title: Bone marrow-derived macrophage - preIL4 [scRNA-seq]

city: South San Francisco

first: Bence

last: Daniel

state: CA

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

data_processing:
Reads were filtered, trimmed, and aligned to the mm10 reference genome using the 10X cellranger count pipeline.
Doublets were called for each sample individually using the R implementation of scrublet, rscrublet.
Gene by barcode counts matrices were loaded into Seurat for additional processing and analysis.
Separate Seurat objects were created for the three sample sets (priming, polarization, and repolarization) and for each individual sample. Barcodes with >12.5% mitochondrial reads, <200 unique features, or a scrublet score >0.25 were removed.
Remaining cells were then clustered and visualized. Cell cycle phase predictions for each cell were performed following the vignette available online: https://satijalab.org/seurat/archive/v3.1/cell_cycle_vignette.html.
Genome_build: mm10
Supplementary_files_format_and_content: 10X Genomics Filtered Gene BC Barcodes, genes and matrix

growth_protocol: Wild type, 2-3 months old female C57Bl6 mice were purchased from Jackson laboratories. Mice were sacrificed and bone marrow was isolated form the tibiae and femora of the animals. Red blood cell lysis was carried out and cells were plated in differentiation media containing 10% FBS, Dulbecco’s Modified Eagle’s Medium (DMEM) and 20ng/ml mouse M-CSF (Peprotech). On the third day of differentiation, media was replaced with fresh differentiation media. Cytokine treatments sorting procedures were carried out on the 6th day of differentiation.

extract_protocol:
10X Genomics Single Cell 5' Library & Gel Bead Kit
Single-cell RNA-seq libraries were prepared using the 10X Single Cell Immune Profiling Solution Kit (v1 Chemistry), according to the manufacturer’s instructions. Briefly, FACS sorted cells were washed once with PBS + 0.04% BSA. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification (98°C for 45 sec; 14 cycles of 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min; 72°C for 1 min). For gene expression library construction, 50 ng of amplified cDNA was fragmented, and end-repaired, double-sided size selected with SPRIselect beads, PCR amplified with sample indexing primers (98°C for 45 sec; 14 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min), and double-sided size selected with SPRIselect beads. Single-cell RNA libraries were sequenced on an Illumina HiSeq 4000 to a minimum sequencing depth of 25,000 reads/cell using the read lengths 28bp Read1, 8bp i7 Index, 91bp Read2.

treatment_protocol: Macrophages were treated with either IL-4 (20ng/ml) or IFNG (20ng/ml) (Peprotech). For polarization we used 24 hours of IL-4 polarization and 3 hours of IFNG polarization in differentiation media that contained 10% FBS, 1% penicillin/streptomycin and M-CSF (20ng/ml). IL-4 priming was performed as follows: macrophages were polarized with IL-4 (20ng/ml) for 24 hours. Cell were washed three times with serum-free DMEM, then differentiation media was replaced, and cells were rested for an additional 24 hours. Repolarization was performed at this point for 3 hours with IFNG (20ng/ml). Macrophage polarization for cell cycle experiments used 3 hours of polarization with either IL-4 or IFNG (both at a 20ng/ml concentration).

value: wild type

value: Bone marrow

tag: cell type

value: Bone marrow-derived macrophage

tag: treatment


title: genomic DNA from ASD patient (ID: 9440)

status: Public on Oct 01 2021

type: genomic

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

country: Brazil

institute: Instituto Butantan

description: whole blood of ASD patients

hyb_protocol: DNA from whole blood samples were treated using the EZ DNA Methylation kit (Zymo Research, Irvine, California,USA). The bisulfite converted DNA was hybridized in the BeadChip Human Methylation 450 microarrays (Illumina Inc., San Diego, California, USA) following the manufacturer’s protocol

scan_protocol: Arrays were imaged using iScan SQ scanner using the GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 IDAT files

data_processing: Bioconductor packages in R (minfi, ComBat and ChAMP)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Automated DNA extraction from peripheral blood was performed using the Maxwell® 1 Instrument (which uses magnetic particles to capture, wash and purify the genomic DNA molecules), following the manufacturer's protocol (Promega Corporation, Madison , Wisconsin, USA). The quality of the extracted DNA was verified by spectrophotometry (NanoDrop® ND-1000, ThermoScientific, Waltham, Massachusetts, USA), in order to guarantee the use of samples with a purity ratio of at least 1.8. DNA quantification was performed using the Qubit® instrument with the dsDNA BR Assay kit (Life Technologies Corporation, Carlsbad, California, USA), according to the manufacturer's instructions.

tag: gender

value: female

tag: age

tag: tissue

value: Whole blood

tag: disease state

value: Autism Spectrum Disorder

tag: cars

tag: iq

tag: snap


title: Δdps RDM deep stationary rep 3 - IPOD RNA-pol ChIP

type: SRA

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were subject to quantitation using kallisto v0.43 and differential expression calling using sleuth 0.30.0
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Culture lysate

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).

tag: strain

tag: genotype

value: {delta}dps

tag: media

value: M9 Rich Defined Media (RDM) + glucose

tag: time of harvest

value: deep stationary phase


title: Bone marrow-derived macrophage - preIL4_IFNG [scRNA-seq]

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus


title: Δdps RDM deep stationary rep 2 - IPOD RNA-pol ChIP


title: Bone marrow-derived macrophage - IL4 [scRNA-seq]


title: genomic DNA from ASD patient (ID: 9378)

description: whole blood of ASD patients

value: male


title: Bone marrow-derived macrophage - IFNG [scRNA-seq]

value: IFNG


title: L_227_05: COVID19 patient 227 day 5

city: San Francisco

first: Zicheng

last: Hu

address: 490 Illinois Street

institute: University of California San Francisco

data_processing:
The transcript level count were quantified using Kallisto v0.46.1.
 Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript count

molecule: total RNA

source_name: Whole blood

extract_protocol:
First the samples were treated with Proteinase K, and then some extractions were performed using Quick-RNA MagBead Kit (R2132) on KingFisher.
Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).

tag: subject

tag: time

value: day 5

tag: Sex

value: Male

tag: symptom severity

value: Moderate Symptomatic

tag: viral shedding


title: genomic DNA from ASD patient (ID: 9365)

description: whole blood of ASD patients


title: Δdps RDM deep stationary rep 1 - IPOD RNA-pol ChIP


title: genomic DNA from ASD patient (ID: 9388)

description: whole blood of ASD patients


title: L_184_00: COVID19 patient 184 day 0

value: day 0

value: Female


title: Δdps RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: logarithmic phase


title: genomic DNA from ASD patient (ID: 9352)

description: whole blood of ASD patients


title: Δdps RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: Bone marrow-derived macrophage - CTR [scRNA-seq]

value: wild type

tag: cell type

tag: treatment

value: CTR


title: genomic DNA from ASD patient (ID: 9400)

description: whole blood of ASD patients

tag: gender

tag: age


title: genomic DNA from ASD patient (ID: 9363)

description: whole blood of ASD patients

tag: tissue

tag: disease state


title: genomic DNA from ASD patient (ID: 9375)

description: whole blood of ASD patients

tag: cars

tag: iq


title: genomic DNA from ASD patient (ID: 9355)

description: whole blood of ASD patients

tag: snap


title: Bone marrow-derived macrophage - IFNG_S_rep2

data_processing:
Fastq files were pseudoaligned to a mm10 transcriptome index.
The abundance of transcripts was quantified using Kallisto v0.43.1 with bias correction.
Transcript-level abundance estimates were imported and summarized using tximport v1.16.1
Differential expression was determined using the DESeq2 package v1.28.11 in Bioconductor v.3.11.
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized bigwig files (.bw); Raw and normalized counts(.xls)

extract_protocol:
Total RNA was isolated with Trizol, followed by precipitation with isopropanol. RNA was washed with 75% Ethanol and pellet was dried and dissolved in nulcease-free water.
Approximately 20ng total RNA was used for library preparation with Ovation Ultralow RNA-seq V2 (Tecan) from two biological replicates. Libraries were generated according to the manufacturer’s instructions. Approximately 50ng amplified cDNA was subjected to Ovation Ultralow V2 library generation and manufacturer’s instructions were followed. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

tag: strain

tag: genotype

value: Bone marrow

value: Bone marrow-derived macrophage

tag: treatment/cell cycle


title: Bone marrow-derived macrophage - IFNG_G2M_rep2


title: WT RDM deep stationary rep 3 - IPOD RNA-pol ChIP

tag: media

tag: time of harvest


title: genomic DNA from ASD patient (ID: 9361)

description: whole blood of ASD patients

value: female

value: Whole blood


title: genomic DNA from ASD patient (ID: 9370)

description: whole blood of ASD patients

value: Autism Spectrum Disorder


title: ihfA::Kan infB::Chlor RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: ihfA::Kan infB::Chlor

value: M9 Rich Defined Media (RDM) + glucose


title: Bone marrow-derived macrophage - IFNG_G1_rep2


title: L_016_05: COVID19 patient 016 day 5

tag: subject

tag: time

tag: Sex


title: L_318_00: COVID19 patient 318 day 0

tag: symptom severity

value: Asymptomatic

tag: viral shedding


title: Bone marrow-derived macrophage - IL4_G2M_rep2

tag: cell type


title: L_143_00: COVID19 patient 143 day 0

tag: age


title: Bone marrow-derived macrophage - IL4_S_rep2

tag: tissue


title: Bone marrow-derived macrophage - IL4_G1_rep2


title: L_154_05: COVID19 patient 154 day 5

tag: disease state


title: L_168_00: COVID19 patient 168 day 0


title: genomic DNA from ASD patient (ID: 9372)

