title: NA18855 Strain Replicate 3

description:
Bulk sample 6
counts.txt.gz
YG-AH-15_S15_L002_R1_001

value: F


title: NA18856 Control Replicate 3

status: Public on Feb 07 2022

type: SRA

city: Chicago

first: Anthony

last: Hung

state: IL

address: 920 E 58th St

country: USA

institute: University of Chicago

description:
Bulk sample 9
counts.txt.gz
YG-AH-18_S18_L002_R1_001

library_source: transcriptomic

data_processing:
Reads from bulk RNA sequencing were mapped to the hg38 genome using STAR (version 2.6.1b). Gene expression levels were quantified using the featureCounts function in Subread (version 1.6.5) using standard parameters to generate the counts.txt file.
Reads from 10X cell barcodes and UMIs from raw scRNA-seq reads were extracted and remaining reads were mapped to genes in the hg38 genome using STARsolo from the STAR software with default parameters (version 2.6.1b) to generate barcodes.tsv, genes.tsv, and matrix.mtx files. Demuxlet was used to deconvolute sample identity of individual cell droplets and detect multiplets in multiplexed samples with default parameters. Previously collected and imputed genotype data for the three Yoruba individuals from the HapMap and 1000 Genomes Project were used as input for demuxlet to generate the demuxlet.best files.
Genome_build: hg38
Supplementary_files_format_and_content: bulk RNAseq - counts.txt file
Supplementary_files_format_and_content: scRNAseq -  barcodes.tsv, genes.tsv, and matrix.mtx files, demuxlet.best files

molecule: total RNA

organism: Homo sapiens

source_name: iPSC-derived chondrogenic cells

growth_protocol: Undifferentiated iPSCs were cultured on Matrigel-coated plates in Essential 8 (E8) medium at 37°C, 5% CO2, and atmospheric O2 until iPSCs reached 30% confluency. E8 medium was subsequently changed to mesenchymal stem cell (MSC) culture medium, which consisted of low glucose Dulbecco’s Modified Eagle Medium (DMEM) with 20% stem cell-qualified fetal bovine serum (FBS), and 100 mg/mL Penicillin/Streptomycin. The MSC medium was changed every day for 3 days, at which point cells were 80-100% confluent. On day 3, cells were detached from the Matrigel-coated petri dishes using a 0.05% Trypsin/EDTA solution and cultured on uncoated polystyrene flasks in MSC medium. The medium was changed every 2-3 days until the cells reached 90% confluency. The cells were then sub-cultured at a ratio of 1:3 until passage 4, at which point cells were classified as iPSC-derived MSCs. iPSC-derived MSCs were detached from culture flasks using 0.05% Trypsin/EDTA and seeded at a density of 250,000 cells/well onto the center of wells of BioFlex Type I Collagen coated 6-well Culture Plates (FlexCell International BF-3001C) using BioFlex cell seeders (FlexCell International). Cells were seeded using a regimen of 15% elongation for 2 hours followed by overnight culture in MSC culture medium. After seeding, cells were cultured in serum-free chondrogenic differentiation medium, consisting of high glucose DMEM, 100 mg/mL Penicillin/Streptomycin, 50mg/mL L-Proline, 200mM GlutaMax, 50mg/mL L-Ascorbic acid-2-Phosphate, 11g/L Sodium pyruvate, 5mM Dexamethasone, 1x ITS Premix, and supplemented with 10 ng/mL TGF-β3. The chondrogenic medium was changed every 2-3 days for 14 days.

extract_protocol:
RNA was extracted from cells following CTS or control treatments using the ZR-Duet™ DNA/RNA MiniPrep kit (Zymo D7001).
Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 & -2002, Illumina)

treatment_protocol: Plates for strained samples were loaded onto the Flexercell baseplate (located in an incubator at 37°C, 5% CO2 , and atmospheric O2), and a vacuum was used to deform the cell culture plate membrane and create uniform biaxial cyclic tensile strain. Specifically, 2.5% elongation (15kPa) of CTS was applied to the cells at a rate of 0.5 Hz for 24 hours. Control samples were cultured in the same incubator without cyclic tensile strain.

tag: cell line

tag: treatment

value: Control

tag: technical replicate

tag: Sex

value: M


title: T20355

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
P.falciparum parasite isolate
H0_sample112

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Uniquely mapped and properly oridented reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
Normalized count - Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 FPKM values for each sample

organism: Plasmodium falciparum

source_name: P.falciparum field isolate from patient

growth_protocol: All samples used in this study (Except ring 3D7 batch controls) were collected from patients involved in Tracking Resistance to Artemisinin Collaboration 2 (TRAC2), a multi-site study that took place between Aug 7, 2015, and Feb 8, 2018. Following collection, blood was subsequently depleted of plasma and buffy coat. Hour 0 samples were additionally purified from white blood cells (WBC) using CF11 columns following the Worldwide Antimalarial Resistance Network (WWARN) protocols. 0.2 to 0.5 mL of packed red blood cells (pRBC) from each sample was homogenized by mixing with 10 volumes of TRIzol (Invitrogen), frozen at -80oC.

extract_protocol:
Total RNA was extracted using Trizol and ZYMO DirectZol96 extraction kit following protocol described in Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020).
Reverse transcription and cDNA synthesis was done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane.

treatment_protocol: In brief, samples were collected from the venous blood of malaria-infected patients at admission to the clinic (Hour 0, 0hr) and 6 hours after their respective treatment (Hour 6, 6hr). Depending on their location, patients were randomly assigned different double or triple Artemisinin Combination Therapy (ACT) as follows: Thailand, Cambodia, Vietnam, and Myanmar - dihydroartemisinin-piperaquine or dihydroartemisinin-piperaquine plus mefloquine; Cambodia - artesunate-mefloquine or dihydroartemisinin-piperaquine plus mefloquine; Laos, Myanmar, Bangladesh - artemether-lumefantrine or artemether-lumefantrine plus amodiaquine.

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: NA18856 Strain Replicate 2

description:
Bulk sample 11
counts.txt.gz
YG-AH-11_S11_L002_R1_001

value: Cyclic Tensile Strain


title: T20356

description:
P.falciparum parasite isolate
H0_sample113


title: NA18855 Strain Replicate 2

description:
Bulk sample 5
counts.txt.gz
YG-AH-09_S9_L002_R1_001


title: NA18855 Strain Replicate 1

description:
Bulk sample 4
counts.txt.gz
YG-AH-03_S3_L002_R1_001


title: T20340

description:
P.falciparum parasite isolate
H0_sample109


title: T20354

description:
P.falciparum parasite isolate
H0_sample111


title: NA18855 Control Replicate 2

description:
Bulk sample 2
counts.txt.gz
YG-AH-10_S10_L002_R1_001


title: T20339

description:
P.falciparum parasite isolate
H0_sample108


title: T20349

description:
P.falciparum parasite isolate
H0_sample110


title: T20334

description:
P.falciparum parasite isolate
H0_sample106


title: NA18855 Control Replicate 3

description:
Bulk sample 3
counts.txt.gz
YG-AH-16_S16_L002_R1_001


title: Motor neuron WT - no_antibody

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

library_source: genomic

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig (wiggle type files using the program wigToBigWig)

molecule: genomic DNA

organism: Mus musculus

source_name: Spinal motor neurons

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Rhee et al., 2016) with some modifications.

extract_protocol:
Cells were lysed and chromatin pellets were isolated, and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against the protein of interest.
ChIP-seq libraries were prepared according to the standard Illumina protocols. Briefly, DNA was end-repaired and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 6 x 10^4 cells per mL (day 0). 1 uM RA and 0.5 uM SAG were added to the medium on day 2. 5 uM DAPT was added on days 4 and 5.

tag: cell type

value: ES-derived spinal motor neurons

tag: strain

tag: chip-seq antibody

value: No antibody (contorol)


title: NA18855 Control Replicate 1

description:
Bulk sample 1
counts.txt.gz
YG-AH-04_S4_L002_R1_001


title: T20338

description:
P.falciparum parasite isolate
H0_sample107


title: T20333

description:
P.falciparum parasite isolate
H0_sample105


title: Motor neuron WT - CTCF_rep1


title: T20327

description:
P.falciparum parasite isolate
H0_sample104


title: T20326

description:
P.falciparum parasite isolate
H0_sample103


title: Motor neuron WT - H3K27ac_rep1


title: T20320

description:
P.falciparum parasite isolate
H0_sample102


title: T20318

description:
P.falciparum parasite isolate
H0_sample101


title: Slc6a20a homozygous 4

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.4.1.1) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage and the pups are weaned on P21.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: whole brain

tag: age

value: ~Postnatal day 120

value: male


title: Slc6a20a homozygous 3


title: 1408501

type: genomic

city: Boston

first: Ze

last: Zhang

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
R studio
Matrix_processed.txt: SeSAMe Processed Average Beta
unmethylated_methylated_signal_intensities.txt

label: Cy5 and Cy3

source_name: Human Peripheral Blood from Glioma Patient

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions.

