title: Lm9252 ChIP Input 2

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: Library name: lm9252-input-rep2

data_processing:
Initial data analysis including adapter trimming, alignment, and peak calling, was carried out as described in Cahn et al. 2024.
After visualizing CENH3/H3 enrichment, centromere regions were computationally estimated as follows: 1) log2(CENH3/H3) was computed across 10 Kbp genome bins, smoothed by 30 Kbp with deepTools v3.5.5  bamCompare; 2) The bin with the highest enrichment per chromosome was selected, and the intersecting MACS2 131 broad peak call with largest (log2(CENH3/H3) * peak_width) as computed by the MaizeCODE pipeline was chosen as the primary peak with bedtools v2.31.1  intersect and awk; 3) all MACS2 peaks within 5 Kbp of each other were merged, and the merged peaks overlapping the primary peak per chromosome were taken as the predicted centromere regions. Predicted transposable elements overlapping these regions were annotated with DANTE v0.2.5
Assembly: Lj8627-REF-CSHL-1.0, Lm9252-REF-CSHL-1.0, Lt9434-REF-CSHL-1.0
Supplementary files format and content: BigWigs:  independently mapped genome coverage from each replicate, and merged coverage for each condition, generated as described in Cahn et al. 2024.
Supplementary files format and content: BEDs:  predicted centromere regions.

organism: Lemna minor

source_name: whole frond

growth_protocol: Sterile cultures were obtained from the Rutgers Duckweed Stock Cooperative and cultivated in 50 mL Schenk and Hildebrandt (SH) medium with 1% sucrose at pH 5.6 at 23°C under a 16 hour photoperiod of approximately 30 μmol/m2/s per second of white fluorescent light.

extract_protocol:
Chromatin extraction and immunoprecipitation was performed as previously described (Parent et al. 2021) with minor modifications. Briefly, two biological replicates of 750 mg whole frond tissue per clone were crosslinked in 1% formaldehyde for 10 min, and ground to a fine powder under liquid nitrogen. Nuclei were extracted in an SDS-Tris buffer, lysed, and sonicated with a Bioruptor Pico (Diagenode) for 12 cycles at 30 Hz, 30 s on, 30 s off.
CENH3 orthologues in S. polyrhiza, W. australiana, L. gibba, and L. japonica were identified by sequence similarity search with O. sativa and A. thaliana sequences. A rabbit polyclonal antibody was raised against the synthesized polypeptide sequence “RTKHISGKRRRTE” unique to the L. minor and L. turionifera CENH3 N-terminal tail (LjCENH3), and then validated by Western blot. Chromatin was cleared with Protein A magnetic beads (Thermo Fisher Scientific) and incubated overnight with following antibodies: LjCENH3 (GenScript), H3 (Sigma, H0164), and H3K4me3 (Sigma, 07-473). Immune complexes were eluted, and crosslinks were reversed with Proteinase K digestion for 2 hrs at 55C with gentle shaking. Overnight NaCl incubation was omitted as in 129. DNA was purified with the ChIP Purification Kit (Zymo), and the NEBNext Ultra II DNA library prep kit (New England Biolabs) was used to construct sequencing libraries. L. turionifera samples in these libraries were from the clone 8133, rather than 9434.

value: whole frond


title: 22BBz CD4, (-) Antigen, 30 min, biol rep 1

status: Public on Feb 04 2025

type: SRA

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

library_source: transcriptomic

data_processing:
The quality of the fastq files was accessed using FastQC  (v.0.11.8), , FastQ Screen (v.0.13.0), and MultiQC (v.1.8)
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the hg38 human reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a)
Differential gene expression analysis was performed using the DESeq2 package.
Pathway enrichment analysis was performed using GSEA and IPA.
Assembly: hg38
Supplementary files format and content: Text file containing raw data matrix

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: CAR T cells were maintained in AIM-V medium supplemented with 5% heat-inactivated FBS, 100 U/mL penicillin, 100 U/mL streptomycin, 5 mL GlutaMax, 10mM HEPES, and 40IU/mL IL-2.

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using Tecan Universal Plus mRNA-Seq according to the manufactuer's protocol.

treatment_protocol: CAR4 and CAR8 cells were stimulated with 22Fc-antigen at 3ug/mL coated 24-well plates for 30mins.

tag: tissue

value: blood

tag: cell type

value: CD8 T cell

tag: genotype

tag: treatment

value: (-) Antigen


title: Lm9252 ChIP Input 1

description: Library name: lm9252-input-rep1

library_source: genomic

molecule: genomic DNA


title: Well P1-11E

city: Worcester

first: Summer

middle: B

last: Thyme

state: MA

address: 55 N Lake Ave

institute: UMass Chan

description: Library name: P1-11E

data_processing:
Demultiplexing, trimming, alignment, filtering, and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci-RNA-seq3_pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 (Lawson et al. 2020).
Assembly: GRCz11
Supplementary files format and content: RDS containing Seurat object with cell-level features, counts, and barcodes
Library strategy: sci-RNA-seq

molecule: polyA RNA

organism: Danio rerio

source_name: 6 dpf head

growth_protocol: Sci-RNA-seq was conducted following the “Tiny-Sci” protocol (Martin et al. 2023). Briefly, Tg(elavl3:KalTA4) fish were crossed with Tg(4xUAS-hmgn6) fish to produce wildtype, elavl3:KalTA4, 4xUAS-hmgn6, and elavl3:KalTA4; 4xUAS-hmgn6 offspring. At 6 dpf, larvae were anesthetized with MS-222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.

extract_protocol:
tiny sci sci-RNA-seq protocol
Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl lysis buffer B in DNA LowBind tubes (Eppendorf, 002431021). Heads were homogenized with a tissue homogenizer at 1 second intervals for 30-45 seconds until no clumps remained. Following fixation with ice-cold methanol and dithiobis (succinimidyl propionate) (DSP, Thermo Fisher, 22586), nuclei were resuspended in sucrose PBS TritonX MgCl2 (SPBSTM) and sonicated for 12 seconds on low at 4°C using a Bioruptor® Pico (Diagenode). Nuclei were resuspended in SPBSTM with dNTPs, and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate (Eppendorf, 0030129512).
Reverse transcription, ligation, final distribution, second-strand synthesis, protease digestion, tagmentation, PCR amplification, and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes (Martin et al. 2023). Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription, ligation, and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1, 10 cycles for Index, and 48 cycles for Read2.

value: 6 dpf head

tag: well

tag: rtindex

value: ACTTGCTAGA


title: lung mait cells, bleomycin d3, rep 1

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. mm10 was used as the reference genome. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: comma-delimited csv file with raw counts for each sample and gene annotation for each gene

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA extraction was performed by single column centrifugation using the RNeasy® Plus Micro Kit (Qiagen, Cat No. 74034) following the manufacturer’s protocol. RNA integrity was assessed by Agilent High Sensitivity RNA ScreenTape Assay on an Agilent 4200 TapeStation following the manufacturer’s protocol (Agilent, Cat. No. 5067-5579, 5580 and 5581).
Total RNA was subsequently submitted to Novogene following their sample preparation and shipping instructions. All further laboratory work was performed by Novogene using their commercial protocol. RNA was reverse transcribed and cDNA amplified by in vitro transcription with the TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa, Cat. No. 634889, for MAIT cell after PR8 IAV challenge), or a low input method using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, Cat. No. 7530, for MAIT cell after bleomycin challenge), or NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Cat. No. 7770, for total lung RNA-seq).

value: Lung

value: MAIT cell


title: Brain,7,Control

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description: Library name: Brain,7,Control

data_processing:
Raw sequencing data (.bcl) was converted to FASTQ with the Dragen Bio-IT platform (v3.9.5).
The quality of RNA-seq data was assessed by FastQC (v0.11.9).
Tissue bulk RNA-seq data were aligned and quantified using a standard protocol of Kallisto (v0.46.2) against Rattus norvegicus genome (mRatBN7.2)  downloaded from Ensembl official website
The output of Kallisto, both estimated counts and TPM (transcript per kilobase million)-based transcript-level expressions were then transformed into gene-level expressions using the Bioconductor package tximport (v1.22.0) with the tx2gene option set to connect transcripts to genes.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-delimited Raw counts for every gene and samples

organism: Rattus norvegicus

source_name: Brain

extract_protocol: RNA sequencing library was prepared with Illumina Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit was used by following the standard protocol provided by the manufacturer

treatment_protocol: Total RNA is extracted from the snap-frozen rat tissues with Zymo Research Quick RNA Miniprep kit (California USA) by following the protocol provided on the manufacturer’s website with slight modifications made to improve the quality and quantity of RNA from each tissue.

value: Brain

value: Tap water

tag: diet

value: Chow


title: lung mait cells, bleomycin d0, rep 3


title: Lm9252 ChIP H3 2

description: Library name: lm9252-h3-rep2


title: Adipose,7,Control

description: Library name: Adipose,7,Control

source_name: Adipose

value: Adipose


title: Well P1-11D

description: Library name: P1-11D

value: ATAAGGAGCA


title: lung mait cells, bleomycin d0, rep 2


title: Lm9252 ChIP H3 1

description: Library name: lm9252-h3-rep1


title: Muscle,4,Control

description: Library name: Muscle,4,Control

source_name: Muscle

value: Muscle


title: Lm9252 ChIP H3K4me3 2

description: Library name: lm9252-h3k4me3-rep2


title: Well P1-11C

description: Library name: P1-11C

value: CAACCGCTAA


title: lung mait cells, bleomycin d0, rep 1


title: Liver,4,Control

description: Library name: Liver,4,Control

source_name: Liver

value: Liver


title: lung mait cells, bleomycin d7, rep 1


title: Well P1-11B

description: Library name: P1-11B

value: ATCATATTAG


title: total lung, WT d21, rep 3

value: Total lung


title: Adipose,8,Control

description: Library name: Adipose,8,Control


title: Brain,4,Control

description: Library name: Brain,4,Control


title: Liver,7,Control

description: Library name: Liver,7,Control


title: Well P1-11A

description: Library name: P1-11A

value: AATTAAGACT


title: total lung, WT d21, rep 2


title: Muscle,7,Control

description: Library name: Muscle,7,Control


title: Lm9252 ChIP H3K4me3 1

description: Library name: lm9252-h3k4me3-rep1

value: whole frond


title: Well P1-10G

description: Library name: P1-10G

value: ATCCATGACT


title: Lm9252 ChIP CENH3 2

description: Library name: lm9252-cenh3-rep2


title: Well P1-11F

description: Library name: P1-11F

value: 6 dpf head

value: AGGTTAGTTC


title: total lung, WT d21, rep 1

value: Lung


title: Adipose,4,Control

description: Library name: Adipose,4,Control


title: Well P1-10F

description: Library name: P1-10F

value: GCTGGAACTT


title: Lm9252 ChIP CENH3 1

description: Library name: lm9252-cenh3-rep1


title: total lung, WT d14, rep 3


title: Liver,3,Control

description: Library name: Liver,3,Control


title: Well P1-10E

description: Library name: P1-10E

value: TATATACTAA


title: Brain,3,Control

description: Library name: Brain,3,Control

value: Brain

value: Tap water


title: Well P1-10D

description: Library name: P1-10D

value: ACCGCCAACC


title: Adipose,3,Control

description: Library name: Adipose,3,Control

value: Adipose

value: Chow


title: total lung, WT d14, rep 1


title: total lung, WT d7, rep 3


title: Muscle,2,Control

description: Library name: Muscle,2,Control

value: Muscle


title: Well P1-10B

description: Library name: P1-10B

value: TTACCGAGGC


title: O-SARS-112dpi-#14

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
Before alignment to the reference genome, raw FASTQ files were processed to trim sequences with low base call quality and remove sequencing adapter contamination( fastq-mcf, http://expressionanalysis.github.io/ea-utils/). Reads shorter than 15 bp were excluded from the FASTQ files. The trimmed reads were then aligned to the reference genome using the open-source short read aligner STAR , with default settings.
Feature counts were obtained by Rsubread v2.16.0 followed by feature annotation using biomaRt_2.54.1. In cases where the gene symbol information for hamster genes was missing, the orthologous human gene symbols were used instead. For the transcriptome analysis, only genes with a biotype of 'protein coding' and counts greater than 10 in at least four samples were included. Differential gene expression analysis was performed using DESeq2 (version 1.36.0) after normalizing gene counts with the rlog function (regularized log transformation). Normalized gene counts were expressed as log2 values.
Assembly: MesAur1.0 (Ensembl, rel. Version 110), ASM985889v3 (Ensembl Covid-19)
Supplementary files format and content: rlog normalized log2 values in Excel format