description: whole blood of ASD patients

tag: gender

value: male

tag: cars


title: genomic DNA from ASD patient (ID: 9368)

description: whole blood of ASD patients

tag: iq

tag: snap


title: WT RDM deep stationary rep 1 - IPOD RNA-pol ChIP

tag: strain

tag: genotype

value: deep stationary phase


title: WT Minimal logarithmic rep 1 - IPOD RNA-pol ChIP

tag: media

value: M9 Minimal Media + glucose


title: WT Minimal logarithmic rep 2 - IPOD RNA-pol ChIP

tag: time of harvest


title: Bone marrow-derived macrophage - CTR_G2M_rep2

tag: treatment/cell cycle


title: L_302_00: COVID19 patient 302 day 0

tag: subject

tag: time

value: Male

value: Moderate Symptomatic


title: Bone marrow-derived macrophage - CTR_S_rep2


title: L_119_05: COVID19 patient 119 day 5

value: day 5

tag: Sex

tag: symptom severity


title: genomic DNA from ASD patient (ID: 9358)

description: whole blood of ASD patients


title: WT (2) RDM logarithmic rep 1 - IPOD RNA-pol ChIP

value: logarithmic phase


title: WT (2) RDM logarithmic rep 2 - IPOD RNA-pol ChIP

value: wild type


title: Bone marrow-derived macrophage - CTR_G1_rep2

tag: cell type


title: genomic DNA from ASD patient (ID: 9339)

description: whole blood of ASD patients

tag: age


title: L_004_00: COVID19 patient 004 day 0

value: day 0

value: Female

tag: viral shedding

tag: tissue


title: L_337_00: COVID19 patient 337 day 0

tag: disease state


title: genomic DNA from ASD patient (ID: 9347)

description: whole blood of ASD patients

tag: gender

tag: cars


title: genomic DNA from ASD patient (ID: 9350)

description: whole blood of ASD patients

tag: iq

tag: snap


title: Bone marrow-derived macrophage - IFNG_G2M_rep1

tag: strain

tag: genotype

value: Bone marrow

value: Bone marrow-derived macrophage


title: L_312_05: COVID19 patient 312 day 5

value: Whole blood


title: WT RDM logarithmic rep 2 - IPOD RNA-pol ChIP

tag: media

tag: time of harvest


title: WT RDM logarithmic rep 3 - IPOD RNA-pol ChIP


title: genomic DNA from ASD patient (ID: 9435)

description: whole blood of ASD patients

value: Autism Spectrum Disorder


title: genomic DNA from ASD patient (ID: 9420)

description: whole blood of ASD patients


title: L_286_00: COVID19 patient 286 day 0

tag: subject


title: Bone marrow-derived macrophage - IFNG_S_rep1

tag: treatment/cell cycle


title: WT RDM logarithmic rep 1 - IPOD RNA-pol ChIP


title: Bone marrow-derived macrophage - IFNG_G1_rep1


title: ΔstpaΔhns RDM logarithmic rep 4 - IPOD interphase

value: {delta}stpa{delta}hns


title: Bone marrow-derived macrophage - IL4_G2M_rep1


title: ΔstpaΔhns RDM logarithmic rep 3 - IPOD interphase

value: M9 Rich Defined Media (RDM) + glucose


title: L_252_05: COVID19 patient 252 day 5

tag: time

tag: Sex


title: Bone marrow-derived macrophage - IL4_S_rep1

tag: cell type


title: genomic DNA from ASD patient (ID: 8355)

description: whole blood of ASD patients

tag: age


title: genomic DNA from ASD patient (ID: 9293)

description: whole blood of ASD patients


title: Bone marrow-derived macrophage - IL4_G1_rep1


title: genomic DNA from ASD patient (ID: 9335)

description: whole blood of ASD patients


title: L_128_05: COVID19 patient 128 day 5

tag: symptom severity

tag: viral shedding


title: L_174_00: COVID19 patient 174 day 0

tag: disease state

value: Severe

tag: tissue


title: L_126_05: COVID19 patient 126 day 5


title: ΔstpaΔhns RDM logarithmic rep 2 - IPOD interphase


title: ΔstpaΔhns RDM logarithmic rep 1 - IPOD interphase


title: L_183_00: COVID19 patient 183 day 0


title: genomic DNA from ASD patient (ID: 9342)

description: whole blood of ASD patients

tag: gender

value: male

tag: cars


title: Bone marrow-derived macrophage - CTR_G2M_rep1


title: genomic DNA from ASD patient (ID: 9303)

description: whole blood of ASD patients

tag: iq

tag: snap


title: L_233_00: COVID19 patient 233 day 0


title: Bone marrow-derived macrophage - CTR_G1_rep1

tag: strain

tag: genotype


title: Bone marrow-derived macrophage - CTR_S_rep1


title: Bone marrow-derived macrophage - RNAPIIpS2_preIL4_IFNG_rep2

data_processing:
Reads were trimmed for quality and adapter sequences using fastp.
Trimmed reads were aligned to the mm10 reference genome using hisat2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized bigwig files; peak files

extract_protocol:
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.

value: Bone marrow-derived macrophage (BMDM)

tag: treatment

value: IFNG

tag: chip antibody

value: Anti-RNA polymerase II antibody (Abcam, ab5095, GR3279013-1)


title: genomic DNA from ASD patient (ID: 9296)

description: whole blood of ASD patients


title: 8h_34 degrees

city: Barcelona

first: Jose

last: Ayte

address: Doctor Aiguader 88

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Sequenced reads were trimmed for adaptor sequence by using Tagdust
Filtered reads were mapped to the reference genome by using Tophat splice mapper (v2.0.5) using the annotation defined in Ensembl database (version ASM294 v1.15)
Mapped reads were filtered removing the multi-mapped ones by using samtools
Introns were only taken into consideration if the sum of spliced and unspliced reads at the conditions 25°C and 34°C was bigger than 50. In order to avoid the division by 0, all read numbers that were equal to 0 were replaced with 1 read.
To determine the splicing efficiency, the ratio of spliced over unspliced reads at the conditions 25°C and 34°C was determined
Genome_build: ASM294v1

organism: Schizosaccharomyces pombe

source_name: pat1_as2 prp2-1 strain in meiosis I, at restrictive temperature (34 degrees)

growth_protocol: The strain was grown in Minimal Media at permissive temperature, arrested in G1 by nitrogen deprivation and the synchronous meiosis was chemically induced.  At the onset of meiosis I, the culture was splitted in two, one was left at permisive temperature and the other half was shifted to restrictive temperature.  Samples were collected after 1 hour.

extract_protocol:
RNA was isolated using standard protocols for S pombe
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mutation

tag: time from induction

value: Synchronous meiosis, collected at the onset of meiosis I after 1 hour at restrictive temperature


title: L_274_00: COVID19 patient 274 day 0

tag: subject

tag: time

tag: Sex

value: Moderate Symptomatic


title: Δstpa RDM logarithmic rep 2 - IPOD interphase

value: {delta}stpa

tag: media

tag: time of harvest

value: logarithmic phase


title: ihfA::Kan infB::Chlor RDM logarithmic rep 2 - IPOD interphase

value: ihfA::Kan infB::Chlor


title: genomic DNA from ASD patient (ID: 9301 or 6322)

description: whole blood of ASD patients

tag: age

tag: disease state


title: 8h_25 degrees

source_name: pat1_as2 prp2-1 strain in meiosis I, at permisive temperature (25 degrees)

value: Synchronous meiosis, collected at the onset of meiosis I


title: Δstpa RDM logarithmic rep 1 - IPOD interphase


title: genomic DNA from ASD patient (ID: 9319)

description: whole blood of ASD patients

tag: gender

tag: tissue


title: genomic DNA from ASD patient (ID: 9299)

description: whole blood of ASD patients

value: female

tag: cars

tag: iq


title: genomic DNA from ASD patient (ID: 9288)

description: whole blood of ASD patients

tag: snap


title: ihfA::Kan infB::Chlor RDM logarithmic rep 1 - IPOD interphase

tag: strain

tag: genotype


title: L_314_05: COVID19 patient 314 day 5

value: day 5

value: Female

tag: symptom severity

tag: viral shedding


title: L_325_00: COVID19 patient 325 day 0

value: day 0

value: Male

value: Whole blood


title: genomic DNA from ASD patient (ID: 9314 or 9041)

description: whole blood of ASD patients

value: Autism Spectrum Disorder


title: Bone marrow-derived macrophage - RNAPIIpS2_preIL4_rep2

value: wild type

value: Bone marrow

tag: cell type

tag: treatment

tag: chip antibody


title: ΔhupA hupB::kan RDM logarithmic rep 2 - IPOD interphase

value: {delta}hupA hupB::kan

value: M9 Rich Defined Media (RDM) + glucose


title: genomic DNA from ASD patient (ID: 9322)

description: whole blood of ASD patients

value: male


title: Bone marrow-derived macrophage - RNAPIIpS2_preIL4_IFNG_rep1

value: Bone marrow-derived macrophage (BMDM)

value: IFNG

value: Anti-RNA polymerase II antibody (Abcam, ab5095, GR3279013-1)


title: ΔhupA hupB::kan RDM logarithmic rep 1 - IPOD interphase

value: logarithmic phase


title: Δhns RDM logarithmic rep 4 - IPOD interphase

value: {delta}hns


title: Bone marrow-derived macrophage - RNAPIIpS2_preIL4_rep1


title: genomic DNA from ASD patient (ID: 9308)

