title: HPC_14div_50mMKCl_6h

description: 14 div + 50mMKCl for 6 hr


status: Public on Jul 25 2023

type: SRA

city: London

first: Fiona

middle: Mary

last: Watt

address: Great Maze Road

country: United Kingdom

institute: Kings College London

description:
CtrlUnwoundedGata6-derivedtomatopositive14
control_g6.txt

library_source: transcriptomic

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Read quality was checked and alinged to GRCm38 reference genome using STAR version 2.2.
Gene specific counts were calculated using featureCounts from Rsubread 2.7 with mm10 Refseq.
All the downstream analysis was performed using Seurat version 3.2.2 and monocle 2.18.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Seurat object with annotations for every sample/cell.

molecule: total RNA

organism: Mus musculus

source_name: Epidermis

extract_protocol:
Single keratinocytes from mouse epidermis were isolated by flow sorting using appropriate markers. Cells were sorted into individual wells of a 96-well plate containing 2ul lysis buffer (0.8% (volume/volume) Triton X-100 and 2U/ul recombinant RNase inhibitor
Libraries were prepared for sequencing using standard Illumina protocols with SmartSeq2 followed by Nextera XT protocol.

treatment_protocol: For lineage-tracing experiments, mice received a topical dose of 4-hydroxy-tamoxifen (1 mg dissolved in 100 µl acetone) applied to clipped back skin

tag: strain

tag: tissue

value: Epidermis

tag: age

value: Day 0 post-wounding

tag: genotype

value: Cre (+/-) tdTomato (+/-)

tag: treatment


title: M_20h_Rep1_exp1

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
exp1
M_20h_Rep1

data_processing:
Reads were trimmed with cudadapt (v. 1.18) to remove Illumina adapter sequences.
Reads were mapped to the ribosomal RNA sequences extracted from ensembl AgamP4 genome using the Ensembl AgamP4 annotation (release 48) with STAR (v. 2.7.3a) with the following parameters: outFilterMultimapNmax 1000000 outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Reads mapping to rRNA were discarded and unmapped reads are used in downstream processing.
Reads were mapped to the ensembl AgamP4 genome using the Ensembl AgamP4 annotation (release 48) together with lncRNA annotation from 10.1186/s12864-015-1507-3 with STAR (v. 2.7.3a) using the following parameters: outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Only uniquely mapped reads were used for downstream analysis.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v. 1.9) and DeepTools (v. 3.1.0)
Primary alignments were assigned to features using subread (v. 1.6.5) with the AgamP4 annotation (release 48) combined with lncRNA annotation 10.1186/s12864-015-1507-3 as a reference.
Assembly: AgamP4
Supplementary files format and content: tab-delimited text file containing raw counts for each sample, bigWig files containing CPM normalized coverage signals of primary alignments

molecule: polyA RNA

organism: Anopheles gambiae

source_name: embryo

growth_protocol: A. gambiae mosquitoes were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).

extract_protocol:
RNA was extracted using Trizol  (Fisher Scientific, Cat. No.15-596-026) and the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. No. R2062).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00).

value: embryo

tag: developmental stage

tag: Sex

value: male


title: RNA_NFIA-Tg_iWAT_rep1

city: Tokyo

first: Yuta

last: Hiraike

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

country: Japan

institute: The University of Tokyo

data_processing:
The sequence reads were aligned to the mm9 genome using STAR (Galaxy Version 2.7.8a+galaxy0).
Assembly and quantification were performed using StringTie (Galaxy Version 2.1.1).
Assembly: mm9
Supplementary files format and content: txt files showing FPKM value of each samples.

source_name: iWAT

growth_protocol: SVF cells were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone.

value: NFIA-Tg

tag: time course

value: iWAT


title: F_20h_Rep4_exp1

description:
exp1
F_20h_Rep4

value: female


title: HPC_14div

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description: 14 div

library_source: genomic

data_processing:
adapter trimming using Methpipe pipeline as described in Lister et al Science 2013
mapping reads to mm10 genome using Bowtie  as described in Lister et al Science 2013
merging mapped runs, convert to .slam, sort, collapse, trim reads using Methpipe pipeline as described in Lister et al Science 2013
stack creation and hammer correction using Methpipe pipeline as described in Lister et al Science 2013
make allC tables and count global statistics using Methpipe pipeline as described in Lister et al Science 2013
convert stacks to bedgraph files using simple awk script
generate bigwigs using bedgraphtobigwig v4
Genome_build: mm10
Supplementary_files_format_and_content: stacks.txt files containing all mapped methylated and total cytosines, bigWigs for coverage containing all mapped cytosines, bigWigs for mC containing percentage of methylated cytosines for contexts CG and CH

molecule: genomic DNA

source_name: E18 primary neurons

growth_protocol: mESC cells lines R1 and G4 were maintained on gamma-irradiated mouse embryonic fibroblasts in mESC medium with LIF. Cells were fed daily and split based on confluency. Neural differentiation was initiated by dissociating the mESC colonies using Accutase and excess feeder cells were removed from the cell suspensions by panning on gelatin-coated plates. Dissociated cells were counted and transferred to ultra-low attachment cell culture plates at a dilution of 220,000 cells/ml, in differentiation medium. Neural induction was continued for 8 days, medium was changed every two days, and supplemented with 5 µM retinoic acid for the final 4 days. Cell aggregates were dissociated using Accutase, single cell selected through a 40 µm cell strainer, and plated onto poly-ornithine / laminin-coated plates in N2 medium. After 2 days, cells were changed into N2B27 which was changed every 4 days for 12 days, following which 50% media changes were performed for the remaining culture time.

extract_protocol:
Quiagen Blood and Tissue DNA Extraction kit with extended Pretinase K and RNAsA treatment steps.
Lucigen Nxseq Ampfree Low DNA Library Kit and Zymo EZ DNA Methylation Direct Kit for MethylC libraries.

treatment_protocol: High potassium-mediated depolarisation was performed by washing cells with low K+ buffer, transferring to high K+ buffer for 5 min, washed again in low K+ buffer and either harvested directly for RNA, immediately fixed for ICC, or chased in growth medium for the appropriate times prior to fixation or RNA extraction.

tag: cell line

value: primary

value: hippocampus


description:
CtrlUnwoundedGata6-derivedtomatopositive12
control_g6.txt


title: F_20h_Rep2_exp1

description:
exp1
F_20h_Rep2


title: RNA_WT_iWAT_rep2

value: WT


description:
CtrlUnwoundedGata6-derivedtomatopositive11
control_g6.txt


title: HPC_1div

description: 1 div


title: RNA_WT_iWAT_rep1


title: F_20h_Rep1_exp1

description:
exp1
F_20h_Rep1


title: M_14h_Rep2_exp1

description:
exp1
M_14h_Rep2


description:
CtrlUnwoundedGata6-derivedtomatopositive9
control_g6.txt


title: Kp209_CSTR-3

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

data_processing:
Adaptor removal; Trim sequences; first base to keep: 14
Drop poor quality reads; Trimmomatic; sliding widow Number of bases to average across: 4 average quality required: 20
Reads mapping; Bowtie2 ;
Count aligned reads in features; Ht-seq count ;
Differentially represented features; DeSeq2 ;
Assembly: NOT PROVIDED
Supplementary files format and content: Gene ID, Normalized counts, DESeq2 results

organism: Klebsiella pneumoniae

source_name: liquid cultures

extract_protocol:
Hot phenol-chloroform RNA extraction and Ribominus 2.0
Collibri stranded RNA library prep kit for illumina (Invitrogen)

tag: strain background

tag: cell type

value: liquid cultures

value: phoQ-mut


description:
CtrlUnwoundedGata6-derivedtomatopositive10
control_g6.txt


title: RNA_WT_iWAT_rep3


title: Kp209_CSTR-2


title: Kp209_CSTR-1


title: MS13-1-MT

city: Seoul

first: jong-seol

last: kang

address: 1 Gwanak-ro, Gwanak-gu

department: Biological sciences

country: South Korea

institute: Seoul National University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdapt version 1.10, in-house python program, and FASTX-Toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to mouse mRNA sequences by Bowtie2 version 2.2.7 (-t -k 2 --very-sensitive).
Tophat version 2.1.1 [command-line parameters: with–no-coverage-search–b2-very-sensitive] was used to align the reads against mouse genome.
RSEM version 1.2.30 was used to estimate transcript abundance. Differentially expressed genes were assessed using the limma package in R, and voom transformation was applied.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Expression_with_read_number_WT_MT.txt

source_name: Skeletal muscle

growth_protocol: All mouse lines were backcrossed onto a C57BL/6 background and were housed and handled according to the guidelines of the Institutional Animal Care and Use Committee (IACUC) at Seoul National University.

extract_protocol:
Skeletal muscles were freshly isolated, and RNA was extracted using Trizol reagent. TruSeq Stranded Total RNA LT sample prep kit (Human Mouse Rat) was used for the construction of library.
Library was constructed following TruSeq Stranded Total RNA Sample prep Guide, Part #15031048 Rev. E.

value: Skeletal muscle

value: 3 months


title: CtrlUnwoundednon-Gata6tomatonegative8

description:
CtrlUnwoundednon-Gata6tomatonegative8
controlng6.txt


title: Kp209-2

value: wild-type


title: F_14h_Rep2_exp1

description:
exp1
F_14h_Rep2


title: CtrlUnwoundednon-Gata6tomatonegative7

description:
CtrlUnwoundednon-Gata6tomatonegative7
controlng6.txt


title: Kp209-3


title: MS15-3-WT

value: wild type


title: MS13-2-MT


description:
CtrlUnwoundedGata6-derivedtomatopositive8
control_g6.txt

value: Epidermis


title: MS15-2-WT


title: M_14h_Rep1_exp1

description:
exp1
M_14h_Rep1


title: MS14-2-MT


title: F_14h_Rep1_exp1

description:
exp1
F_14h_Rep1


title: Kp209-1


title: MS13-3-WT


title: CtrlUnwoundednon-Gata6tomatonegative5

description:
CtrlUnwoundednon-Gata6tomatonegative5
controlng6.txt

value: Day 0 post-wounding


title: CtrlUnwoundednon-Gata6tomatonegative6

description:
CtrlUnwoundednon-Gata6tomatonegative6
controlng6.txt

value: Cre (+/-) tdTomato (+/-)


title: M_11h_Rep3_exp1

description:
exp1
M_11h_Rep3

value: embryo


title: M_11h_Rep2_exp1

description:
exp1
M_11h_Rep2

value: male


title: RNA_WT_adipocytes_day0_rep1

source_name: ingSVF-derived adipocytes

value: day 0

value: ingSVF-derived adipocytes


title: M_11h_Rep1_exp1

description:
exp1
M_11h_Rep1


title: H-5

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Raw data were trimmed by Trim Galore with default settings.
The clean data were mapped to mouse reference genome mm9 using bowtie2 (v2.2.5) with default parameters.
Duplicates were removed using Picard (v2.22.4).
Assembly: mm9
Supplementary files format and content: bigwig files for H3K9me3 signals
Library strategy: CUT&Tag

source_name: GV oocytes

extract_protocol:
The CUT&Tag assay was conducted following the protocol of Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD904) Briefly, 250 GV oocytes were collected and washed once with 500 μl wash buffer before they were bound to activated ConA beads for 10 min at room temperature. After that, cells were incubated with 1 μg anti-H3K9me3 antibody (Active Motif, # 39161) at 4°C overnight. Anti-rabbit IgG was added and incubated for 1 h at 25°C the next day. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25°C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37°C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55°C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water.
15 μl of purifed DNA was mixed with 25 μl of 2× CAM, along with 5 μl of uniquely barcoded i5 and i7 primers from the TruePrep Index Kit V2 for Illumina (Vazyme Biotech, # TD202). A total volume of 50 μl of sample was placed in the Mastercycler® nexus (Eppendorf, #6331000076) using the following program: 72°C for 3 min; 98°C for 3 min; 18 cycles of 98°C for 10 s, 60°C for 5 s, and 72°C for 1 min; and holding at 12°C. To purify the PCR products, 2× volumes of VAHTS DNA Clean Beads (Vazyme Biotech, #N411) were added and incubated at room temperature for 5 min. The beads were washed twice with 200 μl fresh 80% ethanol and eluted in 22 μl ddH2O. All CUT&Tag libraries were sequenced using the Illumina NovaSeq 6000 platform in PE150 mode.

