title: MLL TOPmentation seq for chALL patient sample 3

description: TOPmentation performed in MLL-AF4 patient blasts

value: Bethyl A300-086A


title: H3K79me2 TOPmentation seq for chALL patient sample 3

status: Public on Aug 15 2023

type: SRA

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling and annotation using Homer v4.7
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: MLL-AF4 childhood ALL patient 3 blasts

growth_protocol: Infant (<1 year old) and childhood ALL samples were obtained from Blood Cancer UK Childhood Leukemia Cell Bank, UK (REC: 16/SW/0219). All ALL samples were anonymized at source, assigned a unique study number and linked. Cryopreserved samples were thawed, and immediately processed.

extract_protocol:
Cells were washed with PBS and fixed in 2mM DSG for 30 minutes and 1% FA for 30 minutes. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

tag: disease state

value: acute lymphoblastic leukemia (ALL)

tag: treatment

tag: individual

value: 3-year old MLL-AF4 ALL patient

tag: tissue

value: Bone marrow aspirate

tag: chip antibody

value: Millipore 04-835


title: Stage E7.25 embryo 1 section 7 region L1

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

country: USA

institute: Boston Children’s Hospital

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7L1

library_source: transcriptomic

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

treatment_protocol: Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.

tag: developmental stage

tag: strain

value: embryo


title: Stable MGUS patient_35

type: RNA

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description:
S035
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

hyb_protocol: Double-stranded complementary DNA (cDNA) and biotinylated complementary RNA (cRNA) were hybridized to GeneChip microarrays (Affymetrix, Santa Clara, CA), which were washed and scanned according to procedures developed by the manufacturer.

scan_protocol: The arrays were scanned using Hewlett Packard confocal laser scanner and visualized using Affymetrix 3.3 software (Affymetrix).

data_processing: The data were processed using Microarray Suite version 5.0 (MAS 5.0) with Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was standardized to a value of 100 as a reference point.

label: Biotin

source_name: Bone marrow Stable MGUS patient

label_protocol: Double-stranded cDNA is synthesized from 6 ug total RNA. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. The protocol according to the manufacturer's instructions Expression Analysis Technical Manual, 2001, Affymetrix.

growth_protocol: Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions from bone marrow aspirates in a central laboratory. All samples analyzed by microarray contained more than 85% plasma cells as determined by 2-color flow cytometry (CD38+ and CD45–/dim) performed after selection.

extract_protocol:
Fresh plasma cells were used directly for RNA extraction.
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: cell type

value: Bone marrow plasma cells

value: Stable MGUS


title: sample146, Cluster 1

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.9) and multiqc (v1.6)
Alignment to the human genome using STAR (v2.7.9a)
Read count assessments using htseq-count (v0.11.3)
Assembly: GRCh38.104
Supplementary files format and content: count files, which are text files with counts per gene for each sample

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
2.5mL of whole blood was collected into PAXgene Blood RNA tubes (BD Biosciences; San Jose, CA, USA) and total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen; Germantown, MD, USA)
Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Ipswich, USA) and cDNA libraries were prepared using the NEBNext RNA First Strand Synthesis Module, NEBNext Ultra Directional RNA Second Strand Synthesis Module, and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB; Ipswich, USA)

value: Whole Blood

tag: location

value: Discharged

tag: endotype

value: Cluster 1

tag: batch

value: three

tag: additional metadata

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: Stage E7.25 embryo 1 section 7 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7EP


title: Stable MGUS patient_32

description:
S032
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_34

description:
S034
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_33

description:
S033
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: H3K4me3 TOPmentation seq for chALL patient sample 3

value: Active Motif 39159


title: sample148, Cluster 2

value: Cluster 2


title: sample145, Cluster 2


title: H3K4me1 TOPmentation seq for chALL patient sample 3

value: Diagenode pAb-194-050


title: H3K27me3 TOPmentation seq for chALL patient sample 3

value: Millipore 07-449


title: Stage E7.25 embryo 1 section 7 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7EA


title: sample144, Cluster 1

value: two


title: Stable MGUS patient_30

description:
S030
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_29

description:
S029
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 6 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6R


title: sample143, Cluster 2


title: Stage E7.25 embryo 1 section 7 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_7A


title: sample142, Cluster 1


title: Stable MGUS patient_31

description:
S031
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 6 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6P


title: H3K79me2 TOPmentation seq for chALL patient sample 2

source_name: MLL-AF4 childhood ALL patient 2 blasts

value: acute lymphoblastic leukemia (ALL)

value: 6-year old MLL-AF4 ALL patient


title: Stage E7.25 embryo 1 section 6 region M

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6M


title: H34me1 TOPmentation seq for chALL patient sample 2

value: Bone marrow aspirate


title: H34me3 TOPmentation seq for chALL patient sample 2


title: Stable MGUS patient_28

description:
S028
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample139, Cluster 3

value: Cluster 3


title: sample140, Cluster 2


title: Stable MGUS patient_27

description:
S027
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_25

description:
S025
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample141, Cluster 1


title: Stage E7.25 embryo 1 section 6 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6L

value: embryo


title: Stable MGUS patient_26

description:
S026
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells


title: Stage E7.25 embryo 1 section 6 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6EP


title: H3K27ac TOPmentation seq for chALL patient sample 3

value: 3-year old MLL-AF4 ALL patient

value: Diagenode C15410196


title: sample138, Cluster 3

value: Whole Blood

value: Discharged

value: one


title: H3K27ac TOPmentation seq for chALL patient sample 2


title: Stage E7.25 embryo 1 section 6 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6EA


title: Stage E7.25 embryo 1 section 6 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_6A


title: sample137, Cluster 3

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: MLL TOPmentation seq for chALL patient sample 1

description: TOPmentation performed in MLL-AF4 patient blasts

source_name: MLL-AF4 childhood ALL patient 1 blasts

value: 15-year old MLL-AF4 ALL patient

value: Bethyl A300-086A


title: MLL ChIP seq for iALL patient sample 2

description: ChIP-seq performed in MLL-AF4 patient blasts

source_name: MLL-AF4 infant ALL patient 2 blasts

value: 1-year old MLL-AF4 ALL patient


title: ChIP seq Input for iALL patient sample 2


title: Stable MGUS patient_24

description:
S024
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Stable MGUS


title: Stage E7.25 embryo 1 section 5 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5R


title: Stable MGUS patient_23

description:
S023
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample135, Cluster 1

value: Cluster 1


title: sample136, Cluster 1


title: Stable MGUS patient_20

description:
S020
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample134, Cluster 1


title: AF4 ChIP seq for chALL patient sample 3

value: acute lymphoblastic leukemia (ALL)

value: Abcam ab31812


title: sample133, Cluster 1


title: MLL ChIP seq for chALL patient sample 3

value: Bone marrow aspirate


title: Stage E7.25 embryo 1 section 5 region M

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5M


title: Stage E7.25 embryo 1 section 5 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5P


title: Stage E7.25 embryo 1 section 5 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5L


title: ChIP seq Input for chALL patient sample 3


title: Stable MGUS patient_22

description:
S022
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 5 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5EP


title: AF4 ChIP seq for chALL patient sample 1


title: sample132, Cluster 1


title: MLL ChIP seq for chALL patient sample 1


title: Stage E7.25 embryo 1 section 5 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5EA


title: sample130, Cluster 2

value: Cluster 2


title: ChIP seq Input for chALL patient sample 1


title: Stage E7.25 embryo 1 section 4 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4R

value: embryo


title: sample129, Cluster 1

value: two


title: Stage E7.25 embryo 1 section 5 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_5A


title: Stable MGUS patient_19

description:
S019
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells


title: ATAC-seq for iALL patient sample 2

description: Fragmented genomic DNA

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling using Homer
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)


title: Stable MGUS patient_21

description:
S021
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample128, Cluster 3

value: Hospital

value: Cluster 3


title: sample127, Cluster 1

value: Whole Blood


title: ATAC-seq for chALL patient sample 3

description: Fragmented genomic DNA

value: 3-year old MLL-AF4 ALL patient


title: Stage E7.25 embryo 1 section 4 region M

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4M


title: Stage E7.25 embryo 1 section 4 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4P


title: Stable MGUS patient_18

description:
S018
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ATAC-seq for chALL patient sample 2

description: Fragmented genomic DNA

value: 6-year old MLL-AF4 ALL patient


title: sample126, Cluster 2

value: one

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: polyA-RNA-seq for iALL patient sample 2

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: CPMs

extract_protocol:
RNA was extracted from 1 million cells using the RNeasy mini kit (Qiagen). Poly A purification was conducted using the NEB Poly(A) mRNA magnetic isolation module as per the manufacturer’s protocol.
cDNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).