tag: diagnosis

value: Glioma

value: Peripheral blood

value: Female

tag: karyotype

value: XaXi

value: 1 pre surg

value: 1 new gbm

tag: nontcell

tag: arraytypes

value: IlluminaHumanMethylationEPIC


title: 1407001

value: 2 postsurg/prechemorad

value: 2 new lgg


title: T20314

description:
P.falciparum parasite isolate
H0_sample100

value: In vivo, Blood stage


title: Slc6a20a homozygous 2


title: T20310

description:
P.falciparum parasite isolate
H0_sample99

value: Prior to ACT treatment, 0h


title: Slc6a20a homozygous 1


title: T20305

description:
P.falciparum parasite isolate
H0_sample98


title: 1406701


title: T20304

description:
P.falciparum parasite isolate
H0_sample97


title: 1407801

value: Male

value: XaY


title: Slc6a20a heterozygous 3


title: T20297

description:
P.falciparum parasite isolate
H0_sample96


title: 1407402

value: 8 postsurg/no chemorad


title: Slc6a20a heterozygous 4

value: whole brain


title: T20293

description:
P.falciparum parasite isolate
H0_sample95


title: 1408203

value: 3 postchemorad/pre adj tmz


title: Slc6a20a heterozygous 1

value: ~Postnatal day 120

value: male


title: Slc6a20a heterozygous 2


title: T20290

description:
P.falciparum parasite isolate
H0_sample94


title: 1454302

value: Glioma

value: Peripheral blood


title: Slc6a20a wildtype 4


title: 1408602

value: 9 postsurg/nochemorad/during adjtmz


title: memmix25

description: 12-cell-type artificial mixtures

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R studio

source_name: 12-cell-type artificial mixtures

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: treg

tag: bnv

tag: bmem

tag: nk

tag: mono

tag: neu

tag: eos

tag: bas


title: memmix27

description: 12-cell-type artificial mixtures


title: memmix20

description: 12-cell-type artificial mixtures


title: memmix28

description: 12-cell-type artificial mixtures


title: memmix26

description: 12-cell-type artificial mixtures


title: Slc6a20a wildtype 3

tag: Sex


title: 1407701

value: Female

value: XaXi

value: 1 pre surg

value: 3 rec lgg, still lgg


title: T20289

description:
P.falciparum parasite isolate
H0_sample93

tag: isolate

tag: treatment


title: 1406601

tag: tissue

value: 1 new gbm

value: IlluminaHumanMethylationEPIC


title: memmix19

description: 12-cell-type artificial mixtures


title: T20281

description:
P.falciparum parasite isolate
H0_sample92

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: memmix24

description: 12-cell-type artificial mixtures


title: T20274

description:
P.falciparum parasite isolate
H0_sample91


title: Slc6a20a wildtype 1

tag: strain

tag: age


title: memmix21

description: 12-cell-type artificial mixtures


title: Slc6a20a wildtype 2


title: T20273

description:
P.falciparum parasite isolate
H0_sample90


title: memmix23

description: 12-cell-type artificial mixtures


title: memmix18

description: 12-cell-type artificial mixtures


title: 1408902

tag: diagnosis

value: Male

tag: karyotype

value: XaY

value: 2 postsurg/prechemorad


title: T20267

description:
P.falciparum parasite isolate
H0_sample89


title: 1408201

tag: nontcell

tag: arraytypes


title: MW8_input_S10

first: Isabella

middle: M

last: Salamone

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

description: Male weekly day 8 input

data_processing:
Reads aligned to mm10 with TopHat V2.1.0 using Bowtie2 v2.2.6
Tag directories generated with HOMER makeTagDirectories with two replicate SAM files
Peaks were identified from tag directories of IP and input samples with HOMER findPeaks with parameters -style histone -F 2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of called peaks

source_name: isolated quadriceps myofibers

extract_protocol:
Quadriceps were removed and treated with collagenase II then filtered to isolate myofibers. Cells were lysed (5mM EDTA pH 7.5, 50mM Tris pH 7.5, 0.05% NP-40, 150mM NaCl) and chromatin was sheared via Bioruptor. Chromatin was incubated with anti-H3K27ac antibody (ActiveMotif 39133) overnight and then washed with high salt buffer (50mM Tris pH 7.5, 500mM NaCl, 0.1% SDS, 1% Triton X-100). Immunoprecipitated DNA was purified with Qiagen PCR Purification Kit.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: weekly prednisone

value: isolated quadriceps myofibers


title: T20266

description:
P.falciparum parasite isolate
H0_sample88


title: MW4_input_S05

description: Male weekly day 4 input

value: male


title: 1406802

value: Glioma


title: 1408402

value: Peripheral blood

value: 4 during chemorad


title: memmix17

description: 12-cell-type artificial mixtures

tag: treg

tag: bnv


title: 1405502


title: 1406602


title: memmix22

description: 12-cell-type artificial mixtures

tag: bmem

tag: nk


title: T20263

description:
P.falciparum parasite isolate
H0_sample86


title: MV_input_S02

description: Male vehicle input

value: vehicle


title: MW82_K27ac_S23

description: Male weekly day 8 rep2


title: T20265

description:
P.falciparum parasite isolate
H0_sample87


title: MW6_input_S08

description: Male weekly day 6 input


title: MW81_K27ac_S09

description: Male weekly day 8 rep1


title: 1452101

value: 4 rec lgg, now gbm


title: 1404303

value: Female

value: XaXi


title: T20262

description:
P.falciparum parasite isolate
H0_sample85


title: T20261

description:
P.falciparum parasite isolate
H0_sample84


title: CBmix2a

description: Umbilical cord blood artificial mixtures

tag: bcell

tag: mono

tag: neu


title: 1453601

tag: Sex

value: 1 pre surg

value: 1 new gbm


title: CBmix6b

source_name: Umbilical cord blood artificial mixtures

value: IlluminaHumanMethylationEPIC


title: 1450302

value: 3 rec lgg, still lgg


title: T20257

description:
P.falciparum parasite isolate
H0_sample82

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: MW61_K27ac_S06

description: Male weekly day 6 rep1

tag: treatment


title: 1407803

tag: tissue

value: Male

value: XaY

value: 2 postsurg/prechemorad


title: MW42_K27ac_S04

description: Male weekly day 4 rep2

tag: strain

value: weekly prednisone

value: male

value: isolated quadriceps myofibers


title: MW41_K27ac_S03

description: Male weekly day 4 rep1


title: 1408502

value: Glioma

value: Peripheral blood

tag: age


title: T20258

description:
P.falciparum parasite isolate
H0_sample83


title: T20255

description:
P.falciparum parasite isolate
H0_sample80


title: MV2_K27ac_S22

description: Male vehicle rep2

value: vehicle


title: T20250

description:
P.falciparum parasite isolate
H0_sample79


title: CBmix2b


title: MW62_K27ac_S07

description: Male weekly day 6 rep2


title: MV1_K27ac_S01

description: Male vehicle rep1


title: T20228

description:
P.falciparum parasite isolate
H0_sample77


title: 1453902

tag: diagnosis

value: 8 postsurg/no chemorad


title: T20240

description:
P.falciparum parasite isolate
H0_sample78


title: T20226

description:
P.falciparum parasite isolate
H0_sample76


title: 1454201

tag: karyotype


title: CBmix5b


title: 1453602

value: Female

value: XaXi

value: 4 during chemorad

tag: nontcell


title: T20219

description:
P.falciparum parasite isolate
H0_sample74


title: FW4_input_S16

description: Female weekly day 4 input

value: female


title: FV_input_S13

description: Female vehicle input


title: CBmix5a

tag: arraytypes

value: IlluminaHumanMethylationEPIC


title: CBmix3a


title: 1408401

value: 1 pre surg

value: 1 new gbm


title: CBmix1a


title: FW6_input_S19

description: Female weekly day 6 input


title: FW82_K27ac_S20

description: Female weekly day 8 rep2


title: CBmix1b


title: 1406503

value: Male


title: CBmix4b


title: T20224

description:
P.falciparum parasite isolate
H0_sample75

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: CBmix6a


title: T20218

description:
P.falciparum parasite isolate
H0_sample73


title: 1453901

value: XaY

value: 3 rec lgg, still lgg


title: 1409101


title: CBmix4a


title: FW81_K27ac_S24

description: Female weekly day 8 rep1

value: weekly prednisone

value: isolated quadriceps myofibers


title: FW62_K27ac_S18

description: Female weekly day 6 rep2


title: 1453801

value: Glioma

value: Peripheral blood


title: CBmix3b


title: FW61_K27ac_S17

description: Female weekly day 6 rep1


title: 1407501

value: 4 rec lgg, now gbm


title: T20215

description:
P.falciparum parasite isolate
H0_sample71


title: T20203

description:
P.falciparum parasite isolate
H0_sample69


title: T20200

description:
P.falciparum parasite isolate
H0_sample68


title: 1451902

value: Female

value: 8 postsurg/no chemorad

value: 2 new lgg


title: FV2_K27ac_S12

description: Female vehicle rep2

value: vehicle

value: female


title: 1406803

value: 7 postchemorad/no adjtmz

value: IlluminaHumanMethylationEPIC


title: FW42_K27ac_S15

description: Female weekly day 4 rep2


title: 1451602

value: Male

value: 2 postsurg/prechemorad

value: 1 new gbm


title: 1408701

value: XaY

value: 1 pre surg


title: T20197

description:
P.falciparum parasite isolate
H0_sample66

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: 1450101

value: Glioma

value: 3 rec lgg, still lgg


title: BC16_Hes1GFPhigh_input2

city: Stanford

first: Julien

last: Sage

state: California

address: 265 Campus Drive

institute: Stanford

data_processing:
Alignment using BWA.
Aligned sequences processed using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: TAG directories

source_name: Cell lines

extract_protocol:
Cells were fixed and chromatin sonicated using Diagenode Bioruptor followed by chromatin immunoprecipitation using Rest antibody (Milipore 17-641).
Libraries constructed from ChIP'ed DNA using Ovation Ultralow System V2 kit (Nugen 0344).

tag: hes1-gfp status

value: positive

tag: cancer type

value: Small cell lung cancer

tag: antibody

value: control rabbit IgG (included in Milipore 17-641)


title: BC14_Hes1GFPhigh_input1


title: T20216

description:
P.falciparum parasite isolate
H0_sample72


title: T20196

description:
P.falciparum parasite isolate
H0_sample65


title: 1408301

value: Peripheral blood


title: T20209

description:
P.falciparum parasite isolate
H0_sample70


title: T20195

description:
P.falciparum parasite isolate
H0_sample64


title: FW41_K27ac_S14

description: Female weekly day 4 rep1

value: weekly prednisone

value: isolated quadriceps myofibers


title: BC13_Hes1GFPhigh_ChIP2

value: Rest antibody (Milipore 17-641)


title: T20193

description:
P.falciparum parasite isolate
H0_sample63


title: BC11_Hes1GFPhigh_ChIP1


title: 1406402

value: Female

value: XaXi

value: 4 rec lgg, now gbm

value: IlluminaHumanMethylationEPIC


title: T20189

description:
P.falciparum parasite isolate
H0_sample62


title: 1407101

value: Male

value: XaY


title: 1561_Hesneg_L007

description:
Hes_pos_vs_Hes_neg_ATAC_UP.bed
Hes_pos_vs_Hes_neg_ATAC_DN.bed

data_processing:
DNA reads processing done by Bowtie2 (2.3.4.1) and MACS2.
Differential expression analysis with DESeq2 version 1.28.1
Genome_build: mm10
Supplementary_files_format_and_content: bed files of differentially expressed peaks

source_name: tumors

extract_protocol:
Cells were FACS sorted and processed as outlined in Buenrostro et al., Curr Protoc Mol Biol, 2016.
Library preparations were done as outlined in Buenrostro et al., Curr Protoc Mol Biol, 2016.