organism: Mesocricetus auratus

source_name: lung

extract_protocol:
RNAeasy (Qiagen) was used for RNA extraction
To prepare the RNA sequencing library, 500 ng of total RNA was utilized. mRNA purification was carried out using the Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher), followed by library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) in accordance with the manufacturer’s protocols. The resulting libraries were sequenced on the Illumina NovaSeq 6000 platform, employing the NovaSeq 6000 S1 Reagent Kit (100 cycles) for paired-end runs. On average, each RNA sample yielded approximately 3-5 x 107 reads.

value: lung

tag: time

value: 112 dpi

value: infected SarsCoV2


title: total lung, WT d7, rep 2

value: Total lung


title: Liver,2,Control

description: Library name: Liver,2,Control

value: Liver


title: O-SARS-56dpi-#88

value: 56 dpi


title: Well P1-10C

description: Library name: P1-10C

value: 6 dpf head

value: ACTTAACCTT


title: Brain,2,Control

description: Library name: Brain,2,Control


title: total lung, WT d7, rep 1

value: Lung


title: Well P1-09H

description: Library name: P1-09H

value: AGCTTATCCG


title: O-SARS-56dpi-#87


title: total lung, WT d3, rep 3


title: Muscle,3,Control

description: Library name: Muscle,3,Control


title: Adipose,2,Control

description: Library name: Adipose,2,Control


title: O-SARS-56dpi-#86


title: Well P1-09G

description: Library name: P1-09G

value: CGCTCCTAAC


title: total lung, WT d3, rep 2


title: O-SARS-56dpi-#85


title: O-SARS-112dpi-#19


title: Muscle,1,Control

description: Library name: Muscle,1,Control

value: Tap water


title: O-SARS-112dpi-#16


title: total lung, WT d14, rep 2


title: O-SARS-112dpi-#15


title: Liver,1,Control

description: Library name: Liver,1,Control


title: Well P1-09F

description: Library name: P1-09F

value: CTAACTAGAT


title: total lung, WT d3, rep 1


title: Brain,1,Control

description: Library name: Brain,1,Control

value: Brain


title: total lung, WT d0, rep 3


title: Well P1-09E

description: Library name: P1-09E

value: TCGCTAAGCA


title: Well P1-09D

description: Library name: P1-09D

value: CCGATTCCTG


title: O-SARS-28dpi-#112

value: 28 dpi


title: O-SARS-28dpi-#113

value: lung


title: O-SARS-28dpi-#110


title: Well P1-09C

description: Library name: P1-09C

value: CCAGTTCCAA


title: total lung, WT d0, rep 1


title: Well P1-09B

description: Library name: P1-09B

value: TGCCGGCAGA


title: O-SARS-28dpi-#109

value: infected SarsCoV2


title: total lung, WT d0, rep 2

value: Total lung


title: Liver,11,Control

description: Library name: Liver,11,Control

value: Liver

value: Chow


title: total lung, Mr1KO d21, rep 3


title: Adipose,1,Control

description: Library name: Adipose,1,Control

value: Adipose


title: Muscle,11,Control

description: Library name: Muscle,11,Control

value: Muscle


title: Well P1-10A

description: Library name: P1-10A

value: 6 dpf head

value: TAGATCTACT


title: O-SARS-14dpi-#56

value: 14 dpi


title: Brain,11,Control

description: Library name: Brain,11,Control

value: Tap water


title: total lung, Mr1KO d21, rep 2

value: Lung


title: Well P1-09A

description: Library name: P1-09A

value: ACGGAGGCGG


title: Well P1-08H

description: Library name: P1-08H

value: AGCTCTCCTC


title: total lung, Mr1KO d21, rep 1


title: Adipose,11,Control

description: Library name: Adipose,11,Control


title: O-SARS-14dpi-#55


title: O-SARS-14dpi-#54


title: Muscle,10,Control

description: Library name: Muscle,10,Control


title: Well P1-08G

description: Library name: P1-08G

value: CGGTCAAGAA


title: total lung, Mr1KO d14, rep 3


title: Well P1-08F

description: Library name: P1-08F

value: GATCGCTTCT


title: total lung, Mr1KO d14, rep 2


title: O-SARS-6dpi-#42

value: lung

value: 6 dpi


title: Well P1-08E

description: Library name: P1-08E

value: AACTAGGCGC


title: total lung, Mr1KO d14, rep 1

value: Total lung


title: Brain,10,Control

description: Library name: Brain,10,Control

value: Brain


title: Liver,10,Control

description: Library name: Liver,10,Control

value: Liver

value: Chow


title: Adipose,10,Control

description: Library name: Adipose,10,Control

value: Adipose


title: Well P1-08D

description: Library name: P1-08D

value: 6 dpf head

value: GGCTGAGCTC


title: O-SARS-6dpi-#39

value: infected SarsCoV2


title: total lung, Mr1KO d7, rep 3


title: Well P1-08C

description: Library name: P1-08C

value: AGAACGTCTC


title: total lung, Mr1KO d7, rep 1

value: Lung


title: O-SARS-6dpi-#38


title: O-SARS-6dpi-#41


title: Well P1-08B

description: Library name: P1-08B

value: GCCATTCTCC


title: total lung, Mr1KO d7, rep 2


title: S4-H2

city: Guangzhou

first: Quqian

last: Mo

state: Guangdong Province

address: No.280, Outer Ring East Road, University Town

department: Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine

country: China

institute: Guangdong Pharmaceutical University

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4)
The fragments of genes were counted using stringtie(v1.3.0) followed by TMM (trimmed mean of M values) normalization
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software
Assembly: Rnor_6.0
Supplementary files format and content: xls file include raw counts and FPKM for all samples

source_name: Cardial fIbroblast

growth_protocol: Cardiac fibroblasts were maintained in DMEM containing 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 in 37℃

extract_protocol:
RNA was harvested and extracted using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096).
RNA library for RNA-seq was prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocol.

treatment_protocol: CFs were seeded at a density of 3×105 cells/well in six-well plates and cultured in DMEM containing 5.5 mM glucose(designated N) or 33 mM glucose(designated H) for 24 hours.

tag: cell line

value: Cardial fIbroblast

value: Primary cell

tag: age

value: 20 months

value: DMEM containing 33mM glucose for 24hours


title: Well P1-08A

description: Library name: P1-08A

value: TGCGGACCTA


title: S4-H1


title: total lung, Mr1KO d3, rep 2


title: O-SARS-14dpi-#53

value: lung

value: 14 dpi


title: O-SARS-3dpi-#100

value: 3 dpi


title: Well P1-07G

description: Library name: P1-07G

value: GGCTCTCTAT


title: O-SARS-3-dpi-#27


title: S4-H3


title: Well P1-07F

description: Library name: P1-07F

value: TCTAATAGTA


title: S4-N2

value: DMEM containing 5.5mM glucose for 24hours


title: O-SARS-3-dpi-#25


title: total lung, Mr1KO d0, rep 3

value: Total lung


title: total lung, Mr1KO d3, rep 1


title: O-SARS-3dpi-#99


title: S4-N1


title: O-SARS-1dpi-#76

value: 1 dpi


title: S3-H3

value: 10-13 weeks


title: Well P1-07E

description: Library name: P1-07E

value: 6 dpf head

value: GGTATCCGCC


title: O-SARS-1dpi-#74

value: infected SarsCoV2


title: total lung, Mr1KO d0, rep 1

value: Lung


title: Well P1-07C

description: Library name: P1-07C

value: TCGGCCTTAC


title: S3-H2

value: Cardial fIbroblast

value: Primary cell


title: Well P1-07D

description: Library name: P1-07D

value: GCTAACTTGC


title: Lung, Ext1_KO

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10X scRNA-seq libraries were sequenced on the Illumina Novaseq-6000 platform, and generated reads were de-multiplexed and mapped to the mouse genome using the Cell Ranger pipeline (v7.0.1) and mm10 reference (refdata-gex-mm10-2020-A, 10x Genomics). Seurat (4.1.0) was used for downstream analysis including normalization, batch correction, cell cluster identification and differential expression analysis.
Assembly: mm10
Supplementary files format and content: filtered and raw matrix.h5 files

source_name: whole lung

extract_protocol:
Lung tissues were digested with 5 U/mL Dispase (Corning, 354235), 0.025 mg/mL DNase I (Roche, 10104159001) and 480 U/mL Collagenase type I (Thermo Fisher, 17100017) in PBS solution at 37 °C for 1 h. Lung tissues were then transferred to C-Tubes (Miltenyi,130-093-237) and were mechanically dissociated on a gentleMACS Dissociator (Miltenyi). Samples were passed through 70 μm strainer and were centrifuged at 300 g for 5 min. Samples were treated with 1X RBC lysis buffer (Biolegend, 420301) for 5 min on ice. Cells were then collected in FACS buffer (PBS containing 1mM EDTA, 25mM HEPES and 0.5% BSA) for downstream experiments.
Libraries were constructed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 according to the manufacturer’s protocol

value: whole lung

tag: developmental stage

value: postnatal day 8


title: O-SARS-1dpi-#69

value: lung


title: Well P1-07H

description: Library name: P1-07H

value: AATACCATCC


title: O-SARS-1dpi-#73


title: S3-H1

value: DMEM containing 33mM glucose for 24hours


title: total lung, Mr1KO d3, rep 3


title: S3-N3

value: DMEM containing 5.5mM glucose for 24hours


title: Well P1-07B

description: Library name: P1-07B

value: TAGAATTAAC


title: Lung, Ext1_Ctrl

description: 10x Genomics


title: O-MOCK-112dpi-#8

value: 112 dpi

value: MOCK


title: Well P1-07A

description: Library name: P1-07A

value: 6 dpf head

value: TGAGTCTGGC


title: S4-N3

value: 20 months


title: ATAC, Lung, Ext1_KO,rep2

data_processing:
Libraries were sequenced on the Illumina Nova-seq 6000 platform. FASTQ files were trimmed with Trimgalore to remove adapters and aligned to the mm10 reference genome using bowtie2. MACS2 was used to call peaks. Bigwig files were generated using deepTools.
Assembly: mm10
Supplementary files format and content: narrowPeak file from MACS2 output
Supplementary files format and content: bigwigs normalized with deepTools bamCoverage RPKM

source_name: whole lung from postnatal day 8

extract_protocol:
Lung tissues were digested with 5 U/mL Dispase (Corning, 354235), 0.025 mg/mL DNase I (Roche, 10104159001) and 480 U/mL Collagenase type I (Thermo Fisher, 17100017) in PBS solution at 37 °C for 1 h. Lung tissues were then transferred to C-Tubes (Miltenyi,130-093-237) and were mechanically dissociated on a gentleMACS Dissociator (Miltenyi). Samples were passed through 70 μm strainer and were centrifuged at 300 g for 5 min. Samples were treated with 1X RBC lysis buffer (Biolegend, 420301) for 5 min on ice. Cells were then collected in FACS buffer (PBS containing 1mM EDTA, 25mM HEPES and 0.5% BSA) for downstream experiments.
50,000 cells were captured and nuclei were isolated using lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were subjected to a transposition reaction and library construction using  TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502) and TruePrep® Index Kit V2 for Illumina (Vazyme, TD202).

