title: Time Course IBD.DAY12.SCI133_01_S1

tag: tissue

value: DSS

value: Day 12


title: L6_rep1

status: Public on Sep 03 2021

type: SRA

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

description: LiverL6_rep1_EKDL190133819-1a-AK16538-AK14824_HM55FDSXX_L2

library_source: genomic

data_processing:
Adaptor sequences were trimmed from fastq file
All data were mapped to the hg19 reference genome using bowtie2 using the parameter --very-sensitive
PCR and optical duplicates were removed using Picard v.1.119
The bam file were filtered for alignment quality of >Q10, . Reads mapping to mitochondria were removed
peaks were called using MACS2 with q = 0.01
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Frozen liver tissues samples (n=11) were obtained from the human tissue lab,a biobank for multi-organ donors funded by the excellence of diabetes research in Sweden (EXODIAB), following the Uppsala Regional Ethics Committee approval.3 samples were harvested from donor diagnosed with T2D (HbA1c≥6.5%) and 8 from control donors characterized by normoglycemia (CTRL). Suspension of single nuclei was prepared for each sample using the gentleMACS dissociator (Miltenyi) program E. ~5 mg of frozen liver tissue was transferred into a gentleMACS C-tube with 10 ml of 0,250 M Sucrose solution. The homogenate was filtered using 100 µm MACS SmartStrainers and the volume adjusted to 15 ml with the Sucrose solution. The homogenate was then centrifuged at 600 x g at 4 C in an Eppendorf 5810R Centrifuge and the supernatant was discarded. The nuclei in the pellet were resuspended in 1 ml of PBS with 0,04% BSA and filtered using a 30 µm MACS SmartStrainers. The nuclei suspension was evaluated for purity and concentration using the Countess™ II Automated Cell Counter (Thermo Scientific) via staining with trypan blue.

extract_protocol:
All the libraries are ATAC procol, DNA was purified with MiniElution kit
The ATAC library construction was done with standard ATAC-seq protocol.

treatment_protocol: there is no treaemnt for the cells

tag: donor status

value: Liver


title: L8_rep1

description: LiverL8_rep1_EKDL190133819-1a-AK1554-AK17202_HM55FDSXX_L2

value: control donors characterized by normoglycemia


title: L5_rep1

description: LiverL5_rep1_EKDL190133819-1a-AK16537-AK14824_HM55FDSXX_L2


title: ATAC-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

country: Canada

institute: McGill University Health Centre

description:
Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

data_processing:
Fastq files were trimmed to remove  nextera adaptors  and < phred 10 using cutadapt v2.6 with TrimGalore v0.6.5
Reads were  aligned to both human (hg38) and Mtb (H37rv) genomes using BWA v0.7.17 default parameters. PICARD v2.18.9 was used to mark duplicates and to assess the fragment length distribution. Reads aligning to the mitochondrial genome were removed with samtools v1.9
alignmentSieve v3.3.2 was used to: (i) select unique paired-end reads using the --samFlagExclude 1804; (ii) remove ENCODE hg38 blacklisted regions; and (iii) to extract fragments between 40 – 2000bp in length
Peaks were called with MACS2 v2.2.6 callpeak was used with --call-summits in BAMPE mode. The summit of each peak was extended 250bp in both directions resulting in fixed-width peaks of exactly 501bp. Fiixed-width peaks overlapping in at least two samples were merged with bedtools v2.26
featureCounts v1.6.3 was used to count the number of unique fragments  overlapping the targeted regions.
Libray depth and was calculated via calcNormFactors in edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including the number of fragmentes overlaping assessed peaks for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with normalized peak quantification in log2 scale for every sample. Covariates not regressed out.

source_name: bronchoalveolar lavage

extract_protocol:
Cells were lysed with Trizol and kept at -80°C until extraction.  For ATAC-seq, 50,000 cell were  isolated and incubated with Tn5 transposase for DNA tagmentation.  The fragment length distribution was assessed with the Agilent 2100 Bioanalyzer.
ATACseq libraries were prepared for sequencing using standard paired end sequencing.

treatment_protocol: Bronchoalveolar lavage samples were filtered to remove macro contaminants and alveolar macrophages (AM) cells enrich via tube adhesion method. 1 x 106 AM cells were cultured with media (not challenged) or media + Mtb (challenged) for 20h.

tag: ethnicity

value: Caucasian

tag: Sex

value: M

tag: age

value: hypertension, type.2.diabetes

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

value: yes

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-6 [OHC like cells-6]

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

library_source: transcriptomic

data_processing:
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control.
eads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Cochlear supporting cells with ectopic Atoh1 and Ikzf2

extract_protocol:
Cochlear duct was carefully dissected out and digested by enzymes, wild type adult OHCs and SCs as well as SCs with ectopic Atoh1 and Ikzf2 that were genetically labelled by Tdtomato were manually picked, followed by cDNA generation and amplication via smartseq HT kit (Cat#: 634437, Takara ).
RNA libraries were prepared by tagmentation Kit (Cat#: TD503, Vazyme).

tag: strain

value: post natal day 60

tag: genotype

tag: tissue

value: Cochlea

tag: cell type

value: Cochlear supporting cells


title: Time Course IBD.DAY09.SCI132_18_S18

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

description:
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv

data_processing:
The barcoded sequence was corrected by an edit distance < 2.
The corrected reads were processed using Drop-seq_tools-1.12 (https://github.com/broadinstitute/Drop-seq).
The Drop-seq_tools’ DigitalExpression output was filtered using the numbers of reads, transcripts and genes as well as the percentage of mitochondrial genes for each cell.
The alignment was done with STAR (v2.5b).
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63472/suppl/GSE63472_mm10_reference_metadata.tar.gz
Supplementary_files_format_and_content: count_table.tsv contains digital gene expression for every sample.
Supplementary_files_format_and_content: metadata.tsv contains various annotation, e.g. sample names, time point, treatment, etc.

source_name: Colon

extract_protocol: RNA-seq library was constructed using modified Smart-seq2 method.

treatment_protocol: For time course study, mice were treated with 1.5%DSS for 6 days (Day0 to Day6) then switched to drinking water until Day15. For treatment study, 6 shots of murine recombinant Serpina3n or PBS was intravenously injected (20 μg/kg per day) from Day0 to Day5.

value: Colon

tag: treatment

tag: time point

value: Day 9


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-5 [OHC like cells-5]

tag: age


title: Time Course IBD.DAY09.SCI132_17_S17


title: ATAC-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: active ingredient


title: ATAC-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-4 [OHC like cells-4]

tag: strain

tag: genotype

tag: tissue

tag: cell type


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-3 [OHC like cells-3]

tag: age


title: Time Course IBD.DAY09.SCI132_16_S16

tag: treatment

tag: time point


title: L4_rep1

description: LiverL4_rep1_EKDL190133819-1a-AK1569-AK13180_HM55FDSXX_L2

tag: donor status


title: ATAC-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: sequencing run

tag: lane


title: ATAC-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam


title: Time Course IBD.DAY09.SCI132_15_S15

tag: tissue

tag: treatment

tag: time point


title: Time Course IBD.DAY09.SCI132_14_S14


title: L3_rep2

description: LiverL3_rep2_EKDL190133819-1a-AK11822-AK13180_HM55FDSXX_L2

tag: donor status


title: Time Course IBD.DAY09.SCI132_13_S13


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-2 [OHC like cells-2]

tag: strain

tag: age

tag: genotype

tag: cell type


title: Cochlear SCs (Ikzf2 and Atoh1)-P60-1 [OHC like cells-1]


title: L3_rep1

description: LiverL3_rep1_EKDL190133819-1a-AK1553-AK13180_HM55FDSXX_L2


title: ATAC-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: sequencing run

tag: lane


title: L2_rep1

description: LiverL2rep1_EKDL190133819-1a-AK11820-AK17204_HM55FDSXX_L2


title: Time Course IBD.DAY09.SCI132_11_S11


title: ATAC-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: F

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam


title: ATAC-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: age


title: L1_rep2

description: LiverL1_rep2_EKDL190133819-1a-AK1577-AK13180_HM55FDSXX_L2

tag: donor status

tag: tissue


title: Time Course IBD.DAY09.SCI132_12_S12

tag: treatment

tag: time point


title: L1_rep1

description: LiverL1_rep1_EKDL190133819-1a-N712-AK13180_HM55FDSXX_L2


title: ATAC-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count


title: WT-Cochlear SCs-P60-12 [P60_WT SC-12]

source_name: Wild type cochlear supporting cells

tag: strain

tag: genotype

value: wild type

tag: cell type

value: cochlear supporting cells


title: L4_rep2

description: LiverL4_rep2_EKDL190133819-1a-AK11823-AK13180_HM55FDSXX_L2


title: ATAC-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: sequencing run

tag: lane


title: WT-Cochlear SCs-P60-13 [P60_WT SC-13]

tag: age

tag: tissue


title: WT-Cochlear SCs-P60-15 [P60_WT SC-15]


title: ChIP-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library

data_processing:
Fastq files were trimmed to remove adaptors  and < phred 10 using cutadapt v2.6 with TrimGalore v0.6.5
Reads were  aligned to the human genome (hg38)  using BWA v0.7.17 default parameters. PICARD v2.18.9 was used to mark duplicates. Reads aligning to the mitochondrial genome were removed with samtools v1.9
alignmentSieve v3.3.2 was used to: (i) select unique single-end reads using the --samFlagExclude 1796; (ii) remove ENCODE hg38 blacklisted regions.
Peaks were called with MACS2 v2.2.6 callpeak was used with --call-summits with --shift -37 and --extsize 73 flags. The summit of each peak was extended 250bp in both directions resulting in fixed-width peaks of exactly 501bp. Fiixed-width peaks overlapping in at least two samples were merged with bedtools v2.26
featureCounts v1.6.3 was used to count the number of unique reads overlapping the targeted regions.
Libray depth and was calculated via calcNormFactors in edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including the number of reads overlaping assessed peaks for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with normalized peak quantification in log2 scale for every sample. Covariates not regressed out.