value: GV oocytes

value: Dnmt1f/+,Dnmt3af/+; Blimp1-Cre

tag: antibody


title: H-4


title: F_11h_Rep4_exp1

description:
exp1
F_11h_Rep4

value: female


title: CtrlUnwoundednon-Gata6tomatonegative3

description:
CtrlUnwoundednon-Gata6tomatonegative3
controlng6.txt


title: H-3


title: H-1


title: F_11h_Rep3_exp1

description:
exp1
F_11h_Rep3


title: H-2


title: CtrlH1Blank

description:
CtrlH1Blank
control_g6.txt


title: CtrlUnwoundednon-Gata6tomatonegative2

description:
CtrlUnwoundednon-Gata6tomatonegative2
controlng6.txt


title: F_11h_Rep1_exp1

description:
exp1
F_11h_Rep1


title: AKT+Yap+Sox9KO RNA-seq rep1

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

data_processing:
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using HTSEQ default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python

source_name: Alb-Cre:Sox9(f/f) C57BL/6 background

extract_protocol:
Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) followed by manufacturer’s instructions.
RNA samples from livers were used to generate library using TruSeq kit from Illumina
We used in-house HiSeq2500 platform and sequenced 200 million reads to accurately quantify genes & transcripts

treatment_protocol: Sleeping beauty tranposone containing plasmids along with the transposase in a ratio of 25:1 were diluted in 2 ml of normal saline (0.9% NaCl), filtered through 0.22mm filter (Millipore), and hydrodynamically injected into the lateral tail vein of mice.

tag: gender

value: Male

value: 10-13 weeks

value: Liver

tag: genotype/variation

value: AKT+Yap+Sox9KO mouse


title: AKT+NICD RNA-seq rep2

source_name: C57BL/6 WT

value: AKT+NICD mouse


title: CtrlUnwoundednon-Gata6tomatonegative1

description:
CtrlUnwoundednon-Gata6tomatonegative1
controlng6.txt


title: AKT+NICD RNA-seq rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive7
control_g6.txt


title: WTforH-3


title: M_9h_Rep3_exp1

description:
exp1
M_9h_Rep3


title: WTforH-4


title: WT RNA-seq rep3

value: WT mouse


title: AKT+NICD RNA-seq rep1


title: WTforH-2


title: M_9h_Rep2_exp1

description:
exp1
M_9h_Rep2


title: AKT+Yap+Sox9KO RNA-seq rep3


title: CtrlUnwoundednon-Gata6tomatonegative4

description:
CtrlUnwoundednon-Gata6tomatonegative4
controlng6.txt


description:
CtrlUnwoundedGata6-derivedtomatopositive6
control_g6.txt


title: M_9h_Rep1_exp1

description:
exp1
M_9h_Rep1


title: AKT+Yap+Sox9KO RNA-seq rep2


description:
CtrlUnwoundedGata6-derivedtomatopositive5
control_g6.txt


title: WTforH-1


title: M_9h_Rep4_exp1

description:
exp1
M_9h_Rep4


title: F_9h_Rep3_exp1

description:
exp1
F_9h_Rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive4
control_g6.txt


title: WT RNA-seq rep1


title: R807_10_786OParentalLY2

city: Houston

first: Christine

middle: B.

last: Peterson

state: TX

address: 1400 Pressler St.

department: Biostatistics

institute: University of Texas MD Anderson Cancer Center

data_processing:
Cell line data: Quality control was performed on the read data using the FastQC software.
Cell line data: Reads were aligned to human genome data hg38 using TopHat.
Cell line data: SAM Tools was used to sort the BAM files by read name and convert to SAM files.
Cell line data: HTseq was used to summarize the reads per gene from the aligned BAM files.
Cell line data: The count data were normalized using the variance stabilizing transformation in the DEseq2 R package.
Murine tumor data: Quality control was performed on the read data using the FastQC software.
Murine tumor data: The BBTools Repair utility was used to fix order of paired reads in the samples.
Murine tumor data: Reads were aligned to mouse reference genome GRCm38 using the Star RNASeq alignment software.
Murine tumor data: HTseq was used to summarize the reads per gene from the aligned BAM files.
Murine tumor data: The count data were normalized using the rlog transformation in the DEseq2 R package.
Assembly: Cell line data: hg38
Assembly: Murine tumor data: GRCm38
Supplementary files format and content: csv files with normalized counts for each sample

organism: Homo sapiens

source_name: Kidney

growth_protocol: 786-O cells were maintained in DMEM containing 10% fetal bovine serum at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol: none provided

treatment_protocol:
786-O cells were untreated (Control) or treated with 25nM LY2603618 for 48 hrs.
Renca cells (5 × 105) were suspended in 100 µL Matrigel matrix (Corning, 354234) diluted with PBS at a 1:1 ratio and subcutaneously injected into the backs of mice. After the tumors were palpable (i.e., tumor volume reached approximately 100 mm3), the mice were left untreated or treated with VE822 (60 mg/kg, 5 consecutive days per week) via oral gavage.

value: Kidney

value: Renal cell carcinoma

value: WT


description:
CtrlUnwoundedGata6-derivedtomatopositive3
control_g6.txt

value: Epidermis

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


title: R807_9_786OParentalCon2

value: Untreated


title: R807_2_786OParentalLY


title: R807_1_786OParentalCon


title: mESCs, MTX, 12 hours, rep1 2%IP (Input)

city: Beijing

first: Pei

last: Pei

address: 2 Yabao Road

department: The Central Lab

institute: Capital Institute of Pediatrics

description:
Two group comparison
mtxK79_peaks.txt

data_processing:
CHIP-Seq libraries were prepared according to the protocol and sequenced using Illumina NovaSeq 6000. After passing the quality check, all reads are mapped to mouse genome using Bowtie2 with default parameters. Two mismatches cannot appear in one cohort. The peak of the H3K79me2 on the genome was determined using MACS2 with a false detection rate of 0.05. Each peak-associated gene was identified by an internal program using Entrez gene annotation, where the Shh target gene was defined as a gene containing H3K79me2-peak in its transcription start site (TSS). The data set of H3K79me2 reads per kilobase per million (RPKM) values in the coding region of each gene was normalized.
Assembly: UCSCmm39
Supplementary files format and content: MACS2 peak files

source_name: mtx Input

extract_protocol:
Sv/129 mouse embryonic stem cells (mESCs) were cultured under normal folate medium for at least 2 passages before 1uM methotrexate(MTX) was applied for 24hours. 10^7 mESC cells from normal folate group and MTX group were used to obtain DNA with a concentration of 1 ng / ul and fragments were digested into100-500bp for CHIP(chromatin immunoprecipitation) sequencing.
The ChIP-seq library is constructed from ChIP DNA and control DNA (from an input normal IgG). Construct the libraries according to the manufacturers’ instructions. Perform purification and size selection of the library by Agencourt AMPure XP according to the manufacturer’s instruction. Integrity of the constructed libraries (size distribution and purity) is examined by an Agilent 2100 Bioanalyzer with a High Sensitivity DNA Kit

value: mouse embryonic stem cell

value: MTX

tag: chip antibody


title: F_9h_Rep2_exp1

description:
exp1
F_9h_Rep2

value: embryo


title: mESCs, MTX, 12 hours, rep1 (IP)

description:
Two group comparison
mtxK79_peaks.txt

source_name: mtx K79_IP

value: Di-Methyl-Histone H3(Lys79)(D15E8)XP Rabbit mAb, CST (Cell Signaling Technology), Catalog# 5427


title: mESCs, normal folate, 2%IP, 1week, rep1 (Input)

description:
Two group comparison
ConK79_peaks.txt

source_name: Con Input

value: normal folate culture


title: WT RNA-seq rep2

value: Male

value: 10-13 weeks


title: AA, patient 8

city: San Francisco

first: Eunice

middle: Y

last: Lee

address: 505 Parnassus Ave

institute: University of California, San Francisco

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1
Assembly: mm10, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
For mice, dorsal skin was isolated, subcutaneous fat was removed, and was cut into small pieces prior to digestion with 0.25% collagenase type IV in Dulbecco’s Modified Eagle Medium at 37C for 1 hour in a shaking incubator. Collagenase was neutralized with Advanced RPMI 1640 Medium + 10% FBS and the digested skin was passed through a 70um strainer. The flow through was rinsed twice with centrifugation at 350g, 4C. Single-cell suspensions were stained with anti-CD45-FITC antibody and propidium iodide. CD45+, propidium iodide- cells were isolated via FACS. For human samples, human scalp biopsies were digested using the Whole Skin Dissociation Kit and its accompanying protocol, which involved the use of a gentleMACS Dissociator. Cells were resuspended and washed in 2% FBS in Cell Staining Buffer, then stained with DRAQ5 and SYTOX-Green prior to FACS isolation for DRAQ5- SYTOX-Green- live cells.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits (version 2 for mouse, version 3 for human samples) according to the manufacturer’s instructions, with a target of 5000 cells and 350 million reads

value: Skin

value: Live cells

tag: disease state

value: AA


title: CtrlUnwoundednon-Gata6tomatonegative46

description:
CtrlUnwoundednon-Gata6tomatonegative46
controlng6.txt


title: M_5h_Rep1_exp1

description:
exp1
M_5h_Rep1

value: male


title: Splenocyte naïve, 2 (RNA-seq)

city: Seattle

first: Kathleen

last: Abadie

state: Washington

address: 3720 15th Ave NE

department: Bioengineering

institute: University of Washington

data_processing:
Raw FASTQ files from RNA-seq paired-end sequencing were aligned to the GRCm38/mm10 reference genome using Kallisto (v0.46.1)
Transcript-level abundance estimates generated by Kallisto (HDF5 files) were imported to genes by cells matrices in R using tximport (v1.18.0) for downstream analysis. Transcripts with low counts (<10) were removed.
Differentially expressed genes were identified with DESeq2 (v1.30.1).
Assembly: GRCm38/mm10
Supplementary files format and content: The abundance.h5 file for each sample is a HDF5 binary file containing columns including Ensembl transcript ID and abundance estimates.
Supplementary files format and content: The abundance.tsv file for each sample is a plain text file containing columns including Ensembl transcript ID and abundance estimates.