value: 1-year old MLL-AF4 ALL patient


title: Stable MGUS patient_16

description:
S016
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Stable MGUS


title: Stable MGUS patient_17

description:
S017
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: sample125, Cluster 1

value: Cluster 1


title: Stage E7.25 embryo 1 section 4 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4L


title: Stage E7.25 embryo 1 section 4 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4EP


title: Stable MGUS patient_15

description:
S015
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: polyA-RNA-seq for chALL patient sample 3

value: acute lymphoblastic leukemia (ALL)


title: polyA-RNA-seq for chALL patient sample 2


title: polyA-RNA-seq for chALL patient sample 1

value: 15-year old MLL-AF4 ALL patient


title: Stable MGUS patient_14

description:
S014
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.25 embryo 1 section 3 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3R


title: Stage E7.25 embryo 1 section 4 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4A


title: Tc17-CD5-hi-Ly6c

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

data_processing:
Potentially existing sequencing adapters and raw quality bases in the low reads were trimmed by Skewer. The option -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT were used for the common adapter sequence of the Illumina TruSeqadapters and the option -q 0 -l 25 -k 3 -r 0.1 -d 0.1 was used for trimming low quality 5’ and 3’ ends of the raw reads. The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR software. Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-firststrandwas applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cufflinks with the strand-specific library option, --library-type=fr-firststrandand other default options was used. The gene annotation of the reference genome from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit.
Assembly: UCSC genome in GTF format
Supplementary files format and content: "Processed_Data_File,xlsx" is a spreadsheet (excel) containing expression values of each subsets.

source_name: lymph node

extract_protocol:
RNA was harvested using NucleoZOL (Macherey-Nagel). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted using TRIzol® RNA Isolation Reagents (Life technologies). The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina) according to the manufacturer's protocol. Quality and size of libraries were assessed using Agilent 2100 bioanalyzerDNA kit (Agilent). All libraries were quantified by qPCR using CFX96 Real Time System (Bio-Rad) and sequenced on the NextSeq500 sequencers (Illumina) with a paired-end 75bp plus single 8bp index read run.

treatment_protocol:
Lymph nodes were harvested from C57BL/6 mice, and labeled with antibodies for CD3, CD8a, CD44, CD5, and Ly6C.
Cells were sorted using a BD FACSAria III
FACS-sorted CD44loCD5loLy6C-, CD44loCD5hiLy6C-, and CD44loCD5hiLy6C+ CD8+ TN cells were cultured in anti-CD3ε (2.5 μg/ml) (clone 145-2C11) and anti-CD28 (1 μg/ml) (clone 37.51) coated Nunc MaxiSorpTM Flat-Bottom Plate with recombinant mIL-6 (20 ng/ml) (PeproTech), rmTGF-β (2.5 ng/ml) (PeproTech), anti-IFN-γ (10 μg/ml) (clone XMG1.2), and anti-IL-4 (10 μg/ml) (clone 11B11) for 3 days.

tag: genotype

value: WT

value: lymph node

value: lymphocyte

value: Tc17 differentiation

tag: cell subset

value: CD5hi Ly6C+ CD8+ CD62L+ CD44lo


title: Stable MGUS patient_12

description:
S012
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells


title: Tc17-CD5-hi

value: CD5hi Ly6C- CD8+ CD62L+ CD44lo


title: SHSY5Y_5dPB_rep2_input [ChIP-Seq]

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
Bowtie2 2.4.1 alignment to hg19 genome
Peaks called with MACS2 2.2.7.1 broadPeak mode with input sample reference
Differential Peaks were determined using DiffBind v3.4 on the consensus of broad peaks called in at least 3 of the 5 biological replicates
bigWig files were generated by deeptools with CPM normalisation and mean of the replicates generated with wiggletools
Assembly: hg19
Supplementary files format and content: broadPeak files generated from MACS2
Supplementary files format and content: bigwig files are normalised CPM per sample and the mean average of the 5 replicates
Supplementary files format and content: tables include differential H3K27ac marks from DiffBind for PB v Control for each cell line

growth_protocol: SK-N-BE(2)C, IMR-32 and SH-SY5Y were cultured in DMEM/F12 media with HEPES and l-glut supplemented with 10% FBS

extract_protocol:
cells were fixed for 10 minutes with 1% formaldehyde. 0.125 M Glycine (final) was subsequently used to quench the fixation. Chromatin was extracted from cells and subject to sonication for 30 cycles. 80 ug of chromatin was incorporated into each ChIP that used 2 ug of H3K27ac antibody (ab4729). DNA fragments retrieved from ChIP were purified using GenElute™ Mammalian Genomic DNA Miniprep Kit
Nextflex Rapid DNA kit

treatment_protocol: 1uM palbociclib

value: neuroblastoma cell line

tag: cell line

value: 5d PB

tag: antibody

value: input


title: SHSY5Y_5dPB_rep4_input [ChIP-Seq]


title: SHSY5Y_5dPB_rep1_input [ChIP-Seq]


title: Stage E7.25 embryo 1 section 3 region M

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3M

value: embryo


title: Stage E7.25 embryo 1 section 3 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3P


title: SHSY5Y_control_rep5_input [ChIP-Seq]

value: control


title: Tc17-CD5-lo

value: CD5lo Ly6C- CD8+ CD62L+ CD44lo


title: SHSY5Y_5dPB_rep3_input [ChIP-Seq]


title: SHSY5Y_5dPB_rep5_input [ChIP-Seq]


title: sample131, Cluster 1

value: Whole Blood

value: Discharged

value: one

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: Stage E7.25 embryo 1 section 4 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_4EA


title: Stable MGUS patient_13

description:
S013
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Stable MGUS


title: Stage E7.25 embryo 1 section 3 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3L


title: Stable MGUS patient_11

description:
S011
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_08

description:
S008
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_06

description:
S006
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_10

description:
S010
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: LLS3

city: xianyang

first: ting

last: Ge

address: No. 3 Taicheng Road, Yangling Demonstration Zone, Xianyang City, Shaanxi Province

country: China

institute: College of Animal Science and Technology, Northwest A&F University

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: ASM2241691v1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Ovis aries

source_name: ovary

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: ovary

tag: sample group

value: low-reproduction group (LLS) had 3 sheep which had a litter size of ＜2


title: JQPDPac_1_C5_4R

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
All samples were processed through the computational pipeline developed at the Dana-Farber Cancer Institute Center for Functional Cancer Epigenetics (CFCE) using primarily open-source programs.
Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build mm9 and uniquely mapped, non-redundant reads were retained. These reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with a q-value (FDR) threshold of 0.01.
Assembly: mm9
Supplementary files format and content: bw files were generated using MACS2 using the CHIPS pipeline

source_name: Allograft mammary tumor tissue

growth_protocol: BALBc mice were injected with 200,000 EMT-6 mammary tumors cells (ATTC, CRL-2755). Both inguinal mammary fat pads were injected in each mouse. Tumor development was monitored by palpation and once tumors were palpable, usually about 5-7 days after cancer cell inoculation, treatment was initiated.

extract_protocol:
ATAC-seq was performed following the previously describe Omni-ATAC protocol. Briefly, viably frozen cells were pelleted by centrifugation and cell counts and viability was checked using Countess cell counter and NucBlue stain. 200,000 cells were resuspended in 1 ml of ice cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 800 r.c.f. for 5 min in a pre-chilled (4 °C) fixed-angle centrifuge and the supernatant was carefully aspirated by pipetting. Cell pellets were resuspended in 50 ?l of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting gently and incubated on ice for 3 min. To stop lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added and tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 800 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 ?l of transposition mix (25 ?l 2× TD buffer, 2.5 ?l transposase Tn5 (Illumina 20034197), 16.5 ?l PBS, 0.5 ?l 1% digitonin, 0.5 ?l 10% Tween-20, and 5 ?l water) by pipetting gently. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer at 1,000 r.p.m. Reactions were cleaned up with Qiagen MinElute kit.
Library prep was done with qPCR optimization as described previously (PMID: 25559105). Amplified libraries were purified with Qiagen Qiaquick PCR purification columns as per the kit instructions and were quantified using Qubit.

treatment_protocol: JQ1 was administered as single agents or in combination at the following doses: JQ1 at 50mg/kg by daily gavage,, anti-PD-L1 antibody (clone 10F.9G2, BioXCell) and paclitaxel each at 10mg/kg by i.p. injection twice per week. Treatments were continued until endpoint of the experiment.

value: Allograft mammary tumor tissue

value: CD45 negative cells

value: Wild Type

value: JQ1+Paclitaxel+anti-PD-L1 antibody


title: Stable MGUS patient_05

description:
S005
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

value: Bone marrow plasma cells

tag: disease state


title: Stable MGUS patient_07

description:
S007
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHSY5Y_control_rep1_input [ChIP-Seq]

value: neuroblastoma cell line

tag: treatment


title: Stable MGUS patient_09

description:
S009
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHSY5Y_control_rep3_input [ChIP-Seq]

value: input


title: Stage E7.25 embryo 1 section 3 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3A

value: embryo


title: IMR32_5dPB_rep5_input [ChIP-Seq]

value: 5d PB


title: Stage E7.25 embryo 1 section 2 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2R


title: Stage E7.25 embryo 1 section 3 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3EA


title: LLS2


title: Stable MGUS patient_04

description:
S004
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_03

description:
S003
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: JQPDPac_1_C5_5L


title: JQPD_1_C2_4R

value: JQ1+anti-PD-L1 antibody


title: Stable MGUS patient_02

description:
S002
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: HLS3

value: High-reproduction group (HLS) had a litter size of ≥ 3


title: SHSY5Y_control_rep2_input [ChIP-Seq]

value: control


title: JQPD_1_C2_3L


title: Stage E7.25 embryo 1 section 2 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2P