tag: sequencing lane

value: negative


title: T20199

description:
P.falciparum parasite isolate
H0_sample67

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: 1455301

value: Glioma

value: 1 pre surg

value: 1 new gbm


title: T20172

description:
P.falciparum parasite isolate
H0_sample60


title: 524_Hesnegrep2_L007

value: Small cell lung cancer


title: T20171

description:
P.falciparum parasite isolate
H0_sample59


title: T20181

description:
P.falciparum parasite isolate
H0_sample61


title: 1408601

value: Peripheral blood

value: 2 new lgg


title: 1402304

value: 8 postsurg/no chemorad

value: 3 rec lgg, still lgg


title: FV1_K27ac_S11

description: Female vehicle rep1

value: vehicle

value: female

value: isolated quadriceps myofibers


title: 1561_Hespos_L007

value: positive


title: T20256

description:
P.falciparum parasite isolate
H0_sample81


title: 524_Hesnegrep1_L007


title: 1452002

value: Male

value: 4 rec lgg, now gbm

value: IlluminaHumanMethylationEPIC


title: T20167

description:
P.falciparum parasite isolate
H0_sample58

value: In vivo, Blood stage


title: 524_Hesposrep2_L007


title: T20154

description:
P.falciparum parasite isolate
H0_sample57

value: Prior to ACT treatment, 0h


title: 524_Hesposrep1_L007


title: 1406301

value: Glioma

value: XaY


title: T20150

description:
P.falciparum parasite isolate
H0_sample56


title: T20146

description:
P.falciparum parasite isolate
H0_sample55


title: 521_Hesneg_L007

value: negative


title: 1455501

value: 1 pre surg

value: 1 new gbm


title: T20143

description:
P.falciparum parasite isolate
H0_sample54


title: 1561_Hesneg_L004

value: Small cell lung cancer


title: 1451901

value: Peripheral blood

value: Female

value: XaXi

value: 2 new lgg


title: 1454301


title: T20141

description:
P.falciparum parasite isolate
H0_sample53


title: 1561_Hespos_L004


title: 524_Hesnegrep2_L004


title: T20133

description:
P.falciparum parasite isolate
H0_sample51


title: 1452003

value: 8 postsurg/no chemorad


title: 1406202

value: 2 postsurg/prechemorad


title: 524_Hesnegrep1_L004


title: T20131

description:
P.falciparum parasite isolate
H0_sample50


title: 524_Hesposrep2_L004

value: positive


title: 1407702

value: 3 rec lgg, still lgg


title: FW8_input_S21

description: Female weekly day 8 input

value: weekly prednisone

value: female

value: isolated quadriceps myofibers


title: 1406302

value: Glioma

value: Male

value: IlluminaHumanMethylationEPIC


title: 524_Hesposrep1_L004


title: T20130

description:
P.falciparum parasite isolate
H0_sample49

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: 1406901

value: XaY

value: 1 pre surg


title: 521_Hesneg_L004

value: Small cell lung cancer

value: negative


title: 1407901

value: Peripheral blood

value: Female

value: XaXi


title: T20123

description:
P.falciparum parasite isolate
H0_sample48


title: 521_Hespos_L007

value: positive


title: 1408901

value: 1 new gbm


title: T20122

description:
P.falciparum parasite isolate
H0_sample47


title: 521_Hespos_L004

description:
Hes_pos_vs_Hes_neg_ATAC_UP.bed
Hes_pos_vs_Hes_neg_ATAC_DN.bed


title: T20138

description:
P.falciparum parasite isolate
H0_sample52


title: 1402803

value: 3 postchemorad/pre adj tmz

value: 4 rec lgg, now gbm


title: YT_24_Yap_5days

data_processing:
RNA quantification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.28.1
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

source_name: Cell line

extract_protocol:
RNA was isolated using Allprep DNA/RNA microkit (Qiagen 80284).
Libraries were prepared using TRIO RNA-seq kit (Nugen 0507-32) according to manufacturer's protocol.

tag: cell line

tag: overexpression

tag: bioreplicate

value: Replicate 3


title: T20115

description:
P.falciparum parasite isolate
H0_sample45


title: YT_23_Rest_5days


title: 1455102

value: Glioma

tag: Sex

value: 2 postsurg/prechemorad


title: YT_21_ctrl_5days


title: 1453302

value: 4 during chemorad

value: IlluminaHumanMethylationEPIC


title: T20109

description:
P.falciparum parasite isolate
H0_sample42

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: 1407401

value: Male

value: XaY

value: 1 pre surg

value: 2 new lgg


title: T20106

description:
P.falciparum parasite isolate
H0_sample41

tag: treatment


title: 1455101

tag: tissue

value: Peripheral blood


title: 1453301

value: Female

value: XaXi


title: T20104

description:
P.falciparum parasite isolate
H0_sample40


title: YT_16_Yap_5days

value: Small cell lung cancer

value: Replicate 2


title: 1407601

value: 8 postsurg/no chemorad

value: 4 rec lgg, now gbm


title: YT_17_ctrl_48hrs

value: Replicate 3


title: T20102

description:
P.falciparum parasite isolate
H0_sample38


title: YT_13_ctrl_5days


title: T20103

description:
P.falciparum parasite isolate
H0_sample39


title: T20120

description:
P.falciparum parasite isolate
H0_sample46


title: YT_15_Rest_5days


title: 1451601

value: Glioma

value: 1 new gbm


title: YT_11_Rest_48hrs


title: 1408101

value: IlluminaHumanMethylationEPIC


title: YT_9_ctrl_48hrs


title: 1406702

value: 2 postsurg/prechemorad


title: T20114

description:
P.falciparum parasite isolate
H0_sample44

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: T20101

description:
P.falciparum parasite isolate
H0_sample37


title: YT_8_Yap_5days

value: Replicate 1


title: T20098

description:
P.falciparum parasite isolate
H0_sample36


title: T20111

description:
P.falciparum parasite isolate
H0_sample43


title: 1455801

value: Male

value: XaY

value: 1 pre surg


title: T20095

description:
P.falciparum parasite isolate
H0_sample35


title: 1407902

value: Peripheral blood

value: Female

value: 3 rec lgg, still lgg


title: 1455302


title: T20094

description:
P.falciparum parasite isolate
H0_sample34


title: YT_5_ctrl_5days

value: Small cell lung cancer


title: T20093

description:
P.falciparum parasite isolate
H0_sample33


title: 1407403

value: 8 postsurg/no chemorad

value: 2 new lgg


title: 1405802

value: XaXi


title: T20091

description:
P.falciparum parasite isolate
H0_sample32


title: 1401304

value: Glioma

value: 3 postchemorad/pre adj tmz


title: YT_3_Rest_48hrs


title: YT_1_ctrl_48hrs


title: T20090

description:
P.falciparum parasite isolate
H0_sample31


title: T20086

description:
P.falciparum parasite isolate
H0_sample30


title: 1408801

value: 1 new gbm

value: IlluminaHumanMethylationEPIC


title: 1450303


title: Male weekly rep3

data_processing:
Reads aligned to mm10 with TopHat V2.1.0 using Bowtie2 v2.2.6 with parameters --no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 4 --max-multihits 5
Raw read counts per gene quantified with HTSeq with parameters -f bam -q -m intersection-nonempty -s no -t exon -i gene_id
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

extract_protocol:
Quadriceps were removed and treated with collagenase II then filtered to isolate myofibers. RNA was harvested with TRIzol reagent and PureLink mRNA Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: isolated quadriceps myofibers

tag: strain

value: weekly prednisone

value: male


title: Male weekly rep2


title: Male weekly rep1


title: T20084

description:
P.falciparum parasite isolate
H0_sample29

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: 1454001

value: Male

tag: age

value: XaY

value: 1 pre surg

value: 4 rec lgg, now gbm


title: T20079

description:
P.falciparum parasite isolate
H0_sample28


title: Male vehicle rep3

value: vehicle


title: YT_7_Rest_5days

value: Small cell lung cancer

value: Replicate 1


title: 1454202

tag: diagnosis

value: Peripheral blood

value: 2 postsurg/prechemorad


title: 1408302

value: Glioma

tag: karyotype


title: 1408702

value: 8 postsurg/no chemorad

value: 2 new lgg

tag: nontcell


title: Male vehicle rep2

value: isolated quadriceps myofibers


title: Male vehicle rep1


title: T20078

description:
P.falciparum parasite isolate
H0_sample27


title: T20077

description:
P.falciparum parasite isolate
H0_sample26


title: PCA0612

description: Neu

data_processing:
R studio
SeSAMe Processed Average Beta
Unmethylated and methylated signal intensities

source_name: Human Peripheral blood negatively selected neutrophils, Frozen

tag: mage

tag: purity

value: Mixed

value: Hispanic

value: WHITE

tag: smoker

value: No

tag: bmi

value: Overweight

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: flag

tag: include

value: Yes

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868500150/201868500150_R01C01


title: Male daily rep3

tag: tissue

tag: strain

tag: treatment

value: daily prednisone

tag: Sex

value: male


title: T20070

description:
P.falciparum parasite isolate
H0_sample24

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: T20072

description:
P.falciparum parasite isolate
H0_sample25


title: NKpan2510

description: NK

source_name: Human Peripheral blood CD56+ Natural killers, Frozen

tag: age

tag: mage

tag: purity

value: Indo-European

value: Caucasian

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

tag: treg

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868500150/201868500150_R03C01


title: WB1148

description: Neu

value: Persian

value: Maybe

value: Other myeloid contamination

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868500150/201868500150_R05C01


title: T20068

description:
P.falciparum parasite isolate
H0_sample23

tag: isolate

tag: treatment


title: Male daily rep1

tag: tissue

value: isolated quadriceps myofibers

tag: strain

tag: Sex


title: Mono1972

description: Mono

source_name: Human Peripheral blood CD14+ Monocytes, Frozen

tag: age

tag: mage

tag: purity

value: WHITE

tag: smoker

value: No

tag: bmi

value: Overweight

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

tag: treg

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868590206/201868590206_R06C01