source_name: spleen

extract_protocol:
Sorted cells were centrifuged at 500g for 5 minutes, resuspended in 350 µL of Trizol (Ambion), mixed well, and frozen at -80°C for processing, starting from step 2 of the RNeasy micro kit (Qiagen, #74004) following the manufacturer’s instructions.
After processing, RNA was resuspended in RNase free water, quantified using a NanoDrop 2000c (Thermo Scientific), and shipped on dry ice to Novogene Corporation Inc. (Sacramento, CA) for library preparation and sequencing.

value: spleen

value: CD8+ T cell


title: T cell sci-fate

data_processing:
All data processing steps were performed as in Cao et al., Nature Biotech, 2020 using the mm10 mouse reference genome for alignment. T > C (sense strand) and A > G (antisense strand) mutations were used to identify reads from newly synthesized transcripts, thus generating two digital gene expression matrices from the full sequencing data and newly synthesized RNA data.
Assembly: mm10
Supplementary files format and content: gene_count.mtx.gz is a sparse matrix file for full transcriptome data: each row corresponds to gene id; each column corresponds to each cell; each value in the matrix corresponds to UMI count.
Supplementary files format and content: df_gene.tsv.gz is the gene annotation file for the full transcriptome data including gene id, gene type and gene short name.
Supplementary files format and content: df_cell.tsv.gz is the cell annotation file for the full transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; all_exon are number of UMIs mapping to exon region, all_intron are number of UMIs mapping to intron region, all_reads are number of total UMIs.
Supplementary files format and content: gene_count_newly_synthesized.mtx.gz is a sparse matrix file for newly synthesized transcriptome data: each row corresponds to gene id; each column corresponds to each cell; each value in the matrix corresponds to UMI count.
Supplementary files format and content: df_gene_newly_synthesized.tsv.gz is the gene annotation file for the newly synthesized transcriptome data including gene id, gene type and gene short name.
Supplementary files format and content: df_cell_newly_synthesized.tsv.gz is the cell annotation file for the newly synthesized transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; new_exon are number of newly synthesized UMIs mapping to exon region, new_intron are number of newly synthesized UMIs mapping to intron region, newly_syn_UMIs are number of newly synthesized UMIs.

extract_protocol:
Harvested T cells cells were prepared for sci-RNA-seq as described for the sci-fate protocol (Cao et al., Nature Biotech, 2020). Briefly, cells were fixed with ice-cold 4% PFA for 15 min, washed and flash frozen with PBSR [PBS, pH 7.4, 0.2 mg/mL bovine serum albumin (Fisher), 1% SuperRnaseIn (Thermofisher) and 10 mM dithiothreitol (DTT)]. PFA-fixed cells were thawed, washed, and treated with iodoacetamide (IAA) to attach a carboxyamidomethyl group to 4sU.
A single-cell RNA sequencing library was prepared using the sci-RNA-seq protocol (Cao et al., Science, 2017) and NEBNext High-Fidelity 2X PCR Master Mix (NEB) for PCR. Libraries were sequenced on the Illumina NovaSeq system.

treatment_protocol: Naive CD8 T cells were activated ex vivo with plate-bound anti-CD3 and anti-CD28 in T cell media (TCM) supplemented with 100 U/mL IL-2, 0.5 ng/mL IL-7, 50 ng/mL IL-15, and 0.05 ng/mL IL-12. At days 1, 2, and 4 of activation, two subsequent sci-fate time points were taken as follows: cells were mixed and split into two wells, which had been coated with anti-CD3 and anti-CD28 at day -1 and remained in the incubator with TCM; 4sU was added to one well for a final concentration of 200 µM, and that well was harvested 2 hr later. At that time, 4sU was similarly added to the second well, and that well was harvested 2 hr later. After each 4sU addition, cells were mixed and spun down at 150g for 1 min.


title: M_5h_Rep3_exp1

description:
exp1
M_5h_Rep3


description:
CtrlUnwoundedGata6-derivedtomatopositive1
control_g6.txt

value: Epidermis


title: F_5h_Rep4_exp1

description:
exp1
F_5h_Rep4

value: female


title: CtrlUnwoundednon-Gata6tomatonegative44

description:
CtrlUnwoundednon-Gata6tomatonegative44
controlng6.txt

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


description:
CtrlUnwoundedGata6-derivedtomatopositive2
control_g6.txt


title: M_5h_Rep4_exp1

description:
exp1
M_5h_Rep4


title: AA, patient 5

description: 10x Genomics


title: CTRL, patient 7

description: 10x Genomics


title: M_5h_Rep2_exp1

description:
exp1
M_5h_Rep2


title: CtrlUnwoundednon-Gata6tomatonegative47

description:
CtrlUnwoundednon-Gata6tomatonegative47
controlng6.txt


title: Splenocyte antigen-experienced, 1 (RNA-seq)


title: Splenocyte naïve, 1 (RNA-seq)


title: CtrlUnwoundednon-Gata6tomatonegative42

description:
CtrlUnwoundednon-Gata6tomatonegative42
controlng6.txt


title: CTRL, patient 6

description: 10x Genomics


title: AA, patient 3

description: 10x Genomics


title: F_9h_Rep1_exp1

description:
exp1
F_9h_Rep1


title: F_5h_Rep2_exp1

description:
exp1
F_5h_Rep2


title: AA, patient 4

description: 10x Genomics


title: mESCs, normal folate, 1 week, rep1 (IP)

description:
Two group comparison
ConK79_peaks.txt

value: mouse embryonic stem cell


title: F_5h_Rep1_exp1

description:
exp1
F_5h_Rep1


title: CtrlUnwoundednon-Gata6tomatonegative45

description:
CtrlUnwoundednon-Gata6tomatonegative45
controlng6.txt


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 2 (RNA-seq)


title: Splenocyte antigen-experienced, 2 (RNA-seq)


title: AA, patient 2

description: 10x Genomics


title: CtrlUnwoundednon-Gata6tomatonegative43

description:
CtrlUnwoundednon-Gata6tomatonegative43
controlng6.txt


title: siRNA-SPRTN silenced sample

city: Split

first: Anja

last: Batel

address: Soltanska 2

country: Croatia

institute: MEFST

data_processing:
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGseq R package. The P values were adjusted using the Benjamini and Hochberg methods. Corrected pvalue of 0.005 and |log2 (Fold Change)| of 1 were set as the threshold for significantly differential expression
Assembly: GRCh38.p13
Supplementary files format and content: Processed data is available in excel sheet with columes: Gene (ensembl code), readcount of samples, log2foldchange (log2(sample1.value/sample2.value)), pvalue, padjust, significance (whether this gene is a DEG or not, TRUE means it’s a DEG, FALSE means not), gene name and gene description.

growth_protocol: HepG2 cells were obtained from ATCC and cultivated in EMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) (Sigma), plus 1% penicillin and streptomycin (Capricorn PS-B) .

extract_protocol:
Total RNA was isolated using Trizol (Thermo Fischer Scientiic), according to the manufacturers’ protocol. The concentration of RNA was determined with spectrophotometry (NanoDrop 1000, Thermo Scientific). The quality of RNA was validated on 1% agarose gel with bleach.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: Cells were treated accordingly to the Lipofectamine RNAiMAX reverse transfection of RNAi protocol. Final siRNA concentration was 40 nM, incubation time with transfection mix was 24 h, total incubation time was 72 h (prior to RNA isolation).

value: siRNA for SPRTN


title: F_5h_Rep3_exp1

description:
exp1
F_5h_Rep3

value: embryo


title: CtrlA12Blank

description:
CtrlA12Blank
controlng6.txt


title: control sample

value: negative ctrl siRNA


title: Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 2 (RNA-seq)


title: AA, patient 1

description: 10x Genomics


description:
CtrlUnwoundedGata6-derivedtomatopositive47
control_g6.txt


title: Day3 effector, 2 (RNA-seq)


title: WT BCT-100 replicate 3 run 1

city: Glasgow

first: Kevin

last: Rattigan

address: Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, Bearsden

department: School of Cancer Sciences

institute: University of Glasgow

data_processing:
Sequence reads were checked for QC using fastqc v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore v0.4.4
Trimmed sequence reads were mapped to GRCh38 using hisat2 v2.1.0 and sorted into bam files using samtools v1.15.1
The bam files for two independent runs of each samples were merged using samtools v1.15.1
Read count extraction were performed using featureCounts function in Subread package v2.0.1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count matrix for each Sample

source_name: Blood cell

growth_protocol: Cells were cultured in plasmax. For cell lines, 10% dilayesed FBS was used. For primary samples plasmax was supplemented as described previously (Nature Medicine volume 23, pages1234–1240 (2017))

extract_protocol:
Cell line RNA was harvested using Rneasy mini plus kit (Qiagen) or for primary samples the PicoPure™ RNA Isolation Kit (ThermoFisher) was used. For each sample,either 50, 150 or 500ng total RNA was used to prepare library
Libraries were constructed using the Illumina Stranded mRNA library kit, following manufacturers instructions.

treatment_protocol: The arginine depleting enzyme BCT-100was used to treat (24 hours) on primary normal and CML cells (100ng/mL for primary) as well as the wildtype or ASS1 knock-out K562 cell lines (1000ng/mL for cell lines)

value: Blood cell

value: WT


title: CtrlUnwoundednon-Gata6tomatonegative41

description:
CtrlUnwoundednon-Gata6tomatonegative41
controlng6.txt

source_name: Epidermis


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 2 (RNA-seq)


title: WT BCT-100 replicate 2 run 1


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 1 (RNA-seq)


title: HEK293T,vc-input,rep2

city: Shanghai

first: Xiangyue

state: Shanghai

address: 131 Dong'an Road

institute: Fudan university

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
KAS-seq reads were trimmed from 3' end until the final base had a quality score > 20, using trim_galore, discarding reads left with < 10 bp. Adapter sequence was trimmed by cutadapt.
KAS-seq reads were aligned to the UCSC hg38 genome using Bowtie 2 version 2.4.5. (parameters -X 1500)
To create KAS-seq coverage plots, the reads of mapped KAS-seq were normalized by using RPKM and reformatted in the bigwig file format.
Peaks were called uing MACS2 v2.2.7.1 with the significance cut-off q-value <=0.01. (parameters --broad-cutoff 0.01 -q 0.01)
bigWig files were generated using bamCoverage. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS2 v2.2.7.1.
Assembly: hg38
Supplementary files format and content: bamCoverage output files:co1in_rmdup.bam.RPKM.bigWig, co1ka_rmdup.bam.RPKM.bigWig, co2in_rmdup.bam.RPKM.bigWig, co2ka_rmdup.bam.RPKM.bigWig, vc1in_rmdup.bam.RPKM.bigWig,vc1ka_rmdup.bam.RPKM.bigWig,vc2in_rmdup.bam.RPKM.bigWig,vc2ka_rmdup.bam.RPKM.bigWig.
Supplementary files format and content: MACS2 output files:co1_peaks.narrowPeak, co2_peaks.narrowPeak, vc1_peaks.narrowPeak, vc2_peaks.narrowPeak.
Library strategy: KAS-seq

growth_protocol: 293T cells were maintained under a 5% CO2atmosphere in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin

extract_protocol:
Cells were collected and genomic DNA (gDNA) was isolated from cells by PureLink genomic DNA mini kit (Thermo, K182002)
Eluted DNA and its corresponding input were used for library construction by using First-round random priming and Second-strand synthesis.