description: whole blood of ASD patients


title: Bone marrow-derived macrophage - RNAPIIpS2_IFNG_rep2


title: L_119_00: COVID19 patient 119 day 0

tag: subject

tag: time

tag: Sex

value: Moderate Symptomatic


title: L_285_00: COVID19 patient 285 day 0

tag: age


title: L_195_05: COVID19 patient 195 day 5

tag: disease state

value: day 5


title: L_345_00: COVID19 patient 345 day 0

value: Female


title: Δhns RDM logarithmic rep 3 - IPOD interphase

tag: media

tag: time of harvest


title: Bone marrow-derived macrophage - RNAPIIpS2_IFNG_rep1

tag: tissue


title: Δhns RDM logarithmic rep 2 - IPOD interphase


title: Bone marrow-derived macrophage - RNAPIIpS2_IL4_rep2


title: L_256_00: COVID19 patient 256 day 0

value: day 0


title: Δhns RDM logarithmic rep 1 - IPOD interphase


title: Δhfq RDM logarithmic rep 3 - IPOD interphase

value: {delta}hfq


title: KO_input

city: Hangzhou

first: Jia

last: Xiong

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Macrophage colony-stimulating factor (M-CSF) treated the bone marrow cells for 7 days

data_processing:
Library strategy: m6A-seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeMus musculus (Version: v101).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: mm10
Supplementary_files_format_and_content: Indentification and comparison of different m6A peak between indicated groups:  WT_IPVSWT_input_peak.txt;   KO_IPVSKO_input_peak.txt;   KOVSWT_diffPeak_result.txt;  KOVSWT_diffPeak_Gene_differential_expression.txt

source_name: bone-marrow-derived macrophages

growth_protocol: M-CSF-inudced BMDM in vitro

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630).
Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: bone-marrow-derived macrophages

value: LysM-cre, Mettl3fl/fl


title: L_145_00: COVID19 patient 145 day 0

value: Male

value: Whole blood


title: WT_input


title: L_312_00: COVID19 patient 312 day 0


title: HCT116-shRFWD3_03

type: RNA

city: Chongqing

first: Fenghua

last: Xu

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing

institute: Army Medical Center of PLA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeview human PathArrayTM.

scan_protocol: Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing: The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.

label: 3’ IVT Biotin Label

source_name: HCT-116 cells infected with  shRFWD3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in 1640 medium with 10% FBS, placing in a 37°C incubator containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HCT-116 cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or shRFWD3 lentivirus, culturing in 1640 medium with 10% FBS in a 6-well dish with 2×105 cells per well.

tag: cell

value: HCT-116 cells

tag: lentivirus


title: Δhfq RDM logarithmic rep 2 - IPOD interphase

tag: strain

value: M9 Rich Defined Media (RDM) + glucose


title: Bone marrow-derived macrophage - RNAPIIpS2_CTR_rep2

tag: genotype

value: wild type

value: Bone marrow

value: CTR


title: HCT116-shRFWD3_02

source_name: HCT-116 cells infected with shRFWD3


title: KO_IP


title: HCT116-shRFWD3_01


title: genomic DNA from ASD patient (ID: 9306 or 8088)

description: whole blood of ASD patients

tag: gender

value: female

value: Autism Spectrum Disorder

tag: cars

tag: iq

tag: snap


title: Bone marrow-derived macrophage - RNAPIIpS2_CTR_rep1

tag: cell type

value: Bone marrow-derived macrophage (BMDM)

tag: treatment

tag: chip antibody

value: Anti-RNA polymerase II antibody (Abcam, ab5095, GR3279013-1)


title: WT_IP


title: L_346_00: COVID19 patient 346 day 0

tag: subject

tag: time

tag: Sex

tag: symptom severity

value: Moderate Symptomatic

tag: viral shedding


title: HCT116-shCtrl_02

source_name: HCT-116 cells infected with shCtrl

value: shCtrl


title: HCT116-shCtrl_03


title: J2

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

description:
Undifferentiated Jejunum Control
Line - J2

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids/colonoids were maintained CMGF+ and differentiated according to manuscript

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids on transwells were  treated with various infections or mocks for 6 or 24 hours

tag: segment

value: Jejunum

tag: format

tag: substrate

value: Matrigel

tag: treatment time


title: Δhfq RDM logarithmic rep 1 - IPOD interphase

tag: strain

tag: genotype

value: {delta}hfq

tag: media

tag: time of harvest

value: logarithmic phase


title: L_285_05: COVID19 patient 285 day 5

tag: disease state

value: day 5

value: Male

tag: age

tag: tissue


title: L_115_00: COVID19 patient 115 day 0

value: day 0

value: Whole blood


title: Bone marrow-derived macrophage - RNAPIIpS2_IL4_rep1

value: wild type

tag: cell type

tag: treatment

tag: chip antibody


title: J2_mock_bac_6h

description:
Differentiated Jejunum treated w/ Mock-bac
Line - J2

value: Transwell

value: Collagen IV

value: 6 Hours


title: skin stromal cells, Ms_PBS

first: Ian

middle: Chen

last: Boothby

address: 513 Parnassus Ave, HSW-1201B

data_processing:
Alignment, generation of gene-barcode matrices, and filtering were performed using the cellranger count function in Cellranger 2.1 with default parameters
Genome_build: mm10 (mouse); GrCh38 (human)
Supplementary_files_format_and_content: h5 files for each sample containing raw gene count-barcode matrices

source_name: Skin stromal cells, P22 control

extract_protocol:
10X Chromium 3'-v2 chemistry
cDNA libraries were prepared for sequencing using standard Illumina protocols
single cell RNAseq (10X Chromium 3')

treatment_protocol: skin was finely minced and digested in collagenase XI, Dnase, and hyaluronidase for 45 minutes with shaking at 37C; then filtered, washed in media, and run on a FACS Aria to sort stromal cells

value: 22 days

tag: Sex

value: M

value: skin

tag: site

value: back skin

value: live CD45- CD31- EpCAM- stromal cells

value: PBS


title: Δfis RDM logarithmic rep 1 - IPOD interphase

value: {delta}fis

value: M9 Rich Defined Media (RDM) + glucose


title: WT RDM deep stationary rep 2 - IPOD RNA-pol ChIP

value: deep stationary phase


title: genomic DNA from ASD patient (ID: 9337)

description: whole blood of ASD patients

tag: gender

value: female

value: Autism Spectrum Disorder

tag: cars

tag: iq

tag: snap


title: Δfis RDM logarithmic rep 2 - IPOD interphase

value: logarithmic phase


title: genomic DNA from ASD patient (ID: 9317)

description: whole blood of ASD patients

value: male

value: Whole blood


title: J11

description:
Undifferentiated Jejunum Control
Line - J11

tag: segment

value: Jejunum

tag: format

tag: substrate

value: Matrigel

tag: treatment time


title: L_174_05: COVID19 patient 174 day 5

tag: subject

tag: time

value: day 5

value: Female

tag: symptom severity

value: Severe

tag: viral shedding


title: skin stromal cells, Ms_DT

source_name: Skin stromal cells, Treg-depleted

tag: age

value: 22 days

value: M

tag: tissue

value: skin

tag: cell type

value: DT mediated depletion of Treg cells

tag: strain

tag: genotype

tag: disease state


title: J2_mock_24h

description:
Differentiated Jejunum treated w/ Mock
Line - J2

value: Transwell

value: Collagen IV

value: 24 Hours


title: L_217_00: COVID19 patient 217 day 0

value: day 0

tag: Sex

value: Moderate Symptomatic


title: J2_mock_6h

value: 6 Hours


title: L_316_05: COVID19 patient 316 day 5

value: Male


title: J2_Ito_6h

description:
Differentiated Jejunum treated w/ Ito
Line - J2


title: Liver from treated old mice_rep3

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq and ATAC-seq  reads with Trimmomatic (V0.39).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1). Reads from ATAC-seq were aligned to mm10 using Bowtie2 (V2.3.5.1).
For RNA-seq, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene. For ATAC-seq, MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks.
Genome_build: mm10

source_name: Liver from 20-21 month old mice

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer’s instructions.
Libraries of RNA-seq and ATAC-seq were prepared for sequencing using standard Illumina protocols