title: Stable MGUS patient_01

description:
S001
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHSY5Y_control_rep4_input [ChIP-Seq]


title: JQPDPac_1_C4_1R


title: Stage E7.25 embryo 1 section 3 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_3EP


title: JQPac_1_C3_1R


title: HLS2


title: LLS1


title: Stage E7.25 embryo 1 section 2 region M

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2M


title: JQPac_1_C3_2R


title: IMR32_5dPB_rep2_input [ChIP-Seq]


title: IMR32_5dPB_rep3_input [ChIP-Seq]


title: Stage E7.25 embryo 1 section 2 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2L


title: Liver,180day,rep2,ATAC

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description: ATAC-seq

data_processing:
The adapters and low-quality reads were removed from the ATAC-seq raw data.
Then high-quality reads were aligned to the reference pig genome (Sscrofa 11.1) using Bowtie2.
Mitochondrial alignments, low-quality alignments (q < 10) and PCR duplicates were removed from the mapped reads using SAMtools(v 1.3.1).
The read counts were normalized to 1× depth (reads per genome coverage, RPGC) using the bamCoverage from the deepTools.
ATAC peaks were called using MACS2.
The consensus peaks were identified using the Irreproducible Discovery Rate (IDR) method  (v2.0.2) with default settings, representing a comprehensive set of accessible chromatin regions for the certain tissue or stage.
Assembly: Sscrofa 11.1
Supplementary files format and content: Bigwig file, which were generated from merged bam files of replicates, is the read counts were normalized to 1× depth (reads per genome coverage, RPGC) using the bamCoverage from the deepTools.
Supplementary files format and content: The peaks reproducible between the two biological replicates of the same tissue or stage, termed as consensus peaks, were identified using the Irreproducible Discovery Rate (IDR) method. Column1: Name of the chromosome for common peaks; Colume2:The starting position of the feature in the chromosome; Column3: The ending position of the feature in the chromosome; Column4: Name given to a region (preferably unique) for common peaks. Use '.' if no name is assigned; Column5: Contains the scaled IDR value, min(int(log2(-125IDR), 1000); Column6: Strand; Column7: Measurement of enrichment for the region for merged peaks; Column8: Merged peak p-value; Column9: Merged peak q-value; Column10: Merged peak summit; Column11: Local IDR value; Column12: Global IDR value; Column13: The starting position of the feature in the chromosome for common replicate 1 peaks; Column14: The ending position of the feature in the chromosome for common replicate 1 peaks; Column15: Signal measure from replicate 1;Column16: The summit of this peak in replicate 1; Column17: The starting position of the feature in the chromosome for common replicate 2 peaks; Column18: The ending position of the feature in the chromosome for common replicate 2 peaks; Column19: Signal measure from replicate 2; Column20: The summit of this peak in replicate 2.

organism: Sus scrofa

source_name: Liver

extract_protocol:
Frozen animal tissues were homogenized in a pre-chilled Dounce and centrifuged at in a pre-chilled centrifuge. Avoiding pelleted chunks of connective tissue, 400 ul homogenate of each sample was transferred to a 2 ml Eppendorf tube. Density gradient centrifugation was conducted via mixing the homogenate with 400 ul of 50% Iodixanol solution and then layering 600 ul of 29% Iodixanol solution and 600 ul of 35% Iodixanol solution under the mixture. The nuclei band was collected and 50,000 nuclei were transferred into a tube containing 1 ml of ATAC-RSB and 0.1% Tween-20. After centrifugation, the supernatant was abandoned and Omni-ATAC ATAC-seq reaction mix was added to the pellet. The mixture was resuspended and incubated at 37 °C for 30 min for transposition reaction. After a limited PCR cycle to amplify the fragmented DNA, libraries were purified with the AMPure beads. Library quality was assessed with Qubit.
According to the manufacturer’s instructions, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). The ATAC-seq libraries were sequenced in the 150 bp paired-end sequencing mode with a NovaSeq 6000 platform.

value: Liver

tag: age

value: Postnatal day 180

tag: Sex

value: Female

value: Domestic pig

tag: breed

value: Crossbred pig


title: Stage E7.25 embryo 1 section 2 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2A

tag: developmental stage

tag: tissue


title: Liver,180day,rep1,ATAC

description: ATAC-seq

tag: strain


title: Stage E7.25 embryo 1 section 2 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2EP


title: Stage E7.25 embryo 1 section 2 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_2EA


title: JQPac_1_C3_4L

value: Allograft mammary tumor tissue

tag: cell type


title: Liver,28day,rep2,ATAC

description: ATAC-seq

value: Postnatal day 28


title: Control_3_C9_4R

value: CD45 negative cells

value: Wild Type

value: Vehicle


title: Liver,28day,rep1,ATAC

description: ATAC-seq


title: JQ_1_C1_4L


title: Control_3_C9_4L


title: JQ_1_C1_4R


title: Stage E7.25 embryo 1 section 1 region AP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_1AP


title: Liver,0day,rep2,ATAC

description: ATAC-seq

value: The birth day


title: IMR32_control_rep4_input [ChIP-Seq]

value: neuroblastoma cell line

value: input


title: IMR32_control_rep2_input [ChIP-Seq]


title: HLS1

value: ovary


title: Stage E7.25 embryo 1 section 1 region EAP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_1EAP

value: embryo


title: IMR32_5dPB_rep4_input [ChIP-Seq]

value: 5d PB


title: JQPD_C2_3L_L

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018). Fastq files were aligned to the mouse reference mm9 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out.
Assembly: mm9
Supplementary files format and content: csv file of FPKM table

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The total RNA was measured by Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer's protocol.
The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer's protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500

treatment_protocol: JQ1 was administered as single agents or in combination at the following doses: JQ1 at 50mg/kg by daily gavage, anti-PD-L1 antibody (clone 10F.9G2, BioXCell) and paclitaxel each at 10mg/kg by i.p. injection twice per week. Treatments were continued until endpoint of the experiment.

value: CD45 positive cells

value: JQ1+anti-PD-L1 antibody


title: IMR32_5dPB_rep1_input [ChIP-Seq]


title: JQPD_C2_3R_L


title: Liver,0day,rep1,ATAC

description: ATAC-seq

value: Liver


title: Stage E7.25 embryo 1 section 12 region R

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12R


title: IMR32_control_rep5_input [ChIP-Seq]

value: control


title: IMR32_control_rep1_input [ChIP-Seq]


title: Spleen,0day,rep2,ATAC

description: ATAC-seq

source_name: Spleen

value: Spleen

value: Female

value: Domestic pig


title: Stage E7.25 embryo 1 section 12 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12P


title: JQ_C1_4R_L

value: Allograft mammary tumor tissue


title: Stage E7.25 embryo 1 section 12 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12MP


title: BE2C_7dPB_rep4_input [ChIP-Seq]

value: 7d PB


title: Stage E7.25 embryo 1 section 12 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12MA


title: IMR32_control_rep3_input [ChIP-Seq]


title: JQPac_C3_1R_L

value: Wild Type


title: BE2C_7dPB_rep3_input [ChIP-Seq]


title: BE2C_7dPB_rep2_input [ChIP-Seq]


title: BE2C_7dPB_rep1_input [ChIP-Seq]


title: Lung,0day,rep2,ATAC

description: ATAC-seq

source_name: Lung

value: Lung

value: Crossbred pig


title: Muscle,0day,rep1,ATAC

description: ATAC-seq

source_name: Skeletal Muscle

value: Skeletal Muscle

value: The birth day


title: JQPDPac_C5_4R_L

value: JQ1+Paclitaxel+anti-PD-L1 antibody


title: JQPac_C3_4L_L


title: Ctrl_C9_4L_L

value: Vehicle


title: Stage E7.25 embryo 1 section 11 region R2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11R2

value: embryo


title: Stage E7.25 embryo 1 section 12 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12EP


title: JQ_C1_4L_L

value: CD45 positive cells


title: Lung,0day,rep1,ATAC

description: ATAC-seq


title: BE2C_7dPB_rep5_input [ChIP-Seq]

value: neuroblastoma cell line

value: input


title: Stage E7.25 embryo 1 section 12 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12A


title: JQPDPac_C5_5L_L


title: Ctrl_C9_4R_L


title: Spleen,0day,rep1,ATAC

description: ATAC-seq


title: BE2C_control_rep3_input [ChIP-Seq]

value: control


title: Heart,0day,rep2,ATAC

description: ATAC-seq

source_name: Heart

value: Heart


title: Kidney,0day,rep1,ATAC

description: ATAC-seq

source_name: Kidney

value: Kidney

value: Female


title: BE2C_control_rep5_input [ChIP-Seq]


title: Kidney,0day,rep2,ATAC

description: ATAC-seq

value: Domestic pig


title: Heart,0day,rep1,ATAC

description: ATAC-seq


title: Stage E7.25 embryo 1 section 11 region R1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11R1


title: BE2C_control_rep4_input [ChIP-Seq]


title: BE2C_control_rep1_input [ChIP-Seq]


title: Muscle,0day,rep2,ATAC

description: ATAC-seq


title: Stage E7.25 embryo 1 section 11 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11MA


title: Stage E7.25 embryo 1 section 12 region L

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_12L


title: Stage E7.25 embryo 1 section 11 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11P


title: BE2C_control_rep2_input [ChIP-Seq]


title: Stage E7.25 embryo 1 section 11 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11MP


title: JQPD_3_C2_3R_T

value: Allograft mammary tumor tissue

value: CD45 negative cells

value: JQ1+anti-PD-L1 antibody


title: JQ_C1_4L_T

value: Wild Type


title: SHSY5Y_5dPB_rep4 [ChIP-Seq]

description:
SHSY5Y_5dPB_H3K27ac_ChIP_mean_CPM.bw
SHSY5Y_H3K27ac_5dPBvControl_DiffBind.txt

value: 5d PB


title: SHSY5Y_5dPB_rep5 [ChIP-Seq]


title: JQPD_4_C2_3L_T


title: JQ_C1_4R_T


title: ZM_2

city: tianjin

first: Teng

last: Zhang

address: nanjing road

institute: Tianjin Medical University General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchword
Assembly: mm10
Supplementary files format and content: tab-delimited text file included raw counts for each Sample
Supplementary files format and content: tab-delimited text file included RPKM counts for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer`s protocols.