tag: replicate

value: Rosa26-tdTomato+ lung mesenchymal cells


title: S3-N2

value: 10-13 weeks


title: S3-N1

value: Cardial fIbroblast


title: O-MOCK-112dpi-#6


title: Well P1-06H

description: Library name: P1-06H

value: AGAGCCAAGG


title: total lung, Mr1KO d0, rep 2

value: Lung

value: Total lung


title: S2-H3

value: Primary cell

value: 3-4 weeks


title: ATAC, Lung, Ext1_KO,rep1

value: whole lung

value: postnatal day 8


title: ATAC, Lung, Ext1_Ctrl,rep2


title: Well P1-06F

description: Library name: P1-06F

value: TCAACGTAAG


title: O-MOCK-112dpi-#11

value: lung


title: ATAC, Lung, Ext1_Ctrl,rep1


title: MMA202 gRNA enrichment library

city: Leuven

first: Samantha

last: Pretto

address: ON4 Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

description:
10x Genomics
MMA202_1_barcodes.tsv.gz
MMA202_1_features.tsv.gz
MMA202_1_matrix.mtx.gz
MMA202_1_protospacer_calls_per_cell.csv

data_processing:
Raw reads (.fastq format) from Gene Expression library were mapped to mouse genome (mm10) by CellRanger (v3.1.0). CellRanger feature barcoding analysis pipeline was applied to processes reads from CRISPR Guide Capture library. R package Seurat (R version 3.6.3 and R package Seurat, version v3.2.3) was used to process filterd matrix and perform downstream analysis.
Assembly: refdata-gex-mm10-2020-A from Cell Ranger website
Supplementary files format and content: Filtered cell barodes and count matrix generated by CellRanger. Tab-separated values files and matrix files. Protospacer calling results generated by CellRanger feature barcoding analysis.

source_name: PDAC (KPC_OVA ) primary tumor

extract_protocol:
OT-I Cas9 knockin T cells where transduced with the lentiviral metabolic CRISPR library. Transduced cells were selected based on CD90.1 expression and injected tail vein into recipient mice bearing hortotopic KPC_OVA tumors. The same day treatment with aPD-1 was started. 7 days post adoptive T cells transfer (ACT), mice were sacrificed and CD90.1+ OT-I T cells were sorted from the primary tumor.
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for CRISPR Screening

value: PDAC (KPC_OVA ) primary tumor

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: O-MOCK-56dpi-#84

value: 56 dpi

value: MOCK


title: Well P1-06E

description: Library name: P1-06E

value: 6 dpf head

value: ACGCGAGATT


title: S2-H2

value: Cardial fIbroblast

value: DMEM containing 33mM glucose for 24hours


title: Well P1-06D

description: Library name: P1-06D

value: CATACTCCGA


title: MMA202 CROP-seq


title: S2-H1


title: MMA200 gRNA enrichment library

description:
10x Genomics
MMA200_1_barcodes.tsv.gz
MMA200_1_features.tsv.gz
MMA200_1_matrix.mtx.gz
MMA200_1_protospacer_calls_per_cell.csv

value: IgG


title: Well P1-06C

description: Library name: P1-06C

value: GCAGGTCCGT


title: S2-N3

value: Primary cell

value: 3-4 weeks

value: DMEM containing 5.5mM glucose for 24hours


title: O-MOCK-56dpi-#83


title: O-MOCK-56dpi-#81


title: O-MOCK-112dpi-#7

value: 112 dpi


title: S2-N2


title: O-MOCK-56dpi-#78

value: lung


title: S2-N1


title: Well P1-06G

description: Library name: P1-06G

value: GGAGGATAGC


title: MMA200 CROP-seq

value: PDAC (KPC_OVA ) primary tumor

value: CD90.1+ OT-I T cells


title: O-MOCK-28dpi-#108

value: 28 dpi


title: Well P1-06A

description: Library name: P1-06A

value: GCCGCAACGA


title: O-MOCK-28dpi-#106

value: MOCK


title: Well P1-05H

description: Library name: P1-05H

value: 6 dpf head

value: TTCGCCTCCA


title: MMA198_2 CROP-seq

description:
10x Genomics
MMA198_2_barcodes.tsv.gz
MMA198_2_features.tsv.gz
MMA198_2_matrix.mtx.gz
MMA198_2_protospacer_calls_per_cell.csv

value: Cas9 Knockin OT-I transduced with CRISPR library


title: S1-H3

value: Cardial fIbroblast

value: 0-3 days

value: DMEM containing 33mM glucose for 24hours


title: MMA198_2 gRNA enrichment library


title: O-MOCK-28dpi-#103


title: S1-H1

value: Primary cell


title: O-MOCK-28dpi-#101


title: Well P1-05F

description: Library name: P1-05F

value: CCATTATCTA


title: Well P1-05G

description: Library name: P1-05G

value: TTACCTCGAC


title: S1-N3

value: DMEM containing 5.5mM glucose for 24hours


title: S1-N2


title: O-MOCK-14dpi-#47

value: lung

value: 14 dpi


title: O-MOCK-14dpi-#46


title: O-MOCK-14dpi-#52


title: O4, female, BPA, RNA, rep4

city: Paris

first: Anne-Laure

last: Schang

state: Select Option

address: 4, Avenue de l'Observatoire

department: Faculté de Pharmacie

country: France

institute: Université Paris Cité

description:
library name: Sample_19
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Sequences were aligned to the mm39 murine genome using STAR version 2.5.3a.
Gene expression quantification was performed using htseq-count version 0.6.1p1.
Normalization was performed using DESeq2 version 1.16.1.
Assembly: mm39
Supplementary files format and content: csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

source_name: Brain O4+ oligodendrocytes

extract_protocol:
Brain O4+ oligodendrocytes were isolated by magnetic cell sorting (Miltenyi). RNA were purified using the Macherey Nagel RNA XS Plus kit.
RNA-Seq libraries were generated according to manufacturer's instructions from 100 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94°C for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France). The final libraries were checked for quality, quantified using capillary electrophoresis and sequenced on a Hiseq 4000 sequencer by the GENOMEAST platform.

tag: mouse strain

value: Brain O4+ oligodendrocytes

tag: Stage

value: Post-natal day 16

tag: Sex

value: female

value: BPA (40 µg.kg-1.day-1) from gestational day 7


title: Well P1-05D

description: Library name: P1-05D

value: AGAGAAGGTT


title: Well P1-05E

description: Library name: P1-05E

value: 6 dpf head

value: CTAGTAGTCT


title: Well P1-05B

description: Library name: P1-05B

value: CTTGCGCCGC


title: O-MOCK-14dpi-#45

value: MOCK


title: Well P1-06B

description: Library name: P1-06B

value: GGTACTGCCT


title: S1-H2

value: Cardial fIbroblast

value: 0-3 days

value: DMEM containing 33mM glucose for 24hours


title: Well P1-05C

description: Library name: P1-05C

value: TAGAGTAATA


title: O4, female, BPA, RNA, rep3

description:
library name: Sample_18
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: Well P1-05A

description: Library name: P1-05A

value: CCGAGAATCC


title: S1-N1

value: Primary cell

value: DMEM containing 5.5mM glucose for 24hours


title: O4, female, BPA, RNA, rep2

description:
library name: Sample_16
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Brain O4+ oligodendrocytes


title: MMA198_1 gRNA enrichment library

description:
10x Genomics
MMA198_1_barcodes.tsv.gz
MMA198_1_features.tsv.gz
MMA198_1_matrix.mtx.gz
MMA198_1_protospacer_calls_per_cell.csv

value: PDAC (KPC_OVA ) primary tumor

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: Well P1-04H

description: Library name: P1-04H

value: AGGTTAGCAT


title: MMA198_1 CROP-seq


title: Well P1-04G

description: Library name: P1-04G

value: 6 dpf head

value: ACGAAGTCAA


title: O-MOCK-6dpi-#35

value: lung

value: 6 dpi


title: O-MOCK-6dpi-#32

value: MOCK


title: O-MOCK-6dpi-#31


title: O4, female, BPA, RNA, rep1

description:
library name: Sample_15
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Post-natal day 16

value: female

value: BPA (40 µg.kg-1.day-1) from gestational day 7


title: O-MOCK-6dpi-#29


title: A4

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Human cell line

hyb_protocol: Sample was hybridized to Affymetrix Clariom D Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: Human cell line

label_protocol: 100 ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted following Qiagen protocol (RNeasy Mini Kit, Cat.#74104)

value: Human cell line

tag: condition

value: Control

tag: batch


title: A3

description: Human cell line

tag: tissue


title: O4, male, BPA, RNA, rep4

description:
library name: Sample_13
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

tag: cell type

value: male


title: 5M2

description: Lung metastasis derived from primary tumor 5

source_name: Metastasis from lung

value: Metastasis from lung

value: Metastasis


title: O-MOCK-3dpi-#95

value: 3 dpi


title: O-MOCK-3dpi-#94


title: 6T

description: Primary tumor from muscle (tumor 6)

source_name: Primary tumor from muscle

value: Primary tumor from muscle

value: Tumor


title: Well P1-04D

description: Library name: P1-04D

value: TCCGGCCTCG

tag: genotype


title: O-MOCK-3dpi-#93

tag: treatment


title: 5M3


title: O4, male, BPA, RNA, rep2

description:
library name: Sample_11
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Brain O4+ oligodendrocytes


title: O4, male, BPA, RNA, rep1

description:
library name: Sample_10
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: 5T

description: Primary tumor from muscle (tumor 5)


title: Well P1-04A

description: Library name: P1-04A

value: 6 dpf head

tag: well

value: CTGATGGTCA


title: Well P1-04F

description: Library name: P1-04F

tag: rtindex

value: AATCGATAAT


title: 4M3

description: Lung metastasis derived from primary tumor 4


title: O4, female, control, RNA, rep4

description:
library name: Sample_09
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: O-MOCK-3-dpi-#23