value: liver

tag: treatment


title: L_164_05: COVID19 patient 164 day 5

value: Whole blood


title: Δdps RDM deep stationary rep 2 - IPOD interphase

value: {delta}dps

tag: media

value: M9 Rich Defined Media (RDM) + glucose

tag: time of harvest

value: deep stationary phase


title: Liver from treated old mice_rep2


title: J2_Ito_24h

tag: segment

value: Jejunum

tag: format


title: Δdps RDM logarithmic rep 2 - IPOD interphase

value: logarithmic phase


title: Δdps RDM deep stationary rep 1 - IPOD interphase


title: Liver from treated old mice_rep1


title: Liver from treated old mice_rep4


title: L_120_00: COVID19 patient 120 day 0

value: Female


title: J2_bac_6h

description:
Differentiated Jejunum treated w/ bac
Line - J2

tag: substrate

tag: treatment time


title: Δdps RDM logarithmic rep 1 - IPOD interphase


title: L_295_05: COVID19 patient 295 day 5

tag: subject

tag: time

value: day 5


title: Δdps RDM deep stationary rep 3 - IPOD interphase


title: Liver from control old mice_rep3

value: DMSO


title: J11_mock_bac_6h

description:
Differentiated Jejunum treated w/ Mock-bac
Line - J11

value: Transwell


title: L_128_00: COVID19 patient 128 day 0

tag: symptom severity

tag: viral shedding


title: WT RDM deep stationary rep 2 - IPOD interphase

value: wild type


title: J11_mock_6h

description:
Differentiated Jejunum treated w/ Mock
Line - J11

value: Collagen IV


title: Liver from control old mice_rep2

tag: tissue


title: WT RDM deep stationary rep 3 - IPOD interphase


title: WT RDM deep stationary rep 1 - IPOD interphase


title: L_154_00: COVID19 patient 154 day 0

value: day 0

tag: age


title: J11_mock_24h

value: 24 Hours


title: L_287_05: COVID19 patient 287 day 5

value: Asymptomatic


title: Liver from control old mice_rep4

tag: strain


title: WT Minimal logarithmic rep 2 - IPOD interphase

tag: genotype

value: M9 Minimal Media + glucose


title: J11_Ito_6h

description:
Differentiated Jejunum treated w/ Ito
Line - J11

value: 6 Hours


title: Kidney from treated old mice_rep4

source_name: kidney from 20-21 month old mice

value: kidney


title: WT Minimal logarithmic rep 1 - IPOD interphase


title: Kidney from treated old mice_rep2


title: L_004_05: COVID19 patient 004 day 5

tag: disease state

value: Moderate Symptomatic

value: Whole blood


title: L_218_00: COVID19 patient 218 day 0

tag: Sex

value: Male


title: J11_bac_6h

description:
Differentiated Jejunum treated w/ bac
Line - J11

value: Jejunum


title: L_141_00: COVID19 patient 141 day 0


title: WT (2) RDM logarithmic rep 1 - IPOD interphase

value: M9 Rich Defined Media (RDM) + glucose

value: logarithmic phase


title: I109_mock_6h

description:
Differentiated Ileum treated w/ Mock
Line - I109

value: Ileum


title: HCT116-shCtrl_01

tag: cell

value: HCT-116 cells

tag: lentivirus

value: shCtrl


title: WT RDM logarithmic rep 3 - IPOD interphase

value: wild type

tag: media

tag: time of harvest


title: Liver from control old mice_rep1

value: liver

tag: treatment

value: DMSO


title: I109_Ito_6h

description:
Differentiated Ileum treated w/ Ito
Line - I109

tag: segment

tag: format

value: Transwell

tag: substrate

value: Collagen IV


title: Kidney from treated old mice_rep3


title: WT (2) RDM logarithmic rep 2 - IPOD interphase


title: L_275_05: COVID19 patient 275 day 5

tag: subject

tag: time

value: day 5

value: Female


title: Kidney from control old mice_rep4

value: kidney


title: I109_mock_bac_6h

description:
Differentiated Ileum treated w/ Mock-bac
Line - I109

tag: treatment time

value: 6 Hours


title: L_196_05: COVID19 patient 196 day 5

tag: symptom severity

value: Moderate Symptomatic

tag: viral shedding

tag: tissue

value: Whole blood


title: I109_bac_6h

description:
Differentiated Ileum treated w/ bac
Line - I109


title: Kidney from control old mice_rep1

tag: strain


title: Kidney from control old mice_rep2


title: WT RDM logarithmic rep 2 - IPOD interphase

tag: genotype


title: I109_Ito_24h

value: 24 Hours


title: ΔstpaΔhns RDM logarithmic rep 4 - IPOD input

value: {delta}stpa{delta}hns

value: M9 Rich Defined Media (RDM) + glucose


title: Kidney from control old mice_rep3


title: WT RDM logarithmic rep 1 - IPOD interphase

value: logarithmic phase


title: P9 mice fibroblasts treated mRNA_rep3

source_name: P9 mice skin fibroblasts

value: skin fibroblast


title: ΔstpaΔhns RDM logarithmic rep 3 - IPOD input


title: L_253_05: COVID19 patient 253 day 5

tag: disease state

tag: Sex

tag: age


title: I103_mock_bac_6h

description:
Differentiated Ileum treated w/ Mock-bac
Line - I103

value: Ileum


title: L_273_00: COVID19 patient 273 day 0

value: day 0


title: I103_mock_6h

description:
Differentiated Ileum treated w/ Mock
Line - I103


title: I103_Ito_6h

description:
Differentiated Ileum treated w/ Ito
Line - I103


title: Kidney from treated old mice_rep1


title: L_120_05: COVID19 patient 120 day 5


title: ΔstpaΔhns RDM logarithmic rep 2 - IPOD input

tag: media


title: L_221_05: COVID19 patient 221 day 5


title: L_162_00: COVID19 patient 162 day 0

value: Male


title: P9 mice fibroblasts treated mRNA_rep2


title: P9 mice fibroblasts treated mRNA_rep1


title: ΔstpaΔhns RDM logarithmic rep 1 - IPOD input

tag: time of harvest


title: I103_Ito_24h


title: Δstpa RDM logarithmic rep 2 - IPOD input

value: {delta}stpa


title: P9 mice fibroblasts control mRNA_rep3

tag: treatment

value: DMSO


title: L_134_00: COVID19 patient 134 day 0


title: I103_bac_6h

description:
Differentiated Ileum treated w/ bac
Line - I103

tag: segment

value: Transwell

value: Collagen IV


title: L_314_00: COVID19 patient 314 day 0

value: Female


title: P9 mice fibroblasts control mRNA_rep2


title: D109_mock_6h

description:
Differentiated Duodenum treated w/ Mock
Line - D109

value: Duodenum

tag: format


title: P9 mice fibroblasts control mRNA_rep1


title: L_283_00: COVID19 patient 283 day 0


title: Old liver mRNA_rep3

source_name: liver from old(23-25 month old) mice

value: liver

value: untreated


title: D109_Ito_6h

description:
Differentiated Duodenum treated w/ Ito
Line - D109

tag: substrate

value: 6 Hours


title: Old liver mRNA_rep4


title: ihfA::Kan infB::Chlor RDM logarithmic rep 2 - IPOD input

value: ihfA::Kan infB::Chlor


title: ΔhupA hupB::kan RDM logarithmic rep 1 - IPOD input

value: {delta}hupA hupB::kan


title: L_205_00: COVID19 patient 205 day 0

tag: subject

value: Moderate Symptomatic

value: Whole blood


title: ihfA::Kan infB::Chlor RDM logarithmic rep 1 - IPOD input

value: M9 Rich Defined Media (RDM) + glucose

value: logarithmic phase


title: Old liver mRNA_rep2


title: D109_Ito_24h

value: 24 Hours


title: L_158_05: COVID19 patient 158 day 5

tag: time

value: day 5


title: Δstpa RDM logarithmic rep 1 - IPOD input

value: {delta}stpa


title: ΔhupA hupB::kan RDM logarithmic rep 2 - IPOD input


title: Old liver mRNA_rep1


title: Δhns RDM logarithmic rep 4 - IPOD input

value: {delta}hns


title: D109_bac_6h

description:
Differentiated Duodenum treated w/ bac
Line - D109

value: Transwell

tag: treatment time


title: L_284_00: COVID19 patient 284 day 0

value: day 0

tag: symptom severity


title: D103_mock_bac_6h

description:
Differentiated Duodenum treated w/ Mock-bac
Line - D103

value: Collagen IV


title: L_217_05: COVID19 patient 217 day 5

value: Female

tag: viral shedding


title: Young liver mRNA_rep4

source_name: liver from young(2.5 month old) mice

tag: tissue

value: liver


title: Δhns RDM logarithmic rep 3 - IPOD input

tag: strain


title: D109_mock_bac_6h

description:
Differentiated Duodenum treated w/ Mock-bac
Line - D109

value: Duodenum


title: L_273_05: COVID19 patient 273 day 5


title: Young liver mRNA_rep3

value: untreated


title: D103_mock_6h

description:
Differentiated Duodenum treated w/ Mock
Line - D103

value: 6 Hours


title: L_326_05: COVID19 patient 326 day 5

value: Male


title: D109_mock_24h


title: Δhns RDM logarithmic rep 2 - IPOD input

tag: genotype


title: Δhns RDM logarithmic rep 1 - IPOD input


title: Young liver mRNA_rep1


title: L_320_05: COVID19 patient 320 day 5

tag: disease state

value: Moderate Symptomatic


title: L_266_05: COVID19 patient 266 day 5

tag: Sex

value: Whole blood


title: Δhfq RDM logarithmic rep 3 - IPOD input

value: {delta}hfq

value: M9 Rich Defined Media (RDM) + glucose


title: L_326_00: COVID19 patient 326 day 0

tag: age


title: Old kidney mRNA_rep4

source_name: kidney from old(23-25 month old) mice

value: kidney


title: D103_Ito_24h

description:
Differentiated Duodenum treated w/ Ito
Line - D103

value: 24 Hours


title: L_134_05: COVID19 patient 134 day 5

value: day 5


title: D103_mock_24h


title: Δhfq RDM logarithmic rep 1 - IPOD input

source_name: Culture lysate

tag: media

value: logarithmic phase


title: Δhfq RDM logarithmic rep 2 - IPOD input

tag: time of harvest


title: L_257_05: COVID19 patient 257 day 5

source_name: Whole blood


title: D103_bac_6h

description:
Differentiated Duodenum treated w/ bac
Line - D103

value: Transwell


title: C109_mock_6h

description:
Differentiated Colon treated w/ Mock
Line - C109

value: Colon


title: Old kidney mRNA_rep3

tag: treatment


title: Old kidney mRNA_rep2


title: Old kidney mRNA_rep1


title: L_333_00: COVID19 patient 333 day 0

value: day 0


title: Young liver mRNA_rep2