extract_protocol:
Cells were lysed with Trizol and kept at -80°C until extraction.  For ChIP-seq, AM were crosslinked with 1% w/v formaldehyde for 10 min and then sonicated to 150-500 bp using a S220 (Covaris).
ChIP-DNA was prepared using a manual chromatin immunoprecipitation method with an Antibody-Antigen for H3K27ac (Abcam, Ab4729, GR3211959-1). incubation of 18 hrs., followed by bead incubation for 135 minutes, and 6 x 5-minutes washing steps.
ATACseq libraries were prepared for sequencing using standard single end sequencing.

tag: ethnicity

tag: Sex

value: Atripla

value: Emtricitabine, Tenofovir_DF, Efavirenz

tag: mtb challenged

tag: fragments in clean bam


title: Time Course IBD.DAY06.SCI131_19_S19

description:
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv

tag: treatment

value: DSS

tag: time point

value: Day 6


title: L2_rep2

description: LiverL2rep2_EKDL190133819-1a-AK11822-AK17204_HM55FDSXX_L2

tag: donor status

value: control donors characterized by normoglycemia

value: Liver


title: ATAC-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: Caucasian

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: average tagmented library size


title: ATAC-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: no

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: ATAC-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: age

tag: sequencing run

tag: lane


title: WT-Cochlear SCs-P60-16 [P60_WT SC-16]

tag: strain

tag: genotype

tag: tissue

tag: cell type


title: WT-Cochlear SCs-P60-10 [P60_WT SC-10]


title: ChIP-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: Sex

value: M

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: mtb challenged

tag: fragments in clean bam


title: Time Course IBD.DAY06.SCI131_18_S18

tag: treatment

tag: time point


title: ChIP-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: cd4 count

tag: prescription drugs

value: Genvoya

tag: active ingredient

value: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir

tag: art start year

tag: recreational drugs

value: cannabis

tag: cigarette smoker

value: yes


title: WT-Cochlear SCs-P60-11 [P60_WT SC-11]

tag: strain

tag: age

value: post natal day 60

value: Cochlea


title: ChIP-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

tag: bal sampling date


title: ATAC-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

value: F

tag: average tagmented library size

tag: sequencing run

tag: lane


title: WT-Cochlear SCs-P60-9 [P60_WT SC-9]

tag: genotype

value: wild type

tag: tissue

tag: cell type

value: cochlear supporting cells


title: Time Course IBD.DAY06.SCI131_17_S17

value: Colon

tag: treatment

tag: time point


title: WT-Cochlear SCs-P60-8 [P60_WT SC-8]


title: Time Course IBD.DAY06.SCI131_20_S20

value: DSS


title: ATAC-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: active ingredient

tag: mtb challenged

tag: fragments in clean bam


title: WT-Cochlear SCs-P60-14 [P60_WT SC-14]

tag: strain

tag: age


title: Time Course IBD.DAY06.SCI131_16_S16

value: Day 6


title: Time Course IBD.DAY06.SCI131_15_S15


title: WT-Cochlear SCs-P60-7 [P60_WT SC-7]


title: Time Course IBD.DAY06.SCI131_13_S13


title: ChIP-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: ethnicity

tag: Sex

value: Truvada, Tivicay

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: ATAC-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: average tagmented library size

tag: sequencing run

tag: lane


title: ATAC-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: sexually transmitted infections

tag: quantiferon tb reagent


title: ChIP-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: cd4 count

tag: prescription drugs


title: ChIP-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

value: Viread, Tivicay, Edurant

tag: active ingredient

value: Tenofovir_DF, Dolutegravir, Rilpivirine

tag: mtb challenged


title: ChIP-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library

value: Caucasian

value: no

tag: fragments in clean bam


title: ATAC-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

value: M

tag: age


title: WT-Cochlear SCs-P60-5 [P60_WT SC-5]

tag: strain

tag: genotype

tag: tissue

tag: cell type


title: Time Course IBD.DAY03.SCI131_10_S10

tag: treatment

tag: time point

value: Day 3


title: WT-Cochlear SCs-P60-3 [P60_WT SC-3]


title: Time Course IBD.DAY06.SCI131_12_S12


title: ChIP-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: ethnicity

tag: Sex

value: Triumeq

value: Abacavir, Dolutegravir, Lamivudine

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: ATAC-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: cannabis

value: yes

tag: average tagmented library size

tag: sequencing run

tag: lane


title: ChIP-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: age

tag: active ingredient

tag: mtb challenged

tag: fragments in clean bam


title: ATAC-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity


title: WT-Cochlear SCs-P60-4 [P60_WT SC-4]

tag: strain

value: post natal day 60

tag: genotype

tag: tissue

value: Cochlea

tag: cell type


title: WT-Cochlear SCs-P60-6 [P60_WT SC-6]

value: wild type

value: cochlear supporting cells


title: ATAC-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: Sex

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: WT-Cochlear OHCs-P30-17 [P30_WT OHC-17]

source_name: Wild type cochlear outer hair cells

value: post natal day 30

value: cochlear outer hair cells


title: ChIP-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Genvoya

value: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir


title: ATAC-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: age

value: hypertension, diabetes, gout

tag: active ingredient

tag: average tagmented library size

tag: sequencing run

tag: lane


title: Time Course IBD.DAY03.SCI131_06_S6

value: Colon

tag: treatment

value: DSS

tag: time point


title: Time Course IBD.DAY06.SCI131_11_S11

tag: tissue

value: Day 6


title: Time Course IBD.DAY06.SCI131_14_S14


title: ATAC-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

value: Hispanic

tag: Sex

value: M

value: chlamydia PCR+ and gonorrhea PCR+

value: no

value: Truvada

value: Emtricitabine, Tenofovir_DF

tag: mtb challenged

tag: fragments in clean bam


title: WT-Cochlear SCs-P60-2 [P60_WT SC-2]

tag: strain

value: post natal day 60

tag: genotype

value: Cochlea

tag: cell type


title: ChIP-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

value: Caucasian

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

value: Triumeq

value: Abacavir, Dolutegravir, Lamivudine

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: WT-Cochlear OHCs-P30-15 [P30_WT OHC-15]

tag: age

value: post natal day 30

value: wild type

value: cochlear outer hair cells


title: Time Course IBD.DAY03.SCI131_08_S8

value: Colon

tag: treatment

tag: time point

value: Day 3


title: ATAC-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
Tn5 transposase

tag: ethnicity

tag: prescription drugs

tag: active ingredient

value: cannabis

value: yes

tag: average tagmented library size

tag: sequencing run

tag: lane


title: Time Course IBD.DAY03.SCI131_09_S9

tag: tissue

value: DSS


title: Time Course IBD.DAY03.SCI131_04_S4


title: ATAC-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: Sex

value: M

value: hypertension, diabetes, gout

tag: sexually transmitted infections

tag: mtb challenged

tag: fragments in clean bam


title: WT-Cochlear SCs-P60-1 [P60_WT SC-1]

tag: strain

tag: genotype

tag: cell type

value: cochlear supporting cells


title: Time Course IBD.DAY03.SCI131_07_S7

description:
processed data file: tc_ibd.count_table.tsv
processed data file: tc_ibd.metadata.tsv


title: ATAC-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

tag: age

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date


title: ChIP-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

tag: prescription drugs

value: Kivexa, Reyataz, Norvir

tag: active ingredient

value: Abacavir, Lamivudine, Atazanavir, Ritonavir


title: Time Course IBD.DAY03.SCI131_03_S3

tag: tissue

tag: treatment

tag: time point


title: ChIP-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library

value: Caucasian

tag: Sex

tag: sexually transmitted infections

value: Complera

tag: mtb challenged

tag: fragments in clean bam


title: WT-Cochlear OHCs-P30-12 [P30_WT OHC-12]

tag: strain

tag: age

tag: genotype

value: Cochlea

tag: cell type


title: ChIP-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: quantiferon tb reagent

tag: cd4 count

tag: art start year

tag: recreational drugs


title: sample pool yellow1

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

country: USA

institute: Ohio State University

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Yellow" is a pool of cells from individuals with known genotype.  "Yellow1" indicates it was the first of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.