value: lung

value: MOCK


title: Well P1-04B

description: Library name: P1-04B

value: ACTCAATAGG


title: 4M2


title: 5M1


title: O-MOCK-1dpi-#64

value: 1 dpi


title: Well P1-03H

description: Library name: P1-03H

value: AAGACCGTTG


title: O-MOCK-1dpi-#63


title: O4, female, control, RNA, rep2

description:
library name: Sample_07
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Post-natal day 16

value: female

value: Control


title: O4, male, BPA, RNA, rep3

description:
library name: Sample_12
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: male

value: BPA (40 µg.kg-1.day-1) from gestational day 7


title: O4, female, control, RNA, rep1

description:
library name: Sample_06
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: Well P1-03G

description: Library name: P1-03G

value: ATCGGCTATC


title: O-MOCK-1dpi-#62


title: Well P1-04C

description: Library name: P1-04C

value: TTATCCGGAT


title: Well P1-03F

description: Library name: P1-03F

value: TCCAATCATC


title: O4, male, control, RNA, rep4

description:
library name: Sample_05
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Brain O4+ oligodendrocytes


title: O4, female, control, RNA, rep3

description:
library name: Sample_08
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: O4, male, control, RNA, rep3

description:
library name: Sample_04
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)


title: O-MOCK-1dpi-#66


title: A2

description: Human cell line

value: Human cell line


title: 3T

description: Primary tumor from muscle (tumor 3)

value: Primary tumor from muscle

value: Tumor


title: A1

description: Human cell line


title: 3M2

description: Lung metastasis derived from primary tumor 3

value: Metastasis from lung

value: Metastasis


title: 506_AgedDIOICR

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: biotin

source_name: tumor

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: E0771 cells were cultured in DMEM with 10% FBS and 2mM glutamine, then orthotopically transplanted into C57BL6 mice. Tumors were removed and RNA extracted for analysis

extract_protocol: RNA extracted with trizol reagent then isolated with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: no treatments were applied to injected cells

tag: sample type

value: AgedDIOICR


title: Well P1-03E

description: Library name: P1-03E

value: 6 dpf head

value: GGCAGACGCC


title: 3M1


title: 501_AgedDIOICR


title: 497_AgedDIOICR


title: 500_AgedDIOICR


title: O4, male, control, RNA, rep1

description:
library name: Sample_02
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Post-natal day 16


title: Well P1-03A

description: Library name: P1-03A

value: GATCTTACGC


title: SkinUnk_tdNeg_rep1

city: Göttingen

first: Anja

last: Uhmann

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

institute: University of Göttingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422. The sequencing quality was asserted using FastQC. FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)(version 0.11.5).
Sequences were aligned to the reference genome Mus musculus (mm10 version 96, https://www.ensembl.org/Mus_musculus/Info/Index) using the STAR aligner
Read counting was performed using featureCounts  Read counts were analyzed in the R/Bioconductor environment (version 3.4.4, www.bioconductor.org) using the DESeq2 package version 1.18.1. Candidate genes were filtered using an absolute log2 fold-change >1 and FDR-corrected p-value <0.05. Genes were annotated using the Mus Musculus gene version 96 Gene transfer format (GTF) file.
Assembly: mm10
Supplementary files format and content: text file includes gene expression for each sample

source_name: dorsal skin

extract_protocol:
Epidermal cells were isolated with thermolysin from dorskal skin and sorted by FACS. RNA was harvested using Trizol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® RNA Sample Preparation v2 kit.

value: dorsal skin

tag: cell type_sorted_population

tag: genotype (background)

value: CD4Cre R26-tdT (C57Bl6/N)

tag: treatment age,_sex,_#_of_mice_pooled

value: 29 weeks, male, 2


title: Well P1-03D

description: Library name: P1-03D

source_name: 6 dpf head

value: AAGAAGCTAG


title: SkinUnk_tdPos_rep3

value: 32 weeks, male, 2


title: Well P1-03B

description: Library name: P1-03B

value: CTAAGAGAAG


title: O4, male, control, RNA, rep2

description:
library name: Sample_03
csv file (Column A=ENSEMBL GENE ID, columns B to Q=Raw data, columns R to AG=normalized data, columns AH to AW=normalized and divided by median of transcripts length in kb data)

value: Brain O4+ oligodendrocytes

value: male

value: Control


title: 466_AgedDIOICR


title: SkinUnk_tdNeg_rep2


title: Well P1-02H

description: Library name: P1-02H

value: TCTTGCCGAC


title: Well P1-03C

description: Library name: P1-03C

value: GATACGGAAC


title: 4M1

value: Metastasis from lung

value: Metastasis


title: 505_AgedDIOICR

value: AgedDIOICR


title: Mouse E12.5 Mboat7-/- cortex, biol rep 2

city: Tokyo

first: Nozomu

last: Kono

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: Universtiy of Tokyo

description:
Library name: Sample8
Column name in Mboat7_KO_E12_count_table.txt; KO-E12-5-cortex-2
241023_004_24JU054_E12-5-cortex-4

data_processing:
For E11.5 samples, sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastp.Trimmed seqence reads were mapped to mm10 using Hisat2 and read counts were generated using the feature-counts option from the subRead package. For E12.5 samples. For E12.5 samples, read counts were generated using the nf-core/rnaseq pipeline with the GRCm39 reference genome.
Assembly: mm10/GRCm39
Supplementary files format and content: Tab-delimited text file include raw counts for each sample.

source_name: cortex

extract_protocol:
RNA was harvested using RNeasy mini plus kit (QIAGEN).
Poly(A) selection was performed using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA libraries for RNA-seq were prepared using NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina.

value: cortex


title: 490_AgedDIOAdLib

value: AgedDIOAdLib


title: 2T

description: Primary tumor from muscle (tumor 2)

value: Primary tumor from muscle

value: Tumor


title: 1T

description: Primary tumor from muscle (tumor 1)


title: Well P1-02G

description: Library name: P1-02G

value: 6 dpf head

value: CGGATTAGAA


title: 2M3

description: Lung metastasis derived from primary tumor 2


title: SkinUnk_tdPos_rep2

value: dorsal skin

value: CD4Cre R26-tdT (C57Bl6/N)


title: 479_AgedDIOAdLib


title: 2M1


title: SkinUnk_tdPos_rep1

value: 29 weeks, male, 2


title: 2M2


title: Well P1-02F

description: Library name: P1-02F

value: CGTAGTTACC


title: Mouse E12.5 Mboat7+/- cortex, biol rep 2

description:
Library name: Sample6
Column name in Mboat7_KO_E12_count_table.txt; HT-E12-5-cortex-1
241023_002_24JU054_E12-5-cortex-2


title: 463_AgedDIOAdLib


title: Well P1-02E

description: Library name: P1-02E

value: AACCTGCGTA


title: SkinStem_tdNeg_rep3

value: 32 weeks, male, 2


title: Mouse E12.5 Mboat7+/- cortex, biol rep 1

description:
Library name: Sample5
Column name in Mboat7_KO_E12_count_table.txt; HT-E12-5-cortex-1
241023_001_24JU054_E12-5-cortex-1


title: Well P1-02C

description: Library name: P1-02C

value: CGACGCGACT


title: 461_AgedDIOAdLib


title: non targetting guide control sample 2

description: Library name: sample 5

data_processing:
Raw sequencing reads were mapped to mm10 reference genome by STAR (v2.7.7a) and then RSEM (v1.3.1) was used to quantify gene counts per sample. R package DESeq2 (v1.36.0) performed normalization and differential gene expression analysis, and clusterprofiler (v4.4.4) performed gene sets enrichment analysis.
Assembly: mm10
Supplementary files format and content: Estmated counts, TPM and FPKM per gene from RSEM

extract_protocol:
OT-I Cas9 knockin T cells where transduced with a lentiviral vector containing a non-targeting guide or a sgRNA targeting Elovl1. Transduced cells were selected based on CD90.1 expression and injected tail vein into recipient mice bearing hortotopic KPC_OVA tumors (ACT). The day after, the treatment with aPD-1 was started. 7 days post adoptive T cells transfer (ACT), mice were sacrificed and CD90.1+ OT-I T cells were sorted from the primary tumor. Cells from different mice were kept separetely and were considered as biological replicates.
SMARTer cDNA library preparation

value: PDAC (KPC_OVA ) primary tumor

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: SkinStem_tdPos_rep3


title: non targetting guide control sample 3

description: Library name: sample 6


title: 1M

description: Lung metastasis derived from primary tumor 1

value: Metastasis from lung

value: Metastasis


title: SkinStem_tdNeg_rep2


title: 521_AgedDIOAdLib

value: AgedDIOAdLib


title: Mouse E12.5 Mboat7-/- cortex, biol rep 1

description:
Library name: Sample7
Column name in Mboat7_KO_E12_count_table.txt; KO-E12-5-cortex-1
241023_003_24JU054_E12-5-cortex-3

value: cortex


title: 460_AgedDIOAdLib


title: Well P1-02B

description: Library name: P1-02B

value: AGAGCTATAA


title: SkinStem_tdNeg_rep1


title: Well P1-02D

description: Library name: P1-02D

value: 6 dpf head

value: GAAGATCGAG


title: SkinStem_tdPos_rep1

value: dorsal skin


title: Elovl1 sgRNA sample 3

description: Library name: sample 3


title: SkinStem_tdPos_rep2

value: CD4Cre R26-tdT (C57Bl6/N)


title: 516_AgedControlICR

value: AgedControlICR


title: Well P1-01H

description: Library name: P1-01H

value: AAGCCAGTTA


title: Well P1-02A

description: Library name: P1-02A

value: GCGTTGGAGC


title: Elovl1 sgRNA sample 2

description: Library name: sample 2


title: 515_AgedControlICR


title: 509_AgedControlICR


title: Well P1-01G

description: Library name: P1-01G

value: CATTCAATCA


title: Lj8627 ChIP Input 2

description: Library name: lj8627-input-rep2

organism: Lemna japonica

source_name: whole frond

value: whole frond


title: 495_AgedControlICR


title: 507_AgedControlICR


title: Well P1-01E

description: Library name: P1-01E

value: GGTATGCTTG


title: Lj8627 ChIP H3 2

description: Library name: lj8627-h3-rep2


title: lung mait cells, no BRD509 d7, rep 2

source_name: Lung

extract_protocol:
RNA extraction was performed by single column centrifugation using the RNeasy® Plus Micro Kit (Qiagen, Cat No. 74034) following the manufacturer’s protocol. RNA integrity was assessed by Agilent High Sensitivity RNA ScreenTape Assay on an Agilent 4200 TapeStation following the manufacturer’s protocol (Agilent, Cat. No. 5067-5579, 5580 and 5581).
Total RNA was subsequently submitted to Novogene following their sample preparation and shipping instructions. All further laboratory work was performed by Novogene using their commercial protocol. RNA was reverse transcribed and cDNA amplified by in vitro transcription with the TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa, Cat. No. 634889) or a low input method using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, Cat. No. 7530). First-strand cDNA synthesis and tailing by reverse transcription were performed using SMART (Switching Mechanism at 5’ End of RNA Template) technology. Following first-strand synthesis, cDNA was amplified by PCR to produce the library. Quality control of the library was performed by quantification with a Qubit 2.0 fluorimeter and by qPCR. Insert size was measured by the Agilent 2100 Bioanalyzer automated gel electrophoresis system. The library was sequenced using the NovaSeq platform with Illumina sequencing technology to generate 150bp paired-end reads.

