title: Fetal pancreas, KO

first: Jiajun

last: Sun

state: Shanghai City

address: 197 Rui Jing Er Rd

institute: Shanghai Jiao Tong University Medical School Affiliated Ruijin Hospital

data_processing:
We used BD Rhapsody Sequence Analysis Pipeline 1.8 to process our raw data and the supplementary file cell_barcode_information.xlsx contains the cell barcode sequence for each Cell_Index listed in the processed data files.
We utilized Seurat for subsequent clustering analysis and visualization. Gene expression matrices for each sample was read and converted to Seurat objects. Cells with more than 25% mitochondrial UMI, less than 500 UMI or 200 genes were excluded from the downstream analysis.
Assembly: mm10
Supplementary files format and content: expression matrix files in CSV format

source_name: Pancreatic cell

extract_protocol:
Fetal pancreatic tissue was transferred to a culture dish containing 1XPBS buffer for cleaning. The cleaned tissue was transferred to a 2mL EP tube and 1mL Try.pLE™ Express Enzyme was added. The samples were put into a preheated water bath at 37℃ and digested for 15min at 90rpm (blow with 1mL gun tip every 5min to help digestion). Add 1mL FACS buffer solution to the digested sample to stop the enzymolysis and gently mix; The sample was passed through a 35µm screen, and another 2mL FACS buffer was removed to clean the screen and collect the filtrate. The filtrate was centrifuged at 300×g at 4℃ for 5min to absorb the supernatant, and 1mL of 1×PBS buffer was removed to re-suspend the sample, and then 1×PBS buffer was added to 4mL. The mixture was gently reversed and centrifuged at 300×g at 4℃ for 5min. The supernatant was aspirated and the cells were re-suspended with 1×PBS buffer to the desired volume for further manipulation.
Library was performed according to the manufacter’s instructions (BD Biosciences). Cells were firstly stained with two fluorescent dye, Calcein AM and Draq7, for precisely determination of cell concentration and viability via BD Rhapsody™ Scanner (BD Biosciences). Cells were loaded in one BD Rhapsody micro-well cartridge. Cell capture beads were then loaded excessively to ensure that nearly every micro-well contains one bead, and the excess beads were washed away from the cartridge. After lysing cells with lysis buffer, Cell capture beads were retrieved and washed prior to performing reverse transcription. Microbeads-captured single cell transcriptome were generated into cDNA library containing cell labels and unique molecular identifiers (UMI) information. All procedures were performed with BD Rhapsody cDNA Kit (BD Biosciences, Cat. No. 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat No. 633801) strictly following the manufacturers’ protocol. All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) on the NovaSeq platform (Illumina).

value: Pancreatic cell


title: PIK3R5i#1-Rep2

status: Public on Mar 18 2024

type: SRA

city: Boston

first: Qingyu

last: Luo

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

description:
10_QL
STAR_Gene_Counts

library_source: transcriptomic

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline to generate gene expression data
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus XS (740990.250; Takara Bio) according to the manufacturer’s protocol.
Roche Kapa

tag: cell line

tag: cell type

value: BPDCN

tag: genotype

value: PIK3R5 knockdown

tag: treatment

value: DMSO


title: cCR.ASCC_5

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
QC analysis by fastqc and trimming by trimmomatic
mapping by star and counting by featurecount
generation of bw by sambamba, bedtools and wigtobigwig
Assembly: ensembl release-104
Supplementary files format and content: bw file per fastq file indicating coverage

source_name: primary tumor FFPE

extract_protocol:
Total RNA was isolated from FFPE samples using Qiagen RNeasy FFPE Kit (Qiagen) and depleted from ribosomal RNA (rRNA) to prepare sequencing libraries
Complete Stranded RNA Library

tag: tissue

value: primary tumor FFPE

tag: disease state

value: cCR


title: PF_MYST_overexpression_time point 2

type: RNA

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description: This sample is of Plasmodium falciparum with PfMYST overexpression at second time point.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University. Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions (Roche NimbleGen). Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 4 (dnastar.com).
RMA-normalized, averaged gene-level signal intensity

organism: Plasmodium falciparum

source_name: Plasmodium falciparum PfMYST overexpression, time point 2

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol:
P. falciparum were cultured as described previously (Trager and Jensen, 1976)
The parasite culture was synchronized by sorbital treatment (Lambros and Vanderberg, 1979).

extract_protocol: Total RNA was extracted using the Trizol reagent ((invirtogen.com)

tag: developmental stage

value: early trophozoite

tag: phenotype

value: a faster progression and shorter schizont development time


title: NTC#2+PI3Kγi-Rep1

description:
7_QL
STAR_Gene_Counts

value: WT

value: eganelisib


title: Mouse A3778, PU.1 Transgenic

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

description: scRNA-seq data (10X Chromium)

library_source: transcriptomic single cell

data_processing:
Processing of the sequencing data was performed with the cellranger pipeline (v4.0.0, 10X Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Brain (right hemisphere minus olfactory bulb and cerebellum)

extract_protocol:
Two four-month-old 5XFAD and two four-month-old Pu.1Tg/0;5XFAD mice were anesthetised, transcardially perfused with sterile cold PBS, and then the brain was collected. After removing the cerebellum, the right hemisphere was immediately finely minced on ice and transferred to a polypropylene tube containing 10 ml ice-cold Accutase (Gibco, A11105-01). Tissue was incubated with rocking at 4oC for 30 minutes and then pelleted through centrifugation at 300 g for 5 minutes at 4oC. Supernatant was aspirated and samples were resuspended in 5 ml ice-cold wash buffer [1X HBSS (Gibco, 14175095), 0.04% BSA (Miltenyi, 130-091-376)] and gently dissociated through trituration using a 5 ml serological pipette. 70 µm and 40 µm cell-strainers (Corning, 352350 & 352340) were moistened with 5 ml ice-cold wash buffer and samples were sequentially strained through into fresh polypropylene tubes, each filter was rinsed with an additional 5 ml of ice-cold wash buffer. Cell suspensions were pelleted through centrifugation at 300 g for 10 min at 4oC. The supernatant was aspirated, and cells were resuspended in 1080 µl of degassed MACS Myelin Removal Buffer (1X DPS (Gibco 14190250), 0.5% BSA (Miltenyi, 130-091-376)) and transferred to 2 ml DNA LoBind tubes (Eppendorf, 022431048). 120 µl of myelin removal beads (Miltenyi, 130-096-733) were added to each sample and mixed thoroughly by pipetting. Samples and beads were incubated for 15 min at 4oC with rotating. Samples were transferred to 15 ml polypropylene tubes and washed with 10 ml myelin removal buffer, then pelleted through centrifugation at 300 g for 10 min at 4oC. Supernatant was aspirated and samples were resuspended in 2ml myelin removal buffer. LS columns (Miltenyi, 130-042-401) were loaded into a QuadroMACS separator on a MACS MultiStand with Tube Rack (Miltenyi, 130-090-976 & 130-042-303 & 130-091-052). Columns were equilibrated with three successive 1 ml volumes of myelin removal buffer which were collected in 15 ml polypropylene tubes. Cell suspensions were loaded onto columns and myelin-depleted cell suspensions were washed through using four successive 1 ml volumes of myelin removal buffer. Effluent was made up to 10 ml total volume and cells were pelleted through centrifugation at 300 g for 5 min at 4oC. Supernatant was aspirated to a residual volume of 200 µl and cells were gently resuspended using a pipette. Cells were then pelleted through centrifugation at 300 g for 5 min at 4oC before resuspension in 200 µl resuspension buffer (1X DPS (Gibco 14190250); 0.04% BSA (Miltenyi, 130-091-376)), another centrifugation step using the same settings and finally resuspension in 50 µl resuspension buffer. An aliquot of cells was stained with trypan blue, and the cell concentration and viability were determined by manual counting using a disposable hemocytometer slide (C-Chip, SKC, Inc., Covington, GA) and the 40X objective of an EVOS XL Core microscope
Single cell suspensions were mixed with single cell master mix containing lysis buffer and reverse transcription reagents, following the Chromium Next GEM Single Cell 3’ Reagent Kits User v3.1 (Dual Index) Guide, CG000315 Rev A (10X Genomics, Pleasanton, CA). Each single cell mix was then loaded into a single well of a Single Cell Chip G and run on the Chromium Controller for GEM generation and barcoding. Sample processing and library preparation were performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3’ v3.1 dual index kit (10X Genomics, Inc.) and SPRIselect paramagnetic bead-based chemistry (Beckman Coulter Life Sciences, Indianapolis, IN). The cDNA and library quality were assessed using the Agilent 2100 Bioanalyzer and a High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA) and the final library concentration was determined using a Qubit Fluorometer and the dsDNA HS assay kit (Thermo Fisher Scientific, Waltham, MA). Sequencing was carried out on a NovaSeq 6000 v1.5 S2 100 cycle chip (Illumina) with 28-10-10-91 read setup.

tag: age

value: 4 months

tag: Sex

value: female

value: PU.1 Transgenic

tag: strain


title: Fetal pancreas, WT

city: Shanghai

country: China


title: cCR.ASCC_49


title: PF_MYST_overexpression_time point 1

description: This sample is of Plasmodium falciparum with PfMYST overexpression at first time point.

source_name: Plasmodium falciparum PfMYST overexpression, time point 1

value: ring


title: NTC#1+PI3Kγi-Rep2

description:
6_QL
STAR_Gene_Counts


title: NTC#1+PI3Kγi-Rep1

description:
5_QL
STAR_Gene_Counts


title: Mouse A3774, PU.1 Wildtype

description: scRNA-seq data (10X Chromium)

value: Brain (right hemisphere minus olfactory bulb and cerebellum)

value: Wildtype


title: PF_wildtype_time point 6

description: This sample is of wild-type Plasmodium falciparum 3D7 at six time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 6

value: late schizont

value: normal


title: NTC#2-Rep2

description:
4_QL
STAR_Gene_Counts

value: BPDCN


title: cCR.ASCC_47


title: Mouse A3373, PU.1 Transgenic

description: scRNA-seq data (10X Chromium)


title: PF_wildtype_time point 5

description: This sample is of wild-type Plasmodium falciparum 3D7 at fifth time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 5

value: eraly schizont


title: PF_wildtype_time point 4

description: This sample is of wild-type Plasmodium falciparum 3D7 at fouth time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 4

value: late trophozoite


title: Mouse A3772, PU.1 Wildtype

description: scRNA-seq data (10X Chromium)


title: cCR.ASCC_44

value: primary tumor FFPE


title: NTC#2-Rep1

description:
3_QL
STAR_Gene_Counts

value: DMSO


title: PF_wildtype_time point 3

description: This sample is of wild-type Plasmodium falciparum 3D7 at third time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 3

value: middel trophozoite


title: NTC#1-Rep2

description:
2_QL
STAR_Gene_Counts


title: EFO27_25_Input_H3k4me3

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
EFO27-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_EFO27-25-Input_14Dec2017_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

library_source: genomic

data_processing:
ChIP sequencing data was processed based on ENCODE phase 3 histone ChIP-Seq pipeline with modifications on the peak calling algorithm to retain peaks with p-value < 10e-9.
Reads were aligned to the reference human genome (hg38), filtered by read quality and duplicate reads removed. Peak calling was performed with MACS2 within the AQUOS pipeline, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: narrowpeak

molecule: genomic DNA

source_name: cell line

growth_protocol: FT33, FT246 and FT282 lines were maintained in DMEM-F12 medium (Gibco, Invitrogen, Carlsbad) supplemented with 10% fetal bovine serum (Gibco). The HGSOC cell line UWB 1.289 was cultured in a mixture (1:1) of 50% RPMI and  50% MEGM medium with 3% FBS and Kuramochi was cultured in RPMI-1640 media supplemented with 10% FBS. The remaining cell lines were maintained according to the recommended conditions (ATCC).   All cell lines were thawed and allowed to recover for 1 day before expansion. All cell lines were passaged and plated onto 150mm plates. Cells were harvested at 80% confluency to be fixed, pelleted and snap frozen.