value: spleen

value: WT

value: Cecum Ligation And Puncture


title: ZM_3


title: Stage E7.25 embryo 1 section 11 region L1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11L1

value: embryo


title: Stage E7.25 embryo 1 section 11 region L2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11L2


title: ZM_1


title: Stage E7.25 embryo 1 section 11 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11EP


title: JQPac_C3_1R_T


title: SHSY5Y_5dPB_rep3 [ChIP-Seq]


title: SHSY5Y_5dPB_rep2 [ChIP-Seq]


title: JQPac_C3_4L_T


title: CLP_1

value: saline


title: SHSY5Y_5dPB_rep1 [ChIP-Seq]

value: neuroblastoma cell line


title: Stage E7.25 embryo 1 section 11 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11A


title: JQPac_C3_2R_T


title: CLP_2


title: Stage E7.25 embryo 1 section 11 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_11EA


title: Stage E7.25 embryo 1 section 10 region R2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10R2


title: JQPDPac_C5_4R_T

value: JQ1+Paclitaxel+anti-PD-L1 antibody


title: 37C, biol rep 10

city: Lincoln

first: Hasan

last: Otu

state: NE

address: 430F NH

department: Electrical and Computer Engineering

institute: University of Nebraska-Lincoln

data_processing:
Raw data was initially processed using FastQC (v0.11.9) and Trimmomatic (v0.40) to identify and remove overrepresented artificial sequences such as adapters.
Cleaned reads were further analyzed with Trimmomatic to remove low quality bases. We used the “maxinfo” filtering in palindrome mode with the default parameters. Reads were subject to a quality threshold of 25 and if the retained length was less than 40 bp they were removed from further analysis.
The quality of sequencing data at the sample level before and after trimming and filtering was assessed using our in-house-developed method FQStat. All samples yielded high quality sequences and were carried on for downstream analysis.
Transcript quantification was done using Salmon (v1.6.0) (based on EnsemblBacteria assemblies for the two species. Transcripts per million (TPM) was used as the normalized abundance value for the transcripts.
Assembly: gca_002276955 and gca_900103655
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample

organism:
Lentilactobacillus kefiri
Lactobacillus kefiranofaciens

source_name: Bacteria

growth_protocol: Both L. kefiri and L. kefiranofaciens were separately activated on MRS (Difco, BD Diagnostic, MD, USA) agar plates and incubated anaerobically for 3 days at 30°C. A single colony from each microorganism was picked and transferred into 15 mL Lactobacillus MRS broth and incubated anaerobically at 30°C for 3 days. The two strains of bacteria were subcultured twice until they reached the exponential growth phase.

extract_protocol:
RNA was isolated using Omega Biotek E.Z.N.A.® Total RNA Kit II (Omega Biotek, Inc., Norcross, GA) according to the manufacturer’s protocol. Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Ribosomal RNA depletion was performed with Ribo-Zero Plus rRNA Removal Kit (Illumina Inc., California, USA).
Samples were randomly primed and fragmented based on manufacturer’s recommendation. The first strand was synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42°C. All remaining steps for library construction were performed according to the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final quantity of the libraries was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® [NovaSeq S4] (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads per sample (10M in each direction).

treatment_protocol: All samples were initially inoculated with a mixed culture of L. kefiri and L. kefiranofaciens inoculum blended from 3-day cultures. 20 mL MRS medium was inoculated with 0.5 mL of the combined inoculum and incubated for 3 days, one set of 10 at 30°C, and another set of 10 at 37°C. For controls, L. kefiri and L. kefiranofaciens were inoculated in triplicate for each temperature. The tubes were removed from the incubator after 3 days, and 0.1 mL of each sample was placed in a 96 well plate for OD (600 nm) analysis. Samples were then centrifuged (3000×g, 4°C, 10 min), and the supernatant was removed and frozen for further analysis. The pellet was washed in fresh MRS (pH 5.5), divided in three aliquots, re-pelleted in microcentrifuge tubes, and frozen at -80°C for subsequent transcriptomic, proteomic, and metabolomic analysis.

value: Bacteria

value: JCM5818 and JCM7004


title: SHSY5Y_control_rep4 [ChIP-Seq]

description:
SHSY5Y_control_H3K27ac_ChIP_mean_CPM.bw
SHSY5Y_H3K27ac_5dPBvControl_DiffBind.txt

value: control


title: SHSY5Y_control_rep5 [ChIP-Seq]


title: Stage E7.25 embryo 1 section 10 region R1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10R1

source_name: Mouse embryonic cells


title: SHSY5Y_control_rep3 [ChIP-Seq]


title: CLP_3


title: 37C, biol rep 9

value: JCM5818 and JCM7003


title: JQPDPac_C5_5L_T


title: Stage E7.25 embryo 1 section 10 region P

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10P


title: Stage E7.25 embryo 1 section 10 region MP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10MP


title: Ctrl_C9_4L_T

value: Vehicle


title: SHSY5Y_control_rep2 [ChIP-Seq]


title: SHSY5Y_control_rep1 [ChIP-Seq]


title: Stage E7.25 embryo 1 section 10 region MA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10MA


title: C57Bl/6 Murine Synovial Extravascular CD64-Ly6c- Tissue-Resident Monocyte-Lineage Cells, Replicate 3, Bulk RNA

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description: TR-MC 3

data_processing:
Libraries were demultiplexed using using bcl2fastq v2.17.1.14
Sequenced reads were trimmed using Trimmomatic (version 0.36; Bolger et al., 2014) to remove adapter sequences, low quality bases, and short reads (minimum length = 20bp).
Trimmed reads were aligned to the mouse genome reference mm10 (Mus Musculus/UCSC assembly GRCm38) using Tophat2 (tophat 2.1.0; Trapnell et al 2009; Kim et al 2013).
Aligned reads were mapped to exons using the tool HTSeq-count (Anders et al., 2015)  with the reference transcriptome (Mus Musculus GRCm38.87).
The merged table of gene expression counts across samples was normalized to counts per million (CPM)
Assembly: mm10
Supplementary files format and content: tab-delimited table of CPM values across all samples

source_name: Ankle Joint Synovium

extract_protocol:
RNA was extracted from sorted cells using the PicoPure RNA Isolation kit as per manufacturer's instructions
RNA-seq libraries were prepared using the full-length SMART-seq v4 Ultra Low Input sequencing kit

treatment_protocol: Intra- vs. extra-vascular cells were delineated by intravenous administration of anti-CD45 BUV661 antibody at  796 6μg/mouse in 200μl sterile PBS 5 minutes prior to euthanasia.

value: Ankle Joint Synovium

value: Tissue-Resident Monocyte-Lineage Cells

value: IV anti-CD45 BUV661


title: Stage E7.25 embryo 1 section 10 region L2

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10L2


title: JQPDPac_C4_1R_T

value: Allograft mammary tumor tissue

value: CD45 negative cells

value: Wild Type


title: C57Bl/6 Murine Synovial Extravascular CD64-Ly6c- Tissue-Resident Monocyte-Lineage Cells, Replicate 2, Bulk RNA

description: TR-MC 2


title: Stage E7.25 embryo 1 section 10 region L1

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10L1


title: 37C, biol rep 5

value: JCM5818 and JCM6999

value: WT


title: 37C, biol rep 7

value: JCM5818 and JCM7001


title: 37C, biol rep 6

value: JCM5818 and JCM7000


title: IMR32_5dPB_rep4 [ChIP-Seq]

description:
IMR32_5dPB_H3K27ac_ChIP_mean_CPM.bw
IMR32_H3K27ac_5dPBvControl_DiffBind.txt

value: neuroblastoma cell line

value: 5d PB


title: 37C, biol rep 4

value: Bacteria

value: JCM5818 and JCM6998


title: IMR32_5dPB_rep3 [ChIP-Seq]


title: Stage E7.25 embryo 1 section 10 region EP

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10EP

value: embryo


title: 37C, biol rep 8

value: JCM5818 and JCM7002


title: C57Bl/6 Murine Synovial Extravascular MHCII+ Dendritic Cells, Replicate 3, Bulk RNA

description: DC 3

value: Dendritic Cells


title: IMR32_5dPB_rep2 [ChIP-Seq]