treatment_protocol: Cells were treated with/withiut 0.5 mM vitamin C in the culture medium for 10 min before being subjected to 5 mM N3-kethoxal labeling for another 10 min incubation

value: Human embryonic kidney

value: vitamin C

tag: labeling

value: none (input)


description:
CtrlUnwoundedGata6-derivedtomatopositive45
control_g6.txt

tag: strain


title: HEK293T,vc-kas,rep1


title: Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 1 (RNA-seq)

tag: tissue


title: WT BCT-100 replicate 2 run 2


description:
CtrlUnwoundedGata6-derivedtomatopositive43
control_g6.txt

tag: age


title: Day3 effector, 1 (RNA-seq)


title: HEK293T,vc-input,rep1


description:
CtrlUnwoundedGata6-derivedtomatopositive46
control_g6.txt

tag: genotype


title: HEK293T,control-kas,rep2

tag: treatment

value: control


description:
CtrlUnwoundedGata6-derivedtomatopositive42
control_g6.txt


title: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 1 (RNA-seq)


title: WT BCT-100 replicate 1 run 2


title: Jag1ff/VavCre+ mac 3

city: Chicago

first: Kostandin

middle: V

last: Pajcini

state: IL

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Adaptor trimming performed with FASTQ Toolkit Version: 2.2.0 on BaseSpace (Illumina)
Alignment to mm10 performed using RNA-Seq Alignment Version: 2.0.0 on BaseSpace (Illumina)
Differential expression analysis performed using RNA-Seq Differential Expression Version: 1.0.1 on BaseSpace (Illumina)
Assembly: mm10
Supplementary files format and content: mac_counts.csv.gz

source_name: Fetal liver

extract_protocol:
1-3x10^3 fetal liver-derived CD169+ macrophages from Jag1ff/VavCre- and Jag1ff/VavCre+ E14.5 embryos were sorted into RNA lysis buffer (Invitrogen) and stored at -80ºC until RNA extraction. Total RNA was extracted using PicoPure™ RNA Isolation Kit (ThemoFisher Scientific, USA) with inclusion of DNase treatment step.
RNA sequencing libraries for Illumina sequencing were prepared in one batch using  SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) along with negative and positive controls. We used 1 nanogram of total input RNA and eleven PCR cycles during cDNA amplification.

value: Fetal liver

tag: developmental stage

value: E14.5 embryo

value: macrophages


title: HEK293T,control-input,rep2


title: HEK293T,vc-kas,rep2


title: WT BCT-100 replicate 1 run 1


description:
CtrlUnwoundedGata6-derivedtomatopositive41
control_g6.txt

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Read quality was checked and alinged to GRCm38 reference genome using STAR version 2.2.
Gene specific counts were calculated using featureCounts from Rsubread 2.7 with mm10 Refseq.
All the downstream analysis was performed using Seurat version 3.2.2 and monocle 2.18.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Seurat object with annotations for every sample/cell.

extract_protocol:
Single keratinocytes from mouse epidermis were isolated by flow sorting using appropriate markers. Cells were sorted into individual wells of a 96-well plate containing 2ul lysis buffer (0.8% (volume/volume) Triton X-100 and 2U/ul recombinant RNase inhibitor
Libraries were prepared for sequencing using standard Illumina protocols with SmartSeq2 followed by Nextera XT protocol.

value: Epidermis


title: Jag1ff/VavCre+ mac 2


title: WT Vehicle replicate 3 run 1

value: Vehicle


title: HEK293T,control-kas,rep1


title: WT BCT-100 replicate 3 run 2


description:
CtrlUnwoundedGata6-derivedtomatopositive44
control_g6.txt

value: Day 0 post-wounding


title: HEK293T,control-input,rep1


title: Jag1ff/VavCre+ mac 1


title: CtrlUnwoundednon-Gata6tomatonegative40

description:
CtrlUnwoundednon-Gata6tomatonegative40
controlng6.txt

value: Cre (+/-) tdTomato (+/-)


title: WT Vehicle replicate 2 run 1


title: Jag1ff/VavCre- mac 3


title: WT Vehicle replicate 2 run 2


title: tumor biopsy, pre-afatinib, ID36 [C59]

city: Brussels

first: Jean-Pascal

last: Machiels

address: Avenue Hippocrate 10

country: Belgium

institute: Cliniques Universitaires Saint-Luc

data_processing:
Data was processed using a standard RNAseq pipeline includingFastQCfor the quality control of the raw data, andtrimmomaticto remove low quality reads and trim the adapter from the sequences.hisat2was used to align reads to the genome.featurecountswas used to produce the count matrix. Differential expression analysis was done usingDESeq2Bioconductor package.
Assembly: GRCm38.primary_assembly.genome.fa.gz
Supplementary files format and content: CSV with the matrix of reads counts

source_name: Oral Cavity

extract_protocol:
Total RNA  from bulk fresh-frozen tumor biopsies were extracted using the miRNeasy Mini Kit from Qiagen (Venlo, Netherlands).
with kit 'NEBNext® Ultra™ II mRNA-Seq'

treatment_protocol: Patients with primary squamous cell carcinoma received afatinib for 14 days before surgery (40mg 1x/day)

value: Oral Cavity

tag: time

value: Pre-afatinib

value: afatinib


title: WT Vehicle replicate 3 run 2


title: tumor biopsy, post-afatinib, ID04 [C06]

value: Post-afatinib


title: Jag1ff/VavCre- mac 1


title: CtrlUnwoundednon-Gata6tomatonegative38

city: London

first: Fiona

address: Great Maze Road

institute: Kings College London

description:
CtrlUnwoundednon-Gata6tomatonegative38
controlng6.txt


title: Jag1ff/VavCre- mac 2


title: CtrlUnwoundednon-Gata6tomatonegative39

description:
CtrlUnwoundednon-Gata6tomatonegative39
controlng6.txt


title: WT Vehicle replicate 1 run 1

value: Blood cell


title: Brain,3xDR, rep2, scRNAseq

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

data_processing:
Sample demultiplexing, barcode processing and single-cell 3’ gene counting were carried out with Cell Ranger 5.0.0 (10x Genomics). The 10-bp transcripts/UMI tags were extracted from the reads. Cellranger mkfastq with bcl2fastq 2.0.1 was applied to demultiplex raw base call files from the sequencer into sample-specific FASTQ files
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
In brief, brains without cerebellum and olfactory bulb from 3xDR and control mice were harvested and cut into 1 mm-thickness sections using stainless steel brain matrices. Next, brain slides were incubated in 95% O2 and 5% CO2 bathed Choline Chloride Solution (92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4·7H2O, 0.5 mM CaCl2·2H2O, 12 mM N-acetyl-L-cysteine) with 10 μM NBQX and 50 μM APV and 2% FBS (Gibco, cat: l6140071) for about 30 minutes. After that, brain slides were digested in 20 U/mL papain and 100 U/mL DNase I (Worthington, cat: lK003176) for 30 min at 37 °C, followed by incubation with 1 mg/mL protease (Sigma, cat: P5147) and 1 mg/mL dispase (Worthington, cat: LS02104) at 25°C for 30 min with shaking. Next, brain slides were further tittered using a 1 mL pipette. Single-cell suspensions were then collected and filtered through 40 μm cell strainers (Falcon). The cell debris was removed by 30% Percoll (Millipore, cat: P1644) in Choline Chloride Solution. Finally, cells were resuspended in Choline Chloride Solution for further experiments. Approximately 10^7 cells were obtained from each brain. Approximately 24,000 cells for each mouse were loaded for 10x Genomics library preparation.
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation,so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: brain

value: 6.5 months old

tag: Sex

value: male

value: WT

value: 3 rounds of plx5622 diet


title: tumor biopsy, post-afatinib, ID35 [C57]

source_name: Oropharynx

value: Oropharynx


title: CtrlUnwoundednon-Gata6tomatonegative37

last: Watt

description:
CtrlUnwoundednon-Gata6tomatonegative37
controlng6.txt


title: CtrlUnwoundednon-Gata6tomatonegative36

description:
CtrlUnwoundednon-Gata6tomatonegative36
controlng6.txt


title: tumor biopsy, post-afatinib, ID36 [C58]


title: WT Vehicle replicate 1 run 2

tag: cell line


title: ASS1-KO BCT-100 replicate 3 run 1

value: ASS1 -KO


title: tumor biopsy, pre-afatinib, ID35 [C56]


title: Brain,3xDR, rep1, scRNAseq


title: ASS1-KO BCT-100 replicate 3 run 2


title: CtrlUnwoundednon-Gata6tomatonegative35

description:
CtrlUnwoundednon-Gata6tomatonegative35
controlng6.txt


title: tumor biopsy, post-afatinib, ID33 [C53]


title: Brain, control, rep2, scRNAseq

value: Control diet


title: Brain, control, rep3, scRNAseq


title: CtrlUnwoundednon-Gata6tomatonegative34

description:
CtrlUnwoundednon-Gata6tomatonegative34
controlng6.txt

value: Epidermis


description:
CtrlUnwoundedGata6-derivedtomatopositive40
control_g6.txt


title: ASS1-KO BCT-100 replicate 2 run 1


title: ASS1-KO BCT-100 replicate 2 run 2


description:
CtrlUnwoundedGata6-derivedtomatopositive39
control_g6.txt


title: CtrlUnwoundednon-Gata6tomatonegative33

description:
CtrlUnwoundednon-Gata6tomatonegative33
controlng6.txt


title: tumor biopsy, post-afatinib, ID30 [C51]


title: tumor biopsy, pre-afatinib, ID33 [C52]


title: ASS1-KO BCT-100 replicate 1 run 1


title: tumor biopsy, pre-afatinib, ID30 [C50]


title: ASS1-KO BCT-100 replicate 1 run 2


title: hTauP301L_B6_F_5452

city: Indianapolis

first: Dominic

middle: James

last: Acri

state: Indiana

address: 320 W 15 St, NB Room 107

department: Stark Neurosciences Research Institute

institute: Indiana University School of Medicine

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-8_B6_F_5452

data_processing:
Number of raw reads as mapped by the RNA-seq aligner STARv.2.7.10a
Unique reads as mapped by STARv.2.7.10a
High quality reads from bamutils stats
Reads mapped to each different region of the reference genome from bamutils stats
Reads assigned to genomic regions by featureCounts
Assembly: B6 (C57BL6/J): Statistics of mapping and read distribution across the samples aligned to the UCSC/refGene mm10 reference genome
Assembly: CAST (CAST/EiJ):Statistics of mapping and read distribution across the samples aligned to the CAST/EiJ (Accession: GCA_001624445.1) reference genome
Assembly: PWK (PWK/PhJ): Statistics of mapping and read distribution across the samples aligned to the PWK/PhJ (Accession: GCA_001624775.1) reference genome
Assembly: WSB (WSB/EiJ): Statistics of mapping and read distribution across the samples aligned to the WSB/EiJ (Accession: GCA_001624835.1) reference genome
Supplementary files format and content: 4 tab-delimited text files count values for each Sample, separated by strain/genome assembly

source_name: Brain Cortex

extract_protocol:
RNA was harvested using TRIzol/Chloroform extraction, followed by Zymo Research's RNA Clean-Up & Concentrator-5 kit . 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for mRNA-seq were prepared using KAPA mRNA HyperPrep following manufacturer's protocols.