extract_protocol:
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated  to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K4me1 was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
Sequencing libraries were prepared using a ThruPlex DNA-seq kit (Rubicon R400407), pooled and sequenced on an Illumina HiSeq 5000 for 2 x 150 bp paired-end for an average of 40 million reads (Fulgent Genetics; Temple City, CA).

value: cell line

value: Mucinous serous ovarian cancer

value: H3K4me3 (Millipore 07-473)


title: EFO27_B_H3k4me3


title: cCR.ASCC_40

value: cCR


title: cCR.ASCC_4


title: PF_wildtype_time point 2

description: This sample is of wild-type Plasmodium falciparum 3D7 at second time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 2

value: early trophozoite


title: NTC#1-Rep1

description:
1_QL
STAR_Gene_Counts

value: WT


title: cCR.ASCC_38


title: On- and post-treatment pHLA tetramer+ CD8+ T cells, TCR

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

description: BD Rhapsody Whole Transcriptome Analysis (WTA), Multiplexing and TCR/BCR Full length kit

library_source: other

data_processing:
The BD Rhapsody Sequence Analysis Pipeline (version 1.11, BD Biosciences) was used to map the reads to the human reference genome (GRCh38), assign sample tag calls and process the TCR sequences.
Further processing, e.g. filtering, data integration, clustering and differential gene expression was performed with Seurat (version 4.3.0) and Harmony (version 1.0)
Assembly: GRCh38
Supplementary files format and content: BD Rhapsody output file: Combined_RSEC_MolsPerCell.csv
Supplementary files format and content: BD Rhapsody output file: Sample_Tag_Calls.csv
Supplementary files format and content: BD Rhaspody output file: VDJ_PerCell.csv

molecule: other

source_name: TCR

extract_protocol:
Live, CD3+CD8+ T cells were sorted of PBMC obtained pre-treatment and live, CD3+CD8+tetramer-APC+tetramer-PE+ T cells were sorted of PMBC obtained on-treatment and post-treatment with BD ARIA II cell sorter (BD Bioscience). Sorted cells were pooled and volume of cell suspension was diluted to 600 ml with BD Sample Buffer (BD Bioscience).
Single cell capture and cDNA library preparations were performed using the BD Rhapsody system. First, BD Rhapsody cartridges were primed, and the pooled cells were loaded onto the cartridges and incubated at 4°C for 15 mins. The subsequent steps were performed according to the manufacturer’s instructions (23-21336-01, BD Biosciences). Sample tag and cDNA libraries were generated for both the pre-treatment and on/post-treatment PBMCs (23-21712-00, BD Biosciences), while an additional TCR library was generated for on/post-treatment PBMCs (23-24018(01), BD Biosciences).

value: Blood

value: T cells


title: EFO27_A_H3k4me3


title: PF_wildtype_time point 1

description: This sample is of wild-type Plasmodium falciparum 3D7 at first time point.

source_name: Plasmodium falciparum 3D7 wildtype, time point 1

value: ring


title: MCAS_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
MCAS-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_MCAS-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: MCAS


title: On- and post-treatment pHLA tetramer+ CD8+ T cells, HTO

molecule: protein

source_name: HTO

tag: hto

value: Sample Tag 3 — Human, Sample Tag 4 — Human, Sample Tag 5 — Human, Sample Tag 6 — Human, Sample Tag 7 — Human, Sample Tag 8 — Human, Sample Tag 9 — Human, Sample Tag 10 — Human, Sample Tag 11 — Human, Sample Tag 12 — Human


title: cCR.ASCC_45


title: MCAS_B_H3k4me3


title: PCMs  T748A, LPS 4 hr #2

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

country: Japan

institute: RIKEN Yokohama

data_processing:
Sequence reads were mapped to the mm10 genome using HISAT2
Mapped reads on each gene were counted using featureCounts with default setting
Differential expression analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tabular file including normalized counts of each transcript for all samples

source_name: peritoneal cavity

growth_protocol: Indicated cells were cultured as explained in the text of the related manuscript

extract_protocol:
Trizol reagent followed by addition of chloroform and isolation of total RNA from upper aquous layer
TruSeq stranded mRNA sample prep kit (Illumina, catalog no. 20020594) according to the manufacturer’s instructions

treatment_protocol: Indicated cells were treated as explained in the text of the related manuscript

value: peritoneal cavity

value: macrophages

value: LPS 4 hrs


title: On- and post-treatment pHLA tetramer+ CD8+ T cells, cDNA

molecule: polyA RNA

source_name: RNA


title: MCAS_A_H3k4me3


title: PCMs  T748A, LPS 4 hr #1


title: cCR.ASCC_35

value: primary tumor FFPE


title: cCR.ASCC_34


title: PCMs  Wt, LPS 4 hr #2

value: Wt


title: Baseline CD8+ T cells, HTO

value: Sample Tag 1 — Human, Sample Tag 2 — Human


title: cCR.ASCC_32


title: Baseline CD8+ T cells, cDNA


title: PCMs  Wt, LPS 4 hr #1


title: cCR.ASCC_30


title: HLF cells, co-cultured with CD4+ Tcells, experiment, 3

city: Osaka

first: Hanh

middle: Vinh

last: Ngo

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Hepatology

institute: Osaka Metropolitan University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads'quality, total bases, total reads, GC(%) and basic staticstics are calculated
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome tieh HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts
Expression profiles are represented as read count and normalization values which are calculated based on trasncript length and dept of coverage
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypotheis testing
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Human cancer cell line

growth_protocol: HLFs were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Library Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Reference Guide #1000000040498 v00

treatment_protocol: CD4+ T cells from healthy donor was isolated and activated by anti-CD3 antibody (1ug/mL) and anti-CD28 antibody (5ug/mL) for 24 hours. The next day, activated T cells were co-cultured with pre-seeded HLFs in 24-well plate for 24 hours.

value: Human cancer cell line

value: HLF

value: Human hepatocellular carcinoma cells

value: CD4+ T cells co-culture, 24 hours


title: HLF cells, co-cultured with CD4+ Tcells, experiment, 2


title: cCR.ASCC_36

value: cCR


title: cCR.ASCC_3


title: HLF cells, co-cultured with CD4+ Tcells, experiment, 1


title: PCMs  T748A, LPS 0 hr #2

value: LPS 0 hrs


title: VOA1056_B_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
VOA1056-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_VOA1056-25-Input-H3k27ac_12Dec2017_GRCh38_Primary_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: cell line

value: Low grade serous ovarian cancer

value: H3K4me3 (Millipore 07-473)


title: cCR.ASCC_28


title: GTFR230_A_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
GTFR230-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_GTFR230-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: Mucinous serous ovarian cancer


title: VOA1056_25_Input_H3k4me3


title: PCMs  T748A, LPS 0 hr #1


title: HLF cells, single culture, control, 3

value: single culture, 24 hours


title: VOA1056_A_H3k4me3


title: cCR.ASCC_26


title: PCMs Wt, LPS 0 hr #1

value: peritoneal cavity


title: GTFR230_25_Input_H3k4me3


title: BMDMs T748A, LPS 4 hr #2

source_name: bone marrow

value: bone marrow

value: macrophages


title: PCMs Wt, LPS 0 hr #2


title: OAW42_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
OAW42-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_OAW42-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz


title: cCR.ASCC_25

source_name: primary tumor FFPE

value: primary tumor FFPE


title: OAW42_B_H3k4me3


title: HLF cells, single culture, control, 1


title: GTFR230_B_H3k4me3


title: cCR.ASCC_24


title: BMDMs T748A, LPS 4 hr #1

value: LPS 4 hrs


title: OAW42_A_H3k4me3


title: G62-RNA-seq

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

data_processing:
Reads pairs were aligned to the human reference genome (GRCh38) and transcriptome (Gencode.v29) using STAR (v2.6.0c).
Gene and isoform expression quantification were performed using RSEM (v1.3.3).
Read coverage tracks (BigWig) were generated and normalized by scale factor using the bamCoverage function of deepTools2 (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: *.bw refers a bigwig for each sample which normalized with scale facor and mapping q>20
Supplementary files format and content: all_GSCs_RNAcounts.txt refers a large table with all genes (rows) and their total counts in each GSC (columns).

source_name: glioblastoma stem-like cells

extract_protocol:
GSCs grown to near-confluence in a T25 flask were directly lysed using Trizol (Invitrogen), total RNA was isolated using the DirectZol kit (Zymo).
Standard poly(A)+ selection and library preparation with the TruSeq kit (Illumina).

value: glioblastoma stem-like cells


title: BMDMs Wt, LPS 4 hr #2

value: Wt


title: BMDMs Wt, LPS 4 hr #1


title: cCR.ASCC_22


title: G61-RNA-seq


title: cCR.ASCC_21


title: BMDMs T748A, LPS 0 hr #2


title: cCR.ASCC_20


title: HLF cells, single culture, control, 2

value: Human cancer cell line

value: HLF


title: Kuramochi_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
Kuramochi-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_Kuramochi-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: Kuramochi

value: High grade serous ovarian cancer


title: Kuramochi_B_H3k4me3


title: G452P-RNA-seq


title: cCR.ASCC_27

value: cCR


title: G457-RNA-seq


title: G83-RNA-seq


title: cCR.ASCC_2


title: UWB1.289_25_Input_H3K4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
UWB1.289-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_UWB1.289-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: cell line


title: BMDMs T748A, LPS 0 hr #1

value: LPS 0 hrs


title: BMDMs Wt, LPS 0 hr #1


title: PD.ASCC_38

value: PD


title: G450-RNA-seq


title: BMDMs Wt, LPS 0 hr #2


title: cCR.ASCC_19


title: G452C-RNA-seq


title: RNA_KO-S3D-R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

data_processing:
ChIP-seq analysis: Sequence reads of mouse samples were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1.  Sequence reads of mouse with fly spike-in samples were mapped to the mouse + fruit fly genome (mm10+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID 18798982). ChIP-seq profiles were produced with SeqCode (PubMed ID 34599234). DiffBind (PubMed ID 22217937) was run next over the union of peaks from each pair of replicates of the same experiment to find those peaks that were significantly enriched in both replicates in comparison to the corresponding controls (parameters: categories = DBA_CONDITION, block = DBA_REPLICATE and method = DBA_DESEQ2_BLOCK, P value < 0.05 and FDR < 10-5).
RNA-seq analysis: Sequence reads were mapped against the mm10 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DESeq2 (PubMed ID 25516281) was run to perform differential gene expression analysis of each annotated gene in RefSeq
Assembly: mm10
Supplementary files format and content: Genome-wide profiles (Bedgraph)
Supplementary files format and content: DESeq2 (TXT): columns are gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj

growth_protocol: (mESCs) Serum 20% + LIF. (NPs) mESCs were differentiated as described in https://www.nature.com/articles/nprot.2007.147. Briefly, at day zero mESCs were harvested and seeded in low attachment plates in medium without retinoic acid to allow for the formation of embryoid bodies (EB). EB media was replaced every other day and on day 4 with the addition of retinoic acid. Cells were harvested at day 8 and RNA was extracted for RNA-seq

extract_protocol:
ChIP-seq: ChIP experiments were carried out adapting with modifications a standard protocol in the lab (PubMed ID 34473698)
RNA-seq: RNA extraction was performed using the RNeasy kit (Qiagen, 74134) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.