value: Lung

value: MAIT cell


title: Elovl1 sgRNA sample 1

description: Library name: sample 1

value: PDAC (KPC_OVA ) primary tumor

value: CD90.1+ OT-I T cells

value: Cas9 Knockin OT-I transduced with CRISPR library


title: Well P1-01D

description: Library name: P1-01D

value: TCTGATACCA


title: Lj8627 ChIP Input 1

description: Library name: lj8627-input-rep1

extract_protocol:
Chromatin extraction and immunoprecipitation was performed as previously described (Parent et al. 2021) with minor modifications. Briefly, two biological replicates of 750 mg whole frond tissue per clone were crosslinked in 1% formaldehyde for 10 min, and ground to a fine powder under liquid nitrogen. Nuclei were extracted in an SDS-Tris buffer, lysed, and sonicated with a Bioruptor Pico (Diagenode) for 12 cycles at 30 Hz, 30 s on, 30 s off.
CENH3 orthologues in S. polyrhiza, W. australiana, L. gibba, and L. japonica were identified by sequence similarity search with O. sativa and A. thaliana sequences. A rabbit polyclonal antibody was raised against the synthesized polypeptide sequence “RTKHISGKRRRTE” unique to the L. minor and L. turionifera CENH3 N-terminal tail (LjCENH3), and then validated by Western blot. Chromatin was cleared with Protein A magnetic beads (Thermo Fisher Scientific) and incubated overnight with following antibodies: LjCENH3 (GenScript), H3 (Sigma, H0164), and H3K4me3 (Sigma, 07-473). Immune complexes were eluted, and crosslinks were reversed with Proteinase K digestion for 2 hrs at 55C with gentle shaking. Overnight NaCl incubation was omitted as in 129. DNA was purified with the ChIP Purification Kit (Zymo), and the NEBNext Ultra II DNA library prep kit (New England Biolabs) was used to construct sequencing libraries. L. turionifera samples in these libraries were from the clone 8133, rather than 9434.


title: 470_AgedControlICR


title: lung mait cells, no BRD509 d7, rep 3


title: 511_AgedControlAdLib

value: AgedControlAdLib


title: non targetting guide control sample 1

description: Library name: sample 4


title: Lj8627 ChIP H3 1

description: Library name: lj8627-h3-rep1


title: Lj8627 ChIP H3K4me3 2

description: Library name: lj8627-h3k4me3-rep2


title: lung mait cells, no BRD509 d3, rep 3


title: Well P1-01C

description: Library name: P1-01C

value: 6 dpf head

value: ACTATGCAAT


title: 496_AgedControlAdLib


title: Lj8627 ChIP H3K4me3 1

description: Library name: lj8627-h3k4me3-rep1


title: Well P1-01B

description: Library name: P1-01B

value: TTGACTTCAG


title: Lj8627 ChIP CENH3 2

description: Library name: lj8627-cenh3-rep2


title: 494_AgedControlAdLib


title: lung mait cells, no BRD509 d3, rep 2


title: Well P1-01F

description: Library name: P1-01F

value: TCGCGGTTGG


title: 475_AgedControlAdLib


title: Well P1-01A

description: Library name: P1-01A

value: TCCTACCAGT


title: Lj8627 ChIP CENH3 1

description: Library name: lj8627-cenh3-rep1


title: lung mait cells, no BRD509 d7, rep 1


title: 474_AgedControlAdLib


title: lung mait cells, no BRD509 d0, rep 3


title: Human preterm placenta (35 weeks), sc-RNA-seq

city: Baltimore

first: Bingbing

last: Wang

state: MD

address: 655 W. Baltimore St

department: Ob/Gyn

institute: University of Maryland School of Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: hg38
Supplementary files format and content: cloupe (Loupe browser)

source_name: Primary villous cytotrophoblast

extract_protocol:
Placental villous tissue fragments free of membranes received enzymatic digestions in a solution containing 0.25% trypsin, 0.2% deoxyribonuclease I, 25 mM HEPES, 2 mM CaCl2, and 0.8 mM MgSO4 in 1× Hanks' balanced salt solution at 37oC. To remove tissues that were not digested, we passed them through gauze and a 100-m sieve. After enzymatic digestion, cell pellets resuspended in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS). To further purify cytotrophoblasts, we used a discontinuous density gradient of Percoll (50/45/35/30%) by centrifuging at 1000x g at room temperature for 20 min. Target cells at the interface of fractions of 35/45% were collected
We performed library construction with use of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, CA), which consists of three major steps: GEM generation and barcoding, post-GEM RT cleanup and cDNA amplification, and 3’ gene expression library construction, according to the protocol provided by the manufacturer.

tag: group

value: preterm

value: Primary villous cytotrophoblast


title: 469_AgedControlAdLib


title: Root, Hubei, rep2

city: Lanzhou

first: Chaogui

last: Hu

state: Anning

address: Gansu Agricultural University, Lanzhou 730070, China

institute: Gansu Agricultural University

description: Library name: H-2

data_processing:
Data filtering : FastQC was used to check the quality of the original sequencing data. The Trimmomatic tool was used to perform mass shearing to remove low-quality reads and adaptor sequences to obtain high-quality sequencing data ( Clean data ). Read comparison : The clean reads were aligned to the reference genome using alignment software ( Bowtie2 ). Set appropriate comparison parameters to ensure the accuracy and reliability of the comparison results. Calculate the comparison rate and evaluate the comparison effect. Quantitative gene expression : Genes were quantified using the featureCounts tool to obtain the read count for each gene. The RSEM tool was used to directly calculate gene expression ( FPKM ). Analysis of differentially expressed genes : Differentially expressed genes were analyzed using the DESeq2 tool. The significance threshold ( P value 1 ) was set to screen out the difference between the treatment group and the control group.
Assembly: no
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Angelica pubescens

source_name: root

growth_protocol: After taking a clean plant root sample, the sample should be processed quickly to prevent RNA degradation. Usually, the sample needs to be immediately frozen in liquid nitrogen and stored in a refrigerator at − 80 ° C until RNA extraction is performed.

extract_protocol:
The ground root powder is transferred to a centrifuge tube containing Trizol reagent and vortexed to mix well. The sample was placed at room temperature for 5 minutes to fully crack the sample. Add an equal volume of chloroform, mix well with vortex oscillation, and stand on ice for 5 minutes. Centrifuge at 4 ° C, 12000 rpm for 15 minutes, carefully drawing the upper water phase into a new centrifuge tube. The equal volume of isopropanol was added, vortexed and mixed, and then stood on the ice for 10 minutes. After centrifugation at 12000 rpm for 10 min at 4 °C, the supernatant was discarded and the RNA precipitate was obtained. RNA was washed twice with 75 % ethanol and centrifuged at 12000 rpm for 5 minutes at 4 ° C after each washing. Discard the supernatant and dry the RNA precipitate at room temperature ( pay attention not to over-dry ). The RNA solution was obtained by dissolving RNA with an appropriate amount of water without RNase.
Total RNA extraction, mRNA enrichment and fragmentation, mRNA reverse transcription, end repair and A tail, ligation adapter, PCR enrichment, library quality control.

treatment_protocol: The cleaned root samples were dried with sterile gauze or absorbent paper to absorb the surface moisture, and then immediately frozen in liquid nitrogen. Before RNA extraction, the root sample needs to be ground into powder. Grinding should be carried out in liquid nitrogen to prevent RNA degradation.

value: root

tag: time

value: 2  years


title: Root, Hubei, rep1

description: Library name: H-1


title: lung mait cells, no BRD509 d0, rep 1


title: SBC5, PARPi+4Gy-3

city: Toronto

first: Benjamin

middle: H

last: Lok

state: ON

address: 101 College Street, PMCRT, 13-307

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Raw fastq files were pseudoaligned to the human genome (Gencode v.38) at the transcript level using Kallisto (v. 0.46.1)
Transcript abundances were imported into R using the Bioconductor package tximport to estimate gene-level abundances
Gene level abundances were normalized and assessed for differential expression using DESeq2.
Assembly: Gencode v.38
Supplementary files format and content: Raw gene-level abundances from Kallisto in tab-delimited txt.

growth_protocol: SBC5 cells were maintianed in RPMI medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted by using High Pure RNA Isolation Kit (Roche Life Science, cat#11828665001) according to the manufacturer’s instructions. RNA concentration was measured by NanoDrop 2000 UV-Vis spectrophotometer (Thermo Scientific).
Total RNA-seq library was prepared from 1ug RNA with Illumina TruSeq stranded total RNA library kit (catalog 20020596) according to manufacturer’s protocol. Library quality and yield were determined by Agilent TapeStation and Qubit fluorometer, respectively.

treatment_protocol: SBC5 cells were treated with olaparib or DMSO two hours prior to irradiation. Cells were exposed to the indicated dose of radiation (Gamma ray) with irradiator CS3000. After 3 days, cells were washed with PBS twice and collected.

tag: cell line

value: Small Cell Lung Cancer

value: WT

value: 3 days


title: SBC5, PARPi+4Gy-2


title: Root, Shanxi, rep3

description: Library name: S-3


title: miniTurbo, Biotin, 24to32hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep2

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

description:
Library name: miniTurbo-Biotin-32to40hpi_plusBiotin_RAPA_rep2
miniTurbo_32to40hpi_aBiotin_plusBiotin_plusRAPA_2rep.avg.bedgraph.gz
log2_BDP5-over-miniturbo_32to40hpi_aBiotin_plusBiotin_RAPA_2reps.avg.bedgraph.gz

data_processing:
Sequencing reads were mapped against the reference genome PlasmoDB v26 3D7 with bowtie2 (v2.5.2)
Reads were filtered for mapping quality higher or equal than 30 and mitrochondrial and apicoplast reads were removed with samtools (v1.18)
BigWig files normalised to RPMK were generated with deeptools (v3.5.4)
Bedgraphs were generated for visualisation on UCSC genome browser with bedtools (v2.31.0) normalised to reads per million
Assembly: PlasmoDB v26 3D7
Supplementary files format and content: bedGraph
Library strategy: CUT&Tag

organism: Plasmodium falciparum

source_name: 3D7 wt / mCherry-FRB-miniTurbo

growth_protocol: RPMI 1640 medium supplemented with 0.2% NaHCO3 and 10% human serum at 37 °C under low oxygen conditions (3% O2, 4% CO2 and 93% N2) in human red blood cells at 5% hematocrit. For DiBioCUT&Tag, parasites were grown in biotin-free RPMI supplemented with 0.2% NaHCO3,  200 µM Hypoxyxanthine and 0.5% AlbuMAX TM II. Medium was furthermore supplemented with 250 nM Rapalog 1h before harvest for RAPA samples and 50 µm Biotin 30 min before harvest for plusBiotin samples.