treatment_protocol:
Postnatal Day 0 Intracerebroventricular Injections of Adeno-associated Virus
4x10E10 viral particles of either AAV-eGFP or AAV-hTauP301L was injected into P0 mice of either B6/CAST/PWK/WSB strains which were then aged to 6 months.

tag: injection

value: Brain Cortex

tag: inventory

tag: genetic background

value: F

tag: ID


description:
CtrlUnwoundedGata6-derivedtomatopositive38
control_g6.txt

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


description:
CtrlUnwoundedGata6-derivedtomatopositive37
control_g6.txt


description:
CtrlUnwoundedGata6-derivedtomatopositive36
control_g6.txt


title: hTauP301L_B6_M_5450

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-6_B6_M_5450

value: M


title: hTauP301L_B6_F_5451

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-7_B6_F_5451


title: tumor biopsy, post-afatinib, ID23 [C42]

value: Oral Cavity

value: afatinib


title: ASS1-KO Vehicle replicate 3 run 2

value: Blood cell

tag: cell type

value: Vehicle


title: tumor biopsy, pre-afatinib, ID23 [C41]

value: Pre-afatinib


title: tumor biopsy, post-afatinib, ID03 [C04]

value: Post-afatinib


title: ASS1-KO Vehicle replicate 2 run 1


title: hTauP301L_B6_F_5453

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-9_B6_F_5453


title: Brain, control, rep1, scRNAseq

value: brain

value: 6.5 months old

value: male

value: WT


description:
CtrlUnwoundedGata6-derivedtomatopositive35
control_g6.txt


description:
CtrlUnwoundedGata6-derivedtomatopositive34
control_g6.txt


title: ASS1-KO Vehicle replicate 2 run 2

value: ASS1 -KO


title: hTauP301L_WSB_M_6757

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-46_WSB_M_6757

value: WSB


description:
CtrlUnwoundedGata6-derivedtomatopositive33
control_g6.txt

value: Epidermis


title: hTauP301L_WSB_F_6601

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-43_WSB_F_6601

value: Brain Cortex

value: F


title: ASS1-KO Vehicle replicate 1 run 1


title: tumor biopsy, post-afatinib, ID18 [C33]


title: hTauP301L_WSB_F_6600

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-42_WSB_F_6600


title: tumor biopsy, post-afatinib, ID15 [C31]


title: ASS1-KO Vehicle replicate 1 run 2


title: tumor biopsy, pre-afatinib, ID04 [C05]


title: tumor biopsy, pre-afatinib, ID18 [C32]


title: CML4+Vehicle run 1

value: Primary

value: Progentitor+stem cell


description:
CtrlUnwoundedGata6-derivedtomatopositive32
control_g6.txt

value: Day 0 post-wounding

value: Cre (+/-) tdTomato (+/-)


title: CtrlUnwoundednon-Gata6tomatonegative31

description:
CtrlUnwoundednon-Gata6tomatonegative31
controlng6.txt


title: tumor biopsy, pre-afatinib, ID03 [C03]

value: Oral Cavity

value: afatinib


title: hTauP301L_WSB_M_6597

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-41_WSB_M_6597

value: M


title: CtrlUnwoundednon-Gata6tomatonegative30

description:
CtrlUnwoundednon-Gata6tomatonegative30
controlng6.txt


title: hTauP301L_B6_M_5388

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-3_B6_M_5388


title: CML4+BCT-100 run 1

value: Blood cell


title: tumor biopsy, pre-afatinib, ID11 [C22]

value: Pre-afatinib


title: tumor biopsy, post-afatinib, ID11 [C23]

value: Post-afatinib


title: hTauP301L_WSB_F_5783

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-39_WSB_F_5783


title: CtrlUnwoundednon-Gata6tomatonegative29

description:
CtrlUnwoundednon-Gata6tomatonegative29
controlng6.txt


title: CML4+BCT-100 run 2


title: CtrlUnwoundednon-Gata6tomatonegative28

description:
CtrlUnwoundednon-Gata6tomatonegative28
controlng6.txt


title: CtrlUnwoundednon-Gata6tomatonegative27

description:
CtrlUnwoundednon-Gata6tomatonegative27
controlng6.txt


title: CtrlUnwoundednon-Gata6tomatonegative26

description:
CtrlUnwoundednon-Gata6tomatonegative26
controlng6.txt


title: CtrlUnwoundednon-Gata6tomatonegative32

description:
CtrlUnwoundednon-Gata6tomatonegative32
controlng6.txt


title: hTauP301L_PWK_M_6275

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-33_PWK_M_6275

value: PWK


title: tumor biopsy, post-afatinib, ID01 [C02]


title: tumor biopsy, post-afatinib, ID08 [C17]


title: ASS1-KO Vehicle replicate 3 run 1

value: Vehicle


title: Normal3+Vehicle run 2


title: Normal3+BCT-100 run 1


title: hTauP301L_B6_F_5390

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-4_B6_F_5390


title: hTauP301L_WSB_F_5784

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-40_WSB_F_5784


title: tumor biopsy, pre-afatinib, ID08 [C16]


title: Normal3+BCT-100 run 2


title: CtrlUnwoundednon-Gata6tomatonegative25

description:
CtrlUnwoundednon-Gata6tomatonegative25
controlng6.txt


title: CML4+Vehicle run 2


title: Normal3+Vehicle run 1


title: CML3+Vehicle run 1


title: hTauP301L_PWK_F_6195

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-31_PWK_F_6195


title: hTauP301L_WSB_M_5394

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-37_WSB_M_5394


title: tumor biopsy, pre-afatinib, ID07 [C14]


title: hTauP301L_WSB_M_5782

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-38_WSB_M_5782


title: CML3+Vehicle run 2


title: tumor biopsy, pre-afatinib, ID15 [C30]


title: hTauP301L_PWK_F_6193

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-30_PWK_F_6193


title: tumor biopsy, pre-afatinib, ID01 [C01]


title: hTauP301L_PWK_F_6189

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-28_PWK_F_6189


title: hTauP301L_PWK_F_6196

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-32_PWK_F_6196


title: CML3+BCT-100 run 1


title: OrthoE, Uninfected, replicate 5

city: Palo Alto

first: Tamar

middle: P

last: Feldman

state: CA

address: 240 Pasteur Dr

institute: Stanford University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Data were assessed for quality with FastQC. Adapters were trimmed using TrimGalore. BBTools suite was used to remove human and parasite rRNA reads.
Reads were aligned to a concatenation of the human (GRCh38) and Plasmodium (ASM276v2) genomes using STAR with default settings. Gene counts were generated by the -quantMode flag in STAR.
Assembly: GRCh38, ASM276v2
Supplementary files format and content: tab-delimited text file contains raw gene counts for all samples

source_name: Orthochromatic erythroblast

extract_protocol:
Cells were sorted directly into Buffer RLT (Qiagen) for total RNA extraction with the Rneasy Micro kit (Qiagen).
Paired-end libraries were prepared using the Tecan Trio RNA-seq for low-input samples on the Agilent BRAVO. Custom AnyDeplete probes (Tecan) were added against the human mitochondrial genome, HBB, EEFA1, MALAT1, and HSP90aa1.

value: Orthochromatic erythroblast

tag: day of differentiation

value: Day 14

value: Uninfected


title: hTauP301L_PWK_M_6188

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-27_PWK_M_6188

value: Brain Cortex


title: CML3+BCT-100 run 2


title: tumor biopsy, post-afatinib, ID07 [C15]


title: OrthoE, Uninfected, replicate 3


title: OrthoE, Uninfected, replicate 2


title: OrthoE, Uninfected, replicate 4


title: CML2+Vehicle run 2


title: OrthoE, Uninfected, replicate 1


title: hTauP301L_CAST_F_6200

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-23_CAST_F_6200

value: CAST

value: F


title: CML2+BCT-100 run 1

value: Primary

value: Progentitor+stem cell


title: OrthoE, SRS, replicate 6

value: SRS


title: hTauP301L_CAST_F_6199

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-22_CAST_F_6199


title: hTauP301L_PWK_M_5984

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-25_PWK_M_5984


title: CML2+BCT-100 run 2


title: CML2+Vehicle run 1


title: hTauP301L_PWK_M_5986

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-26_PWK_M_5986


title: OrthoE, SRS, replicate 5


title: Normal2+Vehicle run 2


title: hTauP301L_CAST_M_6067

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-21_CAST_M_6067


title: OrthoE, SRS, replicate 4


title: No Spinal Cord Injury (SCI) S2

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Downsampling of reads to ensure each sample has the same number of reads and read imbalances do not distort upper quartile normalization
Alignment to rat reference genome 'rn6' using ensemble gene annotation and STAR 2.5.4b
Calculation of differentially expressed genes using Cuffdiff 1.3.0
Assembly: rn6

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
Removal of ribosomal RNA using RiboZero kit (Illumina)
Generation of libraries using the Trueseq strandaed total RNA kit (Illumina Inc.)

treatment_protocol: Treat tissue with Cold Active Proteases

value: Spinal cord

value: No Contusion


title: Spinal Cord Injury (SCI) S1

value: Contusion


title: OrthoE, SRS, replicate 3


title: hTauP301L_CAST_M_6063

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-18_CAST_M_6063

value: M


title: Normal2+BCT-100 run 1

value: Blood cell


title: hTauP301L_CAST_F_6201

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-24_CAST_F_6201


title: hTauP301L_CAST_M_6027

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-17_CAST_M_6027


title: OrthoE, SRS, replicate 2


title: Normal2+BCT-100 run 2


title: Normal2+Vehicle run 1


title: hTauP301L_CAST_M_6024

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-16_CAST_M_6024


title: CML1+Vehicle run 1


title: High Osm HP

type: RNA

city: Fukuoka

first: Matsueda

last: Shumei

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu universuty

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: Na 170 mmol/L, Ca 2.5 mmol/L, Pi 3.5 mmol/L

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: umbilical artery smooth muscle cell


title: hTauP301L_CAST_F_5628

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-15_CAST_F_5628


title: No Spinal Cord Injury (SCI) S3


title: HCC827GR

city: Tainan

first: SHANG-YIN

last: WU

address: No.138,Sheng Li Road

department: Oncology

country: Taiwan

institute: National Cheng Kung University Hospital

description: Gene expression data from the gefitinib-resistant cell line, HCC827GR

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA was then pooled and hybridized to Agilent SurePrint G3 Human Gene Exp V3 Array Kit (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Genes are selected from the Features whose Flags are detected in at least one sample. Genes from Flags are Detected with Processed Signal intensities from 70 to anything in at least one sample were further analyzed.