title: T20067

description:
P.falciparum parasite isolate
H0_sample22

tag: isolate


title: Female weekly rep2

tag: treatment

value: weekly prednisone

value: female


title: Female weekly rep3

tag: tissue


title: WB1147

description: Neu

value: Mixed

value: Cauc/Mex/AA

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

value: Yes

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868590243/201868590243_R07C01


title: T20064

description:
P.falciparum parasite isolate
H0_sample21

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: Mono0933

description: Mono

tag: age

tag: mage

tag: purity

value: Indo-European

value: Caucasian

tag: smoker

tag: bmi

value: Obese

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868590243/201868590243_R08C01


title: T20061

description:
P.falciparum parasite isolate
H0_sample19

tag: isolate

tag: treatment


title: Mono1993

description: Mono

value: African-American

value: BLACK OR AFRICAN AMERICAN

value: No

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868590267/201868590267_R07C01


title: Female vehicle rep3

tag: tissue

value: isolated quadriceps myofibers

tag: strain

value: vehicle

tag: Sex

value: female


title: Female weekly rep1

value: weekly prednisone


title: T20063

description:
P.falciparum parasite isolate
H0_sample20


title: Mono2639

description: Mono

tag: age

tag: mage

tag: purity

value: East-Asian

value: Chinese

value: ASIAN

tag: smoker

tag: bmi

value: Normal

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201869680009/201869680009_R07C01


title: Female vehicle rep2

tag: treatment


title: T20060

description:
P.falciparum parasite isolate
H0_sample18

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: Female vehicle rep1

tag: tissue


title: T20053

description:
P.falciparum parasite isolate
H0_sample16


title: Male daily rep2

tag: strain

value: daily prednisone

value: male


title: EOS2272

description: Eos

source_name: Human Peripheral blood CD15+ CD16- Eosinophils, Frozen

value: Jap/Chinese

value: No

value: Obese

value: O+

tag: flag

tag: include

value: Yes

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201869680143/201869680143_R02C01


title: Female daily rep3

value: isolated quadriceps myofibers

tag: Sex

value: female


title: Baso2494

description: Bas

source_name: Human peripheral blood IgE+ CD123+ Basophils, Frozen

tag: age

tag: mage

tag: purity

value: African-American

value: African American

value: BLACK OR AFRICAN AMERICAN

tag: smoker

tag: bmi

value: Overweight

tag: ChIP

tag: arraytypes

tag: fetal

value: Maybe

value: Other myeloid contamination

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201869680143/201869680143_R05C01


title: T20046

description:
P.falciparum parasite isolate
H0_sample14

tag: isolate

value: In vivo, Blood stage

tag: treatment

value: Prior to ACT treatment, 0h


title: Female daily rep2

tag: tissue

tag: strain

value: daily prednisone


title: Baso2477

description: Bas

value: Indo-European

value: Caucasian

value: WHITE

value: Normal

value: A+

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

value: No

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201869680198/201869680198_R06C01


title: T20049

description:
P.falciparum parasite isolate
H0_sample15


title: WB1145

description: Neu

tag: age

tag: mage

tag: purity

value: African-American

value: BLACK OR AFRICAN AMERICAN

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610056/201870610056_R02C01


title: Female daily rep1

tag: tissue

value: isolated quadriceps myofibers

tag: strain

tag: treatment

tag: Sex

value: female


title: NKpan2503

description: NK

value: Portuguese

value: Obese

tag: flag

tag: include

value: Yes

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610056/201870610056_R07C01


title: T20045

description:
P.falciparum parasite isolate
H0_sample13

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: Mono1775

description: Mono

tag: age

tag: mage

tag: purity

value: Mixed

value: Mexican

value: WHITE

tag: smoker

tag: bmi

value: Overweight

value: O+

tag: ChIP

tag: arraytypes

tag: fetal

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610056/201870610056_R08C01


title: Atrial_nuclei_snRNA-seq_G125R

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
We filtered for at least 1000 reads per nucleus using R2 (R2; Genomics analysis and visualization platform (http://r2.amc.nl))
t-Distributed Stochastic Neighbor Embedding (t-SNE) is a dimensionality reduction algorithm that reduces high dimensional datasets to 2 or 3 dimensions.
Differential gene expression in snRNA-seq was determined by Kruskal-wallis test and Bonferroni correction in R2.
Genome_build: mm10

source_name: right atrial nuclei

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines.

extract_protocol:
Nuclei isolation was performed as described above on 3 right atria of each genotype pooled together loaded (resulting in one wildtype sample (containing n=3 RA) and one Tbx5+/G125R sample (containing n=3 RA)). Then nuclei were FACS sorted using a gate for DAPI into 0.4% BSA-PBS solution. Nuclei were counted manually using cell counter and 7000 nuclei were loaded. As per 10x Genomics protocol, sorted single nuclei were processed through the GemCode Single Cell Platform using GemCode Gel Bead, Chip, and Library Kits (10x Genomics). The nuclei were then partitioned into gel beads in emulsion in the GemCode instrument followed by processing. Libraries were sequenced on an Illumina Hiseq 4000 PE150. We filtered for at least 1000 reads per nucleus using R2 (R2; Genomics analysis and visualization platform (http://r2.amc.nl)). t-Distributed Stochastic Neighbor Embedding (t-SNE) is a dimensionality reduction algorithm that reduces high dimensional datasets to 2 or 3 dimensions. Differential gene expression in snRNA-seq was determined by Kruskal-wallis test and Bonferroni correction in R2.
10x Genomics protocol, sorted single nuclei were processed through the GemCode Single Cell Platform using GemCode Gel Bead, Chip, and Library Kits (10x Genomics).

treatment_protocol: Isolated atrial nuclei were fACS sorted and 7000 nuclei were sequenced using 10x Genomics protocol

tag: genotype/variation

value: adult

tag: tissue

value: right atria


title: T20057

description:
P.falciparum parasite isolate
H0_sample17

tag: treatment


title: Neut16936

description: Neu

value: Indo-European

value: non-hispanic white

value: Normal

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

value: No

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201868590206/201868590206_R02C01


title: Atrial_nuclei_snRNA-seq_Control

value: control

tag: age


title: T20026

description:
P.falciparum parasite isolate
H0_sample10

tag: isolate

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: T20030

description:
P.falciparum parasite isolate
H0_sample11


title: Control_Atria_PCM1+_H3K27Ac_4

data_processing:
Library strategy: CUT&RUN
Reads from H3K27ac CUT&RUN data were mapped to mm10 build of the mouse genome using BWA, the default settings were used.
The BEDTools suite was used to distribute the genome wide signal into bins of 500 bp. The background read level was determined per sample per 500 bp by taking the average read count in bins with less than 20 tags. The background level of tags was subtracted per bin per sample. Bins with less than 101 cumulative tags across all 11 samples were discarded as noise.
Differential acetylation was assessed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014). P-values were corrected for multiple testing using the false discovery rate (FDR) method of Benjamini-Hochberg. We have used 0.05 as FDR control level. Continuous bins with differential signal were subsequently merged together using the BEDTools suite
Genome_build: mm10
Supplementary_files_format_and_content: diff_peaks_G125R_H3K27ac_CR.xlsx - Excel file (with differentially acetylated peaks)

source_name: atrial cardiomyocyte nuclei

extract_protocol:
Nuclei were isolated from 8-12 week old control (n=5) and Tbx5+/G125R (n=6) pooled left and right atrium. Nuclei were stained for PCM1 (Pericentreolar material 1). Using FACS sorting the PCM1+ nuclei (cardiomyoycytes) were selected, on which CUT&RUN was performed to determine differential H3K27Ac binding. Protocol was followed as published (Hainer et al., 2019), with 1:00 H3K27Ac incubation overnight. NEBNext Ultra II DNA library Prep Kit for Illumina was used with 15 cycli PCR. Fragment size was determined on a Tapestation high sensitivety chip, DNA concentration was determined with Qubit, and samples were pooled equimolilarly and sequenced PE150 on Hi-seq4000.
NEBNext Ultra II DNA library Prep Kit for Illumina

value: 8-12 week

value: left and right atrium

tag: genotype

value: Control

tag: sorting

value: PCM1 sorted nuclei


title: Control_Atria_PCM1+_H3K27Ac_5

tag: tissue


title: Neut2270

description: Neu

tag: mage

tag: purity

value: Caucasian

value: WHITE

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

value: Yes

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610111/201870610111_R05C01


title: T20024

description:
P.falciparum parasite isolate
H0_sample9

source_name: P.falciparum field isolate from patient

tag: treatment


title: NKpan1879

description: NK

tag: age

value: African-American

value: Irish/AA

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610111/201870610111_R07C01


title: T20022

description:
P.falciparum parasite isolate
H0_sample8

tag: isolate


title: Control_Atria_PCM1+_H3K27Ac_2

tag: tissue

tag: genotype

tag: sorting


title: EOS2275

description: Eos

tag: mage

tag: purity

value: BLACK OR AFRICAN AMERICAN

tag: smoker

tag: bmi

value: Normal

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870620080/201870620080_R02C01


title: NKpan2241

description: NK

tag: age

value: Indo-European

value: No

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/201870610111/201870610111_R01C01


title: Control_Atria_PCM1+_H3K27Ac_1

value: 8-12 week

tag: tissue

value: left and right atrium

tag: genotype

value: Control

tag: sorting


title: EOS2063

description: Eos

tag: mage

tag: purity

value: East-Asian

value: Chinese

value: WHITE

tag: smoker

tag: bmi

value: Overweight

value: O+

tag: ChIP

tag: arraytypes

tag: fetal

tag: eos

tag: gran

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/202163530006/202163530006_R01C01


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_6

tag: age

value: PCM1 sorted nuclei


title: Control_Atria_PCM1+_H3K27Ac_3


title: EOS2042

description: Eos

value: ASIAN

tag: flag

tag: include

value: Yes

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/202163530006/202163530006_R05C01


title: T20020

description:
P.falciparum parasite isolate
H0_sample6

tag: isolate

value: In vivo, Blood stage

tag: treatment

value: Prior to ACT treatment, 0h


title: Tn0082

source_name: Human Peripheral Blood CD8+ CD45RA+ T Cells, Frozen

tag: mage

tag: purity

value: Indo-European

value: Caucasian

tag: smoker

value: No

tag: bmi

value: Normal

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: mono

tag: neu

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203013220070/203013220070_R01C01


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_5

tag: age

value: 8-12 week

tag: tissue

value: left and right atrium

tag: genotype

tag: sorting


title: T20014

description:
P.falciparum parasite isolate
H0_sample4


title: Tem0050

source_name: Human Peripheral Blood CD8+ CD62- CD45RO+ Effector Memory T Cells, Frozen

value: WHITE

value: Overweight

tag: flag

tag: include

value: Maybe

value: CD8T_CM contamination?