title: 37C, biol rep 2

value: JCM5818 and JCM6996


title: C57Bl/6 Murine Synovial Extravascular MHCII+ Dendritic Cells, Replicate 2, Bulk RNA

description: DC 2

value: Ankle Joint Synovium


title: Stage E7.25 embryo 1 section 10 region EA

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10EA


title: Ctrl_C9_4R_T

value: Vehicle


title: IMR32_5dPB_rep1 [ChIP-Seq]


title: Stage E7.25 embryo 1 section 10 region A

description:
E7.25_1_FPKM_Filter_Log2.txt
E7.25_1_10A


title: C57Bl/6 Murine Synovial Extravascular MHCII+ Dendritic Cells, Replicate 1, Bulk RNA

description: DC 1

value: IV anti-CD45 BUV661


title: IMR32_control_rep5 [ChIP-Seq]

description:
IMR32_control_H3K27ac_ChIP_mean_CPM.bw
IMR32_H3K27ac_5dPBvControl_DiffBind.txt

value: control


title: IMR32_5dPB_rep5 [ChIP-Seq]


title: C57Bl/6 Murine Synovial Intravascular CD64-Ly6c- Non-Classical Monocytes, Replicate 2, Bulk RNA

description: NCM 2

value: Non-Classical Monocytes


title: C57Bl/6 Murine Synovial Extravascular CD64-Ly6c- Tissue-Resident Monocyte-Lineage Cells, Replicate 1, Bulk RNA

description: TR-MC 1

value: Tissue-Resident Monocyte-Lineage Cells


title: Stage E6.75 embryo 2 section 8 region EP

description:
E6.75_2.txt
E6.75_2_8EP


title: IMR32_control_rep4 [ChIP-Seq]


title: Stage E6.75 embryo 2 section 8 region P

description:
E6.75_2.txt
E6.75_2_8P


title: Stage E6.75 embryo 2 section 8 region EA

description:
E6.75_2.txt
E6.75_2_8EA


title: C57Bl/6 Murine Synovial Intravascular CD64-Ly6c- Non-Classical Monocytes, Replicate 1, Bulk RNA

description: NCM 1


title: 37C, biol rep 3

value: JCM5818 and JCM6997

value: WT


title: 30C, biol rep 9

value: JCM5818 and JCM6993


title: 30C, biol rep 10

value: JCM5818 and JCM6994


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII- cells, ATAC

description:
ATAC 10x Genomics
C57Bl/6 MHCII- scATAC-seq

library_source: genomic single cell

data_processing:
CITE-seq libraries were processed using cellranger pipeline v6 and reference genome mm10 3.0.0.  ADT reads were assigned to proteins using the included ADT_reference.csv.  Processed files include Unique Molecular Identifier (UMI) counts per genes and ADT counts per protein.
ATAC-seq libraries were processed using the cellranger atac pipeline v.1.1.0 and refdata-cellranger-atac-mm10-1.2.0.  Processed files include fragment counts per peak.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)

extract_protocol:
Synovial tissue was processed into a single-cell suspension and live cells were sorted as indicated for each population
Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) libraries were prepared using 10x Chromium Single Cell 3’ Solution v3. Cellular mRNA and antibody-derived tag (ADT) oligos were indexed with a shared cellular barcode.
single-cell Assay for Transposase Accessible Chromatin (scATAC-seq) libraries were prepared using the 10x Chromium Single Cell ATAC kit

treatment_protocol: To induce serum transfer arthritis (STIA), 85μL/20g K/BxN serum was given intravenously (I.V) to each mouse.  STIA mice were euthanized at peak inflammation (ie. Day 7 post treatment)


title: 30C, biol rep 8

value: JCM5818 and JCM6992


title: Stage E6.75 embryo 2 section 8 region A

description:
E6.75_2.txt
E6.75_2_8A


title: IMR32_control_rep2 [ChIP-Seq]

value: neuroblastoma cell line


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64+ cells, ADT

description:
ADT 10x Genomics
C57BL/6 CD64+ CITE-seq B

library_source: other

data_processing:
CITE-seq libraries were processed using cellranger pipeline v6 and reference genome mm10 3.0.0.  ADT reads were assigned to proteins using the included ADT_reference.csv.  Processed files include Unique Molecular Identifier (UMI) counts per genes and ADT counts per protein.
ATAC-seq libraries were processed using the cellranger atac pipeline v.1.1.0 and refdata-cellranger-atac-mm10-1.2.0.  Processed files include fragment counts per peak.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)
Library strategy: ADT-seq

molecule: protein


title: IMR32_control_rep1 [ChIP-Seq]


title: 37C, biol rep 1

value: Bacteria

value: JCM5818 and JCM6995


title: Stage E6.75 embryo 2 section 7 region P

description:
E6.75_2.txt
E6.75_2_7P

value: embryo


title: 30C, biol rep 6

value: JCM5818 and JCM6990


title: BE2C_7dPB_rep5 [ChIP-Seq]

description:
BE2C_7dPB_H3K27ac_ChIP_mean_CPM.bw
BE2C_H3K27ac_7dPBvControl_DiffBind.txt

value: 7d PB


title: 30C, biol rep 5

value: JCM5818 and JCM6989


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII+ cells, ADT

description:
ADT 10x Genomics
C57Bl/6 MHCII+ CITE-seq B

value: Ankle Joint Synovium


title: Stage E6.75 embryo 2 section 7 region EP

description:
E6.75_2.txt
E6.75_2_7EP


title: 30C, biol rep 4

value: JCM5818 and JCM6988


title: Stage E6.75 embryo 2 section 7 region EA

description:
E6.75_2.txt
E6.75_2_7EA


title: IMR32_control_rep3 [ChIP-Seq]

value: control


title: BE2C_7dPB_rep4 [ChIP-Seq]


title: BE2C_7dPB_rep3 [ChIP-Seq]


title: NR4A1-/- Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 3, Bulk RNA

description: Syn Ly6C- NR4A1-/-  3

data_processing:
Libraries were demultiplexed using using bcl2fastq v2.17.1.14
Sequenced reads were trimmed using BBDuk version 37.22 with the following parameters: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Trimmed reads were aligned to the mouse genome reference mm10 (Mus Musculus/UCSC assembly GRCm38) using STAR (Dobin et al., 2013)
Aligned reads were mapped to exons using the tool HTSeq-count (Anders et al., 2015)  with the reference transcriptome (Mus Musculus GRCm38.87).
The merged table of gene expression counts across samples was normalized to counts per million (CPM)
Assembly: mm10
Supplementary files format and content: tab-delimited table of CPM values across all samples

extract_protocol:
RNA was extracted from sorted cells using the PicoPure RNA Isolation kit as per manufacturer's instructions
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA sequencing kit

value: CD64-Ly6c- Myeloid Cells


title: Stage E6.75 embryo 2 section 7 region A

description:
E6.75_2.txt
E6.75_2_7A

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo


title: 30C, biol rep 7

value: JCM5818 and JCM6991


title: NR4A1-/- Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 2, Bulk RNA

description: Syn Ly6C- NR4A1-/-  2


title: 30C, biol rep 2

value: JCM5818 and JCM6986


title: 30C, biol rep 3

value: JCM5818 and JCM6987

value: WT


title: NR4A1-/- Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 1, Bulk RNA

description: Syn Ly6C- NR4A1-/-  1


title: C57Bl/6 Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 3, Bulk RNA

description: Syn Ly6C- 3


title: BE2C_control_rep5 [ChIP-Seq]

description:
BE2C_control_H3K27ac_ChIP_mean_CPM.bw
BE2C_H3K27ac_7dPBvControl_DiffBind.txt


title: BE2C_7dPB_rep2 [ChIP-Seq]


title: 30C, biol rep 1

value: JCM5818 and JCM6985


title: Stage E6.75 embryo 2 section 6 region EA

description:
E6.75_2.txt
E6.75_2_6EA


title: Stage E6.75 embryo 2 section 6 region EP

description:
E6.75_2.txt
E6.75_2_6EP


title: C57Bl/6 Murine Synovial CD45+CD11b+Ly6g-SiglecF-Cd64-MHCII- cells, ADT

description:
ADT 10x Genomics
C57Bl/6 MHCII- CITE-seq B


title: Stage E6.75 embryo 2 section 6 region A

description:
E6.75_2.txt
E6.75_2_6A


title: C57Bl/6 Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 2, Bulk RNA

description: Syn Ly6C- 2


title: input_SwrA_DS3649_DdegU_rep2

city: Bloomington

first: Ayushi

last: Mishra

state: Indiana

address: Biology Building, BB432, 1001 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. subtilis 3610 (NCBI Reference Sequence CP020102 ) by the using CLC genome browser, rRNA were removed for analysis
Assembly: B. subtilis 3610 (NCBI Reference Sequence CP020102 )
Supplementary files format and content: Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: Bacterial

growth_protocol: Cells were grown in LB, fixed by 3% formaldehyde for 30min at room temperature

extract_protocol:
Wild type and mutant cells of B. subtilis 3610 growing in LB were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

value: Bacterial

value: DdegU

value: none (input)


title: input_SwrA_DS3649_DdegU_rep1


title: BE2C_control_rep3 [ChIP-Seq]

