: cord blood sample

source_name: cord blood 28


title: LKO-Fed-Rep2-RNA-seq


title: genomic DNA from cord blood 24

description: cord blood sample

source_name: cord blood 24


title: genomic DNA from cord blood 23

description: cord blood sample

source_name: cord blood 23


title: LKO-Fed-Rep1-RNA-seq


title: genomic DNA from cord blood 26

description: cord blood sample

source_name: cord blood 26


title: genomic DNA from cord blood 27

description: cord blood sample

source_name: cord blood 27


title: genomic DNA from cord blood 31

description: cord blood sample

source_name: cord blood 31


title: LKO-Fed-Rep4-RNA-seq


title: genomic DNA from cord blood 25

description: cord blood sample

source_name: cord blood 25


title: WT-Fasted-Rep4-RNA-seq

description: male wild type overnight fasted liver total RNA


title: genomic DNA from cord blood 42

description: cord blood sample

source_name: cord blood 42


title: WT-Fasted-Rep3-RNA-seq


title: genomic DNA from cord blood 18

description: cord blood sample

source_name: cord blood 18


title: WT-Fasted-Rep2-RNA-seq


title: genomic DNA from cord blood 20

description: cord blood sample

source_name: cord blood 20


title: WT-Fasted-Rep1-RNA-seq


title: HT_MG-430_PM WT_Splenic_DC_rep3

source_name: CD11c+ splenic DCs

growth_protocol: Lymphocytes from spleenwere enriched using CD4 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions, and then stained and sorted for CD25+CD4+ Tregs. Mouse spleens were digested with Collagenase D (Worthington) and CD11c+ DCs were enriched using CD11c MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions. Enriched cells were stained and sorted for DCs (CD11c+MHC-II+TCRβ–CD19–CD49b–).

tag: cell type

value: dendritic cells (DC)

value: spleen


title: HT_MG-430_PM Lkb1_KO_Splenic_DC_rep2

value: LKB1 KO


title: HT_MG-430_PM Lkb1_KO_Splenic_DC_rep3


title: HT_MG-430_PM Lkb1_KO_Splenic_DC_rep1


title: genomic DNA from cord blood 19

description: cord blood sample

source_name: cord blood 19


title: genomic DNA from cord blood 21

description: cord blood sample

source_name: cord blood 21


title: HT_MG-430_PM WT_Splenic_DC_rep2


title: genomic DNA from cord blood 14

description: cord blood sample

source_name: cord blood 14


title: HT_MG-430_PM WT_Splenic_DC_rep1


title: lc/fas_2dpi_R3

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

department: Horticulture

institute: University of Georgia

data_processing:
Reads were filtered using fqtrim program with QC score< 20 as well as poly-A tail contaminations
Clean reads mapped to ITAG2.4 Released Tomato Genome through Rsubread 3.4
The significance of differentially expressed genes (DEGs) was determined by linear factorial modeling in DEseq2, of which likelihood ratio test was applied.
Genome_build: ITAG2.4 Released Tomato Genome
Supplementary_files_format_and_content: csv text files include read counts per gene for each sample

organism: Solanum pimpinellifolium

source_name: 2dpi floral buds

growth_protocol: Seeds were sown small pots and allowed to germinate under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Columbus, OH, USA, 2016. Approximately 300 first and second inflorescences with only 3-4 visible floral buds were collected from 5 to 7-week old plants that were sown over a six-week window.

extract_protocol:
During the collection, all inflorescences were immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  For the dissection, meristems and buds of different developmental stages were isolated by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. The samples were stored at -80 ℃ prior to the RNA extraction. RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
3'Tag RNA-seq libraries of approximately 300 bp fragments were prepared following the 3’-Tagseq protocol of Meyer et al., (2011)

value: 2dpi floral buds

value: lc and fas double mutants in LA1589 background

tag: cultivar


title: genomic DNA from cord blood 22

description: cord blood sample

source_name: cord blood 22

value: female


title: genomic DNA from cord blood 13

description: cord blood sample

source_name: cord blood 13

value: male


title: lc/fas_SYM_R3

source_name: sympodial shoot apical meristem (SYM)

value: sympodial shoot apical meristem (SYM)


title: WT-Fed-Rep3-RNA-seq

description: male wild type ad lib fed liver total RNA

source_name: liver

value: liver


title: WT-Fed-Rep2-RNA-seq


title: genomic DNA from cord blood 15

description: cord blood sample

source_name: cord blood 15


title: lc/fas_6dpi_R2

source_name: 6dpi floral buds

value: 6dpi floral buds


title: genomic DNA from cord blood 11

description: cord blood sample

source_name: cord blood 11


title: lc/fas_F&IM_R3

source_name: floral and inflorescence meristems (F&IM)


title: WT-Fed-Rep1-RNA-seq

value: Bcl6 fl/fl


title: lc/fas_4dip_R3

source_name: 4dpi floral buds

value: 4dpi floral buds


title: genomic DNA from cord blood 5

description: cord blood sample

source_name: cord blood 5


title: lc/fas_2dpi_R2


title: genomic DNA from cord blood 17

description: cord blood sample

source_name: cord blood 17


title: lc/fas_6dpi_R3


title: genomic DNA from cord blood 4

description: cord blood sample

source_name: cord blood 4


title: lc/fas_F&IM_R2

value: floral and inflorescence meristems (F&IM)


title: lc/fas_SYM_R2