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: eos

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027370053/203027370053_R05C01


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_4

value: PCM1 sorted nuclei


title: T20009

description:
P.falciparum parasite isolate
H0_sample3

tag: isolate

value: In vivo, Blood stage

tag: treatment


title: YT_19_Rest_48hrs

tag: cell line

tag: cancer type

value: Small cell lung cancer

tag: overexpression

tag: bioreplicate

value: Replicate 3


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_3

tag: age

tag: tissue

tag: genotype

tag: sorting


title: Tn0043

tag: mage

tag: purity

value: Indo-European

value: Caucasian

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

value: Yes

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: mono

tag: neu

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027390051/203027390051_R01C01


title: Tem0045

tag: age

value: No

value: Normal

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

tag: bcell

tag: nk

tag: eos

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027390051/203027390051_R08C01


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_2

value: 8-12 week

tag: tissue

value: left and right atrium

tag: genotype

tag: sorting


title: Tn0073

tag: mage

tag: purity

value: WHITE

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027390092/203027390092_R03C01


title: T20021

description:
P.falciparum parasite isolate
H0_sample7

tag: isolate

tag: treatment

value: Prior to ACT treatment, 0h


title: Tn0979

tag: age

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027390094/203027390094_R05C01


title: Control_Atria_PCM1+_4

data_processing:
Reads were mapped to mm10 build of the mouse genome using BWA (Li et al., 2009) using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into sliding window bins of 500bp. Differential peak calling was performed on bins using DESeq2 (Love et al., 2014)
BED files (peaks called differential or stable between G125R heterozygous and control mice).
Genome_build: mm10
Supplementary_files_format_and_content: diff_peaks_G125R_ATAC-seq.xlsx - Excel file (containing differential peaks)

extract_protocol: Isolated nuclei from both atria pooled together per individual were stained for PCM1 (pericentreolar material 1). Samples were FACS sorted and gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. Nuclei were collected and successively washed with PBS and used as input for ATAC-seq using Illumina Tagment DNA enzyme and buffer (20034197) according to protocol. Libraries were sequenced paired end 150bp on an Illumina Hiseq4000.

tag: tissue

tag: genotype

value: Control

tag: sorting

value: PCM1 sorted nuclei


title: Pooled_sample

description: P.falciparum parasite isolate

source_name: Randomly selected P.falciparum field isolates

tag: isolate

value: Lab strain


title: Tn0049

tag: mage

tag: purity

value: Indo-European

value: Caucasian

tag: smoker

tag: bmi

value: Overweight

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203027390100/203027390100_R06C01


title: Control_sample3

description: P.falciparum parasite isolate

source_name: P.falciparum 3D7

value: Lab strain 3D7

tag: treatment


title: Control_sample2

description: P.falciparum parasite isolate


title: Control_Atria_PCM1+_3, rep2

tag: age


title: T20019

description:
P.falciparum parasite isolate
H0_sample5

value: In vivo, Blood stage


title: T20031

description:
P.falciparum parasite isolate
H0_sample12


title: Tem0219

value: No

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

value: Yes

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203028210043/203028210043_R01C01


title: Tem0075

tag: mage

tag: purity

value: WHITE

tag: smoker

tag: bmi

value: Normal

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203028210043/203028210043_R05C01


title: Control_Atria_PCM1+_1, rep2

tag: age

value: 8-12 week

tag: tissue

value: left and right atrium

tag: genotype

value: Control

tag: sorting


title: Control_Atria_PCM1+_3, rep1

value: PCM1 sorted nuclei


title: Treg4722

description: Treg

source_name: Human Peripheral blood CD4+ CD25+ CD127- T regulatory lymphocytes, Frozen

value: Mixed

value: African American/Latino or Hispanic

value: BLACK OR AFRICAN AMERICAN

value: B+

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203496240014/203496240014_R01C01


title: Control_Atria_PCM1+_2


title: Control_sample1

description: P.falciparum parasite isolate

tag: isolate

value: Lab strain 3D7

tag: treatment


title: BGBEAF-32- Dref-  Hi-C replicate 2

city: London

first: Nicolae Radu

last: Zabet

address: 4 Newark Street

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

country: United Kingdom

institute: Queen Mary University of London

data_processing:
HiSeq Control Software HD 3.4.0.38 used for basecalling.
Hi-C analysis: Each pair of the PE reads were aligned separately to Drosophila melanogaster (dm6) genome (Adams et al., 2000; dos Santos et al., 2015) using BWA-mem (Li and Durbin, 2010) (with options -t 20 -A1 -B4 -E50 -L0). HiCExplorer was used to build and correct the contact matrices and detect TADs and enriched contacts (Ramirez et al., 2018). The contact matrices were built at 100 Kb bins for plotting Figures 1, S5 and S6 only, 10Kb for compartments (Rowley et al., 2017) and using the DpnII restriction sites for everything else. Using a minimum allowed distance between restriction sites of 150 bp and a maximum distance of 1000 bp, we obtained a matrix with 217638 bins with a median width of 529 bp.  After filtering, we obtained between 18 M and 65 M reads (see Table S1). The matrices were corrected using the thresholds in Table S2, where values were selected from the diagnostic plots (Figure S8). By using the corrected contact matrices, we detected TADs of at least 5 Kb width using a P-value threshold of 0.01, a minimum threshold of the difference between the TAD-separation score of 0.04, and FDR correction for multiple testing (--step 2000, --minBoundaryDistance 5000 --pvalue 0.01 --delta 0.04 --correctForMultipleTesting fdr). We selected these parameters to ensure that we recover a similar number of TADs as previously reported (Chathoth and Zabet, 2019). Finally, we called strong TAD borders using a stringent value of the threshold of the difference between the TAD separation score of 0.08. This value ensured that we retrieved the strongest half of TADs. The enriched contacts were extracted with HiCExplorer using the observed/expected ratio method.
Chromatin loops: Chromatin loops were called with the HICCUPS tool from the Juicer software suite (Durand et al. 2017) on all mutants as done previously (Chathoth and Zabet, 2019). Loops were called using a 2 kb resolution, 0.05 FDR, Knight-Ruiz normalisation, a window of 10, peak width of 5, thresholds for merging loops of 0.02,1.5,1.75,2 and distance to merge peaks of 20 kb (-k KR -r 2000 -f 0.05 -p 5 -i 10 -t 0.02,1.5,1.75,2 -d 20000).
RNA-seq analysis: Reads were first trimmed using Trimmomatic (v0.39) (Bolger et al., 2014) and then aligned to Drosophila melanogaster (dm6) genome (Adams et al., 2000; dos Santos et al., 2015) using TopHat(v2.1.2) (Kim et al., 2014) with Bowtie2(v2.3.4.1) (Langmead et al., 2012) (Table S3). Finally, we used Picard tools (http://broadinstitute.github.io/picard/) to deduplicate reads and HTseq (Anders et al., 2015) to count reads.
Genome_build: dm6
Supplementary_files_format_and_content: BED files contain the coordinates of TADs; bepe files contain the coordinates of chromatin loops

organism: Drosophila melanogaster

source_name: BGBEAF-32- Dref-  Hi-C

growth_protocol: BG3 cells were grown to 80-90% confluence in Schneider’s Drosophila medium with 10% FBS respectively and antibiotics (Pen-Strep) in 100 mm cell culture plates.

extract_protocol:
Hi-C libraries were generated from 10 million cells by following the Insitu Hi-C protocol as mentioned in (Rao et al. 2014) with minor modifications. Crosslinked cells were lysed and genome was digested using DpnII (NEB) overnight. The overhangs were filled with Bioton-16-dATP (Jena Bioscience) followed by ligation and de-crosslinking with proteinase K digestion. The sample was further sonicated using Bioruptor.
Biotinylated DNA was pulled down using Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602). Selected biotinylated DNA fragments ranging from 200-500bp were then ligated with illumina adaptors (NEB).
RNA extraction: RNA extraction was carried out using Trizol according to manufacturer’s instructions. RNA was further DNase treated and purified using RNeasy Mini kit (Qiagen) following manufacturer's protocol. RNA was assessed qualitatively and quantitatively using Quibit and Bioanalyzer 2100(Agilent).
RNA sequencing: PolyA RNA selection, library preparation and sequencing were carried out by Novogene.

treatment_protocol: Primer sequences for CP190, Chro, Dref and BEAF-32 dsRNAi were obtained from the Drosophila RNAi Screening Center database (http://flyrnai.org) (see Table S5). The primers with T7 promoter sequence were used to amplify the IVT templates from wild type genomic DNA using Dream Taq DNA Polymerase Kit (Thermo Scientific, EP0703). The PCR products were checked by electrophoresis and purified using a Fastgene PCR Purification Kit (Fastgene). The purified PCR products were then used as templates to synthesis dsRNA using the MEGAscript T7 Kit (Life Technologies, AM1334) according to the manufacturer’s recommendations. The BG3 cells were transfected with 50ug of dsRNA using Fugene (Promega) according to manufacturer’s protocol. Cells were harvested after 72 hours and processed for downstream experiments accordingly.