data_processing:
BCL files converted to fastq using cellranger v2.0.1 mkfastq
10X pipestances made using cellranger v2.0.1 count
genetic demultiplexing using freemuxlet:  https://github.com/yelabucsf/popscle
custom analysis using Monocle3 and other tools:  https://github.com/blaserlab/ficlatuzumab_aml
Genome_build: hg19
Supplementary_files_format_and_content: *_barcodes.tsv contains 10X cell barcode data per sample pool.  *_genes.tsv contains gene short names and ensembl ids.  *_matrix.mtx contains cell gene matrices in Matrix Market sparse matrix format.

source_name: pbmc

extract_protocol:
cells were resuspended, pooled and loaded at 40,000-50,000 cells per well on 10X chromium 3' gene expression chips.
single cell gene expression libraries were constructed according to the 10X 3' gene expression user guide.

treatment_protocol: cells were thawed, washed, counted and immediately used for the experiment

value: pbmc


title: WT-Cochlear OHCs-P30-16 [P30_WT OHC-16]

value: post natal day 30

value: wild type


title: ChIP-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

tag: prescription drugs

tag: cigarette smoker

tag: bal sampling date


title: ChIP-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

value: F

value: Complera, Reyataz, Isentress

tag: active ingredient

value: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir


title: ChIP-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: Sex

value: Truvada, Isentress

value: cannabis

value: yes


title: ChIP-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: sexually transmitted infections


title: WT-Cochlear OHCs-P30-14 [P30_WT OHC-14]

tag: tissue

value: cochlear outer hair cells


title: Time Course IBD.DAY03.SCI131_05_S5

value: Colon

tag: treatment

value: DSS

tag: time point

value: Day 3


title: WT-Cochlear OHCs-P30-11 [P30_WT OHC-11]

tag: strain

tag: age


title: ATAC-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library
Tn5 transposase

value: M

value: no

tag: mtb challenged

tag: average tagmented library size

tag: fragments in clean bam

tag: sequencing run

tag: lane


title: sample pool red2

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Red" is a pool of cells from individuals with known genotype.  "Red2" indicates it was the second of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.

tag: cell type


title: WT-Cochlear OHCs-P30-10 [P30_WT OHC-10]

tag: genotype


title: sample pool red1

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Red" is a pool of cells from individuals with known genotype.  "Red1" indicates it was the first of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: sample pool yellow2

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Yellow" is a pool of cells from individuals with known genotype.  "Yellow2" indicates it was the second of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: ChIP-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

value: Caucasian

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

value: Biktarvy

tag: art start year

tag: recreational drugs

tag: cigarette smoker


title: ChIP-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: Sex

tag: sexually transmitted infections

tag: active ingredient

tag: bal sampling date


title: WT-Cochlear OHCs-P30-13 [P30_WT OHC-13]

tag: strain

tag: age

tag: tissue

value: Cochlea


title: Time Course IBD.CONTROL.SCI132_08_S8

tag: time point

value: Day 0


title: sample pool cyan2

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Cyan" is a pool of cells from individuals with known genotype.  "Cyan2" indicates it was the second of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.

tag: cell type

value: pbmc


title: Time Course IBD.DAY03.SCI131_01_S1

tag: treatment


title: ChIP-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

tag: mtb challenged

tag: fragments in clean bam


title: sample pool green1

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Green" is a pool of cells from individuals with known genotype.  "Green1" indicates it was the first of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: WT-Cochlear OHCs-P30-8 [P30_WT OHC-8]

value: post natal day 30

tag: genotype

value: wild type


title: Time Course IBD.CONTROL.SCI132_09_S9


title: WT-Cochlear OHCs-P30-9 [P30_WT OHC-9]


title: ChIP-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

value: F

tag: quantiferon tb reagent

tag: cd4 count

tag: prescription drugs

tag: art start year


title: sample pool green2

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Green" is a pool of cells from individuals with known genotype.  "Green2" indicates it was the second of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: Time Course IBD.CONTROL.SCI132_10_S10


title: ChIP-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: Sex

tag: sexually transmitted infections

tag: recreational drugs

tag: cigarette smoker


title: ChIP-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: age

tag: active ingredient

tag: bal sampling date


title: WT-Cochlear OHCs-P30-7 [P30_WT OHC-7]

tag: strain

tag: tissue

tag: cell type


title: Time Course IBD.CONTROL.SCI132_06_S6

tag: time point


title: WT-Cochlear OHCs-P30-6 [P30_WT OHC-6]


title: Time Course IBD.DAY03.SCI131_02_S2

tag: treatment


title: WT-Cochlear OHCs-P30-5 [P30_WT OHC-5]

tag: genotype


title: Time Course IBD.CONTROL.SCI132_07_S7


title: Time Course IBD.CONTROL.SCI132_05_S5


title: sample pool blue2

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Blue" is a pool of cells from individuals with known genotype.  "Blue2" indicates it was the second of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: Time Course IBD.CONTROL.SCI132_04_S4


title: WT-Cochlear OHCs-P30-4 [P30_WT OHC-4]


title: ChIP-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: ethnicity

tag: quantiferon tb reagent

tag: mtb challenged

tag: fragments in clean bam


title: Time Course IBD.CONTROL.SCI132_03_S3


title: sample pool cyan1

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Cyan" is a pool of cells from individuals with known genotype.  "Cyan1" indicates it was the first of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: sample pool blue1

description:
single cell RNA
total RNA
Explanation of multiplexing strategy: "Blue" is a pool of cells from individuals with known genotype.  "Blue1" indicates it was the first of two replicates from this pool run on the 10X Chromium chip.  Cells have been demultiplexed based on snv data using freemuxlet.  The key for demultiplexing the mixed single cells and attaching patient metadata from this project can be found in cell_metadata.tsv.


title: ChIP-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: Sex

tag: cd4 count

tag: prescription drugs

tag: art start year


title: WT-Cochlear OHCs-P30-3 [P30_WT OHC-3]

tag: age


title: ChIP-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: sexually transmitted infections

tag: active ingredient

tag: recreational drugs

tag: cigarette smoker


title: ChIP-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library

tag: bal sampling date


title: WT-Cochlear OHCs-P30-2 [P30_WT OHC-2]

tag: strain

tag: tissue

tag: cell type


title: Time Course IBD.CONTROL.SCI132_01_S1

tag: time point


title: WT-Cochlear OHCs-P30-1 [P30_WT OHC-1]

tag: genotype


title: SK-N-AS TREATED (30 µM) BG-P400-TAT Rep. Treated 2

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

label: biotin

source_name: Neuroblastoma Primary cell line

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human Neuroblastoma cells (obtained as a gift from Children’s Oncology Group, Texas Tech University Health Sciences Center, Lubbock, TX, USA) were cultured in IMDM medium containing 10% FBS at 37°C and 5% CO2/95% O2.

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

treatment_protocol: Cells were treated with BG-P400-TAT (30 µM) for 48 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

tag: agent

value: BG-P400-TAT (30 microM)

tag: cell line

value: SK-N-AS


title: Time Course IBD.CONTROL.SCI132_02_S2


title: ChIP-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

tag: ethnicity

tag: Sex

tag: quantiferon tb reagent

tag: mtb challenged

tag: fragments in clean bam


title: infected_4_l4

status: Public on Sep 02 2021

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

institute: SUSTech

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC136-indexH11_S24_L004

data_processing:
The raw reads obtained from the run were aligned against the Syrian golden hamster genome (MesAur1.0) in the Basespace platform by Illumina, with the tool “RNA-Seq Alignment”
differential gene-expression analyses were performed using the glmQLFTest method implemented in the edgeR package(v3.28.1)
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Processed data files are in "CSV(Comma-separated values)" format. Each row is a gene and each column is a sample. Values are normalzied counts

organism: Mesocricetus auratus

source_name: lung

extract_protocol:
RNA extraction was performed following instructions from the manufacturer of TRIzol reagent (Invitrogen). Briefly, 1/5 volume of chloroform was added to the lung supernatants in TRIzol, phases were separated by centrifugation and RNA was precipitated by overnight incubation with isopropanol at -20C. The RNA pellet was washed with ethanol 70% and resuspended in RNase-free water. RNA was quantified by nanodrop and resuspended to a final concentration of 100 ng/ul in water.
1 ug of RNA was used as starting material for library preparation. The kit employed was TruSeq RNA Library Prep Kit v2 (Illumina) over polyadenylated RNA and the manufacturer’s instructions were followed. The sequencing was performed on an Illumina NextSeq 500 instrument.