label_protocol: 0.2 μg of total RNA was amplified by a Agilent Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: RPMI-1640 with 10% of fetal bovine serum for HCC827 and HCC827GR.M6. RPMI-1640 with 10% of fetal bovine serum and 1 μM gefitinib for HCC827GR+.

extract_protocol: Qiagen's RNeasy kit was used according to the manufacturer's instructions.

treatment_protocol: HCC827GR was established from HCC827 by long term step-wise treatment with gefitinib and isolated single clones by limiting dilution.HCC827GR maintained in culture medium with or without gefitinib (1 μM) over 6 months to obtain two different sublines, HCC827GR+ and HCC827GR.M6, respectively.

value: Lung

tag: phenotype

value: gefitinib resistance - Yes


title: High Osm

source_name: Na 170 mmol/L, Ca 1.8 mmol/L, Pi 0.9 mmol/L


title: OrthoE, Media, replicate 5

value: Orthochromatic erythroblast

value: Media


title: Low Osm

source_name: Na 126 mmol/L, Ca 1.8 mmol/L, Pi 0.9 mmol/L


title: HCC827GR.M6

description: Gene expression data from the gefitinib-resistant cell line, HCC827GR.M6


title: HCC827

description: Gene expression data from the parental cell line, HCC827

value: gefitinib resistance - No


title: PMY2649_C2

city: Durham

first: Paul

last: Magwene

state: North Carolina

address: 124 Science dr.

department: Biology

institute: Duke University

data_processing:
Reads were aligned using the CNA3 of H99 C. neoformans var. grubii (accession GCA_000149245.3) from the Ensemble Fungi database. Reads were aligned using Kallisto.
Analysis of RNA sequences was performed using Deseq2 in R. Briefly, transcript abundance was normalized using a built in median of ratios method. Samples were normalized based on condition (amobea or control). GO term analysis was performed using the fungidb GeneByLocusTag tool. Correlation of gene expression with BZP4 was performed using the normalized count output from Deseq2.
Assembly: GCA_000149245.3
Supplementary files format and content: tab delimited files containing read counts and TPK values for each gene

organism: Cryptococcus neoformans

growth_protocol: Samples were grown overnight in liquid YPD on a rollerdrum and were added to V8 petri dishes. V8 cultures were grown at 30◦C for 60 hours. Amoeba cultures were collected and suspended at a concentration of 1 × 106 cells/mL. 450 μL of amoeba culture was added to the center of the Cryptococcus lawn with slight agitation to aid in the spread of the culture. Plates were allowed to dry on the benchtop for 30 minutes before being incubated at 25◦C for 48 hours. A consistent area of 30 cm2 was cut from the plates and then scraped to collect cells. Collected cells were resuspended in 1 mL of PBS and were placed in dry ice for 10 minutes. Samples were then lyophilized for 12 - 18 hours.

extract_protocol:
Whole RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen 74904).
Libraries were prepared and sequenced by the using the Illumina NextSeq 500 High Output Kit producing 150-base pair paired end read.

value: yeast

value: control


title: PMY2650_A2

value: amoeba


title: CML1+Vehicle run 2

value: Primary

value: Vehicle


title: hTauP301L_B6_M_6238

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-11_B6_M_6238

value: Brain Cortex


title: HCC827GR+

description: Gene expression data from the gefitinib-resistant cell line, HCC827GR+


title: Low Osm HP

source_name: Na 126 mmol/L, Ca 2.5 mmol/L, Pi 3.5 mmol/L


title: PMY2673_C

source_name: segregant of Bt22xFtc555-1

value: segregant of Bt22xFtc555-1


title: PMY2650_C2


title: hTauP301L_B6_M_6241

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box2-12_B6_M_6241


title: CML1+BCT-100 run 1

value: Progentitor+stem cell


title: PMY2649_A2


title: OrthoE, Media, replicate 4

value: Day 14


title: CML1+BCT-100 run 2


title: OrthoE, Media, replicate 3


title: eGFP_B6_F_7252

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-9_B6_F_7252

value: eGFP

value: F


title: PMY2673_A


title: OrthoE, Media, replicate 2


title: OrthoE, SRS, replicate 1

value: SRS


title: eGFP_B6_M_7250

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-7_B6_M_7250

value: M


title: PMY2911_C


title: Normal1+Vehicle run 2

value: Blood cell


title: PMY2911_A


title: OrthoE, Media, replicate 1

value: Orthochromatic erythroblast


title: eGFP_B6_M_7248

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-5_B6_M_7248


title: Normal1+BCT-100 run 1


title: PolyE, Uninfected, replicate 6

source_name: Polychromatic erythroblast

value: Polychromatic erythroblast

value: Uninfected


title: PMY2771_C

value: yeast


title: PolyE, Uninfected, replicate 5


title: Normal1+BCT-100 run 2


title: PMY2771_A


title: eGFP_WSB_M_7082

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-41_WSB_M_7082

value: WSB


title: ChIP_NFIA-Tg_PPARγ

city: Tokyo

first: Yuta

last: Hiraike

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

institute: The University of Tokyo

data_processing:
The sequence reads were mapped to UCSC build mm9 (NCBI Build 37) assembly using bowtie2 (Galaxy version 2.3.4) with default parameters.
Peak calling was performed using MACS2 (Galaxy version 2.1.1.20160309)
Assembly: mm9
Supplementary files format and content: bigWig files showing the peaks of each samples.

source_name: ingSVF-derived adipocytes

extract_protocol:
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G magnetic beads (Thermo Scientific) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Hiraike Y., Waki H. et.al. 2017).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.

value: NFIA-Tg

tag: time course

value: day 7

value: ingSVF-derived adipocytes

tag: chip antibody

value: anti-PPAR   (4 ug per IP, mix of Santa Cruz Biotechnology, sc-7273, and Perseus    Proteomics, A3409A)


title: ChIP_WT_H3K27Ac

value: WT

value: anti-H3K27Ac (4 ug per IP, Abcam, ab4729)


title: PolyE, Uninfected, replicate 2

value: Day 14


title: PMY2570_C

value: segregant of Bt22xFtc555-1

value: control


title: ChIP_NFIA-Tg_H3K27Ac


title: PMY2869_C


title: eGFP_WSB_F_7085

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-44_WSB_F_7085

value: eGFP

tag: tissue

value: Brain Cortex

value: F


title: PolyE, Uninfected, replicate 3


title: eGFP_WSB_M_7276

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-40_WSB_M_7276

value: M


title: PolyE, Uninfected, replicate 4

value: Polychromatic erythroblast


title: Normal1+Vehicle run 1

value: Blood cell

value: Primary

value: Progentitor+stem cell

value: Vehicle


title: PMY2570_A

value: yeast

value: amoeba


title: PolyE, Uninfected, replicate 1

value: Uninfected


title: ChIP_WT_PPARγ

value: WT

value: day 7

value: ingSVF-derived adipocytes

value: anti-PPAR   (4 ug per IP, mix of Santa Cruz Biotechnology, sc-7273, and Perseus    Proteomics, A3409A)


title: PMY2869_A

value: segregant of Bt22xFtc555-1


title: eGFP_WSB_M_7275

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-39_WSB_M_7275

value: eGFP

value: WSB


title: ChIP_NFIA-Tg_3xFLAG-NFIA

value: NFIA-Tg

value: FLAG M2 (1 ug per IP, Sigma, F3165)


title: PolyE, SRS, replicate 6

value: Polychromatic erythroblast

value: Day 14

value: SRS


title: eGFP_WSB_F_7274

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-38_WSB_F_7274

value: Brain Cortex

value: F


title: PMY2768_C

value: yeast

value: control


title: eGFP_B6_M_7247

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-4_B6_M_7247

value: M


title: ChIP_WT_3xFLAG-NFIA

value: WT


title: PolyE, SRS, replicate 5


title: eGFP_WSB_F_7273

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-37_WSB_F_7273


title: RL603_2017_02_22_G4fans_130616_Day30neuNneg

city: Perth

first: Ryan

last: Lister

address: 35 Stirling Highway

institute: The University of Western Australia

description: ESC-derived wild type neural differentiation, sorted NeuN negative fraction

data_processing:
adapter trimming using Methpipe pipeline as described in Lister et al Science 2013
mapping reads to mm10 genome using Bowtie  as described in Lister et al Science 2013
merging mapped runs, convert to .slam, sort, collapse, trim reads using Methpipe pipeline as described in Lister et al Science 2013
stack creation and hammer correction using Methpipe pipeline as described in Lister et al Science 2013
make allC tables and count global statistics using Methpipe pipeline as described in Lister et al Science 2013
convert stacks to bedgraph files using simple awk script
generate bigwigs using bedgraphtobigwig v4
Genome_build: mm10
Supplementary_files_format_and_content: stacks.txt files containing all mapped methylated and total cytosines, bigWigs for coverage containing all mapped cytosines, bigWigs for mC containing percentage of methylated cytosines for contexts CG and CH

source_name: mESC neural diff 8 days induction

extract_protocol:
Quiagen Blood and Tissue DNA Extraction kit with extended Pretinase K and RNAsA treatment steps.
Lucigen Nxseq Ampfree Low DNA Library Kit and Zymo EZ DNA Methylation Direct Kit for MethylC libraries.

value: mESC neural diff 8 days induction

tag: cell culture

value: in vitro

tag: age

value: 38 days


title: PolyE, SRS, replicate 4

tag: treatment


title: PolyE, SRS, replicate 3


title: eGFP_WSB_F_7272

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-36_WSB_F_7272


title: PMY2765_C

value: segregant of Bt22xFtc555-1


title: PMY2694_C


title: RL602_2017_02_22_G4fans_130616_Day30neuNpos

description: ESC-derived wild type neural differentiation, sorted NeuN positive fraction


title: RL531_G4fans_diff_101116_d8_Pax6_pos

description: NSCs sorted for Pax6 positive

source_name: Pax6+ sorted nuclei from cell cultures

value: Pax6+ sorted nuclei from cell cultures


title: PolyE, SRS, replicate 2


title: PolyE, SRS, replicate 1


title: PMY2765_A

value: amoeba


title: eGFP_B6_M_7241

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-3_B6_M_7241

value: eGFP


title: eGFP_PWK_M_7231

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-34_PWK_M_7231

value: PWK


title: eGFP_PWK_M_7229

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-32_PWK_M_7229


title: PolyE, Media, replicate 5

value: Polychromatic erythroblast

value: Media


title: RL285_2016_06_07_HippN_040516_highK

description: hippocampal neurons, high K+

source_name: cultivated primary neurons 15 days

value: primary

value: hippocampus

value: 33 days


title: PMY2694_A

value: yeast


title: eGFP_WSB_F_7271

description:
WSB_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-35_WSB_F_7271