title: Δfis RDM logarithmic rep 2 - IPOD input

value: {delta}fis


title: C109_mock_24h

tag: segment

value: Collagen IV


title: C109_mock_bac_6h

description:
Differentiated Colon treated w/ Mock-bac
Line - C109

tag: format


title: Young kidney mRNA_rep4

source_name: kidney from young(2.5 month old) mice


title: Δfis RDM logarithmic rep 1 - IPOD input


title: L_284_05: COVID19 patient 284 day 5

value: Female


title: C109_Ito_6h

description:
Differentiated Colon treated w/ Ito
Line - C109

tag: substrate


title: L_345_05: COVID19 patient 345 day 5

tag: subject


title: C109_bac_6h

description:
Differentiated Colon treated w/ bac
Line - C109


title: C109_Ito_24h


title: Δdps RDM deep stationary rep 3 - IPOD input

value: {delta}dps

value: deep stationary phase


title: C103_mock_bac_6h

description:
Differentiated Colon treated w/ Mock-bac
Line - C103

value: 6 Hours


title: L_315_00: COVID19 patient 315 day 0

tag: time

value: Moderate Symptomatic


title: Young kidney mRNA_rep1

value: untreated


title: Young kidney mRNA_rep2


title: Δdps RDM deep stationary rep 2 - IPOD input


title: L_306_05: COVID19 patient 306 day 5

value: Male

value: Whole blood


title: C103_mock_6h

description:
Differentiated Colon treated w/ Mock
Line - C103

tag: treatment time


title: Δdps RDM logarithmic rep 1 - IPOD input

value: M9 Rich Defined Media (RDM) + glucose


title: Δdps RDM logarithmic rep 2 - IPOD input


title: Atf3_nt_mRNA_rep3

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq and ATAC-seq  reads with Trimmomatic (V0.39) and from the RRBS reads with Trim Galore (V0.6.6).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1). Reads from ATAC-seq were aligned to mm10 using Bowtie2 (V2.3.5.1). Reads from RRBS were aligned to mm10 using Bismark (v0.22.3).
For RNA-seq, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene. For ATAC-seq, MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks. For RRBS, DSS (V2.34.0) was used to identify DMRs and DMSs.
Genome_build: mm10

extract_protocol:
Total DNA was extracted from cells using the MasterPureTM Complete DNA & RNA Purification Kit (Cat.No. MC85200). TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer’s instructions.
Libraries of RNA-seq, ATAC-seq and RRBS were prepared for sequencing using standard Illumina protocols

tag: tissue/cell type

value: skin fibroblast

value: Atf3 knockdown control


title: L_248_00: COVID19 patient 248 day 0

tag: symptom severity

tag: viral shedding


title: Atf3_nt_mRNA_rep2

tag: strain


title: WT RDM deep stationary rep 3 - IPOD input

tag: genotype

value: wild type


title: L_301_00: COVID19 patient 301 day 0

tag: disease state

value: Severe

tag: tissue


title: Young kidney mRNA_rep3

value: kidney


title: WT RDM deep stationary rep 2 - IPOD input


title: C103_Ito_6h

description:
Differentiated Colon treated w/ Ito
Line - C103

value: Colon

value: Transwell


title: Atf3_nt_mRNA_rep1


title: L_148_00: COVID19 patient 148 day 0

value: day 0

tag: Sex

tag: age

value: Asymptomatic


title: L_195_00: COVID19 patient 195 day 0


title: Δdps RDM deep stationary rep 1 - IPOD input

value: {delta}dps

tag: media

tag: time of harvest


title: L_294_00: COVID19 patient 294 day 0

value: Female


title: C103_Ito_24h

tag: segment

value: Collagen IV

value: 24 Hours


title: WT Minimal logarithmic rep 2 - IPOD input

value: M9 Minimal Media + glucose

value: logarithmic phase


title: Atf3_sh6_mRNA_rep3

tag: treatment

value: Atf3 knockdown with shRNA


title: Atf3_sh6_mRNA_rep2


title: L_012_00: COVID19 patient 012 day 0

value: Moderate Symptomatic

value: Whole blood


title: WT RDM deep stationary rep 1 - IPOD input

value: M9 Rich Defined Media (RDM) + glucose

value: deep stationary phase


title: WT Minimal logarithmic rep 1 - IPOD input

value: wild type


title: L_286_05: COVID19 patient 286 day 5

value: day 5


title: C103_bac_6h

description:
Differentiated Colon treated w/ bac
Line - C103

value: Colon

tag: format

tag: substrate

value: 6 Hours


title: Re-adapted population: After adapted 46 days with CCNE1 overexpression, allowed to grow w/x induction for 17 days [t4_3]

city: Chapel Hill

first: Jeanette

last: Cook

state: North Carolina

address: 112 Founders Ridge Dr.

department: Biochemistry and Biophysics

institute: University of North Carolina at Chapel Hill

data_processing:
Kallisto (version X) was used, with 100 bootstraps, to estimate transcript abundance and to generate transcripts per million (TPM) tables.
Kallisto output files were imported into a counts matrix for DESeq2 analysis.
Pairwise comparisons between timepoints were performed with DESeq2 with 3 replicates per time point.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file containing TPMs for each sample replicate and log2 fold change (L2FC) values and adjusted P values for each pairwise comparison.

source_name: RPE1-hTERT cells with pINDUCER20-CCNE1 retrovirus

growth_protocol: A pINDUCER20 doxycycline-inducible CCNE1 retrovirus was transduced into RPE1-hTERT cells. Cells were passaged every 3 days and cultured in DMEM with l-glut and pen/strep, plus 10% FBS with 20 ng/ml doxycycline as indicated.

extract_protocol:
Lysates were generated and RNA was extracted from cells using Quick-RNA Miniprep Kit (Zymo Research, Irvine, CA, USA) with chloroform extraction. RNA was quantified with the Qubit RNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA)
Libraries for each sample were prepared, at the same time, using KAPA Hyperprep mRNA Library Kit (Roche) and Illumina adapters (New England Biolabs) starting with 1 µg RNA for each sample.

treatment_protocol: 20 ng/ml dox was added to cultures every 3 days. 10% of cells were passaged to new plate and allowed to grow 72h at 37C, 5% CO2

tag: cell line

value: RPE1-hTERT cells

tag: plasmid construct

value: after growing in dox for 46 days cells were cultured without dox for 17 days


title: Atf3_sh6_mRNA_rep1

tag: tissue/cell type

value: skin fibroblast


title: WT (2) RDM logarithmic rep 2 - IPOD input


title: Re-adapted population: After adapted 42 days with CCNE1 overexpression, allowed to grow w/x induction for 46 days [t4_2]

value: after growing in dox for 42 days cells were cultured without dox for 46 days


title: Atf3_sh5_mRNA_rep3


title: L_256_05: COVID19 patient 256 day 5

tag: subject

tag: time

value: Male

tag: symptom severity


title: WT (2) RDM logarithmic rep 1 - IPOD input

tag: strain

tag: genotype


title: C103_mock_24h

value: Transwell

value: Collagen IV

tag: treatment time

value: 24 Hours


title: L_225_00: COVID19 patient 225 day 0

tag: disease state

value: day 0

tag: Sex

tag: viral shedding

tag: tissue


title: WT RDM logarithmic rep 3 - IPOD input

tag: media

tag: time of harvest

value: logarithmic phase


title: Re-adapted population: After adapted 31 days with CCNE1 overexpression, allowed to grow w/x induction for 18 days [t4_1]

tag: treatment

value: after growing in dox for 31 days cells were cultured without dox for 18 days


title: Adapted population: Day 51 [t3_3]

value: treated with 20 ng/ml dox for 51 days


title: Atf3_sh5_mRNA_rep1

value: Atf3 knockdown with shRNA


title: Tead1_nt_mRNA_rep3

value: Tead1 knockdown control


title: Adapted population: Day 41 [t3_2]

value: treated with 20 ng/ml dox for 41 days


title: L_302_05: COVID19 patient 302 day 5

value: day 5

tag: age

value: Moderate Symptomatic

value: Whole blood


title: WT RDM logarithmic rep 2 - IPOD input

value: wild type

value: M9 Rich Defined Media (RDM) + glucose


title: L_108_00: COVID19 patient 108 day 0


title: WT RDM logarithmic rep 1 - IPOD input


title: Tead1_nt_mRNA_rep2

value: skin fibroblast


title: Adapted population: Day 39 [t3_1]

tag: cell line

value: RPE1-hTERT cells

value: treated with 20 ng/ml dox for 39 days


title: L_329_00: COVID19 patient 329 day 0

value: Male

value: Severe


title: KO5rest

city: Columbus

first: Mireia

last: Guerau

state: OH

address: 460 Medical Center Drive, Rm 329

institute: The Ohio State University

data_processing:
fastq files were aligned to the GRCm38.p3 assembly of the Mus musculus reference from NCBI using version 2.6.0c of the RNA-Seq aligner STAR
Features were identified from the GFF file that came with the assembly from Gencode (Release M19)
Feature coverage counts were calculated using featureCounts
Differentially expressed features were calculated using DESeq2
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: *.cov including raw counts and DESeq produced normalized values

source_name: CD4 T-cells isolated from spleen and lymph nodes

growth_protocol: 5x10^6 whole CD4 T cells from murine spleens and lymph nodes are lysed for RNA

extract_protocol:
RNA was isolated using Direct-zol RNA miniprep kit from Zymo research as per manufacturer's instructions.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol. rRNAremoval was done using Ribo-zero Human/Mouse/Rat Gold kit

tag: background strain

tag: cell type

value: CD4 T-cells

value: iCD4-PRMT5 delta/delta

value: anti-CD3/CD28 treatment for 48hr


title: Tead1_nt_mRNA_rep1

tag: tissue/cell type


title: L_200_00: COVID19 patient 200 day 0

tag: subject

tag: time

value: day 0


title: L_210_00: COVID19 patient 210 day 0

value: Female

tag: symptom severity


title: KO1rest

tag: genotype


title: “Crisis” population: Day 18 [t2_2]