tag: genotype/variation

value: BGBEAF-32- Dref-


title: T20005

description:
P.falciparum parasite isolate
H0_sample2

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: BGBEAF-32- Dref-  Hi-C replicate 1

description:
TADs_BG3_BEAF_DREF_KD_merged_dpnII.bed.gz
TADs_BG3_BEAF_DREF_KD_merged_dpnII_strong.bed.gz
Loops_BG3_BEAF_DREF_KD_HiC_hiccups.bedpe.gz


title: Treg4723

description: Treg

tag: age

tag: mage

tag: purity

value: African-American

tag: smoker

value: No

tag: bmi

value: Overweight

value: O+

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: flag

value: Yes

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203496240017/203496240017_R02C01


title: Tbx5G125R_Atria_PCM1+_4

value: 8-12 week

tag: tissue

value: left and right atrium

tag: genotype

tag: sorting

value: PCM1 sorted nuclei


title: T20004

description:
P.falciparum parasite isolate
H0_sample1

tag: isolate

tag: treatment


title: Tbx5G125R_Atria_PCM1+_H3K27Ac_1

tag: age


title: Bmem0008

description: Bmem

source_name: Human Peripheral blood, CD19+ CD27+ B cells, Frozen

tag: mage

tag: purity

value: Indo-European

value: Caucasian

value: WHITE

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450040/203991450040_R01C01


title: BGCp190- Chro-  Hi-C replicate 2

source_name: BGCp190- Chro-  Hi-C

tag: genotype/variation

value: BGCp190- Chro-


title: BGCp190- Chro-  Hi-C replicate 1

description:
TADs_BG3_Cp190_Chrom_KD_merged_dpnII.bed.gz
TADs_BG3_Cp190_Chrom_KD_merged_dpnII_strong.bed.gz
Loops_BG3_Cp190_Chrom_KD_HiC_hiccups.bedpe.gz


title: Baso2330

description: Bas

tag: smoker

tag: bmi

value: Obese

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450040/203991450040_R03C01


title: Tbx5G125R_Atria_PCM1+_3

tag: age

tag: tissue

tag: genotype

tag: sorting


title: Tbx5G125R_Atria_PCM1+_2


title: BGBEAF-32-  Hi-C replicate 1

description:
TADs_BG3_BEAF_KD_merged_dpnII.bed.gz
TADs_BG3_BEAF_KD_merged_dpnII_strong.bed.gz
Loops_BG3_BEAF_KD_HiC_hiccups.bedpe.gz

source_name: BGBEAF-32-  Hi-C


title: Control_Atria_PCM1+_1, rep1

value: Control


title: BGBEAF-32-  Hi-C replicate 2


title: Bmem0017

description: Bmem

tag: mage

tag: purity

value: No

value: Overweight

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450040/203991450040_R06C01


title: Bn0067

description: Bnv

source_name: Human Peripheral blood, CD19+ CD27- B cells, Frozen

value: African-American

value: African American

value: BLACK OR AFRICAN AMERICAN

tag: smoker

tag: bmi

value: Normal

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: flag

value: Maybe

value: Bmem contamination?

tag: eos

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450040/203991450040_R07C01


title: Tbx5G125R_Left_Atrium_5

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: G125R-whole-tissue-atrial-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).

source_name: left atrium whole tissue

growth_protocol: Murine atrial tissue was obtained between 8-12 weeks of age

extract_protocol:
RNA was extracted using ReliaPrep RNA Tissue Miniprep System (Promega)
Truseq RNA library Prep Kit v2 (Part# 15031048 Rev.E, Illumina) input 300ng

treatment_protocol: Atrial tissue was

tag: Sex

value: Female

tag: age

value: 8-12 week

tag: tissue

value: Left atrium

tag: genotype


title: Bmem0192

description: Bmem

tag: mage

tag: purity

value: Indo-European

value: Caucasian

value: WHITE

value: Obese

tag: include

value: Tcell contamination

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450040/203991450040_R08C01


title: Tbx5G125R_Left_Atrium_4

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx


title: Tbx5G125R_Atria_PCM1+_1

value: left and right atrium

tag: sorting

value: PCM1 sorted nuclei


title: Bn0046

description: Bnv

tag: smoker

value: No

tag: bmi

value: Overweight

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

value: Yes

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R01C01


title: Treg4744

description: Treg

tag: age

tag: mage

tag: purity

value: Mixed

value: African American/ Italian/ French/ Native American

value: O+

value: Cell Pellet

value: IlluminaHumanMethylationEPIC

tag: include

tag: exclude

tag: treg

tag: bnv

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203496240014/203496240014_R07C01


title: Tbx5G125R_Left_Atrium_2

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

tag: tissue

value: Left atrium

tag: genotype


title: WT

city: NEW YORK

first: Cierra

last: Sing

state: NY

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_name feature in the annotation file. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Saccharomyces cerevisiae S288c reference genome available on ENSEMBL
Supplementary_files_format_and_content: csv file show the comparison of gene expression between WT and PQ. The Wald test was used to generate p-values and Log2 fold changes.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in glucose-based rich media (yeast extract/peptone/dextrose, YPD) to mid-log phase (optical density OD600 = 0.3-0.5)

extract_protocol:
RNA was extracted from mid-log phase yeast cells using the RNeasy kit (Qiagen, Germantown, MD)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: growth phase

value: mid-log

value: WT

tag: treatment


title: Prmt1f/f mice-90

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

country: China

institute: Changzheng hospital

data_processing:
(RNA-Seq) Trimmomatic software were used to remove adapter and low quality reads. [Bolger et al., Bioinformatics, 2014]
(RNA-Seq) Quality distribution plot and base content distribution were generated by FASTQC.
(RNA-Seq) STAR is used to align clean reads to reference genome. [Dibin et al., STAR: ultrafast universal RNA-seq aligner.Bioinformatics, 2013]
(RNA-Seq) Read counts for individual transcripts of each sample were produced with HTSeq-count. [Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 2015]
Genome_build: mm10
Supplementary_files_format_and_content: rawcounts

source_name: liver

extract_protocol:
RNA was isolated using TRIzol reagent. A total of 3 μg of RNA per sample was utilized for RNA library preparation with the NEBNext® UltraTM RNA Library Prep Kit for Illumina® for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lrat-Cre; Prmt1f/f mice and  Prmt1f/f mice were treated with TAA (400mg/L, drinking water for 16 weeks) to indeced liver fibrosis

value: liver

value: 10-week old


title: Bmem0055

description: Bmem

value: Indo-European

value: Caucasian

value: WHITE

tag: smoker

value: No

tag: bmi

value: Obese

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R03C01


title: Lrat-Cre; Prmt1f/f mice-88

tag: tissue

tag: age

tag: genotype

value: Lrat-Cre; Prmt1f/f


title: Prmt1f/f mice-42

tag: strain


title: Bmem0187

description: Bmem

tag: mage

tag: purity

value: African-American

value: BLACK OR AFRICAN AMERICAN

tag: smoker

value: Yes

value: Overweight

value: Cell Pellet

tag: include

value: Maybe

value: CD8Tmem contamination?

tag: exclude

tag: treg

tag: bnv

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R05C01


title: Control_Left_Atrium_5

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

value: Left atrium

value: Control


title: Tbx5G125R_Left_Atrium_1

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx


title: Control_Left_Atrium_4

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx


title: Prmt1f/f mice-83

value: liver

value: 10-week old


title: Tbx5G125R_Left_Atrium_3

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx


title: Lrat-Cre; Prmt1f/f mice-82


title: Bn0150

description: Bnv

value: Indo-European

value: Caucasian

value: WHITE

value: No

tag: bmi

value: Normal

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

tag: flag

value: Bmem contamination?

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R06C01


title: Bmem0031

description: Bmem

tag: age

tag: mage

tag: purity

tag: smoker

value: Obese

value: Cell Pellet

tag: include

value: Yes

tag: exclude

tag: treg

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R08C01


title: Lrat-Cre; Prmt1f/f mice-49

tag: strain

tag: tissue

tag: genotype

value: Lrat-Cre; Prmt1f/f


title: Control_Left_Atrium_3

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

value: Left atrium


title: aan1∆

tag: growth phase

value: mid-log

tag: treatment


title: CD4mem 2165

source_name: Human Peripheral Blood CD4+ CD45RO+ T Cells, Frozen

value: Indo-European

tag: bmi

value: Underweight

value: A+

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204086440139/204086440139_R02C01


title: Control_Left_Atrium_2

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

tag: age

tag: tissue

tag: genotype

value: Control


title: Baso 2069

description: Bas

source_name: Human peripheral blood IgE+ CD123+ Basophils, Frozen

tag: mage

tag: purity

value: Caucasian

value: WHITE

tag: smoker

value: No

value: O+

value: IlluminaHumanMethylationEPIC

tag: include

tag: exclude

tag: treg

tag: neu

tag: eos

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204086440139/204086440139_R04C01


title: Control_Left_Atrium_1

description: Tbx5G125R_Whole tissue_RNA_LA_DE.xlsx

tag: Sex


title: Combination anti-PD-1 and anti-PSGL-1 treated tumor-infiltrating immune cells

city: Irvine

first: Roberto

last: Tinoco

state: CA

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

data_processing:
Sorted cells were subjected to 10X Genomics Chromium Single-Cell Platform manipulation, followed by sequencing using an NovaSeq 6000
Raw reads were subjected to QC analysis with FASTQC software and alignment to the reference transcriptome mm10 using a short-read aligner STAR68 via 10X pipeline cellRanger (v.3.1.0) software. The following expression matrices for these studies were: IgG (9726 cells),  PD1 (5614 cells),  PSGL1 (7292 cells),  Combo (4596 cells), all with average read depth of approximately 18,763 reads per cell with 2500 to 3000 median unique molecular identifiers across approximately 15,000 genes each
Gene level expression for each valid cell is then quantified using UMI (Unique Molecular Identifier) and normalization is performed. Dimension reduction is then used to visualize and explore major features in single cell RNA-seq data
PCA, t-distributed Stochastic Neighbor Embedding (t-NSE) and UMAP is performed using cellRanger followed by unsupervised clustering methods such as K mean clustering to identify sub populations and cell types in the sample. Loupe browser is then used to visualize the further explore marker gene expression
For RNA velocity analysis, output files from cellRanger were used to generate looms files with Velocyto (v.0.17.17)
Genome_build: mm10

source_name: Tumor

growth_protocol: B16-GP33 melanoma cells were injected s.c. on 0dpi into the right side flank of C57BL/6 mice. Tumors grew gor 18 days, at which point mice were sacked.

extract_protocol:
Tumors were dissected at 18dpi and processed using tumor digest enzymes A and D in RPMI on the GentleMacs tumor processcor setting 37C_h_TDK_1. Tumor were then passed through 70 micron strainer with sterile wash media (HBSS with 1%FBS, 0.5% HEPES, and 2%PSG). Tumors were spun and resuspended in sterile PBS with 0.04% BSA. Tumor cells were counted and stained with PI for 10 min on ice at 25x10^6 cells/mL. Cells were washed with sterile PBS +0.04% BSA and then stained for CD45.2 (1:300 dilution) with FC block (1:100) at 25x10^6 cells/mL for 20 min on ice. Cells were washed 3x and resuspened in sterile PBS + 0.04% BSA and brought to the flow core at 10x10^6 cells/mL for flow sorting. Purified PI- CD45.2+ cells were sorted for each treatment group. Sorted cells were spun and resuspenede at a concentration of 700 cells/uL.
RNA libraries were prepared using the 10X Genomics Chromium Single-Cell Platform protocol
scRNA-seq

treatment_protocol: Mice were treated with 200ug of IgG, anti-PD-1, anti-PSGL-1, or 200ug each of anti-PD-1 and anti-PSGL-1 antibody at days 8, 10, and 12 post B16-GP33 injection.