tag: sars-cov-2 infection state

value: infected

tag: condition

value: lung

tag: sequencing lane


title: infected_4_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC136-indexH11_S24_L001


title: infected_3_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC135-indexG11_S23_L004


title: infected_4_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC136-indexH11_S24_L002


title: SK-N-AS TREATED (30 µM) BG-P400-TAT Rep. Treated 1


title: infected_3_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC135-indexG11_S23_L001


title: infected_3_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC135-indexG11_S23_L002


title: infected_3_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC135-indexG11_S23_L003


title: infected_2_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC134-indexF11_S22_L003


title: infected_1_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC133-indexE11_S21_L004


title: infected_2_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC134-indexF11_S22_L004


title: infected_2_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC134-indexF11_S22_L001


title: infected_2_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC134-indexF11_S22_L002


title: uninfected_4_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC116-indexD9_S4_L003

value: uninfected


title: infected_1_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC133-indexE11_S21_L003


title: uninfected_4_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC116-indexD9_S4_L002


title: infected_1_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC133-indexE11_S21_L001


title: infected_4_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC136-indexH11_S24_L003


title: uninfected_3_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC115-indexC9_S3_L002


title: uninfected_3_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC115-indexC9_S3_L001


title: uninfected_3_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC115-indexC9_S3_L004


title: infected_1_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC133-indexE11_S21_L002


title: uninfected_4_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC116-indexD9_S4_L001


title: uninfected_4_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC116-indexD9_S4_L004


title: uninfected_1_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC113-indexA9_S1_L004


title: uninfected_2_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC114-indexB9_S2_L001


title: uninfected_2_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC114-indexB9_S2_L002


title: ABBV-744_8_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia99-indexC6_S3_L004


title: uninfected_1_l1

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC113-indexA9_S1_L001


title: uninfected_3_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC115-indexC9_S3_L003


title: SK-N-AS UNTREATED Rep. Untreated 2


title: uninfected_2_l4

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC114-indexB9_S2_L004


title: ABBV-744_8_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia99-indexC6_S3_L003


title: ABBV-744_7_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia98-indexB6_S2_L002


title: ABBV-744_7_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia98-indexB6_S2_L003


title: SK-N-AS UNTREATED Rep. Untreated 1


title: uninfected_2_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC114-indexB9_S2_L003


title: uninfected_1_l3

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC113-indexA9_S1_L003


title: ABBV-744_6_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia97-indexA6_S1_L004


title: uninfected_1_l2

description:
processed data file: Normalized_TPM_infected_vs_uninfected
LC113-indexA9_S1_L002


title: ABBV-744_8_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia99-indexC6_S3_L001


title: ABBV-744_8_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia99-indexC6_S3_L002


title: ABBV-744_7_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia98-indexB6_S2_L001


title: ABBV-744_6_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia97-indexA6_S1_L001


title: Vehicle_8_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia112-indexH7_S16_L001

value: Vehicle


title: Vehicle_8_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia112-indexH7_S16_L002


title: ABBV-744_6_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia97-indexA6_S1_L003


title: Vehicle_7_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia111-indexG7_S15_L004


title: Vehicle_6_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia110-indexF7_S14_L003


title: Vehicle_7_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia111-indexG7_S15_L003


title: ABBV-744_6_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia97-indexA6_S1_L002


title: ABBV-744_7_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia98-indexB6_S2_L004


title: Vehicle_8_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia112-indexH7_S16_L004


title: Vehicle_5_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia109-indexE7_S13_L003


title: Vehicle_7_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia111-indexG7_S15_L001


title: Vehicle_7_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia111-indexG7_S15_L002


title: Vehicle_5_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia109-indexE7_S13_L002


title: Vehicle_6_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia110-indexF7_S14_L004


title: Vehicle_4_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia108-indexD7_S12_L004


title: Vehicle_4_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia108-indexD7_S12_L001


title: Vehicle_8_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia112-indexH7_S16_L003


title: Vehicle_4_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia108-indexD7_S12_L003


title: Vehicle_2_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia106-indexB7_S10_L004


title: Vehicle_2_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia106-indexB7_S10_L003


title: Vehicle_6_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia110-indexF7_S14_L002


title: Vehicle_3_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia107-indexC7_S11_L002


title: Vehicle_5_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia109-indexE7_S13_L001


title: Vehicle_1_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia105-indexA7_S9_L004


title: Vehicle_1_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia105-indexA7_S9_L003


title: Vehicle_3_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia107-indexC7_S11_L004


title: Vehicle_1_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia105-indexA7_S9_L001


title: Vehicle_3_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia107-indexC7_S11_L003


title: ABBV-744_5_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia104-indexH6_S8_L004


title: Vehicle_3_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia107-indexC7_S11_L001


title: ABBV-744_4_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia103-indexG6_S7_L002


title: Vehicle_2_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia106-indexB7_S10_L002


title: ABBV-744_5_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia104-indexH6_S8_L003


title: ABBV-744_3_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia102-indexF6_S6_L004


title: ABBV-744_3_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia102-indexF6_S6_L001


title: ABBV-744_3_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia102-indexF6_S6_L003


title: Vehicle_6_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia110-indexF7_S14_L001


title: ABBV-744_3_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia102-indexF6_S6_L002


title: ABBV-744_2_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia101-indexE6_S5_L003


title: Vehicle_2_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia106-indexB7_S10_L001


title: ABBV-744_2_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia101-indexE6_S5_L004


title: Vehicle_1_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia105-indexA7_S9_L002


title: Vehicle_4_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia108-indexD7_S12_L002


title: Vehicle_5_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia109-indexE7_S13_L004


title: ABBV-744_5_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia104-indexH6_S8_L002


title: ABBV-744_4_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia103-indexG6_S7_L001


title: ABBV-744_5_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia104-indexH6_S8_L001


title: ABBV-744_1_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia100-indexD6_S4_L003


title: ABBV-744_4_l3

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia103-indexG6_S7_L003


title: ABBV-744_2_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia101-indexE6_S5_L002


title: ABBV-744_2_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia101-indexE6_S5_L001


title: ABBV-744_1_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia100-indexD6_S4_L004


title: ABBV-744_4_l4

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia103-indexG6_S7_L004


title: ABBV-744_1_l1

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia100-indexD6_S4_L001


title: ABBV-744_1_l2

description:
processed data file: Normalized_TPM_ABBV_vs_vehicle
Lucia100-indexD6_S4_L002


title: ChIPseq_Dome-SATB2OE_FLAG

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

data_processing:
Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and reads with quality greater than phred 33 were retained. Quality of sequencing reads were determined using fastQC91. High quality sequencing reads were aligned to the zebrafish danRer10 genome version using default parameters of BWA. Aligned reads were subsampled to 40 million reads in each sample using BBMap. RPKM normalized Input signal subtracted BigWig tracks for visualization were generated using the bamCompare tool from deepTools 3.3.2.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

organism: Danio rerio

source_name: Whole embryo

growth_protocol: embryos were grown at 28.5 degrees till the desired stage is reached. Stages were determined visually

extract_protocol:
overexpression of 3xFLAG tagged Satb2, 1000 embryos were harvested for each ChIP reaction at 4.5 hpf (Dome stage) in batches until sufficient amount of input material was generated. Empty pCS2-GFP was used as a control for injections. Pulldowns were performed with 20 µg chromatin and 5 µg anti-H3K4me3 (ab8580, abcam), 5 µg anti-H3K27Ac (ab4729, abcam), 5 µg anti-H3K27me3 (07-449, Millipore) and 5 µg of normal rabbit IgG overnight at 4oC. Antibody-protein complex was captured using 50 µl of pre-blocked Dynabeads A:G mixture for 3 hours at 4oC. Samples were processed further as described in the earlier section.
5 ng of purified ChIP DNA was used for library preparation using NEB ultra II DNA kit (NEB, USA) as described in the earlier section. Sequencing reads (100 bp PE) were obtained on the HiseqX platform at Macrogen Inc, Korea.