tag: plasmid construct

value: treated with 20 ng/ml dox for 18 days


title: KO4rest


title: “Crisis” population: Day 18 [t2_3]


title: “Crisis” population: Day 15 [t2_1]

value: treated with 20 ng/ml dox for 15 days


title: Atf3_sh5_mRNA_rep2

tag: strain

value: Atf3 knockdown with shRNA


title: Tead1_sh4_mRNA_rep2

value: Tead1 knockdown with shRNA


title: Tead1_sh4_mRNA_rep3


title: Tead1_sh4_mRNA_rep1


title: Acute population: Day 2 (“acute” CCNE1 overexpression, 48h) [t1_3]

value: treated with 20 ng/ml dox for 48h


title: L_133_00: COVID19 patient 133 day 0

tag: disease state

tag: Sex

value: Moderate Symptomatic

value: Whole blood


title: L_150_00: COVID19 patient 150 day 0

value: Asymptomatic

tag: viral shedding

tag: tissue


title: Tead1_sh3_mRNA_rep3

value: skin fibroblast


title: Acute population: Day 2 (“acute” CCNE1 overexpression, 48h) [t1_2]

value: RPE1-hTERT cells


title: WT1rest


title: Acute population: Day 2 (“acute” CCNE1 overexpression, 48h) [t1_1]


title: L_282_00: COVID19 patient 282 day 0


title: Tead1_sh3_mRNA_rep2


title: Tead1_sh3_mRNA_rep1


title: Bone marrow-derived macrophage - preIL4_IFNG [scATAC-seq]

data_processing:
Reads were filtered, trimmed, and aligned to the mm10 reference genome using the 10X cellranger atac-count pipeline.
Fragments files were loaded into ArchR for additional processing and analysis.
Separate ArchR projects were created for the three sample sets (priming, polarization, and repolarization) and additionally for each individual sample.
Doublets were identified and removed using ArchR’s default doublet simulation and calling procedures.
Barcodes were removed that had an enrichment of Tn5 insertions in transcription start sites (TSS enrichment) less than 4 or less than 1000 fragments.
Genome_build: mm10
Supplementary_files_format_and_content: Fragment files (.tsv.gz); bigWig (.bw)

extract_protocol:
10X Genomics Single Cell ATAC-seq Library & Gel Bead Kit V2
After cytokine treatments, macrophages were subjected to nuclei isolation according to the protocol of the manufacturer. Nuclei were counted and ~20,000 were submitted for tagmentation. After tagmentation, nuclei were loaded for capture using the 10x Chromium controller. After Gel emulsion generation, linear amplification was performed, followed by DNA purification following the manufacturer’s protocol. The resulting DNA was used for library construction as described on the website of the manufacturer. Libraries were quantified by quantitative PCR and were sequenced on an Illumina Hiseq 2500 sequencer, using the following setup: 50bp read 1N, 8bp i7 index, 16bp i5 index and 50bp read 2N. In this reaction, 1N and 2N refers to the DNA insert sequencing, while i5 and i7 sequencing identifies the individual barcodes of single cells.

value: wild type

value: Bone marrow

value: Bone marrow-derived macrophage


title: Bone marrow-derived macrophage - preIL4 [scATAC-seq]


title: L_173_00: COVID19 patient 173 day 0


title: L_112_05: COVID19 patient 112 day 5

value: day 5

value: Male


title: Control/Baseline population: 0 ng dox (no CCNE1 overexpression) [t0_3]

value: untreated


title: E2f4_nt_mRNA_rep3

value: E2f4 knockdown control


title: Bone marrow-derived macrophage - IL4 [scATAC-seq]


title: WT4rest

value: CD4 T-cells

value: anti-CD3/CD28 treatment for 48hr


title: Control/Baseline population: 0 ng dox (no CCNE1 overexpression) [t0_1]


title: E2f4_nt_mRNA_rep2


title: UM-UC-3 L8 clone

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17

department: Pathology

country: Japan

institute: Sapporo Medical University

data_processing:
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags  and the sequenced CAGE tags were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after  discarding ribosomal or non-A/C/G/T base-containing RNAs.  For tag clustering, CAGE-tag 5‘ coordinates were input for CAGEr clustering (Haberle et al., Nucleic Acids  Research 2015 43:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default  parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes CPM values for each sample.

source_name: urothelial carcinoma cell line

growth_protocol: ALDHhigh clone cells (H-1, H-6, H-10) cells were isolated as AHDLhigh cells by ALDEFLUOR assay and cultured in DMEM/10%FBS.

extract_protocol: Total RNAs were isolated by an Rneasy kit (Qiagen).

value: ALDH low clone, L8


title: WT2rest


title: Bone marrow-derived macrophage - IFNG [scATAC-seq]

value: IFNG


title: B5A-2_L3_360360

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

data_processing:
Normal sequence Illumina Novaseq PE150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with parameters hisat2 -p 8 --dta -x  -1  -2 -S.
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: GRCH38
Supplementary_files_format_and_content: FPKM values for each Sample

growth_protocol: Bel-7402 cells were maintained at 37℃ and 5% CO2 in RPMI modified medium supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA is used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human liver cancer cells


title: UM-UC-3 L3 clone

value: ALDH low clone, L3


title: B5A-1_L3_359359


title: E2f4_nt_mRNA_rep1


title: Bone marrow-derived macrophage - CTR [scATAC-seq]

value: CTR


title: E2f4_sh1_mRNA_rep3

value: E2f4 knockdown with shRNA


title: E2f4_sh1_mRNA_rep2

value: skin fibroblast


title: UM-UC-3 L1 clone

value: ALDH low clone, L1


title: NC-1_L1_353353

value: siControl


title: UM-UC-3 H10 clone

value: ALDH high clone, H10


title: Th1_BATF_KO

city: Onna son

first: Hiroki

last: Ishikawa

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology Graduate University

data_processing:
all raw reads were trimmed by Cutadapt 2.10.
RNA-Seq: trimmed reads were then directly mapped to the UCSC mouse genome mm10, and transcripts were quantified with Salmon 1.3.0 using default settings (k = 31).
RNA-Seq: After transcript quantification, raw feature counts of each transcript were first normalized within and between samples to obtain TPM (Transcripts Per kilobase Million).  conducted with DeSeq2
RNA-SEQ: Differential gene expression analysis was analyzed by DESeq2
ChIP-Seq: Trimmed reads were then mapped to mouse genome mm10 by calling Bowtie2 2.3.4.3 in TopHat2 2.1.1
ChIP-Seq: Peaks were called for each sample replicate using Homer 4.11 with default parameters (FDR < 0.001)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq: csv files include log2FC, pvalue, qvalue for each T helper cell subset
Supplementary_files_format_and_content: ChIP-Seq: bed files include peak annotation for each antibody

source_name: Splenocytes

growth_protocol: Naïve CD4+ T cells were isolaated from mice spleen and cultured under Th0, Th1 and Th2 conditions for 48h.

extract_protocol:
RNA-Seq: QIAGEN RNAeasy. ChIP-Seq: Cell signaling SimpleChIP Plus Enzymatic Chromatin IP Kit (9005S; Cell Signaling)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-Seq, polarized cells were first stained by Zombie-NIR and viable cells were sorted by FACS. Typically, 2e+5 cells were used for one RNA-seq. For ChIP-Seq, 1e+6 cells were directly collected.

tag: polarizing condition

value: Naive CD4+ T cells

tag: antibody

value: Antibody Clone WW8 Santa Cruz

tag: antibody target

value: BATF


title: E2f4_sh1_mRNA_rep1

tag: treatment


title: K562_rep3 Tn5 NakedDNA

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
All reads were trimmed via Trimmomatic version 0.33.0 using the NexteraPE adapter sequence
Trimmed reads were aligned to the mm10 or hg38 genome assembly using Bowtie2 version 2.2.7 with default parameters
Mapped reads were de-duplicated using Picard version 2.9.0 and filtered using samtools version 1.7 with the parameter "-F 780 -q 30"
Processed reads on the forward strand were shifted by +4bp and reads on the reverse strand were shifted by -5bp to get the centers of each Tn5 insertion event (insertion sites)
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: bed files contain the single-base Tn5 insertion sites information. the 5th column indicate Tn5 insertion frequency, the 6th indicate the strand information

source_name: erythromyeloblastoid leukemia cell line

growth_protocol: E14 cells were maintained in 0.2% gelatin (Sigma)-coated plates 2i medium, which consisted of DMEM/F12 supplemented with Neurobasal medium, serum-free N2B27 medium supplemented with 10uM MEK inhibitor PD0325901 and 30uM GSK3 inhibitor CHIR99021 (both from Selleckchem), 2% KnockOutTM serum replacement (Gibco), 0.002% BSA (Gibco), 1mM MTG (Gibco), 1,000 U/ml LIF (Millipore), 0.1mM non-essential amino acid (NEAA) and 2 mM GlutaMAX Supplement (Gibco). Mouse HSPCs were cultured in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/mL mIL-3, 50 ng/ml SCF, 20 ng/ml thrombopoietin (TPO, PeproTech) and 10 ng/ml Flt3 ligand (Flt3-L, PeproTech). The K562 cells were cultured in RPMI-1640 (Giboco) supplemented with 10% FBS.