tag: strain

tag: cell type

value: Immune cells

tag: treatment

value: anti-PD-1 and anti-PSGL-1 antibody


title: anti-PD-1 treated tumor-infiltrating immune cells

value: anti-PD-1 antibody


title: Baso 2182

description: Bas

tag: bmi

value: Overweight

value: Cell Pellet

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

value: Yes

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204086440139/204086440139_R07C01


title: Bn0139

description: Bnv

tag: age

tag: mage

tag: purity

value: Mixed

value: Hispanic

tag: smoker

value: Obese

tag: include

tag: exclude

tag: treg

tag: neu

tag: eos

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/203991450045/203991450045_R07C01


title: Tbx5G125R_Right_Atrium_4

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

source_name: right atrium whole tissue

tag: Sex

value: Female

value: 8-12 week

tag: tissue

value: Right atrium

tag: genotype


title: Baso 2016

description: Bas

value: Indo-European

value: Caucasian

value: WHITE

tag: bmi

value: A+

tag: ChIP

tag: arraytypes

tag: fetal

value: No

tag: flag

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140014/204237140014_R02C01


title: CD4nv 1969

source_name: Human Peripheral Blood CD4+ CD45RA+ T Cells, Frozen

tag: age

tag: mage

tag: purity

tag: smoker

value: Overweight

value: O+

value: IlluminaHumanMethylationEPIC

tag: include

tag: exclude

tag: treg

tag: gran

tag: array

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140011/204237140011_R01C01


title: CD4mem1877

value: Yes

tag: bmi

value: Cell Pellet

tag: ChIP

tag: arraytypes

tag: fetal

value: Maybe

value: Treg contamination?

tag: neu

tag: eos

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140013/204237140013_R04C01


title: Tbx5G125R_Right_Atrium_3

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

tag: Sex

value: Female

tag: age

value: 8-12 week

tag: tissue

tag: genotype


title: BGBEAF-32- Dref-  RNA-seq replicate 2

source_name: BGBEAF-32- Dref-  RNA-seq

tag: genotype/variation

value: BGBEAF-32- Dref-


title: Tbx5G125R_Right_Atrium_1

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

value: Right atrium


title: BGBEAF-32- Dref-  RNA-seq replicate 1


title: CD4nv 2081

tag: mage

tag: purity

value: Indo-European

value: Caucasian

value: WHITE

tag: smoker

value: Obese

value: B+

tag: flag

tag: include

tag: exclude

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140011/204237140011_R04C01


title: CD4nv1906

tag: bmi

value: O+

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

value: No

tag: treg

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140014/204237140014_R03C01


title: BGCp190- Chro-  RNA-seq replicate 2

source_name: BGCp190- Chro-  RNA-seq

tag: genotype/variation

value: BGCp190- Chro-


title: CD4mem 2193

tag: age

tag: mage

tag: purity

tag: smoker

value: A+

value: Cell Pellet

tag: flag

tag: include

value: Yes

tag: exclude

tag: bnv

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140011/204237140011_R02C01


title: Mut tumor AOM/DSS, 76-544

city: Durham

first: Leping

last: Li

state: NC

address: 111 TW Alexander Dr.

department: Biostatistics and Computational Biology

institute: NIEHS

description: Mut tumor AOM/DSS

data_processing:
The quality of reads was evaluated using FastQC (v0.11.5). Reads were aligned using STAR (version 020201).
The STAR index was built using mouse genome (mm10, GENCODE release vM25).
Transcript expression was quantified using the subread package (49) (version 1.6.2) to generate raw counts for 55,293 genes.
Genome_build: mm10, GENCODE release vM25
Supplementary_files_format_and_content: counts text file

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN) and were of sufficient quality. Single-ended (75 base pairs) sequencing was carried out in house using Illumina Nextseq to at least 30 million reads per sample.
Illumina Tru-Seq RNA
Quantification Method:  Qubit fluorometer or Bioanalyzer
Sequencing Format:  Single
Read Length:  75 nt

treatment_protocol: For the AOM model, 2-month-old Dnase1l3 WT and KO mice were injected intraperitoneally with AOM (8 mg/kg, body weight). Colon tissues were isolated 9 hours, or five days after injection. RNA was extracted from the whole colon tissue of Dnase1l3 WT and KO mice at basal condition, after one cycle of AOM/DSS, after three cycles of AOM/DSS and from final tumors from Dnase1l3 WT and KO mice after the three cycles of AOM/DSS.

tag: genotype

value: DNase MUT

tag: tissue

value: tumor only

tag: treatment

value: three cycles of AOM/DSS

tag: group

value: final stage


title: Mut tumor AOM/DSS, 76-543

description: Mut tumor AOM/DSS


title: IgG treated tumor-infiltrating immune cells

tag: strain

tag: cell type

value: Immune cells

value: IgG


title: BGBEAF-32- Dref-  RNA-seq replicate 3

value: BGBEAF-32- Dref-


title: WT tumor AOM/DSS , 77-555

description: WT tumor AOM/DSS

value: DNase WT


title: Control_Right Atrium_4

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

value: Right atrium

value: Control


title: Control_Right Atrium_5

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx


title: Control_Right Atrium_3

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx


title: BGCp190- Chro-  RNA-seq replicate 1

value: BGCp190- Chro-


title: WT tumor AOM/DSS , 81-579

description: WT tumor AOM/DSS


title: WT tumor AOM/DSS , 76-542

description: WT tumor AOM/DSS


title: Tbx5G125R_Right_Atrium_5

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx


title: anti-PSGL-1 treated tumor-infiltrating immune cells

value: anti-PSGL-1 antibody


title: BGBEAF-32-  RNA-seq replicate 3

source_name: BGBEAF-32-  RNA-seq


title: BGCp190- Chro-  RNA-seq replicate 3


title: Mut tumor AOM/DSS, 74-527

description: Mut tumor AOM/DSS


title: CD4mem2075

value: Indo-European

value: Caucasian

value: WHITE

tag: bmi

value: Obese

value: O+

value: Cell Pellet

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

value: No

value: Maybe

value: CD4nv contamination?

tag: treg

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140014/204237140014_R04C01


title: BGBEAF-32-  RNA-seq replicate 2

tag: genotype/variation


title: WT tumor AOM/DSS , 76-541

description: WT tumor AOM/DSS

tag: genotype

value: DNase WT

tag: tissue

value: tumor only

tag: treatment

value: three cycles of AOM/DSS

tag: group

value: final stage


title: BGBEAF-32-  RNA-seq replicate 1


title: Mut colon AOM/DSS late, 76-544

description: Mut colon AOM/DSS late

value: DNase MUT

value: whole colon


title: CD4nv1876

tag: age

tag: mage

tag: purity

value: Indo-European

tag: smoker

tag: bmi

value: Normal

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

value: CD8nv contamination?

tag: exclude

tag: bnv

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140014/204237140014_R06C01


title: Control_Right Atrium_2

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

value: Right atrium

value: Control


title: mem mix1

description: MIX

source_name: artificial mixture of purified leukocytes

value: IlluminaHumanMethylationEPIC

value: No

tag: treg

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R03C01


title: CD4nv1217

tag: age

tag: mage

tag: purity

value: Caucasian

value: WHITE

tag: smoker

value: Yes

tag: bmi

value: A+

value: Cell Pellet

tag: ChIP

tag: arraytypes

tag: fetal

value: Maybe

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204237140015/204237140015_R08C01


title: mem mix15

description: MIX

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R01C01


title: BGWT  RNA-seq replicate 1

source_name: BGWT  RNA-seq

tag: genotype/variation

value: BGWT


title: rpa190-F1205H 1

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

data_processing:
library strategy: NET-seq
Base-calling was performed using bcl2fastq software (version 2.20.00).
Based on the UMI sequence, reads were collapsed via fqtrim (version 0.9.7) with the "-C" option.
Reads containing the sequence and UMI 5'-AGNNNNNNNNTG-3' at the 5' end were identified and removed using cutadapt (version 1.12) with "-g -no-indels" parameters.
The 3' sequence 5'-CTGTAGGCACCAT-3' was removed from reads using cutadapt (version 1.12) with the parameters "-a -no-indels".
Reads were aligned to the Saccharomyces cerevisiae genome assembly R64-1-1 using STAR (version 2.7.1a). The STAR alignIntronMax parameter was set to 1.
Output BAM files were sorted and indexed using SAMtools (version 1.6).
Sorted BAM files were converted to BED files using BEDTools (version 2.26.0).
BEDTools (version 2.26.0) was used to generate genome coverage files, with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.0.2).
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Processed data files are in .csv file format.

source_name: yeast

growth_protocol: Triplicate yeast cultures for each strain were grown at 30ºC with nutation until an OD600 of 0.3 was reached.

extract_protocol:
Extraction methods were based on previously published works from our lab (data available at GSE142457, GSE166983, and GSE175553). Briefly, cells were harvested via filtration, flash frozen, and lysed under cryogenic conditions. Immunoprecipitation for Pol I was performed as previously described and RNA was isolated via acidic phenol/chloroform extraction.
DNA libraries were constructed as previously published (Jacobs and Huffines et al., The small-molecule BMH-21 directly inhibits transcription elongation and DNA occupancy of RNA polymerase I in vivo and in vitro, JBC, 2021). In brief, a DNA linker including a UMI was ligated onto the 3' end of RNA reads. Samples were precipitated, and reads were reverse transcribed. Finally, DNA was circularized, amplified, and sequenced.