treatment_protocol: overexpression of 3XFLAG-SATB2 from 1 cell stage

tag: genotype/varaition

value: Wild-Type

value: AB/TU

tag: antibody

value: anti-FLAG-M2 cat number 3165 Sigma

tag: Stage

value: Dome (4.5 hpf)


title: ChIPseq_Dome-CNT_H3K27me3

tag: strain

value: anti-H3K27me3 cat number 07-449 Millipore


title: ChIPseq_Dome-SATB2OE_SATB2

value: anti-zebrafish Satb2(generated in this study)


title: ChIPseq_14som-SATB2-BR2

description:
processed data file:
14som-SATB2_merged_subtract.bw
14som_SATB2_regulatory_peaks.bed

data_processing:
Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and reads with quality greater than phred 33 were retained. Quality of sequencing reads were determined using fastQC77. High quality sequencing reads were aligned to the zebrafish danRer10 genome version using default parameters of BWA. Aligned reads were subsampled to 40 million reads in each sample using BBMap. Correlation between each replicate was estimated using multiBamSummary and replicates showing very high Pearson correlation (> 0.7) were used for further analysis. Peak calling was performed using MACS2 with default parameters and q value 0.05. Consensus sets of peaks from biological replicates were extracted using a custom R script from Roman Cheplyaka (https://ro-che.info/articles/2018-07-11-chip-seq-consensus). BigWig files were generated first using bamCoverage normalizing to RPKM and then subtracting Input signals using bamCompare utilities from deepTools 3.3.290 and used for visualization with Integrative Genomics Viewer (IGV). Satb2 peaks in regulatory genes were extracted by intersecting with Ensembl of ATAC seq peaks (GSE106428, GSE130944, GSE101779). Further, Satb2 peaks were classified as putative enhancer bound peaks by intersecting Satb2 peaks with a consolidated dataset of H3K4me1 (GSE32483, GSE74231). Promoter bound peaks were assigned as +/- 2 Kb from the TSS of the genes. Peak annotation to the nearest gene was performed using annotate.pl utility from Homer. Motif discovery for a given set of peaks was performed using findMotifsGenome.pl script from Homer and gene ontology was performed using webGestalt utilizing KEGG and Panther databases.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

extract_protocol:
Approximately, 2000 embryos per stage were harvested in 1x E3 medium (composition) and homogenized using glass homogenizer loose piston in the presence of 1 mM PMSF and immediately fixed with 1% methanol free formaldehyde (Thermo Fisher Scientific, USA) at RT for 12 min with constant shaking. Fixation was stopped by addition of glycine to a final concentration of 0.125 M and incubation at RT for additional 5 min. Fixed cells were centrifuged at 500 xg for 5 minutes and washed thrice with ice chilled 1x PBS by centrifugation at 4oC for 5 minutes each. Cells were further lysed in a 6 times bed volume in  the cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% (v/v) NP-40 for 10 minutes on ice and subjected to homogenization in Dounce homogenizer for 10 times with loose piston followed by 3 times with tight piston. Nuclei were collected by centrifugation at 2500 xg, washed with ice cold PBS and resuspended in 8 times the pellet volume in the nuclei lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% (w/v) SDS, 1x protease inhibitor cocktail (PIC: Roche,11873580001)) and incubated further for 30 minutes on ice. The samples were sonicated using the following Covaris S2 sonication conditions: 20% duty cycle, intensity= 5, cycle per burst= 200, time= 40 cycles of 30 seconds ON 30 seconds OFF to obtain an average size of 200-300 base pairs. The samples were centrifuged at 15000 xg for 10 minutes and the chromatin containing supernatant was stored at -80oC till further use. Prior to ChIP setup, supernatant was precleared using a mixture of 1:1 Dynabeads protein A:G beads for 2 hours at 4oC. For each ChIP replicate and mock reaction, 100 μg of chromatin was diluted 1:10 with ChIP dilution buffer (16.7 mM Tris-HCl pH 7.5, 167 mM NaCl, 1.2 mm EDTA, 0.01% (w/v) SDS, 1x PIC) and incubated with either 5 μg of anti-FLAG antibody or 20 μg of anti-Satb2 antibody. For mock ChIP reactions, an equal amount of Rabbit IgG (31235, Invitrogen) was used. Chromatin-antibody complex was incubated overnight at 4°C with constant rotation. Following day, the Chromatin-Antibody complex was captured using 100 μl pre-blocked (with IgG-free BSA and t-RNA) Dynabeads® Protein A:G mix for 4 hours at 4oC. Beads were washed with ice-cold buffers in the following order: 7 minutes 4 times with low salt buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), 10 minutes twice with high salt buffer (20 mM Tris HCl pH 8.0, 200 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), 10 minutes once with LiCl buffer (0.25 M LiCl, 1 mM EDTA, 10 mM Tris HCl pH 8.0, 1% NP-40, 1% sodium deoxycholate) and 10 minutes twice with TE buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA). The TE buffer was removed completely and 150 μL of the elution buffer (0.1M NaHCO3, 1% SDS) was added and vortexed gently to solubilize the beads, followed by incubation at 65oC for 30 minutes at 1000 rpm. The eluate was collected in a fresh tube and the process was repeated with addition of 150 μL of the elution buffer.  To 300 μL of the eluates and 10% input, 20 μL of 5 M NaCl and 2 μL of RNAseA (10mg/ml) was added and the samples were incubated at 65oC overnight with constant shaking at 700-800 rpm. Next, 20 μL of 1 M Tris pH 8.0, 10 μL of 0.5 M EDTA and 2 μL of Proteinase K (20 mg/ml) was added and the samples were further incubated at 42oC for 1 hr at 700-800 rpm. Samples were purified by standard phenol:chloroform extraction method and DNA was precipitated overnight with equal volume of 100% isopropanol in the presence of Glycoblue (Ambion) at -20oC. DNA pellets were eluted in nuclease free water and quantified using Qubit fluorometer (Thermo Fisher Scientific, USA) before proceeding further.
Equal amount of DNA (~5 ng) was used as input for library preparation using Nugen ultra2 ovation kit (Nugen). Number of cycles for amplification of adapter ligated libraries was estimated by the qPCR method as described in the datasheet provided by the manufacturer. Final libraries were purified using HiPrep PCR clean up system (MagBio Genomics, USA). Library concentration was determined using Qubit and average fragment size was estimated using dsDNA HS assay on Bioanalyzer 2100 (Agilent) before pooling libraries at equimolar ratio. Sequencing reads (100 bp PE) were obtained using the HiseqX platform at Macrogen Inc, Korea or Nextseq-550 at IISER Pune.

value: 14 somite (16hpf)


title: ChIPseq_Dome-SATB2OE_H3K27me3


title: ChIPseq_14som_Input


title: ChIPseq_6som_Input

description:
processed data file:
6som-SATB2_merged_subtract.bw
6som_SATB2_regulatory_peaks.bed

value: 6 somite (12hpf)


title: ChIPseq_80epi-SATB2-BR2

description:
processed data file:
80epi-SATB2_merged_subtract.bw
80epi_SATB2_regulatory_peaks.bed

value: zebrafish Satb2(generated in this study)

value: 80% epiboly (8hpf)


title: ChIPseq_Dome-SATB2OE_H3K4me3

value: anti-H3K4me3 cat number ab8580 abcam


title: ChIPseq_Dome-SATB2-BR2

description:
processed data file:
Dome-SATB2_merged_subtract.bw
Dome_SATB2_regulatory_peaks.bed


title: ChIPseq_14som-SATB2-BR1


title: ChIPseq_80epi_Input


title: ChIPseq_Dome-SATB2-BR3


title: ChIPseq_Dome_Input


title: control B4

city: Suzhou

first: Wan-liang

last: Guo

address: 92 Zhongnan Street

institute: Children's Hospital of Soochow University

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
For data analysis, the Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze the array images to get raw data. Genespring (version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 out of 2 conditions have flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, gene ontology (GO) analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs and lncRNAs. Finally, Hierarchical Clustering was performed to display the expression pattern of distinguishable genes among different samples.
normalized with the quantile algorithm

source_name: common bile duct

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA was transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was isolated using TRIZOL (Invitrogen, Carls-bad, CA, USA) according to the manufacturer’s protocol and quantified by the NanoDrop ND-2000 (Thermo Scientific). The RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The tissue of common bile duct of PBM cases were collected and stored at − 80 °C before RNA extraction.