value: embryonic stem cells (ESCs)

tag: chip antibody


title: Hey_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
Hey-A-H3K4me3_8Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x__1_Hey-25-Input_14Dec2017_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: Hey

value: H3K4me3 (Millipore 07-473)


title: cCR.ASCC_18


title: UWB1.289_H3K4me3


title: G412R-RNA-seq


title: RNA_KO-S3D-R1


title: Hey_B_H3k4me3


title: Kuramochi_A_H3k4me3


title: cCR.ASCC_17


title: G402R-RNA-seq


title: RNA_KO-L3D-R2


title: cCR.ASCC_16


title: Hey_A_H3k4me3


title: RNA_KO-L3D-R1


title: cCR.ASCC_15


title: G402-RNA-seq


title: G394-RNA-seq


title: CaOV3_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
CaOV3-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_CaOV3-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz


title: CaOV3_B_H3k4me3


title: RNA_NP_KO-L-R2

value: neuronal precursors (NPs)


title: RNA_NP_KO-L-R1


title: cCR.ASCC_14


title: G390-RNA-seq


title: cCR.ASCC_13


title: RNA_NP_KO-S-R2


title: cCR.ASCC_12


title: G351-RNA-seq


title: RNA_NP_KO-S-R1


title: RMG-II_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
RMG-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_RMG-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: RMG-II

value: Clear cell ovarian cancer


title: G412-RNA-seq


title: cCR.ASCC_11

value: primary tumor FFPE


title: G323-RNA-seq

value: glioblastoma stem-like cells


title: ES2_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
ES2-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_ES2-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz


title: G318-RNA-seq


title: cCR.ASCC_105


title: RNA_NP_WT_R4


title: cCR.ASCC_103


title: RNA_NP_WT_R3


title: RNA_NP_KO_R2


title: JHOC5_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
JHOC5-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_JHOC5-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz


title: cCR.ASCC_102


title: CaOV3_A_H3k4me3


title: cCR.ASCC_101


title: JHOC5_B_H3k4me3


title: G275-RNA-seq


title: RNA_NP_Deltaex4_R2


title: G275R-RNA-seq


title: RMG-II_Input_H3k4me3


title: JHOC5_A_H3k4me3


title: Brain, Young Ethanol

city: Aurora

first: paige

last: Anton

state: COLORADO

address: 12850 E Monteview Blvd, School of Pharmacy V20-3470D

institute: University of Colorado Anschutz

description:
10x Genomics Visium Spatial Transcriptomics
B_Young_Ethanol
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5
Aggr_cloupe.cloupe

data_processing:
FASTQ sequencing files were aligned to the mm10 mouse genome and gene expression counts generated using Space Ranger 2.0.0 (10X Genomics).
The `spaceranger count` command was used to generate tissue slice gene expression count matrices with default settings.
The `spaceranger aggr` command was used to aggregate all slice gene expression count matrices with default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz = list of barcodes
Supplementary files format and content: features.tsv.gz = list of gene IDs
Supplementary files format and content: matrix.mtx.gz = gene count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_feature_bc_matrix.h5 = matrix of detected gene features
Supplementary files format and content: 01f00d4.TIF = high res image of tissue slice
Supplementary files format and content: Aggr_cloupe.cloupe = Gene expresssion data on loupe browser interface
Library strategy: Spatial Transcriptomics

source_name: Murine Brain (Hippocampal)

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Colorado Anschutz Medical Campus. Female C57BL/6 mice were obtained from the National Institutes of Aging (NIA) aged rodent colony and maintained for at least two weeks in an in-house animal facility prior to use.

extract_protocol:
Brain tissue was extracted, and meninges were removed. Left hemispheres were frozen in optimal cutting temperature (OCT) compound and sectioned for spatial transcriptomics. Brain tissue was sectioned coronally (10 um thickness; bregma -2.0 to -2.2) and slices were placed on a 10X Genomics Visium Spatial Gene Expression Slide.
Spatial trancriptomice sequenccing libraries were prepared with 10x Genomic Visium Gene Expression slides to manufacturer's instructions

treatment_protocol: Young (3–4-month-old) and aged (18–20-month-old) mice were randomized (2-3 mice/cage) into vehicle and ethanol treatment groups. All cage mates were matched by weight. Mice received intragastric gavages of vehicle (water) or ethanol (3 g/kg) every-other-day over the course of 18 days, totaling 10 exposures. All mice were allowed ad libitum access to chow and water during the treatment period and housed on a 12-hour/12-hour light/dark cycle. Eighteen hours after the final gavage, mice were anesthetized and sacrificed.

value: Murine Brain (Hippocampal)

value: Female

value: 3 months old

value: Ethanol


title: G23-RNA-seq


title: RNA_NP_Deltaex4_R1


title: EEC16_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
EEC16-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_EEC16-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: Endometriosis


title: G213-RNA-seq


title: cCR.ASCC_10

value: cCR


title: RNA_NP_CSex4_R2


title: cCR.ASCC_1


title: G28-RNA-seq


title: EEC16_A_H3k4me3

value: cell line


title: RNA_NP_CSex4_R1


title: G181-RNA-seq


title: Human_SEOV_12dpi_C

city: Rotterdam

first: Barry

last: Rockx

address: Wytemaweg 80

department: Viroscience

country: Netherlands

institute: Erasmus MC

data_processing:
Assembly: GRCh38
Demultiplexing: Illumina bcl2fastq v2.20.0.422
adapter trimming (Illumina adapter sequences): Cutadapt
alignment: HiSat2 version 2.2.1
expression level counting: htseq-count version 0.12.4
gene filtering: keep only genes with count >=5 in at least 6 samples, separately for the 12 human and the 12 rat samples
Supplementary files format and content: .tsv file: tab-separated text file of raw counts, genes in rows and samples in columns.

source_name: primary lung microvascular endothelial cells

growth_protocol: Commercially available primary cultures of Rattus norvegicus(Cell Biologics) or human (Cell Systems) were propagated in endothelial cell growth medium MV2 (PromoCell) supplemented with 1% penicillin/streptomycin (Lonza) at 37 degrees Celcius in a humidfied CO2 incubator

extract_protocol:
High pure RNA isolation kit (Roche)
Illumina TruSeq Stranded mRNA
ssRNA-seq (stranded RNA-seq)

treatment_protocol: Seoul 80-39 orthohantavirus (SEOV, European Virus Archive Global #008v-EVA1473, P+2) infection with MOI of 1.0 or mock infection with equal amounts of Dulbecco's modified Eagle's medium (Capricorn Scientific) supplemented with 5% fetal calf serum, HEPES, sodium bicarbonate, 1% pen/strep (Lonza) for two hours

tag: timepoint

value: SEOV


title: RNA_NP_KO_R1


title: RNA_NP_WT_R2


title: ES2_H3k4me3


title: G171-RNA-seq


title: RNA_NP_WT_R1


title: Human_SEOV_12dpi_B

value: primary lung microvascular endothelial cells


title: cCR.ASCC_100


title: G163-RNA-seq


title: Human_SEOV_12dpi_A


title: IOSE11_A_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
IOSE11-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_IOSE11-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: Ovarian surface epithelial cell


title: G148-RNA-seq


title: Ring1b_Deltaex4_R2

value: embryonic stem cells (ESCs)

value: Rabbit pAb In-house


title: IOSE4_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
IOSE4-A-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup_pooled.tagAlign_x_IOSE4-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

value: H3K4me3 (Millipore 07-473)


title: Ring1b_Deltaex4_R1


title: EEC16_B_H3k4me3


title: Human_SEOV_4dpi_C


title: G120-RNA-seq


title: G208-RNA-seq


title: Ring1b_CSex4_R2


title: Human_SEOV_4dpi_A


title: G1-RNA-seq


title: Ring1b_CSex4_R1


title: Human_Mock_12dpi_C

value: Mock


title: IOSE11_25_Input_H3k4me3


title: IOSE4_A_H3k4me3


title: G83-HiC

description: CNV-balanced

data_processing:
Hi-C reads were aligned to the reference genome GRCh38 using bwa mem (v0.7.17) with “-SP5M”
Invalid data, including PCR duplicates and read pairs mapping to the same restriction fragment, were removed using pairtools (v0.3.0).
The runHiC (v0.8.4-r1; https://zenodo.org/badge/doi/10.5281/zenodo) and cooler (v0.8.6) packages were used to construct contact matrices at various resolutions.
Raw Hi-C matrices were corrected using a modified matrix balancing method to account for CNV effects and other systematic biases including mappability, GC content, and restriction enzyme sites, all processed via Neoloopfinder (v0.3.0.post4).
Assembly: GRCh38
Supplementary files format and content: .mcool file contains Hi-C contact matrices in a sparse format, storing the non-zero values of the upper triangular matrix in the HDF file.mcoolfiles can include multiple normalisations and resolutions within the same file.

extract_protocol:
Hi-C was performed on 0.5-1 million cells from each GSC line using the Hi-C+ kit (Arima Genomics) according to the manufacturer’s instructions.
Arima-HiC Kit, Library Preparation using KAPA Hyper Prep Kit

tag: assay

value: Hi-C


title: Human_Mock_12dpi_B


title: FT282_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.
rep1-rep2.overlap.bfilt.narrowPeak.gz

value: Fallopian tube derived epithelial cell


title: IOSE4_B_H3k4me3


title: G62-HiC

description: CNV-balanced

value: glioblastoma stem-like cells


title: IOSE11_B_H3k4me3


title: G61-HiC

description: CNV-balanced


title: FT282_B_H3k4me3


title: Human_Mock_12dpi_A


title: Ring1b_WT_R1


title: Human_SEOV_4dpi_B


title: Human_Mock_4dpi_C


title: FT282_A_H3k4me3


title: G457-HiC

description: CNV-balanced


title: Aebp2_Deltaex4_R2

value: Cell Signaling #14129S


title: G452P-HiC

description: CNV-balanced


title: Aebp2_CSex4_R2


title: FT33_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
rep1_rep2.overlap.bfilt.narrowPeak.gz


title: G452C-HiC

description: CNV-balanced


title: Human_Mock_4dpi_B


title: FT33_H3k4me3


title: Human_Mock_4dpi_A


title: Aebp2_CSex4_R1


title: C, Day34

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

department: Graduate School of Medicine

institute: Osaka university

data_processing:
Sequencing was performed on an MGI DNBSEQ-G400 platform in a 100-base single-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
Sequenced reads were mapped to the mouse reference genome sequences (GRCm38) using Hisat2.
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: intestinal tract

extract_protocol:
A moderate amount of intestinal tract was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a TruSeq Stranded mRNA sample preparation kit (Illumina) without RPB (mRNA Purification Beads) process.