value: neuroblastoma cell line


title: Stage E6.75 embryo 2 section 5 region P

description:
E6.75_2.txt
E6.75_2_5P

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

value: embryo


title: input_SwrA_DS2415_DswrA_rep1

value: DswrA


title: input_DegU_SwrA_3610_WT_rep3


title: C57Bl/6 Murine Peripheral Blood Non-Classical Monocytes, Replicate 3, Bulk RNA

description: PB NCM 3

source_name: Peripheral Blood

value: Peripheral Blood

value: Non-Classical Monocytes


title: BE2C_control_rep4 [ChIP-Seq]


title: C57Bl/6 Murine Synovial CD64-Ly6c- Myeloid Cells, Replicate 1, Bulk RNA

description: Syn Ly6C-1

value: Ankle Joint Synovium


title: Stage E6.75 embryo 2 section 6 region P

description:
E6.75_2.txt
E6.75_2_6P


title: Stage E6.75 embryo 2 section 5 region EP

description:
E6.75_2.txt
E6.75_2_5EP


title: C57Bl/6 Murine Peripheral Blood Non-Classical Monocytes, Replicate 2, Bulk RNA

description: PB NCM 2


title: Stage E6.75 embryo 2 section 5 region EA

description:
E6.75_2.txt
E6.75_2_5EA


title: C57Bl/6 Murine Peripheral Blood Non-Classical Monocytes, Replicate 1, Bulk RNA

description: PB NCM 1


title: BE2C_control_rep1 [ChIP-Seq]


title: BE2C_7dPB_rep1 [ChIP-Seq]

value: 7d PB


title: input_DegU_SwrA_3610_WT_rep2


title: BE2C_PBandRA_rep4

description:
BE2C_PBandRA_RNAseq_rawcounts.csv
BE2C_PBandRA_RNAseq_CPM.csv
BE2C_PBandRA_DESeq2output.csv

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
STAR 2.6.1d alignment to hg19 genome
STAR quant mode reverse to obtain gene counts
DESeq2 1.32.0 for differential expression analysis
Assembly: hg19
Supplementary files format and content: csv files include raw counts and counts per million (CPM) for each sample
Supplementary files format and content: csv files include differential expression outputs from DESeq2 for the comparisons: RA v DMSO, PB v DMSO, PB+RA v DMSO, PB+RA v RA and PB+RA v PB

growth_protocol: SK-N-BE(2)C were cultured in DMEM/F12 media with HEPES and l-glut supplemented with 10% FBS

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol with DNase step (Qiagen)
NEB polyA kit & NEB Ultra II directional RNA kit,  paired end sequencing (read length 50)

treatment_protocol: Either 1uM palbociclb, 10uM retinoic acid, 1uM palbociclib + 10uM retinoic acid or DMSO

tag: agent


title: input_DegU_SwrA_3610_WT_rep1


title: Stage E6.75 embryo 2 section 5 region A

description:
E6.75_2.txt
E6.75_2_5A


title: Stage E6.75 embryo 2 section 4 region P

description:
E6.75_2.txt
E6.75_2_4P


title: input_DegU_DS3649_DdegU_rep1


title: NR4A1-/- Murine Peripheral Blood Classical Monocytes, Replicate 3, Bulk RNA

description: PB CM NR4A1-/-  3

value: Classical Monocytes


title: NR4A1-/- Murine Peripheral Blood Classical Monocytes, Replicate 2, Bulk RNA

description: PB CM NR4A1-/-  2


title: BE2C_PBandRA_rep2


title: BE2C_PBandRA_rep3


title: NR4A1-/- Murine Peripheral Blood Classical Monocytes, Replicate 1, Bulk RNA

description: PB CM NR4A1-/-  1


title: input_DegU_DS2415_DswrA_rep3


title: BE2C_PBandRA_rep1


title: Stage E6.75 embryo 2 section 4 region EA

description:
E6.75_2.txt
E6.75_2_4EA


title: BE2C_control_rep2 [ChIP-Seq]

value: control


title: Stage E6.75 embryo 2 section 4 region EP

description:
E6.75_2.txt
E6.75_2_4EP


title: input_DegU_DS2415_DswrA_rep2


title: BE2C_PB_rep4

value: palbociclib


title: input_DegU_DS2415_DswrA_rep1


title: C57Bl/6 Murine Peripheral Blood Classical Monocytes, Replicate 3, Bulk RNA

description: PB CM 3


title: Stage E6.75 embryo 2 section 4 region A

description:
E6.75_2.txt
E6.75_2_4A


title: C57Bl/6 Murine Peripheral Blood Classical Monocytes, Replicate 2, Bulk RNA

description: PB CM 2


title: BE2C_PB_rep3


title: BE2C_PB_rep1


title: Stage E6.75 embryo 2 section 3 region EP

description:
E6.75_2.txt
E6.75_2_3EP


title: Stage E6.75 embryo 2 section 3 region P

description:
E6.75_2.txt
E6.75_2_3P


title: C57Bl/6 Murine Peripheral Blood Classical Monocytes, Replicate 1, Bulk RNA

description: PB CM 1


title: BE2C_PB_rep2


title: WGS_DK9524_DdegU_DswrA_Physpank_degU32_rep1

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. subtilis 3610 (NCBI Reference Sequence CP020102 ) by the using CLC genome browser, rRNA were removed for analysis
Assembly: B. subtilis 3610 (NCBI Reference Sequence CP020102 )
Supplementary files format and content: Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.
Library strategy: WGS

value: none (WGS sequencing)


title: SLAM-seq_Dome, omf201, replicate3

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

data_processing:
T-to-C conversion rates in 3'UTRs were calculated using the SLAM-DUNK package with default settings. The 4.3.2 transcript annotation by Lawson et al (doi: 10.7554/eLife.55792) was used.
Assembly: GRCz11
Supplementary files format and content: slamDunkResults.tar.gz has Tab-separated tcount files containing the SLAMSeq statistics per Ensembl gene UTR.
Library strategy: SLAM-seq

organism: Danio rerio

source_name: whole organism

growth_protocol: Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10-hour light and 14-hour dark cycles.

extract_protocol:
The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 (74104; Qiagen).
The QuantSeq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (Lexogen). RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single-ended reads.

treatment_protocol: Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. 2-cell embryos were injected with 50 pmoles of 4-Thiouridine (S4U). Embryos were incubated at 28.5. Prior to collection, all clutches were visually examined to ensure synchronous development, and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at -80°C for later processing for mRNA.

value: whole organism

tag: time

value: rif1 omf201/omf201

tag: cell cycle_phase

value: Asynchronous


title: Stage E6.75 embryo 2 section 3 region A

description:
E6.75_2.txt
E6.75_2_3A


title: WGS_DK9525_DswrA_Physpank_degQ_rep1

value: Bacterial

tag: genotype

value: DswrAPhyspankdegQ


title: WGS_DK9523_DdegU_Physpank_degU32_rep1


title: BE2C_RA_rep4


title: Stage E6.75 embryo 2 section 3 region EA

description:
E6.75_2.txt
E6.75_2_3EA


title: SLAM-seq_Dome, omf201, replicate2


title: SLAM-seq_256Cell, omf201, replicate3


title: ChIP_SwrA_DS3649_DdegU_rep3

value: DdegU

value: ChIP using anti-SwrA


title: BE2C_RA_rep3

value: neuroblastoma cell line


title: BE2C_RA_rep2


title: SLAM-seq_256Cell, omf201, replicate2


title: Stage E6.75 embryo 2 section 2 region EP

description:
E6.75_2.txt
E6.75_2_2EP

value: embryo


title: Stage E6.75 embryo 2 section 2 region P

description:
E6.75_2.txt
E6.75_2_2P


title: SLAM-seq_Dome, wildtype, replicate3

value: WT


title: ChIP_SwrA_DS3649_DdegU_rep2


title: ChIP_SwrA_DS3649_DdegU_rep1


title: Stage E6.75 embryo 2 section 2 region EA

description:
E6.75_2.txt
E6.75_2_2EA


title: BE2C_RA_rep1


title: ChIP_SwrA_DS2415_DswrA_rep2

value: DswrA


title: Stage E6.75 embryo 2 section 2 region A

description:
E6.75_2.txt
E6.75_2_2A


title: BE2C_DMSO_rep4

value: DMSO


title: SLAM-seq_256Cell, wildtype, replicate3


title: ChIP_SwrA_DS2415_DswrA_rep1


title: SLAM-seq_256Cell, wildtype, replicate2


title: BE2C_DMSO_rep2


title: SLAM-seq_Dome, wildtype, replicate2


title: ChIP_SwrA_3610_WT_rep3


title: Stage E6.75 embryo 2 section 1 region EP

description:
E6.75_2.txt
E6.75_2_1EP


title: BE2C_DMSO_rep1


title: WGS_DK9504_Physpank_degQ_rep1

value: PhyspankdegQ


title: Stage E6.75 embryo 2 section 1 region EA

description:
E6.75_2.txt
E6.75_2_1EA


title: BE2C_DMSO_rep3


title: SLAM-seq_Dome, omf201, replicate1


title: Stage E6.75 embryo 2 section 1 region P

description:
E6.75_2.txt
E6.75_2_1P


title: ChIP_SwrA_3610_WT_rep1


title: ChIP_SwrA_3610_WT_rep2


title: Stage E6.75 embryo 2 section 1 region A

description:
E6.75_2.txt
E6.75_2_1A


title: SLAM-seq_Dome, wildtype, replicate1


title: Stage E6.75 embryo 1 section 8 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_8P


title: ChIP_DegU_DS3649_DdegU_rep2

value: ChIP using anti-DegU


title: SLAM-seq_256Cell, omf201, replicate1


title: SLAM-seq_256Cell, wildtype, replicate1


title: ChIP_DegU_DS3649_DdegU_rep1


title: 1Cell, omf201, replicate3

data_processing:
Raw reads were trimmed with bbmap.
Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR.
To identify potential internal priming sites in polyA genomic sequences, a custom R script was developed and implemented. Once internal priming sites were identified, the same script was used to remove reads that mapped to these sites.
Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al (doi: 10.7554/eLife.55792) was used.
Assembly: GRCz11
Supplementary files format and content: Counts.csv has read counts at 3' ends of transcripts assigned to Ensembl gene IDs.