tag: tissue

value: common bile duct

value: normal


title: ChIPseq_14som-SATB2-BR3


title: ChIPseq_Dome-CNT_H3K4me3


title: control B2


title: PBM A6

value: PBM


title: PBM A3


title: ChIPseq_80epi-SATB2-BR1


title: ChIPseq_6som-SATB2-BR2


title: ChIPseq_512_Input

description:
processed data file:
512-SATB2_merged_subtract.bw

value: 512 cell


title: ChIPseq_6som-SATB2-BR1


title: ChIPseq_Dome-SATB2-BR1


title: ChIPseq_512-SATB2-BR3


title: control B3


title: ChIPseq_512-SATB2-BR1


title: ChIPseq_512-SATB2-BR2


title: PBM A4


title: control B5


title: ChIPseq_Dome-CNT_H3K27Ac

value: anti-H3K27Ac Cat number ab4729 abcam


title: Exo-KO-152: Sidt1/Sidt2 double knock-out dendritic exosomes, mouse 152

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the moues genome by Rsubread version 1.16.1
Fragment (read pair) counts wre summarized by Entrez Gene ID using the Rsubread featureCounts function
Genes were identified using Rsubreads inbuilt RefSeq annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: Bone marrow

growth_protocol: To obtain bone-marrow-derived dendritic cells (BMDCs),  femurs from C57Bl/6 mice were flushed with Dulbecco’s modified Eagle’s medium (DMEM). The resulting bone marrow cells were resuspended, counted, plated at a density of 2 million cells per 10 cm petri dish, and then cultured for 7 days at 37 degrees C with 5% CO2 in DMEM supplemented with 10% fetal calf serum and 10% X-63 (GM-CSF-containing) supernatant to allow the cells to differentiate into DCs. After isolating the BMDCs, we also performed ultrafiltration and differential ultracentrifugation of culture supernatant from these mouse BMDCs to obtain exosomes.

extract_protocol:
Total RNA was extracted from cells using Tri-Reagent (Sigma-Aldrich) as per the manufacturers’ instructions. SEV RNA was extracted using Trizol LS (Invitrogen) then purified further using Qiagen RNA Mini kit. RNA yield was quantified using NanoDrop and RNA quality was assessed using either the TapeStation System 2200 or the Bioan-alyser (Agilent Technologies). To remove contaminating DNA, 1μg RNA was treated with 1μl (2 U) of DNAse I (Ambion) in a 20μl reaction incubated at 37 °C for 30 minutes and 1μl DNAse inactivation reagent added.
RNA libraries were prepared from 200ng of total RNA using a TruSeq RNA puri-fication kit, and RNA-seq was performed on an Illumina NextSeq platform, generating 80 base pair (bp) paired-end reads.

treatment_protocol: Not applicable

tag: mouse id

tag: cell type

value: Dendritic exosomes

value: Sidt1/Sidt2 double knock-out

tag: mouse gender

value: Male


title: control B1


title: PBM A1


title: Exo-KO-153: Sidt1/Sidt2 double knock-out dendritic exosomes, mouse 153

tag: genotype


title: Cells-KO-151: Sidt1/Sidt2 double knock-out dendritic cells, mouse 151

value: Dendritic cells


title: Cells-WT-42: Wild type dendritic cells, mouse 42

value: Wild type

value: Female


title: Exo-WT-46: Wild type dendritic exosomes, mouse 46


title: Cells-WT-46: Wild type dendritic cells, mouse 46


title: Cells-WT-33: Wild type dendritic cells, mouse 33


title: Exo-WT-33: Wild type dendritic exosomes, mouse 33


title: Exo-KO-151: Sidt1/Sidt2 double knock-out dendritic exosomes, mouse 151


title: Exo-WT-42: Wild type dendritic exosomes, mouse 42


title: Cells-KO-152: Sidt1/Sidt2 double knock-out dendritic cells, mouse 152


title: DPSCs_7d_rep1

city: shaanxi,xi'an

first: min

last: xiao

address: Fourth Military Medical University

institute: Fourth Military Medical University

description: Long noncoding RNAs expression after 7d without SDF-1α-irradiated human dental pulp stem cells

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed LncRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs between the two samples were identified through Fold Change filtering.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each RNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen) and purified with a Takara Kit (Takara, Dalian, China) according to the manufacturer protocol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

treatment_protocol: Dental pulp stem cells were isolated and cultured from healthy third molars,then incubated with or without 100ng/mL SDF-1α for 7days. The samples cultured at 37 ℃ in a 5% CO2 incubator.

value: dental pulp

value: dental pulp stem cells (DPSCs)

tag: age

tag: treatment

value: control


title: Cells-KO-153: Sidt1/Sidt2 double knock-out dendritic cells, mouse 153


title: WGBS_Iridophore, rep2

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter-trimmed with cutadapt.
RNA-seq reads were aligned to danRer10 genome using STAR.
WGBS reads were aligned to danRer10 using bismark with standard parameters.
omniATAC-seq reads were aligned to danRer10 using bwa-mem.
Genome_build: danRer10
Supplementary_files_format_and_content: bigWig, bedGraph, and text files.

source_name: Iridophore cells

extract_protocol:
Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP-positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab (Higdon et al. 2013). Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol-chloroform:isoamyl alcohol (PCI) extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC-seq protocol was followed to extract materials for ATAC-seq.
RNA-seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation-Direct kit (Zymo, D5020) and processed with TruSeq DNA Methylation Kit (Illumina, 15066014) to generate Illumina-compatible WGBS libraries. Published omniATAC-seq was followed to generate ATAC-seq data.

treatment_protocol: Tg(crestinA:EGFP) embryos at designated biological time points were dechorionated with Pronase, rinsed with egg water to remove the chorion, and collected into 1.5ml Eppendorf tubes on ice. 4-5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice.

tag: developmental stage

value: 4-5 dpf

value: Iridophore cells


title: WGBS_Iridophore, rep1


title: PBM A2


title: ChIPseq_Dome-SATB2OE_H3K27Ac

value: Wild-Type

value: AB/TU

value: Dome (4.5 hpf)


title: WGBS_24hpf_NCC, rep2

source_name: Neural crest cells

value: 24 hpf

value: Neural crest cells


title: WGBS_24hpf_NCC, rep1


title: WGBS_Melanophore, rep1

source_name: Melanophore cells

value: Melanophore cells


title: WGBS_15somite_NCC, rep1

value: 15 somite


title: WGBS_15somite_NCC, rep2


title: WGBS_Melanophore, rep2


title: DPSCs_7d_rep3


title: DPSCs_7d_100ng/mL SDF-1α_rep2

description: Long noncoding RNAs expression after 7d in 100ng/mL SDF-1α-irradiated human dental pulp stem cells

source_name: DPSCs，7days,100ng/mL SDF-1α


title: DPSCs_7d_100ng/mL SDF-1α_rep3


title: RNA-seq_24hpf_NCC, rep1

description: mRNA


title: RNA-seq_24hpf_NCC, rep2

description: mRNA


title: RNA-seq_Melanophore, rep1

description: mRNA


title: DPSCs_7d_100ng/mL SDF-1α_rep1


title: RNA-seq_Iridophore, rep2

description: mRNA


title: RNA-seq_15somite_NCC, rep1

description: mRNA


title: DPSCs_7d_rep2


title: omniATAC-seq_24hpf_NCC, rep1

description: DNA (open chromatin)


title: omniATAC-seq_Iridophore, rep1

description: DNA (open chromatin)


title: omniATAC-seq_Iridophore, rep2

description: DNA (open chromatin)


title: omniATAC-seq_Melanophore, rep2

description: DNA (open chromatin)


title: omniATAC-seq_Melanophore, rep1

description: DNA (open chromatin)