value: intestinal tract

value: control mice reared on normal feed until day 34


title: G450-HiC

description: CNV-balanced


title: Ring1b_WT_R2


title: Aebp2_WT_R2


title: FT246_25_Input_H3k4me3

description:
ChIP-Seq for H3K4me3 with Replicate 1 (R1) and Input available. Fastq provided for Replicate 1 (R1) and Input.
FT246-H3k4me3_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign_x_FT246-25-Input_5Jan2018_GRCh38_CGC_BWAmem.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz


title: G412-HiC

description: CNV-balanced


title: FT246_H3k4me3


title: G402R-HiC

description: CNV-balanced


title: Aebp2_Deltaex4_R1


title: 1KR, Day33

value: fed methionine-deficient diet until day 28, normal diet until day 33 and free-drinking DSS from day 18


title: H2Aub_Deltaex4_R2

value: Cell Signaling# 8240


title: Aebp2_WT_R1


title: H2Aub_CSex4_R2


title: 3KR, Day33

value: fed methionine-, tryptophan-, and niacin-deficient diet until day 28, normal diet until day 33 and free-drinking DSS from day 18


title: 3K, Day28

value: fed methionine-, tryptophan-, and niacin-deficient diet until day 28 and free-drinking DSS from day 18


title: H2Aub_CSex4_R1


title: G402-HiC

description: CNV-balanced


title: 2K, Day28

value: fed tryptophan- and niacin-deficient diet until day 28 and free-drinking DSS from day 18


title: 2KR, Day33

value: fed tryptophan- and niacin-deficient diet until day 28 , normal diet until day 33 and free-drinking DSS from day 18


title: G412R-HiC

description: CNV-balanced


title: G390-HiC

description: CNV-balanced


title: 1K, Day28

value: fed methionine-deficient diet until day 28 and free-drinking DSS from day 18


title: H2Aub_WT_R1

value: embryonic stem cells (ESCs)


title: H2Aub_WT_R2


title: H2Aub_Deltaex4_R1


title: R, Day28

value: fed normal diet until day 28 and free-drinking DSS from day 18


title: JI92, Embryo, DevStage 3, replication 1 [E_JI92.3.1]

city: Troubsko

first: Oldrich

last: Trneny

address: Zahradni 1

country: Czech Republic

institute: Agricultural research Ltd.

description:
gene_count_pea_dormancy.csv
fpkm_pea_dormancy.csv

data_processing:
Raw sequence reads were cleaned with adapter quality trimming process using BBDuk from BBTools (minlen=25 qtrim=rl trimq=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo)
Sequences were mapped to reference sequence using HISAT2 v2.1.0
Reference sequence-guided assembly was performed using StringTie v2.1.0
Genotype transcripts were compared with reference transcripts using gffcompare
Merging all transcripts from all samples was performed using StringTie v2.1.0.
Read count was done by StringTie v2.1.0 using prepDE.py script
Normalization of genes count to FPKM values were performed using Ballgown v2.20.0 R package.
Assembly: Cameor v1a
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes FPKM normalized counts for all samples

organism: Lathyrus oleraceus

source_name: embryo

growth_protocol: glasshouse grown plants (spring period of February-June), UP Olomouc, CZ in 5 liters pots with substrate

extract_protocol:
Total RNA was isolated using PureLink™ Plant RNA Reagent (Invitrogen). Residual DNA was removed by Baseline-ZERO DNase (Epicenter) treatment followed by phenol/chloroform extraction.
Library preparation started with QC of RNA by Nanodrop, Agarose gel electrophoresis RNA degradation and contamination test and Agilent 2100 integrity checks and quantification. mRNA from organisms was enriched using oligo(dT) beads. Fragmentation of mRNA was done  by fragmentation buffer. The cDNA is synthesized by using mRNA template and random hexamers primer and a custom second-strand synthesis buffer with dNTPs, RNase H and DNA polymerase I. Finally, series of terminal repair, A ligation and sequencing adaptor ligation were performed. cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: no specific treatment to plants, well watered and fertilized, minimalization of stress conditions

value: embryo

value: DevStage 3


title: Mtf2_Deltaex4_R2

value: Protein Tech  #16208-1-AP/ Drosophila H2Av (Active Motif 61686)


title: JI1794, Embryo, DevStage 3, replication 2 [E_JI1794.3.2]

organism: Lathyrus oleraceus subsp. biflorus


title: JI92, Seed Coat, DevStage 3, replication 2 [SC_JI92.3.2]

source_name: seed coat

value: seed coat


title: Mtf2_Deltaex4_R1


title: JI1794, Embryo, DevStage 3, replication 1 [E_JI1794.3.1]


title: G394-HiC

description: CNV-balanced

value: glioblastoma stem-like cells

value: Hi-C


title: RR, Day33

value: intestinal tract

value: fed normal diet until day 33 and free-drinking DSS from day 18


title: JI92, Seed Coat, DevStage 3, replication 1 [SC_JI92.3.1]


title: Cameor, Embryo, DevStage 3, replication 2 [E_Ca.3.2]

value: Cameor


title: JI1794, Seed Coat, DevStage 3, replication 2 [SC_JI1794.3.2]


title: Mtf2_CSex4_R2


title: Mtf2_CSex4_R1


title: JI1794, Seed Coat, DevStage 3, replication 1 [SC_JI1794.3.1]


title: JI92, Embryo, DevStage 3, replication 2 [E_JI92.3.2]


title: JI64, Embryo, DevStage 3, replication 2 [E_JI64.3.2]


title: Cameor, Seed Coat, DevStage 3, replication 2 [SC_Ca.3.2]


title: JI64, Embryo, DevStage 3, replication 1 [E_JI64.3.1]


title: Cameor, Embryo, DevStage 3, replication 1 [E_Ca.3.1]


title: Cameor, Seed Coat, DevStage 3, replication 1 [SC_Ca.3.1]


title: Mtf2_WT_R1


title: JI64, Seed Coat, DevStage 3, replication 2 [SC_JI64.3.2]


title: Jarid2_Deltaex4_R2

value: Novus #NB100-2214/ Drosophila H2Av (Active Motif 61686)


title: JI261, Embryo, DevStage 5, replication 2 [E_JI261.5.2]

value: DevStage 5


title: Jarid2_Deltaex4_R1


title: Jarid2_CSex4_R2


title: Cameor, Seed Coat, DevStage 5,  [SC_Ca.5]


title: Cameor, Embryo, DevStage 1, replication 1 [E_Ca.1.1]

value: DevStage 1


title: JI92_17, Seed Coat, DevStage 4, replication 2, year 2017 [SC_JI92_17.4.2]

value: DevStage 4


title: Jarid2_CSex4_R1


title: Jarid2_WT_R2


title: JI261, Embryo, DevStage 4, replication 2 [E_JI261.4.2]


title: Mtf2_WT_R2


title: Jarid2_WT_R1


title: JI92_17, Seed Coat, DevStage 4, replication 1, year 2017 [SC_JI92_17.4.1]


title: JI92_17, Seed Coat, DevStage 2, replication 2, year 2017 [SC_JI92_17.2.2]

value: DevStage 2


title: JI261, Embryo, DevStage 4, replication 1 [E_JI261.4.1]


title: JI92_17, Seed Coat, DevStage 2, replication 1, year 2017 [SC_JI92_17.2.1]


title: JI92_17, Seed Coat, DevStage 1, replication 2, year 2017 [SC_JI92_17.1.2]


title: JI64, Seed Coat, DevStage 3, replication 1 [SC_JI64.3.1]


title: JI261, Embryo, DevStage 3, replication 2 [E_JI261.3.2]


title: H3K27me3_S-3D_R1

value: H3K27me3 (Millipore 07-449) / Drosophila H2Av (Active Motif 61686)


title: H3K27me3_L-3D_R1

value: embryonic stem cells (ESCs)


title: JI261, Embryo, DevStage 3, replication 1 [E_JI261.3.1]


title: Cameor, Seed Coat, DevStage 4, replication 2 [SC_Ca.4.2]


title: JI261, Seed Coat, DevStage 5, replication 1 [SC_JI261.5.1]


title: JI92_17, Seed Coat, DevStage 1, replication 1, year 2017 [SC_JI92_17.1.1]


title: Cameor, Seed Coat, DevStage 4, replication 1 [SC_Ca.4.1]


title: H3K27me3_S_R1


title: H3K27me3_S_R2


title: H3K27me3_L_R2


title: JI261, Seed Coat, DevStage 5, replication 2 [SC_JI261.5.2]


title: JI261, Seed Coat, DevStage 4, replication 2 [SC_JI261.4.2]


title: JI92, Embryo, DevStage 5, replication 2 [E_JI92.5.2]


title: H3K27me3_WTforSL


title: H3K27me3_L_R1


title: JI261, Embryo, DevStage 5, replication 1 [E_JI261.5.1]


title: JI261, Seed Coat, DevStage 4, replication 1 [SC_JI261.4.1]


title: JI261, Seed Coat, DevStage 3, replication 2 [SC_JI261.3.2]


title: ES_+2D_RNAseq_rep3

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

data_processing:
Basic quality control for raw sequencing reads were performed using FastQC(v0.11.9). Sequencing adaptors and low-quality reads/bases were further removed using trimmomatic (v0.39).
Clean reads were then aligned to the mouse reference genome (mm10) using STAR (v2.7.5a) and only uniquely mapped reads were retained.
Raw counts for each gene were estimated using htseq-count (v0.13.5) from the aligned bam files.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for every gene and every sample

source_name: Mouse embryonic stem cell

extract_protocol:
Cell RNA were extracted and purified by Total RNA Extraction Kit (LS1040, Promega).
RNA-seq libraries were constructed according to the standard protocol of NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, 7530L).