extract_protocol:
For nuclei isolation, parasite cultures were lightly crosslinked with 0.1% formaldehyde (Sigma, F8775), incubating for 2 min at 37 °C while shaking. Crosslinking was stopped by addition of glycine to 0.125 M final concentration. Samples were handled on ice from here onwards. Cells were harvested by 440 g centrifugation for 8 min at 4 °C, and washed with ice-cold PBS. Centrifugation was repeated and the pellet was washed with PBS supplemented with 1x EDTA-free Protease Inhibitor (Roche, 04693132001). Parasites were extracted by adding saponin (0.05% total concentration) and incubating at room temperature (RT) for 10 min. Nuclei were isolated by carefully transferring the extracted parasite mixture on top of a 0.25 M to 0.1 M sucrose gradient in cell lysis buffer (10 mM Tris pH 8, 3 mM MgCl2, 0.2% NP-40, 1x EDTA free Protease inhibitor (Roche, 04693132001); 15 mL 0.25 M Sucrose and 17.5 mL 0.1M Sucrose for 50 mL tubes, 4 mL 0.25 M Sucrose and 6 mL 0.1 M Sucrose for 15 mL tubes) and centrifuging for 12 min, 3100 g, 4 °C with acceleration and deceleration set to 1 (Eppendorf 5910 Ri, Rotor S-4x400). Supernatant was removed and nuclei washed in cell lysis buffer (10 min, 3500 g, 4 °C; Heraeus Fresco 21). Nuclei were counted in an automatic hemocytometer (BioRad, TC10 Automated Cell Counter) and were directly used for CUT&Tag. Optionally, nuclei were washed with cell lysis buffer containing 20% Glycerol and nuclei pellet was snap frozen in liquid nitrogen prior to storage at -80°C. For parasite isolations, parasite cultures were harvested by 440 g centrifugation for 8 min at RT and pellet was resuspended in 1 mL of 0.15% Saponin/PBS per 10 mL culture and incubated for 5 min on ice. Samples were vortexed shortly every minute. Samples were washed three times with ice-cold PBS (3500 g centrifugation for 3 min at 4 °C; Heraeus Fresco 21). Intact parasites were counted in an automatic hemocytometer and were directly used for CUT&Tag. Optionally, parasites were washed with PBS containing 20% Glycerol and parasite pellets snap frozen in liquid nitrogen prior to storage at -80 °C. Nuclei or whole parasite were resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor) containing 0.1% Triton X-100 and permeabilized for 10 min on ice. Nuclei / parasites were pelleted by centrifugation (3500 g, 10 min, 4 °C) and resuspended in CUT&Tag wash buffer. Concanavalin A beads (Bangs Laboratories, BP531) were activated by resuspending into 10 volumes of Bead Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), washed once on a magnetic rack and resuspended in the starting volume of bead slurry. Purified nuclei or parasites were bound to 10 µL beads per reaction by incubating for 10 min rotating at RT. The supernatant was removed and 50 µL antibody buffer (CUT&Tag wash buffer; 2 mM EDTA, 0.1% BSA) with primary Antibody (0.25 µL polyclonal rabbit αHP1; 0.5 µg αH3K9me3, Abcam 8988; 0.5 µL αBiotin (Cell Signaling Technology #D5A7; for DiBioCUT&Tag); 0.25µg αGFP, Roche 11814460001; or 0.5 µg normal rabbit IgG (MERCK, #12-370)) was added and incubated nutating over night at 4 °C. Unbound primary antibody was removed by washing once with 100 µL CUT&Tag wash buffer and samples were then incubated with secondary antibody (1.2 µg guinea pig anti-rabbit antibody, Antibodies-Online ABIN101961; or 0.5 µg goat anti-mouse antibody, EpiCypher 13-0048; in 100 µL CUT&Tag wash buffer, 1:100 dilution) for 1h on RT, nutating. The nuclei or parasites were washed on a magnetic stand twice with 100 µL CUT&Tag wash buffer and once with 100 µL CUT&Tag 300 Wash Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor). For all following wash steps CUT&Tag 300 wash buffer was used in order to quench potential affinity of protA-Tn5 to accessible chromatin regions. 2.5 µL commercial proteinA/G-Tn5 fusion protein (CUTANA™ pAG-Tn5 for CUT&Tag, Epicypher, 15-1017) was added in 50 µL CUT&Tag 300 wash buffer and incubated nutating for 1 h. Unbound proteinA/G-Tn5 fusion protein was removed by thrice washing with 100 µL CUT&Tag 300 wash buffer. The supernatant was removed and the nuclei or parasites were resuspended in 200 µL freshly prepared tagmentation buffer (CUT&Tag 300 wash buffer, 10 mM MgCl2). To perform tagmentation, samples were incubated in a PCR thermocycler (BioRad, T100) at 37 °C for 1h. Tagmentation was stopped and nuclei or parasite lysis was facilitated by addition of 10 µL of 0.5M EDTA pH8, 3 µL of 10% SDS and 1 µL of 50 mg/mL proteinase K. Samples were briefly vortexed and then incubated at 55 °C for 1 h. DNA fragments were extracted utilizing the DNA Clean & Concentrator - 5 kit (Zymogen, D4014) following manufactures instructions. DNA was eluted from the column with 26 µL of prewarmed elution buffer and DNA concentrations were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231).
Libraries were generated using maximal 50 ng of extracted DNA from CUT&Tag experiments and tagged fragments were amplified with unique combinations of i5 and i7 barcoded primers, enabling tracing the DNA fragments originating from separate experiments in the sequencing data. PCRs were performed in a total reaction volume of 50 µL using Kapa HiFi polymerase (use non-hotstart version for gap filling; Roche, KK2102) in a thermocycler with the following program: 58 °C for 5 min, 62 °C for 5 min (gap filling), 98 °C for 2 min, 12-16 cycles of 98 °C for 20 second and 62 °C for 10 seconds, 62 °C for 1 min and hold at 4 °C. Post-PCR DNA cleanup was performed by adding 50 µL (1x volume) of AMPure XP bead slurry (Beckman Coulter, A63882) and incubating for 10 min at RT, washing twice with 80% EtOH on a magnetic rack, and eluting in 16.5 µL of 10 mM Tris-HCl pH 8 for 5 min at RT. DNA concentrations of libraries were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231) and library fragment size distribution was accessed by microfluidic gel electrophoresis (Agilent 2100 Bioanalyser) with the corresponding High Sensitivity DNA Kit (Agilent, 5067-4626). Sequencing was performed using an Illumina NextSeq 2000 instrument for 3-10 M reads per CUT&Tag sample; 59bp paired-end reads were generated.
(DiBio)CUT&Tag, ChIPseq

value: 3D7 wt / mCherry-FRB-miniTurbo

tag: cut&tag antibody

value: Biotin (CST, #D5A7)

tag: starting material

value: isolated nuclei


title: 439_YoungDIOICR

value: YoungDIOICR


title: 435_YoungDIOICR


title: miniTurbo, Biotin, 24to32hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: miniTurbo-Biotin-32to40hpi_plusBiotin_noRAPA_rep2
miniTurbo_32to40hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: SBC5, PARPi+4Gy-1


title: lung mait cells, no BRD509 d3, rep 1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. mm10 was used as the reference genome. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: comma-delimited csv file with raw counts for each sample and gene annotation for each gene

value: Lung

value: MAIT cell


title: Root, Hubei, rep3

description: Library name: H-3


title: miniTurbo, Biotin, 32to40hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-32to40hpi_plusBiotin_RAPA_rep1
miniTurbo_32to40hpi_aBiotin_plusBiotin_plusRAPA_2rep.avg.bedgraph.gz
log2_BDP5-over-miniturbo_32to40hpi_aBiotin_plusBiotin_RAPA_2reps.avg.bedgraph.gz


title: SBC5, DMSO+4Gy-3


title: Root, Shanxi, rep1

description: Library name: S-1


title: 428_YoungDIOICR


title: Human term placenta (38 weeks), sc-RNA-seq

description: 10X Genomics

value: term


title: 458_YoungDIOICR


title: lung mait cells, no BRD509 d0, rep 2


title: SBC5, DMSO+4Gy-2


title: miniTurbo, Biotin, 32to40hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-32to40hpi_plusBiotin_noRAPA_rep1
miniTurbo_32to40hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: 418_YoungDIOICR


title: SBC5, DMSO+4Gy-1


title: 414_YoungDIOICR


title: miniTurbo, Biotin, 32to40hpi, noBiotin, noRapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-32to40hpi_noBiotin_noRAPA_rep1
miniTurbo_32to40hpi_aBiotin_noBiotin_noRAPA_rep1.bedgraph.gz


title: Root, Gansu, rep3

description: Library name: G-3


title: Root, Gansu, rep2

description: Library name: G-2


title: Well P1-04E

description: Library name: P1-04E

data_processing:
Demultiplexing, trimming, alignment, filtering, and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci-RNA-seq3_pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 (Lawson et al. 2020).
Assembly: GRCz11
Supplementary files format and content: RDS containing Seurat object with cell-level features, counts, and barcodes
Library strategy: sci-RNA-seq

extract_protocol:
tiny sci sci-RNA-seq protocol
Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl lysis buffer B in DNA LowBind tubes (Eppendorf, 002431021). Heads were homogenized with a tissue homogenizer at 1 second intervals for 30-45 seconds until no clumps remained. Following fixation with ice-cold methanol and dithiobis (succinimidyl propionate) (DSP, Thermo Fisher, 22586), nuclei were resuspended in sucrose PBS TritonX MgCl2 (SPBSTM) and sonicated for 12 seconds on low at 4°C using a Bioruptor® Pico (Diagenode). Nuclei were resuspended in SPBSTM with dNTPs, and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate (Eppendorf, 0030129512).
Reverse transcription, ligation, final distribution, second-strand synthesis, protease digestion, tagmentation, PCR amplification, and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes (Martin et al. 2023). Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription, ligation, and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1, 10 cycles for Index, and 48 cycles for Read2.

value: 6 dpf head

value: TAGCCGTCAT


title: miniTurbo, Biotin, 32to40hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep2

description:
Library name: miniTurbo-Biotin-24to32hpi_plusBiotin_RAPA_rep2
miniTurbo_24to32hpi_aBiotin_plusBiotin_RAPA_2rep.avg.bedgraph.gz


title: SBC5, PARPi+0Gy-3


title: 457_YoungDIOAdLib

value: YoungDIOAdLib


title: Root, Gansu, rep1

description: Library name: G-1


title: 455_YoungDIOAdLib


title: SBC5, PARPi+0Gy-2


title: Root, Chongqing, rep3

description: Library name: C-3


title: Root, Shanxi, rep2

description: Library name: S-2


title: miniTurbo, Biotin, 32to40hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: miniTurbo-Biotin-24to32hpi_plusBiotin_noRAPA_rep2
miniTurbo_24to32hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: SBC5, PARPi+0Gy-1


title: miniTurbo, Biotin, 24to32hpi, noBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: miniTurbo-Biotin-24to32hpi_noBiotin_noRAPA_rep2
miniTurbo_24to32hpi_aBiotin_noBiotin_noRAPA_2rep.avg.bedgraph.gz


title: Root, Chongqing, rep2

description: Library name: C-2


title: SBC5, DMSO+0Gy-3


title: Root, Chongqing, rep1

description: Library name: C-1


title: SBC5, DMSO+0Gy-2


title: 413_YoungDIOAdLib


title: M. bovis challenged cow, rep2 [WT02]