value: Brain Cortex

value: WSB

value: F


title: PMY2581_C

value: control


title: RL530_G4fans_ESCs_101116_p30_Nanog_pos

description: ESCs sorted for Nanog positive

source_name: Nanog+ sorted nuclei from cell cultures

value: Nanog+ sorted nuclei from cell cultures

value: in vitro


title: PMY2581_A

value: segregant of Bt22xFtc555-1


title: eGFP_PWK_M_7228

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-31_PWK_M_7228

value: M


title: PolyE, Media, replicate 4

value: Day 14


title: eGFP_PWK_M_7227

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-30_PWK_M_7227

value: eGFP


title: RL283_2016_06_07_CortN_040516_highK

description: cortical neurons, high K+

value: cortex


title: PMY2768_A

value: amoeba


title: PolyE, Media, replicate 3

value: Polychromatic erythroblast

value: Media


title: PMY2865_C


title: eGFP_PWK_F_7226

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-29_PWK_F_7226

value: PWK


title: RL284_2016_06_07_HippN_040516_lowK

description: hippocampal neurons, low K+

value: primary

value: hippocampus

value: 33 days


title: PolyE, Media, replicate 2


title: RL282_2016_06_07_CortN_040516_lowK

description: cortical neurons, low K+


title: eGFP_PWK_F_7225

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-28_PWK_F_7225

value: Brain Cortex


title: PolyE, Media, replicate 1


title: eGFP_PWK_F_7234

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-24_PWK_F_7234

value: F


title: PMY2813_C

value: yeast

value: control


title: BasoE, Uninfected, replicate 4

source_name: Basophilic erythroblast

value: Basophilic erythroblast

value: Day 7

value: Uninfected


title: BasoE, Uninfected, replicate 3


title: PMY2813_A

value: segregant of Bt22xFtc555-1


title: eGFP_PWK_F_7232

description:
PWK_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-22_PWK_F_7232

value: eGFP


title: RL275_2016_06_07_R1p33_290316_Day38lowK

description: low K+

value: mESC neural diff 8 days induction

value: in vitro

value: 38 days


title: RL280_2016_06_07_Hipp200K_040416_E18

description: hippocampus sample

source_name: primary neurons

value: 18 days


title: eGFP_CAST_M_7820

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-19_CAST_M_7820

value: CAST

value: M


title: BasoE, Uninfected, replicate 2


title: PMY2650_C


title: RL274_2016_06_07_G4p31_170316_Day26highK

description: high K+

value: 26 days


title: PMY2776_C


title: eGFP_CAST_F_7822

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-21_CAST_F_7822


title: eGFP_CAST_M_7819

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-18_CAST_M_7819


title: R1p20_190116_Dayminus1

description: ESC before induction

source_name: cultivated ES cells

value: cultivated ES cells

value: passage 20


title: PMY2776_A

value: amoeba


title: R1D0_170116_Day18plusVE

description: PSA-NCAM sorted +VE fraction

source_name: cultivated adherent neurons

value: cultivated adherent neurons


title: BasoE, SRS, replicate 6

value: SRS


title: PMY2865_A

value: yeast


title: eGFP_CAST_F_7818

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-17_CAST_F_7818

source_name: Brain Cortex

value: Brain Cortex

value: F


title: PMY2650_A


title: RL281_2016_06_07_Cort200k_040416_E18

description: cortex sample

value: primary

value: cortex


title: RL276_2016_06_07_R1p33_290316_Day38highK

description: high K+

value: mESC neural diff 8 days induction


title: eGFP_CAST_M_7817

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-16_CAST_M_7817

value: eGFP


title: BasoE, SRS, replicate 4

value: Basophilic erythroblast

value: Day 7


title: BasoE, SRS, replicate 3


title: eGFP_CAST_M_7621

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-14_CAST_M_7621

value: CAST


title: PMY2649_C

value: control


title: BasoE, SRS, replicate 2


title: R1D0_170116_Day18minusVE

description: PSA-NCAM sorted -VE fraction

value: in vitro

value: 18 days


title: F1339 Dnmt1 Cut&Tag no3

city: Cleveland

first: Sudipta

last: Biswas

state: Ohio

address: 9500 Euclid Ave

department: Translational Hematology & Oncology Research

institute: Cleveland Clinic

data_processing:
methods
Data processing was on the Galaxy platform (usegalaxy.org)54. To trim the adapters, we used Cutadapt. Sequencing reads were mapped to mm10 or GRCh37/hg19 genomes using Bowtie255. Heatmaps of coverage around gene transcription start sites were created using EASEQ56
Assembly: mm10 or GRCh37/hg19
Library strategy: Cut & Tag

source_name: lung

growth_protocol: H82 and F1339 cells were maintained in RPMI media supplemented with 10% FBS and antibiotics at 37C incubator with 5% CO2.

extract_protocol: The Cleavage Under Targets and Tagmentation (CUT&Tag) procedure in triplicate, following the manufacturer’s protocol for the CUT&Tag-ITTM Assay Kit from Active Motif (cat no # 53165), and using DNMT1 antibody (Active Motif cat no # 39204), was applied to murine F1339 and human H82 SCLC cells. Libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer’s protocols. Sequencing on NextSeq 550 followed the manufacturer’s protocols through the Genomics Core Facility at Case Western Reserve University.

value: lung

value: SCLC


title: R1D0_170116_Day28lowK

description: low K+

value: cultivated adherent neurons

value: 28 days


title: BasoE, Uninfected, replicate 1

value: Uninfected


title: eGFP_CAST_F_7622

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-15_CAST_F_7622

value: Brain Cortex


title: PMY2649_A

value: yeast

value: amoeba


title: BasoE, SRS, replicate 1

value: SRS


title: F1339 Dnmt1 Cut&Tag no2


title: eGFP_CAST_M_7620

description:
CAST_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-13_CAST_M_7620

value: M


title: MFP5L_tumor_margin

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

hyb_protocol: Labelled RNA (300 ng) was then hybridized to SurePrint G3 Hmn GE 8x60K Microarrays (Cat. #: G4851A, Agilent Technologies) 60K whole mouse genome microarray gene expression chips (Agilent Technologies) in a rotating hybridization oven for 17 hours at 65°C.

scan_protocol: Microarray chips were washed, dried and scanned (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90050).

data_processing: Microarray data were extracted using Feature Extraction Software v.9.5.3.1 (Agilent Technologies). Processing of the output files was done with the R Bioconductor package LIMMA. (Linear Models for Microarray Data), version 3.14.4. The raw data were normalized using half background correction (offset of 50), LOESS within array and quantile between array normalization

source_name: 4T1-2792, primary tumor, margin

label_protocol: Extracted RNA (5 ng) or universal mouse reference RNA (Cat. #: 740100, Stratagene) was linearly amplified using the RiboAmp HS PLUS RNA Amplification Kit (Cat. #: KIT0525, Applied Biosystems) and profiles of amplified RNA (aRNA) were assessed using the 2100 Bioanalyzer platform (Agilent). Microdissected aRNA (5 μg) was then labelled with Cy3dye (Cat. #: KIT0609, Applied Biosystems) while universal mouse reference aRNA was labelled with Cy5dye (Cat. #: KIT0610, Applied Biosystems).

growth_protocol: All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.

extract_protocol: RNA was extracted from microdissected material  using a PicoPure RNA Isolation Kit  (Cat. #: KIT0204, Applied Biosystems).

treatment_protocol: 4T1-2776 and 4T1-2792 cells were inejcted into the mammary fat pad of Balb/c mice and grown as priamry tumors or were grown as metastasis in the liver after splenic injection. Tumor samples were harvested and processed for laser-capture microdissection.

value: mammary fat pad tumor

tag: gender

value: female


title: BasoE, Media, replicate 6

value: Basophilic erythroblast

value: Day 7

value: Media


title: eGFP_B6_F_7255

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-12_B6_F_7255

value: eGFP

value: F


title: eGFP_B6_F_7254

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-11_B6_F_7254


title: BasoE, SRS, replicate 5


title: MFP5L_tumor_core

source_name: 4T1-2792, primary tumor, core


title: MFP3L_tumor_margin


title: F1339 Dnmt1 Cut&Tag no1

value: lung


title: BasoE, Media, replicate 5


title: eGFP_B6_F_7253

description:
B6_ILMN_1462_Kim_mRNAseq64_Aug2022_STAR_featureCounts_raw-counts.txt
Box1-10_B6_F_7253


title: MFP3L_tumor_core


title: T cells, Trib1_KO

city: Philadelphia

first: Warren

last: Pear

address: 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
FASTQ file generation and alignment to GRCm38 were performed using Cell Ranger v3.0.2 with default arguments.
Consensus TCR annotations were generated using Cell Ranger v3.0.2 with default arguments.
Assembly: GRCm38
Supplementary files format and content: Csv file of consensus TCR annotations per barcoded cell.
Library strategy: scTCR-seq

source_name: Spleen

extract_protocol:
Activated (CD44+) T cells (TCRb+) were FACS sorted from spleens of control or Trib1 cKO mice at day 15 post-clone 13 infection. Two biological replicates were pooled for each genotype. Cells were washed twice with RPMI, counted and single-cell TCR-seq was performed according to 10X Genomics protocols, targeting 5000 cells for loading.
Library construction was performed using the Chromium Single Cell 5' Library and Gel Bead Kit according to the manufacturer's protocol. The final pooled library (control and Trib1 cKO samples) was sequenced on a NextSeq 500 using paired-end sequencing on one 300 cycle high output FlowCell (Illumina).

value: Spleen

tag: strain

tag: infection

value: LCMV cl13

tag: time

value: 15 days post-infection

tag: genotype

value: CD4-Cre Trib1 F/F

value: 7-8 weeks


title: T cells, control

value: CD4-Cre Trib1 +/+


title: BasoE, Media, replicate 4


title: Mouse ES-cell derived NPCs [OPC_d3A3L_pCdkn2a_H3K27ac]

city: Boston

first: Gilbert

middle: Joseph

last: Rahme

state: MA

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq data were aligned to hg19 or mm10 using BWA aln 0.7.4, requiring minimal mapping quality of 10.
PCR duplicates were removed with picard tools 2.9.2
ChIP-Seq density tracks were generated by bedgraph to BigWig format after RPM normalization
Assembly: hg19 for human samples, mm10 for mouse samples
Supplementary files format and content: ChIP-seq density tracks in bigwig format, and peak files in bed format

source_name: OPCs

growth_protocol: Human NPCs (Bys012) were cultured wiith ATCC formluated media following manufacturer's guidelines. Mouse NPCs were culture with DMEM:F12, 1X N2, 1X B27, 1% penicillin/streptomycin, 20 ng/ml of EGF, 20 ng/ml FGF2, and 1 μg/ml laminin. Mouse OPCs were cultured with DMEM:F12, 1X N2, 1X B27, 1% penicillin/streptomycin, 10 ng/ml PDGFB, 20 ng/ml FGF2 , and 1 μg/ml laminin.

extract_protocol:
For ChIP-seq, cultured cells were fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80 C for at least overnight. Sonication of tumor specimens and cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418).  H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3' A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

value: H3K27ac (Active motif 39133)

value: OPCs


title: R1D0_170116_Day28highK

description: high K+

tag: cell line

value: cultivated adherent neurons

value: in vitro

value: 28 days


title: AG_mutant

city: Bunkyo-ku

first: Yuya

last: Nagaoka

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

data_processing:
To process Hi-C data, we used Juicer version 1.6 and Juicer tools version 2.13.07.
Sequenced reads were aligned to the reference mouse genome (mm10) by BWA version 0.7.17.
25-kbp resolution contact matrix with SCALE normalization was generated.
TADs (25-kbp resolution) and loops (5-kbp, 10-kbp and 25-kbp resolutions) were called by ArrowHead and HiCCUPS,  respectively.
Log-scaled relative contact frequency and insulation score (500-kbp distance) were calculated by CustardPy.
Assembly: mm10
Supplementary files format and content: .hic files were generated by juicertools with default parameters.
Supplementary files format and content: Control.hic, NUP98-HOXA9.hic and AG_mutant.hic were generated by merging fastq files from Arima-HiC-mouse-01 and Arima-HiC-mouse-02, Arima-HiC-mouse-03 and Arima-HiC-mouse-04 or Arima-HiC-mouse-05 and Arima-HiC-mouse-06.