value: Mouse embryonic stem cell

value: mESC-treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days

tag: time

value: Day 2


title: Cameor, Seed Coat, DevStage 2, replication 1 [SC_Ca.2.1]


title: ES_+2D_RNAseq_rep2


title: JI92, Embryo, DevStage 5, replication 1 [E_JI92.5.1]

value: embryo


title: JI261, Seed Coat, DevStage 1, replication 2 [SC_JI261.1.2]

value: seed coat


title: ES_+2D_RNAseq_rep1


title: JI92, Embryo, DevStage 4, replication 2 [E_JI92.4.2]


title: JI261, Seed Coat, DevStage 1, replication 1 [SC_JI261.1.1]


title: JI92, Embryo, DevStage 4, replication 1 [E_JI92.4.1]


title: JI64_17, Seed Coat, DevStage 4, replication 2, year 2017 [SC_JI64_17.4.2]


title: ES_-2D_RNAseq_rep3

value: mESC-untreated

value: Day -2


title: ES_-2D_RNAseq_rep2


title: Cameor, Seed Coat, DevStage 2, replication 2 [SC_Ca.2.2]


title: JI261, Seed Coat, DevStage 3, replication 1 [SC_JI261.3.1]

value: DevStage 3


title: ES_-2D_RNAseq_rep1


title: JI64_17, Seed Coat, DevStage 4, replication 1, year 2017 [SC_JI64_17.4.1]


title: JI64_17, Seed Coat, DevStage 2, replication 2, year 2017 [SC_JI64_17.2.2]


title: JI92, Embryo, DevStage 2, replication 1 [E_JI92.2.1]


title: JI92, Seed Coat, DevStage 5,  [SC_JI92.5]


title: JI92, Seed Coat, DevStage 4, replication 1 [SC_JI92.4.1]


title: JI64_17, Seed Coat, DevStage 2, replication 1, year 2017 [SC_JI64_17.2.1]


title: DUXKO_c19_TSC.2

source_name: induced TSC

tag: cell source

value: Dux-KO-c19 induced TSC

value: induced TSC


title: MG1_TS_C2.3

value: NaB induced TSC


title: JI92, Seed Coat, DevStage 4, replication 2 [SC_JI92.4.2]


title: JI92, Embryo, DevStage 2, replication 2 [E_JI92.2.2]


title: JI1794, Embryo, DevStage 5, replication 2 [E_JI1794.5.2]

value: DevStage 5


title: JI64_17, Seed Coat, DevStage 1, replication 1, year 2017 [SC_JI64_17.1.1]

value: DevStage 1


title: DUXKO_c19_TSC.1


title: JI92, Seed Coat, DevStage 2, replication 2 [SC_JI92.2.2]


title: MG1_TS_C2.2


title: MG1_TS_C2.1


title: Cameor, Seed Coat, DevStage 1, replication 2 [SC_Ca.1.2]

value: Cameor


title: JI1794, Embryo, DevStage 5, replication 1 [E_JI1794.5.1]


title: JI1794, Embryo, DevStage 4, replication 2 [E_JI1794.4.2]

value: DevStage 4


title: MG1_TS_C1.5


title: JI92, Seed Coat, DevStage 2, replication 1 [SC_JI92.2.1]

value: DevStage 2


title: JI92, Seed Coat, DevStage 1, replication 2 [SC_JI92.1.2]


title: JI1794, Embryo, DevStage 4, replication 1 [E_JI1794.4.1]


title: JI1794, Embryo, DevStage 2, replication 2 [E_JI1794.2.2]


title: MG1_TS_C1.4


title: JI92, Seed Coat, DevStage 1, replication 1 [SC_JI92.1.1]


title: MG1_TS_C1.3


title: JI1794, Seed Coat, DevStage 5, replication 2 [SC_JI1794.5.2]


title: JI1794, Embryo, DevStage 2, replication 1 [E_JI1794.2.1]


title: Cameor, Embryo, DevStage 5, replication 2 [E_Ca.5.2]


title: RoB-positive3

city: Burnaby

first: Sanam

last: meraj

email: smeraj@sfu.ca, sammeraj26@gmail.com

state: British Columbia

address: 8888 university drive

department: Biological Sciences

country: Canada

institute: simon fraser university

data_processing:
We used the gene hit counts table for downstream differential expression (DE) analysis, using DESeq2 (48) to compare gene expression among groups of samples. We used the Wald's test to generatep-values and Log2 Fold Changes (Log2FC). We considered genes to be differentially expressed (DE) when adjustedp-values were < 0.05 and the overall absolute Log2FC was > 1. The data for immune transcripts were mined to evaluate their expression levels, and are reported as transcripts per million (TPM).
Assembly: Cimex_lectularius_Clec_2.1 reference genome available on ENSEMBL
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Cimex lectularius

source_name: RoB; body minus head and midgut tissues

growth_protocol: Bed bug colonies were maintained as previously described (46). Briefly, colonies were kept in the insectary of Simon Fraser University (SFU) at a temperature of ∼24 °C, ambient relative humidity, and a photoperiod of 14 h light to 10 h dark. Groups of 150 bed bugs were maintained in 50-mL glass jars fitted with a square of cardboard (2 cm × 2 cm) at the bottom and a strip of cardboard (2 cm × 4 cm) diagonally across the jar. Bed bugs in separate jars were fed on the forearm of a volunteer (Regine Gries) once every month. For feeding, jars were covered with fine mesh, inverted, and pressed against the forearm so that the bed bugs could feed through the mesh.

extract_protocol:
Midgut and RoB tissues (RoB = rest of the body: bodies without heads and midgut tissues) of treatment and control bed bugs were dissected 12 h after an immune challenge, and total RNA was extracted using TRizol reagent (Invitrogen) following the manufacturer’s recommendations. The samples were quantified on a Nanodrop 1000 spectrophotometer v. 3.7 (Thermo Fisher Scientific, USA). RNA samples were used to generate complementary DNA (cDNA) for analysis using quantitative real-time polymerase chain reaction (qPCR) and transcriptome assembly.
We created a de novo transcriptome assembly from RNA extracted from midgut and RoB tissues of male bed bugs 12 h after ingesting blood containing E. coli or B. subtilis. RNA purification, first and second strand synthesis, adaptor ligation, quantification, validation, and Illumina sequencing were all done at GENEWIZ LLC. (South Plainfield, NJ, USA). The RNA samples were sequenced using a paired-end (PE) configuration, consisting of two 150 base pair (bp) strands. HiSeq Control Software (HCS) was used for image analysis and base calling. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and demultiplexed with bcl2fastq 2.17 software (Illumina Inc, San Diego, CA, USA). For index sequence identification, one mismatch was allowed. After examining the quality of raw data, adapter sequences and nucleotides of poor quality were removed from sequence reads using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genome available on ENSEMBL, using STAR aligner v.2.5.2b which utilizes a splice aligner to detect splice junctions and incorporates them to help align the entire read sequences to generate Binary Alignment Map (BAM) files. In the Subread package version 1.5.2, we used the ‘Counts’ feature to calculate the unique gene count. Only reads predicted to fall within exons were counted.

treatment_protocol: Microbes (Escherichia coli(K12/D31) andBacillus subtilis (ATCC 6633)) were grown in separate Lysogeny Broth (LB) (47) for 17 h at 30 °C in a shaking incubator (220 revolutions per minute). Subsequently, aliquots of these bacteria were reinoculated into fresh broth and incubated 4 h under the same conditions to reach the log phase of growth. The bacteria were then washed three times in sterile phosphate buffered saline (PBS; 0.01 M phosphate buffer, 2.7 mM potassium chloride, 0.137 M sodium chloride, pH 7.4), and were diluted in sterile defibrinated rabbit blood to a final concentration of ~1 × 106cells/mL. Male bed bugs (food-deprived >20 days) fed 1 h on defibrinated, microbe-laced (E. coliorB. subtilis) rabbit blood in a water-jacketed membrane feeder (Thermo Fisher Scientific Isotemp 2150 B14, USA) set to 37 °C, with stretched out parafilm as the membrane. Control bed bugs ingested sterile blood. Fully engorged bed bugs were separated and housed in glass jars until analysis. Each experiment had five replicates, with each replicate containing five insects in treatment and control samples.

value: RoB; body minus head and midgut tissues

value: WT

value: Ingestion of Gram-negative (Gr–) bacterium Escherichia coli


title: RoB-positive2


title: MG1_TS_C1.1


title: MG1_TS_C1.2


title: OGTS.2

source_name: TSC

value: TSC derived from mouse blastocyst

value: TSC


title: Cameor, Embryo, DevStage 5, replication 1 [E_Ca.5.1]

value: embryo


title: RoB-negative2

value: Ingestion of Gram-positive (Gr+) bacterium Bacillus subtilis


title: Cameor, Embryo, DevStage 4, replication 1 [E_Ca.4.1]


title: Cameor, Embryo, DevStage 4, replication 2 [E_Ca.4.2]


title: OGTS.1


title: JI1794, Seed Coat, DevStage 4, replication 2 [SC_JI1794.4.2]

value: seed coat


title: JI1794, Seed Coat, DevStage 4, replication 1 [SC_JI1794.4.1]


title: RoB-negative3


title: JI1794, Seed Coat, DevStage 5, replication 1 [SC_JI1794.5.1]


title: RoB-control3

value: Ingestion of sterile blood


title: JI1794, Seed Coat, DevStage 2, replication 2 [SC_JI1794.2.2]


title: RoB-negative1


title: Cameor, Embryo, DevStage 2, replication 2 [E_Ca.2.2]


title: Cameor, Embryo, DevStage 2, replication 1 [E_Ca.2.1]


title: Cameor, Embryo, DevStage 1, replication 2 [E_Ca.1.2]


title: JI1794, Seed Coat, DevStage 2, replication 1 [SC_JI1794.2.1]


title: Mac_572, WT, D20 post-influenza

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

institute: University of Pennsylvania

data_processing:
Reads were aligned to the mm10 mouse genome using Kallisto and imported into R Studio for analysis via the TxImport package.
Transcripts with low counts were filtered out if they had 1) zero reads in any sample, or 2) less than at least one count per million in at least two samples.  Data was then normalized using the trimmed mean of M values normalization method in the EdgeR package.
Mean-variance trend fitting, linear modeling, and Bayesian statistics for differential gene expression analysis were performed using the Voom, LmFit, and eBayes functions, respectively, of the Limma package, yielding differentially expressed genes between Sparcl1-OE and WT groups.
Assembly: mm10
Supplementary files format and content: abundance.tsv files generated from Kallisto alignment and csv files of normalized RPKM values

source_name: Sorted primary cells

extract_protocol:
RNA extracted and amplified (10 ng RNA/sample) using SMART-Seq® HT kit (Takara Bio, #634455) according to the manufacture’s instruction
PolyA-selected RNA was used to generate libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions

tag: cell line

value: Sorted primary cells

value: pulmonary macrophages

tag: infection

value: Influenza

value: Day 20


title: RoB-control2

tag: genotype


title: RoB-positive1

tag: treatment


title: Mac_571, OE, D20 post-influenza

tag: cell type


title: RoB-control1

tag: tissue


title: JI1794, Seed Coat, DevStage 1, replication 2 [SC_JI1794.1.2]

tag: developmental stage

value: DevStage 1


title: Cameor, Seed Coat, DevStage 1, replication 1 [SC_Ca.1.1]

value: Cameor


title: Mac_541, OE, D20 post-influenza


title: midgut-positive3

source_name: midgut

value: midgut


title: Mac_569, OE, D20 post-influenza


title: JI1794, Seed Coat, DevStage 1, replication 1 [SC_JI1794.1.1]


title: PI358617, Embryo, DevStage 1, replication 1 [E_PA.1.1]

organism: [Pisum sativum] subsp. abyssinicum


title: midgut-positive2


title: PI358617, Seed Coat, DevStage 5, replication 2 [SC_PA.5.2]

value: DevStage 5


title: Mac_575, WT, D20 post-influenza


title: JI64, Embryo, DevStage 4, replication 2 [E_JI64.4.2]

value: DevStage 4


title: RNA_KO_S_R2

data_processing:
ChIP-seq analysis: Sequence reads of mouse samples were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1.  Sequence reads of mouse with fly spike-in samples were mapped to the mouse + fruit fly genome (mm10+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID 18798982). ChIP-seq profiles were produced with SeqCode (PubMed ID 34599234). DiffBind (PubMed ID 22217937) was run next over the union of peaks from each pair of replicates of the same experiment to find those peaks that were significantly enriched in both replicates in comparison to the corresponding controls (parameters: categories = DBA_CONDITION, block = DBA_REPLICATE and method = DBA_DESEQ2_BLOCK, P value < 0.05 and FDR < 10-5).
RNA-seq analysis: Sequence reads were mapped against the mm10 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DESeq2 (PubMed ID 25516281) was run to perform differential gene expression analysis of each annotated gene in RefSeq
Assembly: mm10
Supplementary files format and content: Genome-wide profiles (Bedgraph)
Supplementary files format and content: Peaks (BED)
Supplementary files format and content: DESeq2 (TXT): columns are gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj

growth_protocol: Serum 20% + LIF

value: embryonic stem cells (ESCs)


title: midgut-positive1

value: WT

value: Ingestion of Gram-negative (Gr–) bacterium Escherichia coli


title: midgut-negative2


title: JI64, Embryo, DevStage 2, replication 2 [E_JI64.2.2]

value: DevStage 2


title: PI358617, Seed Coat, DevStage 4, replication 2 [SC_PA.4.2]


title: JI64, Embryo, DevStage 2, replication 1 [E_JI64.2.1]

value: embryo


title: RNA_KO_S_R1


title: RNA_KO_L_R2


title: PI358617, Seed Coat, DevStage 5, replication 1 [SC_PA.5.1]


title: RNA_KO_L_R1


title: PI358617, Embryo, DevStage 3, replication 2 [E_PA.3.2]

value: DevStage 3


title: JI64, Embryo, DevStage 1, replication 2 [E_JI64.1.2]


title: RNA_KO_R3


title: midgut-negative1

value: Ingestion of Gram-positive (Gr+) bacterium Bacillus subtilis


title: midgut-control3

value: Ingestion of sterile blood


title: JI64, Embryo, DevStage 1, replication 1 [E_JI64.1.1]


title: JI64, Embryo, DevStage 4, replication 1 [E_JI64.4.1]


title: PI358617, Embryo, DevStage 3, replication 1 [E_PA.3.1]


title: JI64, Seed Coat, DevStage 5, replication 2 [SC_JI64.5.2]

value: seed coat


title: RNA_KO_R1


title: RNA_KO_R2


title: PI358617, Seed Coat, DevStage 3, replication 2 [SC_PA.3.2]


title: midgut-negative3


title: PI358617, Seed Coat, DevStage 4, replication 1 [SC_PA.4.1]


title: PI358617, Seed Coat, DevStage 2, replication 2 [SC_PA.2.2]


title: JI64, Seed Coat, DevStage 5, replication 1 [SC_JI64.5.1]


title: RNA_Deltaex4_R2


title: PI358617, Seed Coat, DevStage 3, replication 1 [SC_PA.3.1]


title: JI64, Seed Coat, DevStage 4, replication 2 [SC_JI64.4.2]


title: RNA_Deltaex4_R1


title: PI358617, Seed Coat, DevStage 2, replication 1 [SC_PA.2.1]


title: Vero HSV1 8h rep1

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
*library strategy: GRO-seq
Reads were trimmed using HOMER 4.3 software to remove poly-A tails and reads shorter than 25 nt were discarded. Quality control using FastQC tool, bases with poor quality were trimmed using FastX toolkit so that minimum 97 % of all bases in one read have to have a minimum phred quality score of 10. Alignments to ChlSab1.1 genome were done using bowtie-0.12.7 allowing up to two mismatches and up to three locations per read and the best alignment was reported. Differentially expressed genes were detected using ChlSab1.1.95.gtf coordinates, analyzeRNA.pl workflow of HOMER 4.3 and edgeR v3.2.2.
Assembly: ChlSab1.1
Supplementary files format and content: tab-delimited text file containing RPKMs for each sample and results from differential expression analysis

organism: Chlorocebus aethiops

source_name: Kidney

extract_protocol:
Both infected and noninfected samples of VERO cells (ATCC CCL-81) were prepared as two biological replicates. Infected sample replicates were infected independently with MOI 5. Cell nuclei were extracted post-infection at the indicated times. Cells were washed with PBS and scraped into swelling buffer containing 10 mM Tris-HCl (pH 7.5), 2 mM MgCl2, 3 mM CaCl2, 1 U/ml SUPERase-In and 1 U/ml RNAsin plus in ultrapure water (Gibco 15564-027, Invitrogen AM9530G, Sigma-Aldrich 21115-100ml, Invitrogen 10977-035, Invitrogen AM2694, Promega N2611). Cells were centrifuged at 400 x g for 10 minutes. Formed cell pellet was resuspended into swelling buffer containing 10 % glycerol and 4 U/ml SUPERase-In (ACROS ORGANICS 327255000, Invitrogen AM2694). Nuclei were extracted by incubating the cells in swelling buffer supplemented 10 % glycerol and 1% Igepal (Igepal®CA-630 I8896-50ml) for 5 minutes. Lysis buffer composted of swelling buffer, 0.5 % Igepal, 10% glycerol, 1 U/ml SUPERase-In and 1 U/ml RNAsin plus was added to the extracted nuclei. Nuclei were washed once with lysis buffer. Isolated nuclei were resuspended into freezing buffer containing 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 50 mM Tris-HCl (pH 8.3) and 2 U/ml SUPERase-In (Invitrogen AM9260G, Gibco 15564-027 Invitrogen 15568-025) and frozen.
Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNAseH treated, circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.

value: Kidney

value: Vero

value: epithelial cell

value: HSV1 infection, 8h pi


title: JI64, Seed Coat, DevStage 2, replication 2 [SC_JI64.2.2]


title: Vero HSV1 8h rep2


title: PI358617, Seed Coat, DevStage 1, replication 2 [SC_PA.1.2]

value: DevStage 1


title: RNA_CSex4_R2


title: Vero HSV1 4h rep2

value: HSV1 infection, 4h pi


title: Vero HSV1 4h rep1


title: RNA_CSex4_R1


title: RNA_WT_R3


title: JI64, Seed Coat, DevStage 2, replication 1 [SC_JI64.2.1]


title: midgut-control2

value: midgut


title: midgut-control1


title: Vero mock rep2

value: mock


title: PI358617, Embryo, DevStage 5, replication 1 [E_PA.5.1]

value: DevStage 5


title: JI64, Seed Coat, DevStage 1, replication 2 [SC_JI64.1.2]


title: JI64, Seed Coat, DevStage 1, replication 1 [SC_JI64.1.1]


title: Vero mock rep1


title: RNA_WT_R2

value: embryonic stem cells (ESCs)


title: PI358617, Embryo, DevStage 4, replication 2 [E_PA.4.2]

value: DevStage 4


title: RNA_WT_R1


title: EP cells H3K4me3_CUT_Tag rep 2

first: Qirui

last: Wang

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: CUT&Tag-seq sample for ctrl

data_processing:
libraries were sequenced on Illumina® platform
The raw reads were filtered to clean reads with fatsp software.
Then, the clean reads were mapped to the mouse genome GRCm39 using bowtie2 software.
MACS2 and ChIPseeker software were used for peak identification and annotation, respectively.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Epidermis, FACS-sorted,P0

extract_protocol:
P0 mice were euthanized and the back skin was carefully removed using scissors and forceps. The extracted back skin was then placed into a culture dish with the dermal side facing downwards. Next, to separate the epidermis from the dermis, the dispase II was used to incubate these skin tissues overnight at 4°C. The following day, the skin was transferred to a new culture dish and the epidermis was carefully separated from the dermis using forceps. Subsequently, the separated epidermis was finely diced and incubated with 0.25% trypsin solution at 37 °C for 5 minutes. The digested solution was then filtered and subjected to centrifugation at 500g for 5 minutes at 4 °C, leading to the enrichment of primary epidermal keratinocytes in the resultant cell pellet. We further used fluorescence-activated cell sorting (FACS) to isolate cells that specifically express integrin α6 (CD49f), which were progenitor cells of the epidermis and hair placodes/germs. NovoNGS High-Sensitivity CUT&Tag 3.0 Kit is used to extract DNA fragments.
We constructed the libraries using the NovoNGS High-Sensitivity CUT&Tag 3.0 Kit (Novoprotein, N259-YH01) according to the manufacturer’s instructions. In Brief, epidermal basal layer cells (approximately 20,000 cells per sample) isolated by the above method were bound with Concanavalin A-coated beads. Then, they were incubated with primary antibody anti-H3K4me3 (1:50; Invitrogen, MA5-11199) for 2 hours at room temperature. The beads were washed several times with wash buffer and then incubated with secondary antibody goat anti-rabbit Immunoglobulin G (1:100; Invitrogen, 31210) for 1 hour at room temperature. After washing again several times, these beads were incubated with the ChiTag pAG-Tn5 transposon for 1 hour at room temperature. Then, tagmentation buffer (containing MgCl2) was added and incubated at 37°C for 1 hour, and this process was stopped by adding 10% SDS and incubating at 55°C for 10 minutes. The DNA fragments were then purified and extracted using Tagment DNA Extraction Beads. A 50 ul PCR amplification system was prepared: 33 μl DNA fragments, 2.5 μl i5 primer (10μM, N501), 2.5 μl i7 primer (10μM, N701 or N702) and 10 μl 5×mpliMix buffer. The number of cycles of amplification was determined by agarose gel electrophoresis.

value: Epidermis, FACS-sorted,P0

value: epidermal progenitor cell

value: H3K4me3 (Invitrogen,MA5-11199)


title: JI64, Seed Coat, DevStage 4, replication 1 [SC_JI64.4.1]


title: PI358617, Embryo, DevStage 4, replication 1 [E_PA.4.1]

value: embryo


title: blastoid-scRNA-seq

description: blastoid.processed_data.tar.gz (contains raw counts and a meta file for blastoid-scRNAseq data)

data_processing:
Raw sequencing data were first preprocessed with Cell Ranger pipeline (version 3.1.0) to generate the feature-barcode unique molecular identifier (UMI) count matrix for each sample.
We next utilized the 'cellranger aggr' function to combine results of all samples (D-2 to D10) together to get the final UMI count matrix with sequencing depth normalized.
Subsequent analyses were mainly using the Seurat package (version 3.2.3).
Assembly: mm10
Supplementary files format and content: raw umi-count matrix for cells from blastoid

source_name: Mouse blastoid

growth_protocol: Mouse embryonic stem cells were first cultured in ESC medium and then tranferred to TSC F4H medium.

extract_protocol: Cells purfied by FACS were used for scRNA-seq library construction.scRNA-seq libraries were constructed according to the standard protocol of Chromium Next GEM Chip G Single Cell Kit (1000121, 10x Genomics) .

treatment_protocol: Mouse ES cells were plated into one well of the 6-well culture dishes and incubated with ESC medium (0.5 mM sodium butyrate) for 2 days. Subsequently, cells were digested with 0.05% trypsin and resuspended by 1×TSC medium with 0.5 mM NaB and transferred to 6-well plates coated with irradiated MEF cells. Change the medium every two days. After 4 days of incubation, cells were digested and resuspended by 1.5×TSC medium with 0.5 mM NaB and transferred to a new 6-well with MEF cells, continue cultured for 4 to 6 days, and changed the medium every two days.

value: Mouse blastoid

value: mESCs were treated with 0.5 mM NaB for 2 days in ESC medium, followed by culturing in TSC medium for 8 days. After that, cells were transferred to AggreWell 400 with iblastoid medium and cultured for 6 days.


title: PI358617, Embryo, DevStage 2, replication 2 [E_PA.2.2]

value: DevStage 2


title: TA_9_L

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
The gene expression matrices were generated from raw reads using scopetools (https://anaconda.org/singleronbio/scopetools). The first step involved filtering out reads without polyT tails and extracting cell barcodes and unique molecular identifiers (UMIs). Adapters and polyA tails were trimmed before aligning the reads to the pre-mRNA reference. Then reads with the same cell barcode, UMI, and gene were grouped together to count the number of UMIs per gene per cell.
Assembly: scRNA-seq: mm39
Supplementary files format and content: scRNA-seq: tar file containing barcodes.tsv, genes.tsv, and matrix.mtx