city: Knoxville

first: Aga

middle: Edema

last: Gelgie

state: Tennessee

address: 2506 River Dr

department: Animal Science

institute: The University of Tennessee

data_processing:
Raw reads were trimmed and quality filtered using fastp (v0.23.4) as described elsewhere. For read mapping, a custom reference genome was developed by appending M. bovis PG45 (Accession No. NC_014760) reference genome to Bos taurus ( ARS-UCD2.0 ; RefSeq accession GCF_002263795.3 ). Spliced Transcripts Alignment to a Reference (STAR) and BWA-MEM2 were used to map reads to the combined Bos taurus and M. bovis. Reads were counted within genes for the separate Bos taurus and M. bovis annotations, respectively, using featureCounts. Differentially expressed genes (DEGs) were called using DESEq2 with log fold changes shrunken by apeglm method. An alpha level of 0.001was used for DESeq2 independent filtering and as the false discovery rate (FDR)-adjusted p-value cutoff for calling DEGs. Functional overrepresentation analysis of up-regulated and down-regulated genes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) with the clusterProfiler R package. Pathways with FDR adjusted P value (q value ) of < 0.05  were considered significantly enriched.
Assembly: a custom reference genome was developed by appending M. bovis PG45 (Accession No. NC_014760) reference genome to Bos taurus ( ARS-UCD2.0 ; RefSeq accession GCF_002263795.3 )
Supplementary files format and content: Excel file which includes raw counts for each sample

organism:
Bos taurus
Mycoplasmopsis bovis

source_name: mammary gland

growth_protocol: M. bovis strain PG45 (ATCC 25523) (250 µL of 10*8 CFU/mL) was inoculated into 5 mL of Friis broth and incubated at 37oC in 5% CO2:95% air incubator. Bovine mammary epithelial cell lines were seeded in 75 cm*2 tissue culture flask at a concentration of 2.0 x 10*6 cells/mL in 37oC, 5% CO2:95% air incubator.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen GmbH, Germantown, MD) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research) according to the manufacturer’s procedure.

treatment_protocol: Once MAC-T cells growth reached 85 - 95% confluency, cells were infected at a MOI of 150 (150 M. bovis : 1 cell) for 24 h. Bacterial suspension was divided into aliquots of 5 mL containing 1 x 10*6 CFU and two contralateral quarters (right-front and left-rear) of 2 cows were infused. One cow received intramammary infusion of 5 mL sterile endotoxin free 1  PBS (pH 7.4) into similar quarters and used as a control.

value: mammary gland

value: Bos taurus+M.bovis

value: M bovis infected


title: SBC5, DMSO+0Gy-1


title: miniTurbo, Biotin, 24to32hpi, noBiotin, noRapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-24to32hpi_noBiotin_noRAPA_rep1
miniTurbo_24to32hpi_aBiotin_noBiotin_noRAPA_2rep.avg.bedgraph.gz


title: M. bovis challenged cow, rep1 [WT01]


title: 415_YoungDIOAdLib


title: miniTurbo, Biotin, 24to32hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-24to32hpi_plusBiotin_noRAPA_rep1
miniTurbo_24to32hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: PBS challenged cow, control, rep2 [PBS02]

organism: Bos taurus

value: control/no treatment


title: 453_YoungControlICR

value: YoungControlICR


title: PBS challenged cow, control, rep1 [PBS01]


title: 448_YoungControlICR


title: 3D7-BDP5-FKBP, Biotin, 32to40hpi, plusBiotin, noRapa, DiBioCUT&Tag

description:
Library name: 3D7-BDP5-FKBP-Biotin-32to40hpi_plusBiotin_noRAPA
3D7-BDP5-FKBP_32to40hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz

source_name: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo


title: 3D7-BDP5-FKBP, GFP, 32to40hpi, noBiotin, noRapa, DiBioCUT&Tag

description:
Library name: 3D7-BDP5-FKBP_aGFP-32to40hpi_noBiotin_noRAPA
3D7-BDP5-FKBP_32to40hpi_aGFP_noBiotin_noRAPA.bedgraph.gz

value: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo


title: MAC-T cell only, control, rep2 [MACT02]

source_name: MAC-T

value: MAC-T

value: bovine mammary epithelial cells

value: Bos taurus


title: MAC-T cells infected by M. bovis, 24 h incubation, rep1 [INF01]


title: 420_YoungControlICR


title: 440_YoungDIOAdLib


title: RNA-Seq G5A-KO_bz3

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

description: Library name: sample12

data_processing:
reads were mapped to toxoplasma genome TGM49_v55 (toxodb.org) with hisat2 using default settings
get feature counts with htseq-count
differential expression with DESeq2
Assembly: TGM49 version 55 (toxodb.org)
Supplementary files format and content: tabular, feature (gene) counts

molecule: cytoplasmic RNA

organism: Toxoplasma gondii

source_name: PrudeltaKu80deltaHX (parental)

growth_protocol: parasites innoculated onto confluent human foreskin fibroblasts in DMEM+5%FBS (no antibiotic). After 4hrs, media changed to same (for unstressed) or to RPMI pH8.3 (stressed) for 48h prior to harvest

extract_protocol:
infected HFF monolayer was scraped and syringed lysed (23gauge), pelleted and washed twice in PBS prior to resuspension in Trizol. Total RNA isolated according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: parasites grew in tachyzoite (DMEM pH 7.4, 5% FBS, 5%CO2) or bradyzoite-inducing (RPMI pH8.3, 5%FBS, ambient CO2) media for 48hrs prior to harvest

value: PrudeltaKu80deltaHX (parental)

value: stressed tachyzoites

value: RPMI pH8.3, 5% FBS, ambient CO2 / 48hr


title: miniTurbo, Biotin, 24to32hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep1

description:
Library name: miniTurbo-Biotin-24to32hpi_plusBiotin_RAPA_rep1
miniTurbo_24to32hpi_aBiotin_plusBiotin_RAPA_2rep.avg.bedgraph.gz

value: 3D7 wt / mCherry-FRB-miniTurbo

value: Biotin (CST, #D5A7)

value: isolated nuclei


title: 427_YoungDIOAdLib


title: 3D7-BDP5-FKBP, Biotin, 32to40hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-32to40hpi_plusBiotin_noRAPA_rep2
3D7-BDP5-FKBP_32to40hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: 3D7-BDP5-FKBP, Biotin, 32to40hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-32to40hpi_plusBiotin_RAPA_rep2
3D7-BDP5-FKBP_32to40hpi_aBiotin_plusBiotin_RAPA_2rep.avg.bedgraph.gz
log2_BDP5-over-miniturbo_32to40hpi_aBiotin_plusBiotin_RAPA_2reps.avg.bedgraph.gz


title: MAC-T cell only, control, rep1 [MACT01]


title: RNA-Seq G5A-KO_bz2

description: Library name: sample11


title: 3D7-BDP5-FKBP, Biotin, 32to40hpi, noBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-32to40hpi_noBiotin_noRAPA_rep2
3D7-BDP5-FKBP_32to40hpi_aBiotin_noBiotin_noRAPA_2rep.avg.bedgraph.gz


title: Drosophila heads, UAS-bchs::HAcontrol (neuron dataset), sample 5

city: Leipzig

first: Diana

last: Le Duc

address: Philipp-Rosenthal-Str. 55

institute: Institute of Human Genetics,University of Leipzig Medical Center

data_processing:
STAR,HTSEQ
Assembly: BDGP6.46 (GCA_000001215.4)

organism: Drosophila melanogaster

source_name: adult heads

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to protocol (neuronal Bchs overexpression dataset) or exchanging the first step of homogenization in RLT buffer with the following Trizol protocol (glial Bchs overexpression dataset). Heads were homogenized in 500 µl Trizol, centrifuged for 5 min at 10000 rpm at 4°C, supernatant was tranferred to a new tube, 200 µl Chloroform (Carl Roth, No. 6340.1) was added and the tube was shaked. An incubation step at room temperature for 3 min was followed by centrifugation for 5 min at 10,000 rpm at 4°C. The upper aqueous phase was transferred in a new tube and it was continued with the RNeasy Micro Kit protocol.
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA).

value: adult heads


title: 408_YoungControlICR


title: 405_YoungControlICR


title: RNA-Seq G5A-KO_bz1

description: Library name: sample10


title: 3D7-BDP5-FKBP, Biotin, 24to32hpi, plusBiotin, noRapa, DiBioCUT&Tag

description:
Library name: 3D7-BDP5-FKBP-Biotin-24to32hpi_plusBiotin_noRAPA
3D7-BDP5-FKBP_24to32hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: Drosophila heads, UAS-bchs::HAcontrol (neuron dataset), sample 4


title: 404_YoungControlICR


title: RNA-Seq G5A-KO_tz3

description: Library name: sample9

value: tachyzoites

value: DMEM pH 7.4, 5% FBS, 5% CO2 / 48hr


title: 449_YoungControlAdLib

value: YoungControlAdLib


title: Drosophila heads, UAS-bchs::HAcontrol (neuron dataset), sample 3


title: MAC-T cells infected by M. bovis, 24 h incubation, rep2 [INF02]

value: Bos taurus+M.bovis

value: M bovis infected


title: RNA-Seq G5A-KO_tz2

description: Library name: sample8


title: 3D7-BDP5-FKBP, Biotin, 24to32hpi, plusBiotin, Rapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-24to32hpi_plusBiotin_RAPA_rep2
3D7-BDP5-FKBP_24to32hpi_aBiotin_plusBiotin_RAPA_2rep.avg.bedgraph.gz


title: Drosophila heads, UAS-bchs::HAcontrol (neuron dataset), sample 2


title: 3D7-BDP5-FKBP, Biotin, 24to32hpi, plusBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-24to32hpi_plusBiotin_noRAPA_rep2
3D7-BDP5-FKBP_24to32hpi_aBiotin_plusBiotin_noRAPA_2rep.avg.bedgraph.gz


title: 446_YoungControlAdLib


title: Drosophila heads, UAS-bchs::HAcontrol (neuron dataset), sample 1


title: 424_YoungControlAdLib


title: RNA-Seq G5A-KO_tz1

description: Library name: sample7


title: Drosophila heads, nSyb-Gal4 control, sample 5


title: 421_YoungControlAdLib


title: RNA-Seq G5A-HA_bz2

description: Library name: sample5

value: GCN5A-3xHA tag


title: MDV infected, replicate 3, scRNA seq

city: Athens

first: Deborah

last: Velez-Irizarry

state: GA

address: 934 College Station Road

department: US National Poultry Research Center

institute: USDA, Agricultural Research Service

description: 10X Genomics

data_processing:
Raw Illumina sequences were demultiplexed and converted to single cell feature counts using CellRanger v7.0.0 (10X Genomics).
Assembly: Sequence reads were mapped to an amalgamated reference genome that included the reference Gallus gallus (GCF016699485.2) and Gallid alphaherpesvirus 2 (GCF000846265.1).
Supplementary files format and content: HDF5 files with gene counts per cell, barcode ids, gene information, and sample metadata.

organism: Gallus gallus

source_name: spleen

extract_protocol:
Whole spleens were subsequently collected for each bird, and splenic-derived leukocytes were isolated. Briefly, individual spleens were homogenized and filtered through a 40µM cell strainer to obtain single-cell suspensions. Mononuclear leukocytes were enriched with a density gradient cell separation protocol using Histopaque-1077 medium (MilliporeSigma, Burlington, MA). Six single-cell suspensions (2 x 10^5 cells from 3 control and 3 MDV-infected samples) were transferred the same day on ice for sequencing.
Chromium Next GEM Single Cell 3’ kit v3.1 was used to prepare the single-cell libraries on the 10X Genomics platform (10X Genomics Inc., Pleasonton, CA) with a target number of 10k cells per sample. The 10X single-cell libraries were sequenced on the NovaSeq 6000 system (paired-end 28bp x 90 bp) (Illumina, San Diego, CA).