extract_protocol:
DNA was purified with QIAamp DNA Mini Kit (QIAGEN) and 50ng DNA was used for the following procedure.
The DNA was added with a 50ul Transposition reaction mix (5 μL TTE Mix V50, 10 μL 5 X TTBL and use ddH2O from Vazyme TD501) and followed with incubation at 55C for 10 min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction, and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina).

tag: cell line

value: erythromyeloblastoid leukemia cell line


title: Control/Baseline population: 0 ng dox (no CCNE1 overexpression) [t0_2]

value: RPE1-hTERT cells

value: untreated


title: Th1_IRF4_WT

value: Junbfl/fl

tag: cell type

value: Antibody Clone M-17 Santa Cruz


title: L_136_05: COVID19 patient 136 day 5

data_processing:
The transcript level count were quantified using Kallisto v0.46.1.
 Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript count

extract_protocol:
First the samples were treated with Proteinase K, and then some extractions were performed using Quick-RNA MagBead Kit (R2132) on KingFisher.
Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).

value: day 5

value: Male

tag: age

value: Moderate Symptomatic

value: Whole blood


title: E2f4_OE_control_RRBS_rep2

tag: tissue/cell type

value: Vector overexpression as control


title: Th1_BATF_WT


title: K562_rep2 Tn5 NakedDNA


title: UM-UC-3 H6 clone

value: ALDH high clone, H6


title: K562_rep1 Tn5 NakedDNA


title: E2f4_OE_control_RRBS_rep1

value: skin fibroblast


title: E2f4_OE_passaging_control_RRBS_rep2

value: P3 passaging fibroblasts


title: NC-2_L1_354354

value: Human liver cancer cells

value: siControl


title: Th1_JunB_WT

value: Naive CD4+ T cells

value: Antibody Clone 210 Santa Cruz

value: JunB


title: E2f4_OE_passaging_control_RRBS_rep1


title: Th1_IRF4_KO


title: UM-UC-3 H1 clone

value: ALDH high clone, H1


title: E2f4_OE_RRBS_rep2

value: E2f4 overexpression


title: SP1-ERT2-3HA ChIP-seq 4OHT 360min

first: Yuko

last: Hasegawa

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to the custom genome containing hg38 and sacCer3 assembly using bowtie2 using parameter --sensitive.
PCR duplicates were removed using picard MarkDuplicates and mapped reads with low quality score (less than 30) were excluded using samtools.
Peaks calling was performed with MACS2 using input from each expetiment as a reference with the following setting: -q 0.01.
bedGraph files were created by MACS2 pileup.
Values in bedGraph were normalized to reference-adjusted reads per million (RRPM) calculated as deviding human ChIP-seq score by total yeast mapped read number.
bedGraph files were converted to bigWig by UCSC bedGraphToBigWig program.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, Scores represent Reference-adjusted RPM

growth_protocol: K562 cells expressing SP1-ERT2-3HA were routinely cultured in phenol-red free IMDM containing 10% FBS.

extract_protocol:
Protein-DNA complexes were isolated with HA antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645).

treatment_protocol: Cells were treated with EtOH or 100nM 4OHT.

tag: chip antibody

value: HA (F-7) (sc-7392, Santa Cruz)


title: UM-UC-3 wild type

value: wild type


title: SP1-ERT2-3HA ChIP-seq 4OHT 1440min


title: E2f4_OE_RRBS_rep1


title: SP1-ERT2-3HA ChIP-seq 4OHT 90min


title: Tracheal chondroblasts, BMP4_Control_1

city: Cincinnati

first: John

middle: M.

last: Snowball

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

description: Processed data file: chondroblasts_raw_counts.txt

data_processing:
FASTQ files were trimmed using TrimGalore and aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.txt  (text file of RNA raw counts)

source_name: Bmp4flox/flox, γSMAeGFP

extract_protocol:
RNA was isolated using trizol according to manufacturer’s instructions
SMART-Seq v4 Ultra Low Input Kit for Sequencing
Illumina Nextera XT library was used for sequencing library preparation

treatment_protocol: e13.5 tracheas were dissected out of Bmp4flox/flox, γSMAeGFP and  Bmp4flox/flox, Foxg1Cre+, γSMAeGFP embryos and tracheal cells isolated by FACS.

value: control

value: trachea

value: chondroblast


title: Tracheal chondroblasts, BMP4_Control_3


title: Tracheal chondroblasts, BMP4_Control_2


title: Tracheal chondroblasts, BMP4_Mutant_2

source_name: Bmp4flox/flox, Foxg1Cre+, γSMAeGFP

value: mutant


title: input DNA 1440min


title: E2f4_OE_control_mRNA_rep2

value: Vector overexpression


title: Tracheal chondroblasts, BMP4_Mutant_1


title: E2f4_OE_control_mRNA_rep1


title: A3250_parental_tumor_rep3

city: New York

first: Mihaela

last: Skobe

state: NY

address: 1425 Madison Ave, Rm 15-20F

department: Oncological Sciences

institute: The Icahn School of Medicine at Mount Sinai

data_processing:
Illumina NextSeq 500
Sequenced reads were mapped to human genome hg38 using RNA STAR.
The resulting reads were then processed by featureCounts to produce raw counts and gene lengths.
Fragments per kilobase of transcript per million (FPKM) was calculated by normalizing gene count against gene length.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated text file includes FPKM values for each sample

source_name: inflammatory breast cancer

growth_protocol: A3250 tumor cells were maintained as adherent cultures in standard tissue culture dishes, in high-glucose DMEM supplemented with 4 mM L-glutamine, 10% FBS, and 1X antibiotics (100 U/ml penicillin, 100 U/ml streptomycin)

extract_protocol:
Tumors were harvested and samples preserved in RNAlater™ Solution (Invitrogen AM7020). RNA was extracted using Qiagen Allprep uniersal kit, as recommended by the manufacturer.
RNA-Seq libraries were prepared for sequencing using NEXTflex rapid directional RNA-Seq kit (PerkinElmer)

treatment_protocol: Tumor cells were harvested for RNA-Seq analysis at 80% confluency under standard culture conditions, no treatment. To generate tumors, A3250 tumor cells (1 x 10E6 cells in 100 µl PBS) were injected into the fourth mammary fat pads of eight to nine-week-old SCID mice. Tumors were harvested at 5-6 weeks post-injection, when they reached 4-5 mm in diameter.

value: SCID mice

value: A3250 tumor

value: 6 weeks post-injection

value: parental

value: A3250 IBC Cell line


title: P7 mice fibroblasts RRBS_rep3

source_name: P7 mice fibroblasts RRBS

value: skin fibroblast

value: untreated


title: MDR-CLL3

first: Catherine

last: Wu

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1).
Count value was used to measure gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for all samples

source_name: CLL

growth_protocol: RNA-seq was performed on purified splenic B cells or CLL cells (1x106) from WT or knockout mice.

extract_protocol:
Harvested spleens were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells were immunomagnetically selected from the resulting cell suspension using the MACS B cell Isolation Kit. Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina).

value: CLL cell

value: MDR fl/fl

value: 15 months


title: input DNA 360min

value: HA (F-7) (sc-7392, Santa Cruz)


title: input DNA 90min


title: E2f4_OE_mRNA_rep2

value: E2f4 overexpression


title: MDR-CLL2


title: A3250_parental_tumor_rep2


title: A3250_parental_tumor_cells_in _vitro

value: A3250 cells


title: A3250_parental_tumor_rep1


title: P7 mice fibroblasts RRBS_rep1


title: P5 mice fibroblasts RRBS_rep3

source_name: P5 mice fibroblasts RRBS


title: P7 mice fibroblasts RRBS_rep2


title: E2f4_OE_mRNA_rep1


title: CD19-Cre3

source_name: B cell

value: Splenic B cell

value: wild type


title: CD19-Cre2


title: MDR-CLL1


title: P5 mice fibroblasts RRBS_rep2


title: CLL_hom1

value: Dnmt3a fl/fl


title: CD36

city: Århus N

first: Trine Line

middle: Hauge

last: Okholm

address: Palle Juul-Jensens Boulevard 99

department: Department of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

data_processing:
Fastq files demultiplexed using Illumina’s bcl2fastq v2.20.0.422
Adapters removed using Trim Galore v0.4.1
Reads mapped using TopHat2 (version 2.1.1) and Bowtie2 (version 2.1.0.0)
Read counts were estimated using HTSeq (v0.6.1p1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: cell line

extract_protocol:
RNA was extracted from cells dissolved in Trizol (Invitrogen) according to manufacturers protocol except for using two chloroform extractions instead of one. After isopropanol precipitation RNA pellets were dissolved in nuclease free water (Ambion)
Libraries were prepared for sequencing using the standard protocol QuantSeq 3'mRNA-SEQ Library Prep Kit (Lexogen). Input was 1,000 ng RNA and 11 PCR cycles were applied.