source_name: EB3-derived FLAG-NUP98-HOXA9 (AG mutant) expressing stable cell line #1 and #2, combined

extract_protocol:
Cells were collected and crosslinked with 37% formaldehyde solution. DNA isolated from the crosslinked cells was digested with two restriction enzymes (^GATC and G^ANTC).
After incorporating biotinylated nucleotides into the digested DNA ends, both ends were ligated to spatially proximal ends. The ligated DNA was mechanically sheared into an average size of 400-500 bp and the ligation junctions were enriched with streptavidin magnetic beads. The sequencing libraries were prepared from enriched DNA fragments with a TruSeq DNA PCR-Free Library Prep Kit (Illumina) and amplified for 4 PCR cycles.

value: Mouse embryonic stem cells (mESCs)


title: MFP2L_tumor_margin

value: mammary fat pad tumor

value: female


title: BasoE, Media, replicate 3

value: Basophilic erythroblast

value: Day 7

value: Media


title: Mouse ES-cell derived NPCs [OPC_3A3L_pCdkn2a_H3K27ac]


title: 92_9LM_distant_10_days

source_name: 4T1-2792, liver met, distant, 10 days

value: liver tissue


title: NUP98-HOXA9

source_name: EB3-derived FLAG-NUP98-HOXA9 expressing stable cell line #1 and #2, combined


title: Control

source_name: Parental ES (EB3) and EB3-derived control stable cell line (Empty vector), combined


title: BasoE, Media, replicate 1


title: Mouse ES-cell derived NPCs [OPC_3A3L_NT_H3K27ac]


title: ProE, Uninfected, replicate 4

source_name: Proerythroblast

value: Proerythroblast

value: Uninfected


title: 92_7LM_margin_3_weeks

source_name: 4T1-2792, liver met, margin, 3 weeks

value: liver metastasis


title: Mouse ES-cell derived NPCs [OPC-NT-H3K27ac]


title: ProE, Uninfected, replicate 5


title: AG_mutant#1

source_name: EB3-derived FLAG-NUP98-HOXA9 (AG mutant) expressing stable cell line #1


title: 92_9LM_core_10_days

source_name: 4T1-2792, liver met, core, 10 days


title: Mouse ES-cell derived NPCs [OPC-Insulator-CTCF]

value: CTCF (CST 3418)


title: Mouse ES-cell derived NPCs [OPC-RFXmotif-H3K27ac]


title: 92_9LM_adjacent_10_days

source_name: 4T1-2792, liver met, adjacent, 10 days


title: NUP98-HOXA9#2

source_name: EB3-derived FLAG-NUP98-HOXA9 expressing stable cell line #2


title: AG_mutant#2

source_name: EB3-derived FLAG-NUP98-HOXA9 (AG mutant) expressing stable cell line #2


title: Mouse ES-cell derived NPCs [OPC-NT-CTCF]


title: ProE, Uninfected, replicate 3


title: 92_7LM_core_3_weeks

source_name: 4T1-2792, liver met, core, 3 weeks


title: NUP98-HOXA9#1

source_name: EB3-derived FLAG-NUP98-HOXA9 expressing stable cell line #1


title: ProE, Uninfected, replicate 2


title: 92_6LM_margin_2_weeks

source_name: 4T1-2792, liver met, margin, 2 weeks


title: Mouse ES-cell derived NPCs [OPC-H3K27ac]


title: MFP2L_tumor_core

source_name: 4T1-2792, primary tumor, core


title: ProE, Uninfected, replicate 1


title: BasoE, Media, replicate 2

source_name: Basophilic erythroblast


title: Mouse ES-cell derived NPCs [OPC-CTCF]

source_name: OPCs


title: ProE, SRS, replicate 6

value: SRS


title: Control#1

source_name: Parental ES (EB3)

value: Parental ES (EB3)


title: Mouse ES-cell derived NPCs [NPC-H3K27ac]

source_name: NPCs

value: H3K27ac (Active motif 39133)

value: NPCs


title: 92_6LM_distant_10_days

source_name: 4T1-2792, liver met, distant, 10 days


title: ProE, SRS, replicate 5


title: Sorted Tcon cells Green_A1

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Sorted Tcon cells

data_processing:
Illumina DRAGEN to convert BCL to fastq files and trime for adapters
Read count extraction and normalization were performed using STAR v.2.7.1 and DESeq2 v1.34
Assembly: GENCODE GRCh38.p13 and GENCODE GRCm39 respectively
Supplementary files format and content: Tab-delimited text files include count values for each sample and decoder included information on the sample

source_name: Tcons

extract_protocol:
Mouse Tregs, exTregs, Tcons, human Tregs, Tnaive and Th1 were directly sorted in 750uL of TRIzol LS (ThermoFisher). Next, RNA was extracted using the miRNeasy micro kit (Qiagen). RNA quality was measured by using 2100 TapeStation (Agilent  Technologies). Samples with high quality RNA (RNA integrity number >8.0) were used for the  next steps. Low-input human exTregs were sorted in duplicate (1,000 cells twice) in 20uL of  lysis buffer as described previously 25 .
For both TRIzol LS and low-input samples, double-  stranded (ds)-cDNA was prepared using the SuperScript II reverse transcriptase  (ThermoFisher) according to the manufacturer’s instructions. cDNA was amplified using 15  cycles and eluted in 24 μl. 100ng of resulting cDNA was processed using the Illumina DNA Prep  Kit (Cat#20018704, Illumina) following manufacturer’s instructions. Samples were pooled and  loaded onto an Illumina NovaSeq6000, and sequenced with 50 base pair paired-end reads  (PR50).

tag: tissue type

value: Spleen

value: Tcons


title: 92_6LM_core_10_days


title: Sorted Tcon cells Green_A3

description: Sorted Tcon cells


title: Sorted Tcon cells Green_A2

description: Sorted Tcon cells


title: ChIP-seq DNMT1

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description: ChIP-seq DNMT1

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference mm10 by BWA (version 0.7.17) and sorted by SAMtools (version 1.9)
Aligned reads were filtered by SAMtools (version 1.9, samtools view -b -h -q 30 -F 256 $BAMinput > $BAMfilter) and marked duplicates by picard tools (version 2.18.12)
Peak calling was performed by MACS2 (version 2.1.1.20160309) comparing treated library and the corresponding input library
Assembly: mm10
Supplementary files format and content: BW file generated by deeptools (version 3.3.0, bamCoverage -b $BAMsort -o $BWfile)

source_name: liver

growth_protocol: Regular chow diet

extract_protocol:
Tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: University of Pittsburgh animal protocol

value: Male

value: 2 months

tag: antibody


title: ChIP-seq input

description: ChIP-seq input

value: Input


title: 92_6LM_adjacent_2_weeks

source_name: 4T1-2792, liver met, adjacent, 2 weeks

value: female


title: ProE, SRS, replicate 2

source_name: Proerythroblast

tag: cell type

value: Day 7


title: Sorted Tcon cells Green_A4

description: Sorted Tcon cells


title: 92_6_adjacent_10_days


title: Mouse ES-cell derived NPCs [NPC-CTCF]


title: Zymoseptoria pseudotritici Zp13, incompatible wheat infection stage A, 10 days post inoculation, replicate 2

city: Kiel

first: Janine

last: Haueisen

address: Am Botanischen Garten 1-9

department: Botanical Institute

institute: Christian-Albrechts University of Kiel

data_processing:
We assessed the quality of the sequencing data with FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/) and applied a stringent trimming and filtering protocol using FASTX‐toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_ toolkit/) and Trimmomatic (Bolger, Lohse, & Usadel, 2014) v0.33.
Reads were mapped to the reference genome assemblies (Feurtey et al., 2020; Goodwin et al., 2011) using hisat2 v2.2.0 (Kim et al., 2019).
Read alignments were stored in SAM format, and indexing, sorting, and conversion to BAM format were performed using SAMtools v1.10 (Li et al., 2009).
Relative abundances of transcripts for predicted genes were calculated in RPKM using Cuffdiff2 v2.2.1 (Trapnell et al., 2013).
Total read counts per gene were estimated with HTSeq v0.11.3 (Anders et al., 2015).
Assembly: SMRT-seq assembled genomes of Za17 & Zp13: https://doi.org/ 10.5281/zenodo.3820378
Supplementary files format and content: Za17_expression_values.csv: csv file, contains normalized RPKM values calculated using Cuffdiff2
Supplementary files format and content: Zp13_expression_values.csv: csv file, contains normalized RPKM values calculated using Cuffdiff2

organism: Zymoseptoria pseudotritici

source_name: Infected leaf tissue of Triticum aestivum Obelisk

growth_protocol: Cells of Z. pseudotritici and Z. ardabiliae were inoculated from cryostocks onto YMS agar (0.4% [w/v] yeast extract, 0.4% [w/v] malt extract, 0.4% [w/v] sucrose, 2% [w/v] bacto agar) and grown at 18°C for 5 days. Single cells were grown in liquid YMS (200 rpm, 18°C) and harvested by centrifugation (3500 rpm for 10 min).

extract_protocol:
Total RNA from Zymoseptoria spp.‐infected wheat material collected during one infection experiment was isolated using the TRIzol™ reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's instructions. One biological sample consists of material from three inoculated second leaves that were pooled and homogenized in liquid nitrogen. One hundred milligram of the resulting powder was used for RNA extraction.
Preparation of strand‐specific RNA‐seq libraries including polyA enrichment was performed at the Max Planck Genome Center, Cologne, Germany (http://mpgc.mpipz. mpg.de), using the NEBNext UltraTM Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol (New England Biolabs, Frankfurt/Main, Germany) with an input of 1 µg total RNA.

treatment_protocol: Seedlings of the Triticum aestivum cultivar Obelisk (Wiersum Plantbreeding, Winschoten, Netherlands) were cultivated, maintained and brush-inoculated as described in (Fagundes et al., 2020). Fungal inoculum was adjusted to 10x8 cells/ml in 0.1% [v/v] Tween 20 (Roth, Karlsruhe, Germany). Plants were grown with a 16-h light period and either maintained in a plant growth chamber environment (22°C [day]/20°C [night], 70% humidity) for up to 4 weeks post inoculation.

value: Infecting hyphae

value: WT

value: incompatible wheat infection 10 dpi


title: 92_6LM_core_2_weeks

source_name: 4T1-2792, liver met, core, 2 weeks


title: Zymoseptoria pseudotritici Zp13, incompatible wheat infection stage A, 10 days post inoculation, replicate 1

value: Infected leaf tissue of Triticum aestivum Obelisk