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: thalamus

extract_protocol:
Cartilage were lysesd and pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. Tissues were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until tissues were dissociated into single cells via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS.
Chromium Single Cell 3' Reagents Kits version 2

value: thalamus

value: unilateral ACES, for the contralateral hemisphere collection


title: TA_9_R

value: ACES bilaterally


title: Suz12_KO_R1

value: Polyclonal rabbit antibody designed for this work (peptide GFSEINSKEKALETDSVC)


title: Suz12_Deltaex4_R2


title: Suz12_KO_R2


title: TA_8_R

value: unilateral ACES, for the ipsilateral hemisphere collection


title: EP cells H3K4me3_CUT_Tag rep 1

description: CUT&Tag-seq sample for ctrl


title: PI358617, Embryo, DevStage 1, replication 2 [E_PA.1.2]

value: DevStage 1


title: PI358617, Embryo, DevStage 5, replication 2 [E_PA.5.2]


title: ES+NaB_+2D_Input-rep2

data_processing:
Raw sequencing reads were first subjected to basic quality control using FastQC (v0.11.9). Sequencing adapters and low-quality reads/bases were removed using Trim Galore (v0.6.4_dev).
Clean reads were then aligned to the mouse reference genome (mm10) using bowtie2 (v2.4.2, --maxins 2000 --no-unal --no-mixed --no-discordant). Only uniquely mapped reads with mapQ >= 30 were retained. Duplicated reads were also discarded.
Aligned bam files of two replicates except for day -2 input (only input-rep1 was used considering low quality of input-rep2) were merged by samtools (v1.10). Normalized ChIP-seq signal (CPM, counts per million mapped reads) was calculated using bamCompare in deepTools (v3.5.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files with normalized ChIP-seq signal (CPM)

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed according to the standard protocol of EZ-Magna ChIPTM A/G kit (Millipore-17-10086).

treatment_protocol: Mouse ES cells were plated into one well of the 6-well culture dishes and incubated with ESC medium (0.5 mM sodium butyrate) for 2 days. Subsequently, cells were digested with 0.05% trypsin and resuspended by 1×TSC medium with 0.5 mM NaB and transferred to 6-well plates for 2 days.

value: Mouse embryonic stem cell

value: mESC-treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days

value: Day 2


title: Suz12_CSex4_R1

value: embryonic stem cells (ESCs)


title: Suz12_Deltaex4_R1


title: TA_7_R

value: Sham


title: PI358617, Seed Coat, DevStage 1, replication 1 [SC_PA.1.1]

value: seed coat


title: ES+NaB_+2D_Input-rep1


title: TA_7_L


title: ES_-2D_Input-rep1

value: mESC-untreated

value: Day -2


title: TA_2_L


title: Suz12_WT_R2


title: ES+NaB_+2D_H3K9ac-rep2


title: G323-HiC

description: CNV-balanced

value: glioblastoma stem-like cells

value: Hi-C


title: TA_10_R


title: G351-HiC

description: CNV-balanced


title: Suz12_WT_R1


title: TA_1_L


title: ES+NaB_+2D_H3K9ac-rep1


title: PI358617, Embryo, DevStage 2, replication 1 [E_PA.2.1]

value: embryo

value: DevStage 2


title: H3K27me3_KO_R3

value: H3K27me3 (Millipore 07-449) / Drosophila H2Av (Active Motif 61686)


title: G28-HiC

description: CNV-balanced


title: HP_8_R

source_name: hippocampus

value: hippocampus


title: ES_-2D_H3K9ac-rep1


title: H3K27me3_KO_R2

value: H3K27me3 (Millipore 07-449)


title: HP_7_R


title: H3K27me3_KO_R1


title: HP_7_L

value: unilateral ACES, for the contralateral hemisphere collection


title: G275-HiC

description: CNV-balanced

source_name: glioblastoma stem-like cells


title: H3K27me3_Deltaex4_R3


title: H3K27me3_Deltaex4_R2


title: ES_-2D_H3K27ac-rep2


title: G213-HiC biorep2

description: CNV-balanced


title: HP_2_L

value: unilateral ACES, for the ipsilateral hemisphere collection


title: G23-HiC

description: CNV-balanced


title: H3K27me3_CSex4_R2


title: HP_1_L


title: HP_10_R

value: ACES bilaterally


title: ES_-2D_H3K27ac-rep1

value: Mouse embryonic stem cell


title: G213-HiC biorep1

description: CNV-balanced


title: G275R-HiC

description: CNV-balanced


title: D10_NaB_mESC_TSC medium+10D

data_processing:
Raw sequencing data were first preprocessed with Cell Ranger pipeline (version 3.1.0) to generate the feature-barcode unique molecular identifier (UMI) count matrix for each sample.
We next utilized the 'cellranger aggr' function to combine results of all samples (D-2 to D10) together to get the final UMI count matrix with sequencing depth normalized.
Subsequent analyses were mainly using the Seurat package (version 3.2.3).
Genome_build: mm10
Supplementary_files_format_and_content: raw umi-count matrix for cells from blastoid

extract_protocol:
Cells purfied by FACS were used for scRNA-seq library construction.
scRNA-seq libraries were constructed according to the standard protocol of Chromium Next GEM Chip G Single Cell Kit (1000121, 10x Genomics) .

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 10 days

value: Day 10


title: CT_9_L

source_name: cortex

value: cortex


title: G318-HiC

description: CNV-balanced


title: G208-HiC biorep2

description: CNV-balanced


title: D4_NaB_mESC_TSC medium+4D

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 4 days

value: Day 4


title: H3K27me3_WT_R2

value: embryonic stem cells (ESCs)


title: CT_9_R


title: ES_-2D_H3K9ac-rep2

value: mESC-untreated

value: Day -2


title: H3K27me3_WT_R3


title: H3K27me3_CSex4_R1


title: ES+NaB_+2D_H3K27ac-rep2

value: mESC-treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days

value: Day 2


title: G171-HiC

description: CNV-balanced

value: glioblastoma stem-like cells

value: Hi-C


title: H3K27me3_Deltaex4_R1

value: H3K27me3 (Millipore 07-449)


title: CT_7_R

value: Sham


title: CT_8_R

value: unilateral ACES, for the ipsilateral hemisphere collection


title: G181-HiC

description: CNV-balanced


title: ES+NaB_+2D_H3K27ac-rep1


title: D2_NaB_mESC_TSC medium+2D

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days


title: MG1-NaB-GFPpositive rep2

data_processing:
Basic quality control for raw sequencing reads were performed using FastQC(v0.11.9). Sequencing adaptors and low-quality reads/bases were further removed using trimmomatic (v0.39).
Clean reads were then aligned to the mouse reference genome (mm10) using STAR (v2.7.5a) and only uniquely mapped reads were retained.
Raw counts for each gene were estimated using htseq-count (v0.13.5) from the aligned bam files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts for every gene and every sample

source_name: 2C-like cell

growth_protocol: Mouse embryonic stem cells were cultured in ESC medium, and mouse trophoblast stem cells were cultured in TSC F4H medium.

treatment_protocol: Mouse ES cells were plated into one well of the 6-well culture dishes and incubated with ESC medium (0.5 mM sodium butyrate) for 2 days.

value: Mouse embryonic stem cell

value: GFP positive cell from mESC after treated with 0.5 mM NaB for 2 days

value: 2C-like cell


title: D1_NaB_mESC_TSC medium+1D

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 1 day

value: Day 1


title: CT_7_L

value: cortex

value: unilateral ACES, for the contralateral hemisphere collection


title: G163-HiC

description: CNV-balanced


title: H3K27me3_WT_R1

value: embryonic stem cells (ESCs)


title: D8_NaB_mESC_TSC medium+8D

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 8 days

value: Day 8


title: CT_2_L


title: G148-HiC

description: CNV-balanced


title: G208-HiC biorep1

description: CNV-balanced


title: D0_NaB_mESC

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium

value: Day 0


title: CT_10_R

value: ACES bilaterally


title: D6_NaB_mESC_TSC medium+6D

value: mESC, treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 6 days

value: Day 6


title: G120-HiC

description: CNV-balanced

value: glioblastoma stem-like cells

value: Hi-C


title: MG1-GFPnegative rep2

source_name: mESC

value: Mouse embryonic stem cell

value: GFP negative cell from mESC

value: mESC


title: MG1-GFPnegative rep1


title: D-2_mESC

value: untreated mESC

value: Day -2


title: G1-HiC

description: CNV-balanced


title: PAO1 ∆pqsA +AiiA Rep 1

status: Public on Mar 17 2024

city: Seattle

first: Nicole

middle: E

last: Smalley

state: Washington

address: 1705 NE Pacific St Health Sci Bldg  K-359

department: Pulmonary, Critical Care and Sleep Medicine

institute: University of Washington

description: OD 2.0 cells grown in buffered LB +AiiA lactonase (100 ug/ml)

data_processing:
Trim Galore! (Babraham Bioinformatics, Cambridge UK) set to paired-end reads default parameters was used to remove adapters.
Trimmed reads were mapped to PAO1 NCBI Reference Sequence: NC_002516.2 before transcript enumeration using StrandNGS software version 3.3.1 RNAseq quantification set to default parameters.
Raw transcript counts were normalized and differential expression analysis was done using DESeq2 (Love & Huber, 2014).
Assembly: PAO1 NCBI Reference Sequence: NC_002516.2
Supplementary files format and content: Raw transcript counts in .txt file format
Supplementary files format and content: DESeq2-normalized transcript counts in .csv file format

organism: Pseudomonas aeruginosa

growth_protocol: From ovenight cultures of single colonies grown in LB-MOPS, starter cultures for RNAseq were inoculated into 5 mL fresh LB-MOPS at OD 0.01 and grown to logarithmic phase (OD 0.1-0.4). This log-phase culture was then subcultured back to an OD of 0.005 to 25 mL LB-MOPS in 250 mL baffled flasks and grown at 37˚C with shaking at 225 RPM until collection at OD 2.0.

extract_protocol:
2 mL of OD 2.0 cultures were collected, the cells were pelleted by centrifugation and immediately frozen using liquid nitrogen, then stored at -80ºC. The RNA extraction was performed using RNeasy Mini kit (Qiagen), followed by DNA depletion with Turbo DNase (Ambion). The DNA-free RNA was concentrated by MinElute Cleanup kit (Qiagen).
rRNA depletion and strand-specificTruSeq RNA Library Kit preparation were performed according to Illumina protocols by the sequencing vendor Azenta (South Plainfield, NJ; formerly Genewiz).

treatment_protocol: Flasks were supplemented with either 100 ug per ml AiiA lactonase or the equivalent volume of lactonase buffer (20 mM Tris-HCL, 100 mM NaCl, pH 7.4, 10% glycerol).