title: RNA-seq_Melanophore, rep2

description: mRNA


title: ORR_OvarianFollicleCell_MS_Replicate2

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Bam files were aligned to dm6 (Dos Santos et al., 2015) by BWA mem (v0.7.17) (Li, 2013) and duplicate reads are marked with Picard Tools command ‘MarkDuplicates’.
Coordinates of uniquely-mapping, non-duplicate, reads with a MAPQ >10 were extracted with samtools (Li et al., 2009) view (v1.11) (-F 1024 -F 256 -F 128 -q 10).
RT was generated from a modified version of TIGER (Koren et al., 2021). Alignability filtering was performed against dm6 using a read length of 100bp. The uniquely aligning sample reads were then partitioned into windows of 1000 uniquely alignable base pairs. GC correction was performed with standard segmentation (TIGER command ‘TIGER_segment_filt’, using the MATLAB function ‘segment’) parameters which temporarily removed eUR and PH regions for determining GC content bias. GC correction was then applied to all data (PH and eUR included). From the GC-corrected data in 1kbp windows, eUR regions were defined in WT fat body and salivary gland samples as regions of continuous low DNA copy number. In this, the raw DNA copy number data in 1kb windows were segmented (TIGER command ‘TIGER_segment_filt’, R2 = 0.04, standard deviation threshold = 1) to identify regions of at least one standard deviation below the mean.  From these regions, only those ≥ 50 kbp in length without gaps ≥10 kbp (≥10 continuous 1kbp windows above the segmentation standard deviation cutoff) were called as eUR regions. This method provided the most accurate prediction of eUR regions by visual inspection. These predicted eUR regions overlapped with the smaller panel of previously published UR regions (J. Nordman et al., 2011) in fat body and salivary glands. The predicted and previously published eUR regions were merged with bedtools (Quinlan & Hall, 2010) merge (v2.29.2) to finalize eUR zones in fat body and salivary gland. Standard TIGER data filtering removes outlier windows attributed to noise or copy number variations. To still filter outliers, eUR and PH regions must be removed and filtered separately from the rest of the chromosome (arm regions). The eUR (as defined in the previous paragraph) and PH regions were removed from the GC-corrected data. In the arm-only regions, outliers were removed with segmentation (standard deviation threshold = 2, R2 = 0.06). eUR regions then separately filtered for outliers in a similar manner (standard deviation threshold = 3, R2 = 0.06). All segmentation parameters were chosen to optimize outlier removal via visual interpretation. The segmentation filtered arm, PH, and eUR regions were merged to form the final rawRT data. This data was used for all the statistical analysis including variant calling between salivary gland and fat body samples. RT values were generated by smoothing the filtered data with a cubic smoothing spline (MatLab command ‘csaps’, smoothing parameter = 1x10-15). Only zones of >20 continuous 1kbp windows were included and smoothing was not performed over gaps of >5kpb. The smoothed profiles were then normalized to an individual chromosomal mean of zero and a standard deviation of one. In comparing TIGER profiles of salivary glands and fat body to G1/S profiles of wind disc and follicle cells, the variable copy number of eUR and PH regions distorts normalization. Therefore, a second normalization was performed based only on the arm regions of chromosomes. The arm regions were first normalized to a mean of zero and a standard deviation of one. The mean shift and standard deviation values based on the arm regions were then applied to the eUR and PH regions. All regions were then merged and smoothed for visualization using identical parameters.
Quantile normalization was performed for comparisons between TIGER and non-TIGER samples through the preprocess Core R package to equalize the dynamic range of RT values (Bolstad 2016).
The stats (v3.6.2) statistical package was used to identify 50-kb windows with significantly altered RT values, by one-way ANOVA test [aov, P value adjusted for multiple testing with BH post-HOC correction {P < (0.01/2400)}]. Adjacent windows were merged and >200kb regions were called as variant.
BEDTools intersect (v2.26.0) was used to determine overlap of windows with -f 0.5 parameters (Quinlan and Hall 2010).
Merging of adjacent RT windows was done by BEDTools merge (v2.27.1) with -d 11 parameters.
Genome_build: dm6
Supplementary_files_format_and_content: text

organism: Drosophila melanogaster

source_name: Adult ovarian follicle cell

extract_protocol:
Adult female flies were fattened for 2 days on wet yeast and ~200 pairs of ovaries were dissected out by hand dissection. Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

value: Ovarian follicle cell

value: Oregon-R

tag: Sex

value: Adult

tag: phase

value: S phase


title: ORR_SalivaryGland_Replicate1

description: All_samples_rawRT_values.txt - column orr_sg_rep1, All_samples_RT_values.txt - column orr_sg_rep1

source_name: female 3rd instar larval salivary gland

extract_protocol:
Salivary glands were dissected in EBR from ~20 3rd instar female larvae prior to wandering per genotype, wild type -OregonR, Rif1 - Rif11/Rif2, and SuUR - SuURES. Tissues were pelleted, resuspended in LB3, dounce homogenized and sonicated using a Bioruptor 300 (Diagenode) for 10 cycles of 30’’ on and 30’’ off at maximal power. Lysates were treated with RNase and Proteinase K and genomic DNA was isolated by phenol-chloroform extraction.
Illumina libraries were prepared using NEBNext DNA Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers protocol, for subsequent whole genome sequencing on Illumina Novaseq 6000 sequencing platform.

value: salivary gland


title: ORR_OvarianFollicleCell_MS_Replicate1

value: Female


title: RNA-seq_15somite_NCC, rep2

description: mRNA


title: SUUR_SalivaryGland_Replicate1

description: All_samples_rawRT_values.txt - column suur_sg_rep1, All_samples_RT_values.txt - column suur_sg_rep1

value: SuUR


title: omniATAC-seq_15somite_NCC, rep2

description: DNA (open chromatin)


title: Rif1null_SalivaryGland_Replicate2

description: All_samples_rawRT_values.txt - column rif1_sg_rep2, All_samples_RT_values.txt - column rif1_sg_rep2


title: SUUR_SalivaryGland_Replicate2

description: All_samples_rawRT_values.txt - column suur_sg_rep2, All_samples_RT_values.txt - column suur_sg_rep2


title: RNA-seq_Iridophore, rep1

description: mRNA


title: omniATAC-seq_15somite_NCC, rep1

description: DNA (open chromatin)


title: omniATAC-seq_24hpf_NCC, rep2

description: DNA (open chromatin)


title: ORR_SalivaryGland_Replicate2

description: All_samples_rawRT_values.txt - column orr_sg_rep2, All_samples_RT_values.txt - column orr_sg_rep2


title: ORR_FatBody_Replicate1

description: All_samples_rawRT_values.txt - column orr_fb_rep1, All_samples_RT_values.txt - column orr_fb_rep1

source_name: female 3rd instar larval fat body

extract_protocol:
Fat bodies were dissected in EBR from 25 OregonR female larvae per replicate 96 hours after egg laying (AEL). Tissues were pelleted, resuspended in LB3, dounce homogenized and sonicated using a Bioruptor 300 (Diagenode) for 10 cycles of 30’’ on and 30’’ off at maximal power. Lysates were treated with RNase and Proteinase K and genomic DNA was isolated by phenol-chloroform extraction.
Illumina libraries were prepared using NEBNext DNA Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers protocol, for subsequent whole genome sequencing on Illumina Novaseq 6000 sequencing platform.

value: fat body


title: Rif1null_SalivaryGland_Replicate1

description: All_samples_rawRT_values.txt - column rif1_sg_rep1, All_samples_RT_values.txt - column rif1_sg_rep1


title: ORR_FatBody_Replicate2

description: All_samples_rawRT_values.txt - column orr_fb_rep2, All_samples_RT_values.txt - column orr_fb_rep2


title: YUGEN8_replicate 1

city: Copenhagen

first: victor

last: oria

state: Zealand

address: Ole Maaløes Vej 5, 4th Floor

department: BRIC

country: Denmark

institute: University of Copenhagen

hyb_protocol: Affymetrix GeneChip® WT Plus Reagent Kit (ThermoFisher, Santa Clara, CA) was used for the preparation of samples and generation of ss-cDNA for hybridization250 ng of total RNA were used for input. All the reactions and hybridizations were carried out according to the manufacturer's protocol. Affymetrix GeneChip Human Gene 2.0 ST Array were washed using the GeneChip® Fludics Station 450

scan_protocol: GeneChip Scanner 3000

data_processing: The raw data was first processed with R package oligo (Carvalho BS, Irizarry RA (2010). “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics, 26 (19), 2363-7. ISSN 1367-4803, doi: 10.1093/bioinformatics/btq431) and then normalized with RMA (Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. doi:10.1093/nar/gng015).

source_name: Cultured cell line

label_protocol: Biotin

growth_protocol: Opti-MEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution

extract_protocol: Total RNA extraction using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol. Extracted RNA was treated with RNAse Free DNAse kit to remove traces of geomic DNA prior to analysis

value: Cell line


title: YUGEN8_replicate 3


title: Clone 2B_replicate 3


title: Clone 1A_replicate 2


title: Clone 2A_replicate 2


title: Clone 1A_replicate 3


title: CLL633_mRNA

city: Memphis

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

hyb_protocol: Products were hybridized to Affymetrix Human Gene 2.0 ST arrays according to the manufacturer's protocol

data_processing:
Gene expression levels were determined using the Applied Biosystems Transcriptome Analysis Console (v4.0.2.15) using rma normalization, HuGene2.0.na36 annotations, and default settings.
probe group file: HuGene-2_0-st.pgf
meta-probeset file: HuGene-2_0-st-v1.na36.transcript.csv

source_name: CD19+ B cells

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit

extract_protocol: RNA was purified using Qiagen RNAeasy Kits according to the manufacturer's protocol

value: Peripheral blood

tag: disease state

value: chronic lymphocytic leukemia


title: CLL612_mRNA


title: TS110514_MEM_mRNA

source_name: CD19+/CD27+/CD5- B cells

value: Tonsil

value: healthy


title: TS102214_MEM_mRNA


title: CLL674_mRNA


title: Clone 2A_replicate 1


title: Clone 1A_replicate 1


title: Clone 2B_replicate 1


title: TS081414_NAIVE_mRNA

source_name: CD19+/CD27-/CD5- B cells


title: CLL679_mRNA


title: TS081414_MEM_mRNA


title: CLL668_mRNA


title: Clone 2B_replicate 2


title: YUGEN8_replicate 2


title: Clone 2A_replicate 3


title: CLL634_mRNA


title: CLL600_mRNA


title: TS102214_NAIVE_mRNA


title: CLL597_mRNA


title: CLL589_mRNA


title: Tumor_CD11b+F4/80high [Mp-Picro_6]

first: Katsuyuki

last: Shiroguchi

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

institute: RIKEN

description: rep1-6: independent library preparations;