title: BGWT  RNA-seq replicate 2


title: BGWT  RNA-seq replicate 3


title: rpa190-F1205H 2


title: B6_uninf_2

city: Philadelphia

first: Rina

last: Matsuda

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

description:
gran_filtered_normalized.xlsx
gran_filtered.xlsx

data_processing:
fastq files were aligned to mouse reference genome GRCm38 using Kallisto version 0.46.2
genes with <1 CPM in 3 samples were filtered out
expression data was normalized by TMM method using edgeR package in R
data were variance-stabilized using VOOM function in the Limma package in R
differentially expressed genes (³2-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each sample, with or without normalization

source_name: small intestine punch biopsy

growth_protocol: Mice were bred at the University of Pennsylvania and housed under specific pathogen free conditions. Female mice at 8 weeks of age were used for this experiment.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded Total RNA Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Yersinia pseudotuberculosis strain 32777 was cultured to stationary phase at 28°C and 250 rpm shaking for 16 hours in 2xYT broth supplemented with 2 μg/ml triclosan (Millipore Sigma). Mice were fasted for 16 hours and subsequently inoculated by oral gavage with 200 μl bacterial suspension in phosphate-buffered saline (PBS). All bacterial strains were administered at 2x10^8 colony-forming units (CFU) per mouse. At day 5 post-infection, mice were killed by CO2 inhalation. Small intestines were isolated and contents were flushed with PBS. Tissue was opened longitudinally, and 2mm punch biopsies were taken of granulomas, non-granulomas, or uninfected tissue. 5 biopsies were pooled per sample. Biopsies were collected into RNAlater buffer (Sigma-Aldrich), kept overnight at 4C, then transferred to -80C for storage prior to RNA extraction.

tag: background strain

tag: genotype

value: wild-type

tag: treatment

value: uninfected


title: B6_uninf_3


title: Mut colon AOM/DSS late, 75-535

description: Mut colon AOM/DSS late

value: DNase MUT

tag: tissue

value: whole colon

value: three cycles of AOM/DSS

tag: group

value: final stage


title: WT 3


title: Mut colon AOM/DSS late, 76-543

description: Mut colon AOM/DSS late


title: mem mix6

description: MIX

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: age

tag: mage

tag: purity

tag: smoker

tag: bmi

value: IlluminaHumanMethylationEPIC

value: No

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R02C01


title: mem mix8

description: MIX

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R04C01


title: WT colon AOM/DSS late, 77-555

description: WT colon AOM/DSS late

tag: genotype

value: DNase WT

tag: tissue

tag: treatment

tag: group


title: WT 2

tag: genotype/variation


title: mem mix4

description: MIX

tag: age

tag: mage

tag: purity

tag: smoker

tag: bmi

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R05C01


title: Control_Right Atrium_1

description: Tbx5G125R_Whole tissue_RNA_RA_DE.xlsx

tag: Sex

value: Female

value: 8-12 week

value: Right atrium

tag: genotype

value: Control


title: WT tumor AOM/DSS , 75-534

description: WT tumor AOM/DSS

tag: tissue

value: tumor only

tag: treatment


title: B6_uninf_1

tag: background strain

value: wild-type


title: rpa190-F1205H 3

tag: genotype/variation


title: Mut colon AOM/DSS late, 74-527

description: Mut colon AOM/DSS late

tag: group


title: WT 1


title: mem mix7

description: MIX

tag: age

tag: mage

tag: purity

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R07C01


title: mem mix16

description: MIX

tag: smoker

tag: bmi

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361720136/204361720136_R06C01


title: mem mix9

description: MIX

tag: age

tag: mage

tag: purity

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361730134/204361730134_R02C01


title: WT colon AOM/DSS late, 76-541

description: WT colon AOM/DSS late

tag: genotype

tag: tissue

value: whole colon

tag: treatment

value: three cycles of AOM/DSS

tag: group


title: B6_nongran_2

tag: background strain

value: Yp infected non-granuloma


title: RIPK1 KO CD45- rep1

first: Jingya

last: Qiu

address: 421 Curie Blvd, 532

department: Radiation Oncology

description: CD45- sorted non-immune cells from cancer cell specific RIPK1 knockout tumor, replicate 1

data_processing:
Raw bcl files demultiplexed using cellranger mkfastq (version 2.1.0)
fastq reads aligned, filtered, and quantified into gene-barcode matrices using cellranger count (version 2.1.0)
Raw UMI counts were normalized using Seurat's SCT normalization procedure
Gene expression was denoised using SAVERCAT
Genome_build: mm10
Supplementary_files_format_and_content: hdf5 feature barcode matrices generated with cellranger version 2.1.0
*10x SCT transformed data.rds: normalized counts (Seurat SCT)
*SAVERCAT Denoised.rds: denoised estimates (SAVERCAT)
*SAVERCAT sampled estimates.rds: sampled estimates (SAVERCAT)
*SAVERCAT and Seurat Metadata.txt: metadata

source_name: subcutaneous tumor

growth_protocol: Wild-type or RIPK1 knockout TSA cancer cells were subcutaneously injected into Balb/c syngeneic mice and grown for 14 days in vivvo before tumor harvest and cell sorting for CD45 positive or CD45 negative populations.

extract_protocol:
Mice were euthanized and tumors were harvested and dissociated using type IV collagenase solution supplemented with DNAseI. Cells were stained with CD45.2 antibody and live dead aqua and sorted for either CD45+ or CD45- live cell populations. Single cell suspensions were loaded into the 10x Genomics Chromium Controller to generate single cell emulsions.
Libraries were prepared from single cell emulsions using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) following the manufacturer’s protocol.

tag: tumor type

value: Breast Cancer

tag: injected cell line

value: TSA

tag: ripk1 expression status in cancer cells

value: RIPK1 deleted

tag: sorted cell population

value: CD45 negative non-immune cells


title: RIPK1 KO CD45- rep2

description: CD45- sorted non-immune cells from cancer cell specific RIPK1 knockout tumor, replicate 2


title: WT colon AOM/DSS late, 81-581

description: WT colon AOM/DSS late

value: DNase WT

value: final stage


title: B6_nongran_3


title: Mut colon AOM/DSS early, 115-804

description: Mut colon AOM/DSS early

value: DNase MUT

value: one cycle of AOM/DSS

value: early stage of AOM/DSS with 5 days recovery


title: WT CD45- rep2

description: CD45- sorted non-immune cells from RIPK1 wild type tumor, replicate 2

value: Wild Type


title: Mut colon AOM/DSS early, 115-803

description: Mut colon AOM/DSS early


title: Mut colon AOM/DSS early, 116-813

description: Mut colon AOM/DSS early


title: mem mix13

description: MIX

tag: smoker

tag: bmi

value: IlluminaHumanMethylationEPIC

value: No

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361730134/204361730134_R01C01


title: B6_gran_2

tag: background strain

tag: genotype

value: wild-type

tag: treatment

value: Yp infected granuloma


title: B6_gran_3


title: B6_gran_1


title: B6_nongran_1


title: mem mix10

description: MIX

tag: age

tag: mage

tag: purity

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

tag: fetal

tag: flag

tag: include

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361730134/204361730134_R05C01


title: mem mix14

description: MIX

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: nk

tag: mono

tag: neu

tag: eos

tag: gran

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361730134/204361730134_R03C01


title: RIPK1 KO CD45+ rep1

description: CD45+ sorted immune cells from cancer cell specific RIPK1 knockout tumor, replicate 1

tag: tumor type

value: Breast Cancer

tag: injected cell line

tag: ripk1 expression status in cancer cells

tag: sorted cell population

value: CD45 positive immune cells


title: WT colon AOM/DSS late, 76-542

description: WT colon AOM/DSS late

tag: genotype

tag: tissue

value: whole colon

tag: treatment

value: three cycles of AOM/DSS

tag: group


title: TKO_YT29_Hes1GFP_nonNE

source_name: Cell lines

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

tag: derived from pooled tumors from a mouse or single tumor

value: Pooled

tag: cancer type

value: Small cell lung cancer

value: Hes1-GFP reporter

tag: cell population

value: Hes1GFP nonNE


title: Mut colon AOM/DSS early, 116-811

description: Mut colon AOM/DSS early

value: DNase MUT

value: one cycle of AOM/DSS

value: early stage of AOM/DSS with 5 days recovery


title: mem mix5

description: MIX

tag: age

tag: mage

tag: purity

tag: smoker

tag: bmi

tag: ChIP

tag: arraytypes

value: IlluminaHumanMethylationEPIC

tag: fetal

value: No

tag: flag

tag: include

tag: exclude

tag: treg

tag: bnv

tag: bmem

tag: bcell

tag: array

tag: slide

tag: basename

value: I:/Dropbox (Christensen Lab)/Extended library/Raw_Data/Raw_Data/204361730134/204361730134_R08C01


title: WT colon AOM/DSS early, 116-812

description: WT colon AOM/DSS early

tag: genotype

value: DNase WT

tag: tissue

tag: treatment

tag: group


title: WT CD45+ rep2

description: CD45+ sorted immune cells from RIPK1 wild type tumor, replicate 2

tag: tumor type

tag: injected cell line

value: TSA

tag: ripk1 expression status in cancer cells

value: Wild Type

tag: sorted cell population


title: WT CD45- rep1

description: CD45- sorted non-immune cells from RIPK1 wild type tumor, replicate 1

value: Breast Cancer

value: CD45 negative non-immune cells


title: TKO_YT28_Hes1GFP_NE

tag: derived from pooled tumors from a mouse or single tumor

tag: cancer type

tag: cell population

value: Hes1GFP NE


title: WT colon AOM/DSS early, 97-686

description: WT colon AOM/DSS early

value: whole colon


title: TKO_YT19_Rest_nonNE

value: Single

value: Rest floxed

value: nonNE


title: TKO_YT15_Rest_nonNE

value: Pooled

value: Small cell lung cancer


title: RIPK1 KO CD45+ rep2

description: CD45+ sorted immune cells from cancer cell specific RIPK1 knockout tumor, replicate 2

value: RIPK1 deleted

value: CD45 positive immune cells


title: MUT colon basal, 125-872

description: MUT colon basal

value: DNase MUT

value: basal condition

value: basal control


title: WT colon AOM/DSS early, 97-685

description: WT colon AOM/DSS early

value: DNase WT

value: one cycle of AOM/DSS

value: early stage of AOM/DSS with 5 days recovery


title: TKO_YT14_Rest_nonNE


title: TKO_YT20_Rest_nonNE


title: WT CD45+ rep1

description: CD45+ sorted immune cells from RIPK1 wild type tumor, replicate 1

value: Breast Cancer

value: TSA

value: Wild Type