value: spleen

value: lymphocytes

tag: age

value: 20 days

tag: days post_infection

value: 2,000 pfu JM/102W strain MDV


title: MDV infected, replicate 2, scRNA seq

description: 10X Genomics

tag: tissue


title: 406_YoungControlAdLib


title: RNA-Seq G5A-HA_bz1

description: Library name: sample4

value: PrudeltaKu80deltaHX (parental)

tag: cell type


title: Drosophila heads, nSyb-Gal4 control, sample 3

tag: genotype


title: MDV infected, replicate 1, scRNA seq

description: 10X Genomics

tag: treatment


title: 403_YoungControlAdLib


title: Drosophila heads, nSyb-Gal4 control, sample 4


title: RNA-Seq G5A-HA_tz3

description: Library name: sample3


title: control uninfected, replicate 3, scRNA seq

description: 10X Genomics


title: RNA-Seq G5A-HA_tz2

description: Library name: sample2


title: Drosophila heads, nSyb-Gal4 control, sample 2


title: Drosophila heads, nSyb-Gal4 control, sample 1


title: NHP Liver, PCSK9-EE-V2 1.5mpk, 3

city: Boston

first: Frederic

last: Tremblay

address: 201 Brookline Ave, Suite 1101

institute: Chroma Medicine

data_processing:
A nf-core Methyl-Seq pipeline was used for initial read alignment and estimation of methylation calls using Bismark, aligned to the Ensembl Cyno_6.0 reference genome without deduplication.
IGV was used to visualize the methylation bedgraphs in the region surrounding the PCSK9 TSS.
Average % methylation of CpGs with coverage in all conditions in a 500bp region centered on the gRNA binding sites (Chr1:169045699-169046199) was calculated for each condition using R.
Assembly: Cyno_6.0
Supplementary files format and content: bedgraph, CpG methylation

organism: Macaca fascicularis

source_name: Liver

extract_protocol:
Genomic DNA was extracted from NHP liver biopsies using DNAdvance Kit (Beckman Coulter).
Genomic DNA is denatured and treated with sodium bisulfite and heat to deaminate unmethylated cytosines to uracil using the EZ-96 Methylation-Gold MagPrep bisulfite conversion kit (Zymo Research). Primers were designed to amplify the region around the NHP PCSK9 TSS, as seven short, partially overlapping, amplicons. Amplicons were generated using Platinum Taq polymerase (Invitrogen) and pooled for each condition so that each sample contained all associated amplicons and used as input for NEBNext Ultra II DNA library prep, amplified with unique dual indexes to allow for multiplexing. Libraries were sequenced using an Illumina Nextseq 2000 instrument (2x150bp PE reads) to a read depth of at least 9 million read pairs per sample.

treatment_protocol: The cynomolgus monkey studies were conducted at Altasciences according to the IACUC guidelines. All monkeys were genotyped at the PCSK9 locus to ensure the DNA sequence at the sites where gRNAs bind have no mutations. Monkeys were randomly assigned to groups based on established social unit. Pretreatment medications of diphenhydramine (5 mg/kg), dexamethasone (1 mg/kg), and famotidine (0.5 mg/kg) were administrated to all monkeys via intramuscular injection one day and 30-60 min before the start of infusion. The LNP formulations or saline vehicle were administered by intravenous infusion for 1 hour. During the study, liver biopsy collections were performed under general anesthesia by ultrasonographic-guided percutaneous biopsy using a 16-gauge biopsy needle. Samples were flash frozen in liquid nitrogen, maintained on dry ice, then stored in a freezer set to maintain at -80°C.

value: Liver

value: PCSK9-EE-V2, 1.5 mpk


title: RNA-Seq G5A-HA_tz1

description: Library name: sample1


title: Drosophila heads, neuronal Bchs overexpression, sample 5


title: control uninfected, replicate 1, scRNA seq

description: 10X Genomics


title: control uninfected, replicate 2, scRNA seq

description: 10X Genomics


title: NHP Liver, PCSK9-EE-V2 1.5mpk, 2


title: PRU_bz

description: Library name: sample14

data_processing:
reads were mapped to toxoplasma genome (TGME49 version 67) using bowtie2 v2.5.3 allowing for dovetailing
duplicates removed using MarkDuplicates v3.1.1.0
genome coverage using bamCoverage v3.5.4 normalizing to 65Mb genome size
Assembly: TGME49 version 67 (toxodb.org)
Supplementary files format and content: bigwig, genome coverage for each sample
Library strategy: CUT&Tag

extract_protocol:
infected HFF monolayer was scraped and syringed lysed (23gauge), pelleted and washed twice in PBS. Nuclei were isolated and processed according to manufacturer's CUT&Tag protocol (Active motif cat# 53160)
Illumina-compatible libraries constructed using Active motif CUT&Tag module (cat# 53160)

value: stressed tachyzoite

value: wildtype

value: RPMI pH8.3, 5% FBS, ambient CO2 / 48hr


title: NHP Liver, PCSK9-EE-V2 1.5mpk, 1


title: RNA-Seq G5A-HA_bz3

description: Library name: sample6

value: stressed tachyzoites


title: Drosophila heads, neuronal Bchs overexpression, sample 4

value: adult heads


title: PRU_tz

description: Library name: sample13

value: tachyzoite

value: DMEM pH 7.4, 5% FBS, 5% CO2 / 48hr


title: 5% CO2, pH 7.0, Rep 2,  part 2

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Reads from each lane were combined into individual files using standard UNIX commands
Trimmomatic (v0.33)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie (v1.1.2) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
HTSeq software suite (v0.6.0) was used to analyze aligned and determine counts per gene feature in the M. tuberculosis CDC1551 genome
edgeR (v3.2) was used to normalize data by estimating effective library sizes using trimmed mean M-values
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the GLM functionality edgeR package
Assembly: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary files format and content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates

organism: Mycobacterium tuberculosis

source_name: Bacterial Cell

growth_protocol: M. tuberculosis CDC1551  was maintained in vented T-25 culture flasks in 7H9 Middlebrook medium supplemented with 10% oleic acid-albumin-dextrose-catalase (OADC), 0.05% Tween-80, and 0.2% glycerol and incubated at 37 °C with 5% CO2, unless noted otherwise. For experiments requiring buffered medium, 100 mM 3-(N-morpholino)propanesulfonic acid (MOPS) or 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) was added to 7H9 medium for buffering to pH 7.0 or pH 5.7, respectively. Cultures were grown to mid-late log phase (OD600 0.5-1.0) for use in experiments described below.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: M. tuberculosis CDC1551 ultures were seeded at a starting OD600 of 0.2  in 8 mL of 7H9 buffered media and grown at 37°C in standing T-25 culture flasks. Two biological replicates of the following culture conditions were examined: i)  0.5% CO2 at pH 5.7, ii)  5% CO2 at pH 5.7, , iii) 0.5% CO2 at pH 7.0, iv) 5% CO2 at pH 7.0. Cultures were incubated for six days, after which total bacterial RNA was extracted as previously described [1]

tag: strain

tag: condition


title: NHP Liver, PCSK9-EE-V2 1.0mpk, 3

value: PCSK9-EE-V2, 1.0 mpk


title: Drosophila heads, neuronal Bchs overexpression, sample 3


title: 5% CO2, pH 7.0, Rep 2, part 1


title: NHP Liver, PCSK9-EE-V2 1.0mpk, 2


title: G5B-HA_bz3

description: Library name: sample12

value: GCN5B-3xHA tag


title: Drosophila heads, neuronal Bchs overexpression, sample 2


title: G5B-HA_bz2

description: Library name: sample11


title: 5% CO2, pH 7.0, Rep 1,  part 2


title: 3D7-BDP5-FKBP, Biotin, 24to32hpi, noBiotin, noRapa, DiBioCUT&Tag, rep2

description:
Library name: 3D7-BDP5-FKBP-Biotin-24to32hpi_noBiotin_noRAPA_rep2
3D7-BDP5-FKBP_24to32hpi_aBiotin_noBiotin_noRAPA_2rep.avg.bedgraph.gz

value: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo

value: Biotin (CST, #D5A7)

value: isolated nuclei


title: NHP Liver, PCSK9-EE-V2 1.0mpk, 1

description: Sample was resequenced to improve coverage, data was merged for analysis


title: Drosophila heads, neuronal Bchs overexpression, sample 1


title: NHP Liver, PCSK9-EE-V2 0.5mpk, 3

value: PCSK9-EE-V2, 0.5 mpk


title: G5B-HA_bz1

description: Library name: sample10


title: 5% CO2, pH 7.0, Rep 1, part 1


title: Drosophila heads, UAS-bchs::HAcontrol (glia dataset), sample 5


title: G5B-HA_tz3

description: Library name: sample9


title: 5% CO2, pH 5.7, Rep 2,  part 2


title: Drosophila heads, repo-Gal4 control, sample 5


title: NHP Liver, PCSK9-EE-V2 0.5mpk, 2


title: 5% CO2, pH 5.7, Rep 2, part 1


title: G5B-HA_tz2

description: Library name: sample8


title: Drosophila heads, glial Bchs overexpression, sample 5


title: Drosophila heads, UAS-bchs::HAcontrol (glia dataset), sample 4


title: 5% CO2, pH 5.7, Rep 1, part 1


title: G5A-HA_bz3

description: Library name: sample6

value: GCN5A-3xHA tag


title: 5% CO2, pH 5.7, Rep 1,  part 2


title: 0.5% CO2, pH 7.0, Rep 2,  part 2


title: NHP Liver, Vehicle, 1

value: Vehicle


title: G5A-HA_bz2

description: Library name: sample5

value: PrudeltaKu80deltaHX (parental)


title: Drosophila heads, glial Bchs overexpression, sample 4


title: G5A-HA_bz1

description: Library name: sample4


title: M. bovis only, control, rep1 [MB01]

organism: Mycoplasmopsis bovis

source_name: strain PG45 (ATCC 25523)

value: strain PG45 (ATCC 25523)

value: WT

value: control/no treatment


title: M. bovis only, control, rep2 [MB02]


title: Drosophila heads, UAS-bchs::HAcontrol (glia dataset), sample 3


title: G5A-HA_tz3

description: Library name: sample3


title: 0.5% CO2, pH 7.0, Rep 2, part 1


title: 0.5% CO2, pH 7.0, Rep 1,  part 2


title: 0.5% CO2, pH 7.0, Rep 1, part 1


title: G5A-HA_tz2

description: Library name: sample2


title: NHP Liver, PCSK9-EE-V2 0.5mpk, 1

value: Liver


title: 0.5% CO2, pH 5.7, Rep 2,  part 2


title: G5A-HA_tz1

description: Library name: sample1


title: G5B-HA_tz1

description: Library name: sample7


title: Drosophila heads, repo-Gal4 control, sample 3


title: Drosophila heads, UAS-bchs::HAcontrol (glia dataset), sample 2


title: Drosophila heads, glial Bchs overexpression, sample 3