value: Lab master strain PAO1

value: PAO1 pqsA deletion

value: AiiA lactonase treated - AHL QS off


title: PAO1 ∆pqsA +AiiA Rep 2


title: PAO1 ∆pqsA +Buffer Rep 2

description: OD 2.0 cells grown in buffered LB

value: untreated - AHL QS on


title: PAO1 ∆pqsE +AiiA Rep 1

value: PAO1 pqsE deletion


title: PAO1 ∆pqsE +Buffer Rep 2

description: OD 2.0 cells grown in buffered LB


title: PAO1 ∆pqsR +Buffer Rep 1

description: OD 2.0 cells grown in buffered LB

value: PAO1 pqsR deletion


title: PAO1 ∆pqsE +AiiA Rep 2


title: PAO1 ∆pqsA +Buffer Rep 1

description: OD 2.0 cells grown in buffered LB


title: PAO1 +Buffer Rep 2

description: OD 2.0 cells grown in buffered LB

value: PAO1 wildtype


title: PAO1 ∆pqsE +Buffer Rep 1

description: OD 2.0 cells grown in buffered LB


title: PAO1 ∆pqsR +AiiA Rep 1


title: MG1-NaB-GFPpositive rep1

value: GFP positive cell from mESC after treated with 0.5 mM NaB for 2 days

value: 2C-like cell


title: RNaseIII-CLASH_vancomycin_2

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
library strategy: RNase III-CLASH
BBDuk was used to trim the 5’ adapter sequence of the raw data using the parameters ‘ktrim=l k=23 mink=11 hdist=1’ followed by quality trimming with the parameters ‘qtrim=rl trimq=30’(Bushnell, 2014).
BBmerge was used to merge the paired-end reads using the default parameters (Bushnell et al, 2017)
RNase III-RNA and RNA-RNA interactions were determined using the pipeline Hyb-CRAC-R avaiable at https://github.com/IgnatiusPang/Hyb-CRAC-R
Assembly: GCF_000145595.1 with additional custom annotations of 5'UTRs and 3'UTRs from PMID: 35732665
Supplementary files format and content: Final_RATT_VISACLASH.txt, RNA-RNA interactions recovered from RNase III_CLASH. Format as per https://github.com/IgnatiusPang/Hyb-CRAC-R
Supplementary files format and content: Sa_JKD6008_annot_updated.gtf; updated annotation file in GTF format

organism: Staphylococcus aureus subsp. aureus str. JKD6008

source_name: strain JKD6008 (vancomycin intermediate, VISA)

growth_protocol: S. aureus str. JKD6008 was grown in Muller-Hinton media to an OD600 of 0.8 before treatment

extract_protocol:
as per CLASH protocol (PMID: 37925184)
Libraries were prepared using RNase III-CLASH (PMID: 37925184). This technique captures RNA-RNA interactions associated with RNase III

treatment_protocol: Where applicable, cultures were treated with 8ug/ml of vancomycin for 30mins and then harvested into GTC-phenol buffer.

value: VISA

value: 2ug/ml vancomycin for 10mins


title: RNaseIII-CLASH_vancomycin_3

value: strain JKD6008 (vancomycin intermediate, VISA)


title: RNaseIII-CLASH_vancomycin_4


title: PAO1 +Buffer Rep 1

description: OD 2.0 cells grown in buffered LB


title: CT_1_L

value: cortex

value: Sham


title: RNaseIII-CLASH_vancomycin_1


title: JKD6008_untagged_bkg_4

description: Not included in the final processed data


title: RNaseIII-CLASH_no_treatment_2

value: no treatment


title: RNaseIII-CLASH_no_treatment_1


title: JKD6008_untagged_bkg_3


title: JKD6008_untagged_bkg_2


title: S_aureus_JKD6008_ribo_seq_2

description: Ribo-seq data. Reads represent ribosome protected fragements.

data_processing:
*library strategy: Ribo-seq
Reads were trimmed using BBTools (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) using the parameters ‘ktrim=r k=23 mink=11 hdist=1’ and the quality trimming of the 5’ and 3’ ends was conducted using the parameters ‘qtrim=rl trimq=30’.
paired-end reads were merged into a single FASTQ file with BBmerge using the default parameters
BBmap parameters ‘slow sam=1.3 trd’ was then used to map the reads back to the JKD6008 genome
The output sam file was converted into a bam file format using samtools. This bam file was then converted into a bed file using bedtools and read counts for each feature was computed using bedtools coverage.
Assembly: GCF_000145595.1
Supplementary files format and content: read count table (column1=gene name, column2=raw read count)

extract_protocol: Ribo-seq. RNA was extracted as per Winton Wu, Chi Nam Ignatius Pang, Daniel Mediati, Jai Justin Tree bioRxiv 2023.08.23.554412; doi: https://doi.org/10.1101/2023.08.23.554412

treatment_protocol: no treatment


title: PAO1 ∆pqsR +Buffer Rep 2

description: OD 2.0 cells grown in buffered LB


title: JKD6008_untagged_bkg_1


title: PAO1 +AiiA Rep 2


title: PP_B_brain_injury_5 [RNA_S5219Nr11]

city: Essen

first: Vikramjeet

last: Singh

state: Nordrhein-Westfalen

address: Universitätsstr. 2

department: Institute for Experimental Immunology and Imaging

institute: University Duisburg-Essen

data_processing:
The quality of sequenced reads was determined with FastQC (version v0.11.9) 7 and Illumina adapters and low-quality reads -Phred score under 20- were trimmed with Trimmomatic (version 0.39) 8. Kallisto (version 0.48.01) 7 was used to pseudo-align reads to the GRCm38 release 102 genome assembly from ENSEMBL 9 and subsequently to quantify transcript expression as transcripts per million (TPM).  Transcripts with less than 1 TPM across all 12 samples were removed and in R (version 4.1.2) 10, a Wald Test from package Sleuth (version 0.30.0) 11 was used to analyze differential expression between the sham-operated and brain injured sample groups at the gene level, with significance set at a p-value < 0.05. Gene Ontology (GO) 12, 13. Biological Process enrichment analysis was also performed in R, with package clusterprofiler (version 4.0.5) 14, 15 and significance was defined as FDR-adjusted p-value < 0.05. In gene set enrichment analysis (GSEA), the dot size indicates the ratio of the overlap of differentially expressed genes with single GO term gene sets to the overlap of differentially expressed genes with the sum of all unique GO term genes queried.
Assembly: GRCm38 release 102
Supplementary files format and content: Delimited file containing normalized expression values per sample in TPM (Transcripts Per Kilobase Million).

source_name: B cell

extract_protocol:
RNA was isolated from MACS-purified B cells using RNeasy Micro Kit according to the protocols provided by the supplier (Cat. 74004, Qiagen). Briefly, cells were lysed in lysis buffer on ice and centrifuged to remove cell debris. RNA was precipitated with 70% ethanol and passed through the RNA columns. After two washing steps, genomic DNA was removed using RNase-free DNase set (Cat. 9254, Qiagen). The columns containing RNA were washed with buffers and supplemented with centrifugation steps. In the end, RNA from columns was collected using RNase-free water in new Eppendorf tubes and stored at -80°C until further used for the analysis.
cDNA

value: B cell

value: Brain injury


title: S_aureus_JKD6008_ribo_seq_1


title: PP_B_brain_injury_4 [RNA_S5219Nr10]


title: PP_B_brain_injury_3 [RNA_S5219Nr9]


title: PAO1 +AiiA Rep 1

value: Lab master strain PAO1


title: PP_B_brain_injury_1 [RNA_S5219Nr7]


title: PP_B_brain_injury_2 [RNA_S5219Nr8]


title: PP_B_sham_5 [RNA_S5219Nr5]


title: PP_B_sham_2 [RNA_S5219Nr2]


title: PP_B_sham_3 [RNA_S5219Nr3]


title: PP_B_sham_4 [RNA_S5219Nr4]


title: PAO1 ∆pqsR +AiiA Rep 2


title: PP_B_sham_1 [RNA_S5219Nr1]


title: m6A-seq of chromatin associated RNAs with FP treatment, Rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using Hisat2.
Assembly: GRCm39
Supplementary files format and content: coverage files containing read coverage at individual sites, which are seperated by comma

source_name: mouse embryonic fibroblasts cells

growth_protocol: MEF cells were grown in DMEM (BI) medium containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Cells were washed with chilled PBS and pelleted by centrifugation before they were subjected to cell membrane lysis buffer (0.15% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25 μM α-amanitin, 10 U SUPERase_In) and incubated on ice for 5 min. Cell lysates were then added to 2.5 volumes of chilled sucrose cushion (10 mM Tris-HCl pH 7.0, 150 mM NaCl, 25% sucrose, 25 μM α-amanitin, 20 U SUPERase_In) and the mixture was centrifuged at 4 °C with 16,000 ×g for 10 min. The supernatant was the cytoplasmic fraction, and the pellet was regarded as cell nuclei. The nuclear pellet was then washed with nuclear wash buffer (0.1% Triton X-100, 1 mM EDTA, in 1× PBS, 25 μM α-amanitin, 10 U SUPERase In, and protease inhibitor mix) twice and pelleted by centrifugation at 1150 ×g for 2 min. The supernatant was discarded, and the pellet was subjected to chilled glycerol buffer (20 mM Tris-HCl pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT, 25 μM α-amanitin, 10 U SUPERase_In). Equal volumes of chilled nuclei lysis buffer (1% NP-40, 20 mM HEPES pH 7.5, 300 mM NaCl, 1 M urea, 0.2 mM EDTA, 1 mM DTT, 25 μM α-amanitin, 10 U SUPERase_In) were then added to the nuclei suspension and incubated on ice for 2 min followed by centrifugation at 4 °C at 18,500 ×g for 2 min. The pellet was subjected to chilled chromatin resuspension solution (25 µM α-amanitin, 20 units SUPERase_In, 1× protease inhibitor mix (in 1× PBS)) to obtain the insoluble chromatin-associated fraction and subjected to RNA extraction using TRIzol Reagent.
For m6A immunoprecipitation, 50 μg chrRNA samples were fragmented by RNA fragmentation buffer (100 mM Tris-HCl pH 7.0 and 100 mM ZnCl2) at 94 °C for 30 s. Flowing standard ethanol precipitation and 1/20 of the fragmented RNA was saved as the input. The remaining fragmented RNA was immunoprecipitated with anti-m6A antibody (Abcam) in IP buffer (0.1% NP-40, 10 mM Tris-HCl pH 7.0, 150 mM NaCl) at 4 °C for 4 h. Dynabeads protein A/G (NEB) were washed, added to the mixture and incubated for 2 h at 4 °C with rotation. The m6A-containing RNA fragment was eluted twice with 6.7 mM N6-methyladenosine 5’-monophosphate sodium salt at 4 °C for 1 h and precipitated with ethanol at -80 °C overnight. RNA was dissolved in 10 μl nuclease-free water and subjected to reverse transcription for qPCR (see reverse transcription and quantitative Real Time-PCR). For chrRNA m6A-seq, cDNA library construction and sequencing were performed at LC-BIO Biotech Ltd. (Hangzhou, China). Paired-end 2 × 150 bp sequencing on an Illumina NovaSeq™ 6000 platform was also performed on libraries.

treatment_protocol: For flavopiridol treatment assays, MEF cells at around 80% confluence were replenished with fresh medium 2 hours before harvesting. Subsequently, the cells were treated with 300 nM flavopiridol for a duration of 30 min.

value: mouse embryonic fibroblasts cells

value: 300 nM flavopiridol , 30 min


title: RNA-seq of chromatin associated RNAs with FP treatment, Rep1