treatment_protocol: Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection, all clutches were visually examined to ensure synchronous development, and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at -80°C for later processing for mRNA.


title: SHSY5Y_5dPB_rep3

description:
SHSY5Y_PB_RNAseq_rawcounts.csv
SHSY5Y_RNAseq_CPM.csv
SHSY5Y_PB_RNAseq_DESeq2output.csv

data_processing:
TrimGalore 0.6.4 for adapter and quality trimming
STAR 2.6.1d alignment to hg19 genome
STAR quant mode reverse to obtain gene counts
DESeq2 1.32.0 for differential expression analysis
Assembly: hg19
Supplementary files format and content: csv files include raw counts and counts per million (CPM) for each sample
Supplementary files format and content: csv files include differential expression outputs from DESeq2 for the comparisons: 24hPB v Control, 5/7d PB v Control and 5/7d PB v 24h PB

extract_protocol:
Cells were lysed using RLT buffer and RNA extracted following the RNeasy Protocol with DNase step (Qiagen)
NEB polyA kit & NEB Ultra II directional RNA kit, paired end sequencing on a NovaSeq (read length 100)

tag: time point


title: SHSY5Y_5dPB_rep4

tag: cell line


title: Stage E6.75 embryo 1 section 8 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_8EP


title: ChIP_DegU_DS2415_DswrA_rep3


title: SHSY5Y_5dPB_rep2


title: Stage E6.75 embryo 1 section 8 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_8EA


title: 1Cell, omf201, replicate2


title: SHSY5Y_5dPB_rep1


title: 1Cell, omf201, replicate1


title: Stage E6.75 embryo 1 section 8 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_8A


title: SHSY5Y_24hPB_rep5


title: ChIP_DegU_DS2415_DswrA_rep2


title: SHSY5Y_24hPB_rep4


title: SHSY5Y_5dPB_rep5


title: Stage E6.75 embryo 1 section 7 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_7P


title: ChIP_DegU_DK9525_DswrA_Physpank_degQ_rep3


title: Stage E6.75 embryo 1 section 7 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_7EP


title: 1Cell, wildtype, replicate4


title: 1Cell, wildtype, replicate3


title: SHSY5Y_24hPB_rep3


title: ChIP_DegU_DK9525_DswrA_Physpank_degQ_rep2


title: Stage E6.75 embryo 1 section 7 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_7EA


title: 1Cell, wildtype, replicate1


title: Stage E6.75 embryo 1 section 7 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_7A


title: ChIP_DegU_DK9525_DswrA_Physpank_degQ_rep1


title: 1Cell, wildtype, replicate2


title: Stage E6.75 embryo 1 section 6 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_6P


title: SHSY5Y_control_rep5

value: control


title: Stage E6.75 embryo 1 section 6 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_6EP


title: 24hpf, omf201, replicate4

value: 24 hpf


title: 24hpf, omf201, replicate3


title: ChIP_DegU_DK9524_DdegU_DswrA_Physpank_degU32_rep2


title: SHSY5Y_control_rep4


title: ChIP_DegU_DK9524_DdegU_DswrA_Physpank_degU32_rep3


title: SHSY5Y_24hPB_rep2

value: palbociclib


title: ChIP_DegU_DS2415_DswrA_rep1


title: ChIP_DegU_DK9524_DdegU_DswrA_Physpank_degU32_rep1


title: Stage E6.75 embryo 1 section 6 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_6EA


title: SHSY5Y_control_rep3


title: ChIP_DegU_DK9523_DdegU_Physpank_degU32_rep3


title: Stage E6.75 embryo 1 section 6 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_6A


title: Stage E6.75 embryo 1 section 5 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_5P


title: ChIP_DegU_DK9523_DdegU_Physpank_degU32_rep2


title: SHSY5Y_control_rep1


title: Bud, omf201, replicate4

value: whole organism

value: 10 hpf


title: 24hpf, omf201, replicate1

value: rif1 omf201/omf201

value: Asynchronous


title: Bud, omf201, replicate3


title: SHSY5Y_24hPB_rep1


title: IMR32_5dPB_rep5

description:
IMR32_PB_RNAseq_rawcounts.csv
IMR32_RNAseq_CPM.csv
IMR32_PB_RNAseq_DESeq2output.csv


title: Stage E6.75 embryo 1 section 5 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_5EA


title: ChIP_DegU_DK9504_Physpank_degQ_rep3

value: Bacterial


title: ChIP_DegU_DK9523_DdegU_Physpank_degU32_rep1


title: Bud, omf201, replicate2


title: IMR32_5dPB_rep4


title: ChIP_DegU_DK9504_Physpank_degQ_rep2


title: Bud, omf201, replicate1


title: Stage E6.75 embryo 1 section 5 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_5A


title: IMR32_5dPB_rep2


title: 24hpf, omf201, replicate2


title: Shield, omf201, replicate4

value: 6 hpf


title: IMR32_5dPB_rep3


title: ChIP_DegU_DK9504_Physpank_degQ_rep1


title: Stage E6.75 embryo 1 section 4 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_4P


title: ChIP_DegU_3610_WT_rep3


title: Stage E6.75 embryo 1 section 4 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_4EP


title: Stage E6.75 embryo 1 section 4 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_4EA


title: ChIP_DegU_3610_WT_rep2


title: Shield, omf201, replicate3


title: Stage E6.75 embryo 1 section 5 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_5EP


title: Stage E6.75 embryo 1 section 4 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_4A


title: IMR32_24hPB_rep5


title: IMR32_5dPB_rep1


title: Pbn rep3

city: changsha

first: Huilin

middle: huilin

last: Yang

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

data_processing:
Illumina Novaseq platform were used for basecalling.
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
The left files (read1 files) from all libraries samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to by default and all other parameters set default.
Assembly: unigene.fasta includes gene_ids after Corset (PMID: 25063469) de-redundancy; Trinity.fasta: splicing assembly.
Supplementary files format and content: readcount.txt: Tab-delimited text file includes read counts for each Sample.
Supplementary files format and content: processed_data_files.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Araneus ventricosus

source_name: cerebral ganglia

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cerebral ganglia

value: lead


title: IMR32_24hPB_rep4

value: neuroblastoma cell line


title: Shield, omf201, replicate1


title: Shield, omf201, replicate2


title: Dome, omf201, replicate3


title: Pbn rep2


title: Pbn rep1


title: Stage E6.75 embryo 1 section 3 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_3EA

value: embryo


title: IMR32_control_rep5


title: 256Cell, omf201, replicate3


title: Stage E6.75 embryo 1 section 3 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_3EP


title: Pba rep3

source_name: ampullate gland

value: ampullate gland


title: IMR32_24hPB_rep1


title: IMR32_24hPB_rep2


title: Dome, omf201, replicate1


title: IMR32_control_rep4


title: 256Cell, omf201, replicate2


title: Pba rep1


title: ChIP_DegU_3610_WT_rep1

value: WT


title: Pba rep2


title: Stage E6.75 embryo 1 section 2 region EP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_2EP


title: IMR32_24hPB_rep3


title: Stage E6.75 embryo 1 section 2 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_2P


title: Stage E6.75 embryo 1 section 2 region EA

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_2EA


title: Dcn rep3

value: cadmium and lead


title: IMR32_control_rep3


title: 256Cell, omf201, replicate1


title: IMR32_control_rep2


title: Stage E6.75 embryo 1 section 3 region P

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_3P


title: Dcn rep2


title: Stage E6.75 embryo 1 section 2 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_2A


title: Stage E6.75 embryo 1 section 3 region A

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_3A


title: Dome, omf201, replicate2


title: IMR32_control_rep1


title: Dcn rep1


title: Stage E6.75 embryo 1 section 1 region AP

description:
E6.75_1_FPKM_Filter_Log2.txt
E6.75_1_1AP


title: SHSY5Y_control_rep2

description:
SHSY5Y_PB_RNAseq_rawcounts.csv
SHSY5Y_RNAseq_CPM.csv
SHSY5Y_PB_RNAseq_DESeq2output.csv


title: 24hpf, wildtype, replicate2


title: BE2C_7dPB_rep5

description:
BE2C_PB_RNAseq_rawcounts.csv
BE2C_RNAseq_CPM.csv
BE2C_PB_RNAseq_DESeq2output.csv