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of clusters for each gene was counted, which provides the number of molecules detected for each gene
The number of RNA molecules for each gene and index was listed
Genome_build: mm10
Supplementary_files_format_and_content: The copy number of detected RNA molecules for genes and indexes (tubes) are summarized

molecule: polyA RNA

source_name: Tumor macrophages in picrotoxin-treated WT mice

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: One hundred of CD45+CD11b+F4/80high cells were isolated from tumor using FACS cell sorter

tag: agent

value: picrotoxin


title: CLL583_mRNA


title: Tumor_CD11b+F4/80high [Mp-DMSO_6]

source_name: Tumor macrophages in DMSO-treated WT mice

value: DMSO


title: Tumor_CD11b+F4/80high [Mp-Picro_5]


title: Tumor_CD11b+F4/80high [Mp-Picro_2]


title: Tumor_CD11b+F4/80high [Mp-DMSO_3]


title: CC012314_mRNA

source_name: CD19+/CD10+/CD44low/CXCR4- B cells


title: Tumor_CD11b+F4/80high [Mp-DMSO_2]


title: CB012314_mRNA

source_name: CD19+/CD10+/CD44low/CXCR4+ B cells


title: CB020514_mRNA


title: CLL580_mRNA


title: CC021314_mRNA


title: Tumor_CD11b+F4/80high [Mp-Picro_4]


title: CB011514_mRNA


title: CB021314_mRNA


title: Tumor_CD11b+F4/80high [Mp-DMSO_5]


title: Tumor_CD11b+F4/80high [Mp-DMSO_4]


title: CC012214_mRNA


title: Tumor_CD11b+F4/80high [Mp-DMSO_1]


title: Tumor_CD11b+F4/80high [Mp-Picro_1]


title: CC020514_mRNA


title: Tumor_CD11b+F4/80high [Mp-Picro_3]


title: Mp-uMTgaba_6

description:
rep1-6: independent library preparations;
Tumor_CD11b+F4/80high

source_name: Tumor macrophages in muMt-/- mice implanted with GABA

treatment_protocol: One hundred of CD45+CD11b+F4/80high or CD45+TCRbeta+CD8+ cells were isolated from tumor using FACS cell sorter

tag: cell markers

value: Tumor macrophages

value: muMt-/-

value: implanted with GABA pellet


title: Mp-uMTgaba_4


title: CC011514_mRNA


title: Mp-uMTgaba_5


title: CB012214_mRNA


title: Mp-uMTgaba_3


title: Mp-uMT_4

source_name: Tumor macrophages in muMt-/- mice


title: Mp-uMTgaba_1


title: Mp-uMTgaba_2


title: Mp-uMT_6


title: ChIPseq_E13_5_dTelInput

description:
processed data file:
E13_5_SATB2_merged_subtract.bw

source_name: Dorsal Telencephalon

extract_protocol:
To obtain genome wide binding sites for SATB2 during early neurogenesis, SWR/J mice were incrossed and embryos were isolated at desired stage of development. For experiments with E9.5 head tissue and trunk (visceral organs were discarded) were dissected under stereo microscopes with fine forceps and collected in ice chilled 1x PBS containing 0.5% glucose. Tissues from 10-12 embryos were pooled together for each replicate and crosslinked using 1% methanol free formaldehyde for 8 minutes followed by quenching with 125 mM glycine for an additional 5 minutes at RT. For experiments at E13.5, dorsal telencephalon was isolated and processed as described above. Chromatin isolation and ChIP experiment was performed as described in experiments for zebrafish Satb2 with modifications as follows. 100 µg of precleared chromatin was used for each IP reaction and 10 µg of anti-Human SATB2 antibody was used for pulldown. Equal amount of anti-Rabbit IgG (Invitrogen) was used as a control for each ChIP experiment. Antibody-protein complex was captured using 100 µl of pre-blocked Dynabeads protein A:G mixture for 4 hours at 4oC. Samples were processed further as described in the earlier section.
Equal amount of DNA (~5 ng) was used as an input for library preparation and libraries were prepared using NEB ultra II DNA library prep kit (NEB, USA). Sequencing reads (76 bp PE) were obtained on the Nextseq 550 platform at IISER, Pune.  Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and were aligned to mouse mm10 genome using default parameters of BWA. Aligned reads were subsampled to 25 million reads for each sample using BBMap. QC, peak calling and BigWig generation was performed as described in the above sections.  Equal amount of DNA (~5 ng) was used as an input for library preparation and libraries were prepared using NEB ultra II DNA library prep kit (NEB, USA). Sequencing reads (76 bp PE) were obtained on the Nextseq 550 platform at IISER, Pune.  Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and were aligned to mouse mm10 genome using default parameters of BWA. Aligned reads were subsampled to 25 million reads for each sample using BBMap. QC, peak calling and BigWig generation was performed as described in the above sections.

tag: genotype/varaition

value: Wild-Type

value: SWR/J


title: Mp-uMT_3


title: ChIPseq_E9_5_TrunkInput

description:
processed data file:
E9_5_Trunk_SATB2_merged_subtract.bw

source_name: Trunk tissue

tag: antibody


title: ChIPseq_E9_5_TrunkSATB2_BR2

value: anti-Human Satb2(generated in this study)

tag: Stage


title: Mp-uMT_1


title: ChIPseq_E13_5_dTelSATB2_BR1

tag: strain


title: ChIPseq_E13_5_dTelSATB2_BR2


title: Mp-WT_3

source_name: Tumor macrophages in WT mice

value: WT


title: Mp-WT_5


title: Mp-uMT_2


title: ChIPseq_E9_5_TrunkSATB2_BR1


title: Mp-WT_6


title: ChIPseq_E9_5_HeadSATB2_BR2

description:
processed data file:
E9_5_Head_SATB2_merged_subtract.bw

source_name: Head tissue


title: Mp-WT_1


title: Mp-WT_2


title: CD8T-uMTgaba_6

description:
rep1-6: independent library preparations;
Tumor_CD8+

source_name: Tumor CD8+ T cells in muMt-/- mice implanted with GABA

value: Tumor CD8+ T cells


title: Mp-WT_4


title: ChIPseq_E9_5_HeadInput


title: CD8T-uMTgaba_5


title: WT_IgG

data_processing:
library strategy: CUT & RUN
Paired-end reads were mapped to the human genome GRCh38 using Bowtie2 (v2.3.4.1) with options: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1000.
Sparse Enrichment Analysis for CUT&RUN (SEACR, https://seacr.fredhutch.org/) was used for peak calling
Genome_build: GRCh38
Supplementary_files_format_and_content: Peaks calling data files are in bed format. Raw singal files are in bedgraph format

extract_protocol:
CUT&RUN was performed with 1 million Calu-3 cells. Cells were removed from the plate by treatment with Versene (Life Technologies 15040066) for 20 minutes and resuspended in fresh media. They were spun down and washed twice with DPBS before proceeding with the CUTANA CUT&RUN kit (Epicypher 14-0050)
The experiment was performed with the included IgG and H3K4Me control antibodies and the BRD2 antibody (abcam 197865) as well as E.coli spike-in DNA according to the kit protocol.

tag: cell line

tag: perturbation

value: control

value: IgG


title: CD8T-uMTgaba_4

tag: cell type


title: CD8T-uMTgaba_3


title: CD8T-uMTgaba_1


title: CD8T-uMTgaba_2


title: WT_H3K4ME


title: WT_BRD2_1


title: CD8T-uMT_6

source_name: Tumor CD8+ T cells in muMt-/- mice


title: CD8T-uMT_4


title: WT_H2AZ_3


title: WT_H2AZ_1


title: BRD2KD_IgG

value: BRD2 knockdown


title: WT_H2AZ_2


title: CD8T-WT_6

source_name: Tumor CD8+ T cells in WT mice


title: CD8T-uMT_2


title: CD8T-uMT_3


title: CD8T-uMT_1


title: BRD2KD_H2AZ_1


title: BRD2KD_H2AZ_2


title: BRD2KD_BRD2_3


title: CD8T-WT_4


title: CD8T-uMT_5


title: WT_BRD2_2


title: CD8T-WT_5


title: CD8T-WT_3


title: BRD2KD_H3K4ME


title: CD8T-WT_2


title: BRD2KD_BRD2_2


title: BRD2KD_H2AZ_3


title: BRD2KD_BRD2_1


title: Hep3B_sh1_2

city: Nanjing

first: Anliang

last: Xia

address: 321 Zhongshan Road

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: Hep3B cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hep3B cells

value: HCC-derived cells

value: treated with shlnc-CTHCC lentivirus for 72 hours


title: Hep3B_sh1_1


title: Hep3B_shNC3

value: treated with shNC lentivirus for 72 hours


title: Hep3B_shNC1