title: 24hpf, wildtype, replicate1


title: BE2C_7dPB_rep4


title: Dca rep2


title: Bud, wildtype, replicate3


title: Bud, wildtype, replicate4


title: BE2C_7dPB_rep3


title: UVC_NMT_A5

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Replicate 1

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
FASTA file of lesion-containing dinucleotide sequence extracted using BEDTOOLS2 fastaFromBed
Damage-containing dinucleotide sequences counted using custom perl script
Assembly: dinucounts.txt: contains counts of 2 bp lesions
Supplementary files format and content: BED: contains locations of 2 bp CPD lesions
Library strategy: CPD-seq

organism: Saccharomyces cerevisiae

source_name: Yeast genomic DNA

growth_protocol: Yeast cultures (BY4741) were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A (ThermoFisher Scientific) at 37˚C for ~1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and dissolved in sterile deionized H2O.
The methylated CPD-seq procedure is adopted from own CPD-seq method. Briefly, for a subset of samples, DNA was methylated in vitro with purified M. SssI methyltransferase enzyme. DNA samples were then sonicated to create fragments <1 kb in length. DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP or dideoxy-GTP. CPD lesions were cleaved with purified T4 endonuclease V. DNA was then ligated to a second adaptor A which are biotinylated and barcoded. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different samples and experiments. DNA was purified with Streptavidin beads and amplified for up to 8 cycles in a PCR reaction with primers complimentary to both A and trP1 adaptors, and the resulting DNA libraries were used for DNA sequencing. Following enzyme treatments, DNA was purified using Ampure XP beads and/or phenol:chloroform:isoamyl alcohol and ethanol precipitation.

treatment_protocol: 60mL of BY4741 were collected for an unirradiated sample (no UV) and two naked DNA samples (20mL per sample). DNA was isolated via phenol:chloroform:isoamyl extraction and ethanol precipitation. Naked DNA was then methylated in vitro with purified M. SssI CpG methyltransferase enzyme in 75uL reactions consisting of 1X NEBuffer2 (50mM NaCl, 10mM Tris-HCl, 10mM MgCl2, 1mM DTT, pH 7.9 @ 25C), 160uM S-adenosylmethionine (SAM), 15uL methyltransferase, 15ug previously purified DNA (UVB replicate #2 & UVC replicate #1), and sterile water up to 75uL. This reaction was run in quadruplicate for a total of 60ug DNA methylated. For the first replicate with UVB, the 75uL methyltransferase reaction instead contained 10uL of enzyme and 40ug of DNA along with 1X NEbuffer2, SAM, and water, done twice in parallel for a total of 80ug methylated DNA. Naked DNA was then irradiated with either 500 J/m2 UVB or 90J/m2 UVC. Non-methylated DNA cohorts were incubated in 75uL reaction as well, without SAM or methyltransferase and with 60ug or 80ug of DNA, respectively per replicate. Reactions were incubated at 37C for 4hrs, heat-killed at 65C for 20m for UVB replicate #1 or 37C overnight, heat-killed for 20m at 65C for replicate #2 (UVB) and replicate #1 with UVC. For the overnight reactions, additional 160uM SAM was spiked in after 4hrs. Methylation status was verified via methylation-sensitive restriction enzyme digests.

value: Wild-type

value: UVC irradiated 90 J/m2

tag: cpg methylation


title: 24hpf, wildtype, replicate4

value: 24 hpf


title: UVC_MT_A6

description: Replicate 1

value: Yes


title: 24hpf, wildtype, replicate3

value: whole organism


title: UVC_No_A4

description: Replicate 1


title: Ckn rep3

value: untreated


title: Dca rep1


title: BE2C_7dPB_rep1

value: palbociclib


title: Bud, wildtype, replicate1

value: 10 hpf

value: Asynchronous


title: Bud, wildtype, replicate2


title: BE2C_24hPB_rep5


title: Ckn rep1


title: Ckn rep2


title: Shield, wildtype, replicate4

value: 6 hpf


title: Dca rep3


title: UVB_No_A1

description: Replicate 2


title: BE2C_24hPB_rep4


title: UVB_NMT_A2

description: Replicate 2

value: UVB irradiated 500 J/m2


title: BE2C_24hPB_rep3


title: WT_NoUV_A1_1bp

description: Replicate 1


title: UVB_MT_A3

description: Replicate 2


title: Cka rep2


title: Shield, wildtype, replicate1


title: WT_NMT_500UVB_A2_1bp

description: Replicate 1


title: BE2C_7dPB_rep2


title: BE2C_24hPB_rep2


title: Dome, wildtype, replicate4


title: Cka rep1


title: BE2C_24hPB_rep1


title: Cdn rep3

value: cerebral ganglia

value: cadmium


title: WT_MT_500UVB_A3_1bp

description: Replicate 1


title: BE2C_control_rep5

value: neuroblastoma cell line

value: control


title: db-retina, scRNA-seq

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

institute: Nanjing university

description: 10x Genomics

data_processing:
scRNA-seq samples: the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
RNA-seq samples: CLC Genomics Workbench v 11.0.1, sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05), trimmed sequence reads were mapped to  hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8), read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files for scRNA-seq samples.
Supplementary files format and content: Tab-delimited text files include RPKM values for RNA-seq samples.

source_name: retina

growth_protocol: HMC and HRPC were  maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
21 weeks old wide type (wt) and leptin receptor-deficient (db/db) in C57BLKs/J background mice were sacrificed. Kidneys were perfused with PBS, followed by dynabead perfusion. Minced kidneys were digested with 1 mg/ml collagenase II , 1 mg/ml Protease E  plus 50 units/ml DNase I  at 37 °C for 5 min. Separated glomeruli were washed three times, then placed in 2 ml digestion buffer and incubated for an additional 30 minutes at 37℃ with rotating. Globes were removed and dissected in PBS on ice. Retina tissues were dissociated with dissociation system containing 2 mg/ml collagenase  II  and 200 units/ml DNase I at 37℃ for 30 minutes on a rotator. The retinal cells were then sorted by magnetic bead separation using PE anti-mouse CD140b antibody and PE-anti PECAM1 antibody.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HMC and HRPC was induced by treatment of 100 µg/ml AGEs for 6 hours while 100 µg/ml BSA as control.

value: retina

value: 21 weeks old

value: leptin receptor-deficient


title: Cdn rep2


title: Cka rep3

value: ampullate gland


title: Cdn rep1


title: wt-retina, scRNA-seq

description: 10x Genomics

value: wide-type


title: BE2C_control_rep3


title: BE2C_control_rep4


title: Dome, wildtype, replicate1

value: WT


title: 256Cell, wildtype, replicate3

value: whole organism


title: Cda rep3


title: Dome, wildtype, replicate3


title: db-kidney,  rep 1, scRNA-seq

description: 10x Genomics

source_name: kidney

value: kidney


title: BE2C_control_rep2


title: Dome, wildtype, replicate2


title: Shield, wildtype, replicate3


title: Cda rep2


title: 256Cell, wildtype, replicate2


title: BE2C_control_rep1


title: wt-kidney, rep 2, scRNA-seq

description: 10x Genomics


title: db-kidney,  rep 2, scRNA-seq

description: 10x Genomics


title: 256Cell, wildtype, replicate1


title: Cda rep1


title: T. gondii VEG WT, Control Conditions, Rep 3

status: Public on Aug 14 2023

city: Pittsburgh

first: Jon

middle: P

last: Boyle

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
For H. hammondi vs. T. gondii comparisons, data were reduced to include only genes that could be matched between T. gondii and H. hammondi based on synteny.  "Species specific" genes are included in the counts file but not subject to further analysis
Assembly: T. gondii and H. hammondia verson 43
Supplementary files format and content: Counts files have raw counts for each transcripts
Supplementary files format and content: Analyzed files have statistical analyses and log-transformed data

organism: Toxoplasma gondii

source_name: replicating tachyzoites under different conditions

growth_protocol: in vitro derived tachyzoites or in vitro derived sporozoites

extract_protocol:
Qiagen Rneasy
NEB Next or Illuina Tru Seq stranded mRNA
200 bp insert

treatment_protocol: control conditions or high pH, low C02, low serum conditions

value: tachyzoites and/or bradyzoites

value: VEG

value: control media conditions


title: T. gondii VEG ROCY1 KO, Switch Conditions, Rep 1

value: replicating tachyzoites under different conditions

value: high pH, low C02, low serum conditions


title: T. gondii VEG WT, Control Conditions, Rep 2


title: T. gondii VEG WT, Switch Conditions, Rep 3


title: T. gondii VEG ROCY1 KO, Control Conditions, Rep 2


title: T. gondii VEG ROCY1 KO, Switch Conditions, Rep 3


title: T. gondii VEG ROCY1 KO, Control Conditions, Rep 1


title: T. gondii VEG WT, Control Conditions, Rep 1


title: T. gondii VEG ROCY1 KO, Switch Conditions, Rep 2


title: T. gondii VEG BFD1 KO, Switch Conditions, Rep1


title: T. gondii VEG BFD1 KO, Switch Conditions, Rep2


title: T. gondii VEG BFD1 KO, Control Conditions, Rep 2


title: T. gondii in vitro bradyzoite induction conditions 1

source_name: freshly excysted sporozoites

value: freshly excysted sporozoites

value: sporozoites grown in vitro


title: T. gondii in vitro bradyzoite induction conditions 2


title: T. gondii in vitro control conditions 3