value: bladder carcinoma

tag: sirna

tag: triplicate

value: C

tag: time


title: CLL_hom3

tag: strain

tag: genotype


title: CD34

value: A


title: P5 mice fibroblasts RRBS_rep1


title: P3 mice fibroblasts RRBS_rep3

source_name: P3 mice fibroblasts RRBS


title: CD30


title: P3 mice fibroblasts RRBS_rep2


title: CD29

value: B


title: CLL_het1

value: Dnmt3a fl/+

value: 8 months


title: CD19-Cre1


title: P3 mice fibroblasts RRBS_rep1

value: skin fibroblast


title: CLL_het2


title: CD28


title: CD24


title: CD35


title: P1 mice fibroblasts RRBS_rep3

source_name: P1 mice fibroblasts RRBS

value: untreated


title: B2_Dnmt3a_2

value: 4 months


title: CLL_hom2

value: CLL cell


title: B2_Dnmt3a_1


title: P7 mice fibroblasts mRNA_rep4

source_name: P7 mice fibroblasts mRNA


title: CD22


title: P1 mice fibroblasts RRBS_rep2


title: B1_Dnmt3a_3


title: CD18


title: P7 mice fibroblasts mRNA_rep3


title: B1_Dnmt3a_2


title: CD17


title: CD16


title: P7 mice fibroblasts mRNA_rep2


title: CD23


title: B1_Dnmt3a_1


title: CD33

value: scr


title: CLL_het3


title: P7 mice fibroblasts mRNA_rep1


title: B2_Cre3


title: B2_Dnmt3a_3


title: B2_Cre1


title: P1 mice fibroblasts RRBS_rep1


title: P5 mice fibroblasts mRNA_rep2

source_name: P5 mice fibroblasts mRNA


title: P5 mice fibroblasts mRNA_rep3


title: P5 mice fibroblasts mRNA_rep4


title: CD27


title: CD32


title: CD31


title: B1_Cre3


title: B2_Cre2


title: CD25


title: P3 mice fibroblasts mRNA_rep3

source_name: P3 mice fibroblasts mRNA


title: P3 mice fibroblasts mRNA_rep4


title: B1_Cre1


title: CD21


title: CD20


title: B1_Cre2


title: KO4-ZC109

first: Alain

last: Laederach

state: NC

institute: UNC-Chapel Hill

data_processing:
461,851,481 reads were sequenced using an Illumina HiSeq by Genewiz (https://www.genewiz.com/). On average, 50-60 million reads per sample (4 WT and 4 L2-cKO) were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. In all cases over 97.5% of the trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (43). 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. Only unique reads that fell within exon regions were counted in a strand-specific manner since the library was strand specific.
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 (44). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.csv (Matrix table with raw gene counts for every gene and every sample), normalized_counts.csv, Differential_expression_analysis_table.csv

source_name: Spleen Organoid

growth_protocol: Conditional Zfp36l2 knockout mice carrying the loxP sites flanking exon 2 of Zfp36l2 (Zfp36l2fl/+) were generated by Xenogen Biosciences (Cranbury, NJ) using standard embryonic stem (ES) cell targeting techniques. Mice carrying both Zfp36l2 alleles containing loxP sites were kindly obtained from Dr. Blackshear by MTA and are referred here as Zfp36l2fl/fl (23). B6.CTg(CMV-Cre)1Cgn/J (stock#006054) mice were purchased from Jackson Laboratory. Deletion of Zfp36l2 by conditional knockout was obtained by crossing the CMV-Cre transgenic females with the Zfp36l2 floxed males (Zfp36l2fl/fl) to generate Zfp36l2fl/-;CMV-Cre in the first generation (F1). When Zfp36l2fl/-;CMV-Cre (F1) females were mated with Zfp36l2fl/-;CMV-Cre (F1) males, animals of both sex carrying the recombined Zfp36l2 alleles were generated on the second generation (Zfp36l2-/-;CMV-Cre), these animals are referred here as L2-cKO. Animals carrying both WT copies of Zfp36l2, as well as the Tg.CMV-Cre, were used as WT littermate controls for experiments (Suppl. Fig. 6). Animals were housed in the Dental School vivarium of UNC’s School of Medicine, Chapel Hill. All experiments were in revised and approved by Institutional Animal Care and Use Committee (IACUC) from the University of North Carolina at Chapel Hill.  Mice were genotyped by polymerase chain reaction. For the Zfp36l2flox,+ or-  the following primers used:  F: 5' AGATACCAAACACTTAGGTCTCAGATGAG 3' R: 5' CGACCATTACAGGACCCAGAAA 3'. For the presence of the Tg.CMV-Cre, we used as primers: F: 5' TGGGCCAGCTAAACATGCTT 3' and R: 5' GGTGTTATAAGCAATCCCCAGA 3'.

extract_protocol:
Trizol Plus RNA extraction kit (Thermo Fisher)
NEBNext Ultra II library prep kit with polyA RNA selection

tag: gender

value: M

value: Spleen Organoid


title: CD15


title: KO2-ZC159


title: P3 mice fibroblasts mRNA_rep2


title: KO3-ZC151

value: F


title: CD26


title: KO1-ZC158


title: CD14


title: P1 mice fibroblasts mRNA_rep3

source_name: P1 mice fibroblasts mRNA


title: WT3-ZC162

value: WT


title: WT3-ZC143


title: P5 mice fibroblasts mRNA_rep1


title: CD13


title: WT2-ZC161


title: CD19


title: CD9


title: WT1-ZC128


title: P3 mice fibroblasts mRNA_rep1


title: CD8


title: A2-SA-4

city: Baltimore

first: Xintong

last: Dong

state: MD

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 6000, 100-base-paired-end data producing FASTQ files
Mapping with STAR - 2.7.3a using default parameters
Count quantification to annotation model (Partek E/M), mm10_refseq_v93 transcript counts with default parameters
Partek Flow normalized to FPKM at default parameters
FPKMs log2 quantile normalzed with Partek GS v7.0 and 1-way two-tailed t-test run
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Log2 quantile normalized FPKM

source_name: Skin

extract_protocol:
Skin tissue was homogenized in Trizol and chloroform. RNA was extracted from the aqueous phase, mixed with 70% Ethanol and purified using the Qiagen Rneasy kit.
Library was constructed using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit with standard protocol

treatment_protocol: 3e7 colony forming units of S. aureus (US300 LAC::lux) were intradermally injected into the back skin of mice.

value: skin

value: Mrgpra2 dKO

value: 8 weeks old

value: S. aureus infected


title: A2-SA-5


title: P1 mice fibroblasts mRNA_rep4


title: WT_NAIVE_LY6GHIGH_2

city: London

first: Venizelos

last: Papayannopoulos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

extract_protocol:
Nuclear RNA was isolated using Qiagen RNeasy mini kit (#74104) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Nugen cDNA synthesis kit

value: Primary cells from spleen

value: Neutrophils

tag: infection status

value: naive

tag: ly6g status


title: P1 mice fibroblasts mRNA_rep2

data_processing:
Sequencing adapters and low quality reads were removed from the raw RNA-seq and ATAC-seq  reads with Trimmomatic (V0.39) and from the RRBS reads with Trim Galore (V0.6.6).
Reads from RNA-seq were aligned to mm10 with Hisat2 (V2.2.1). Reads from ATAC-seq were aligned to mm10 using Bowtie2 (V2.3.5.1). Reads from RRBS were aligned to mm10 using Bismark (v0.22.3).
For RNA-seq, HTSeq-count (V0.12.4) was used to calculate the count of reads for each gene. For ATAC-seq, MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks. For RRBS, DSS (V2.34.0) was used to identify DMRs and DMSs.
Genome_build: mm10

extract_protocol:
Total DNA was extracted from cells using the MasterPureTM Complete DNA & RNA Purification Kit (Cat.No. MC85200). TRIzol reagent (Invitrogen) was used to extract total RNA according to the manufacturer’s instructions.
Libraries of RNA-seq, ATAC-seq and RRBS were prepared for sequencing using standard Illumina protocols


title: A2-SA-6

tag: tissue


title: WT_NAIVE_LY6GHIGH_1


title: A2-SA-2


title: A2-SA-3


title: WT_INFECTED_LY6GLOW_3

value: infected


title: A2-SA-1


title: P1 mice fibroblasts mRNA_rep1

value: skin fibroblast


title: CD1

value: bladder carcinoma

value: No

value: A


title: A2-con-6

value: Naive


title: CD71

value: B


title: CD3

value: C


title: CD7

value: scr


title: CD70


title: WT_INFECTED_LY6GLOW_2

value: WT


title: WT_NAIVE_LY6GHIGH_3


title: CD72


title: A2-con-3

value: skin


title: A2-con-4

value: Mrgpra2 dKO


title: CD66


title: WT_INFECTED_LY6GLOW_1


title: WT_INFECTED_LY6GHIGH_2


title: WT_INFECTED_LY6GHIGH_1


title: CD64


title: CD65


title: CD2


title: WT_INFECTED_LY6GHIGH_3


title: Def-SA-6

value: Def cKO

value: 8 weeks old


title: CD59


title: WT_NAIVE_GCSFCLODRONATE_LY6GLOW_3

value: Primary cells from spleen


title: Def-SA-5

value: S. aureus infected


title: CD60


title: A2-con-2


title: WT_NAIVE_GCSFCLODRONATE_LY6GLOW_2

value: Neutrophils

value: naive


title: WT_NAIVE_GCSFCLODRONATE_LY6GLOW_1


title: CD58


title: WT_NAIVE_GCSFCLODRONATE_LY6GHIGH_3


title: CD54


title: CD52


title: A2-con-5


title: Def-SA-2


title: Def-SA-3


title: WT_NAIVE_GCSFCLODRONATE_LY6GHIGH_2


title: WT_NAIVE_GCSFCLODRONATE_LY6GHIGH_1


title: TCRaKO_NAIVE_LY6GHIGH_3

value: TCRaKO


title: Def-con-6


title: TCRaKO_NAIVE_LY6GHIGH_2


title: Def-SA-1


title: CD69

value: bladder carcinoma


title: Def-con-5


title: CD67


title: TCRaKO_NAIVE_LY6GHIGH_1


title: TCRaKO_INFECTED_LY6GLOW_3

value: infected


title: TCRaKO_INFECTED_LY6GLOW_1


title: Def-con-4


title: Def-con-3


title: Def-con-2


title: TCRaKO_INFECTED_LY6GLOW_2


title: UCT25T25minusVitD

city: Faridabad

first: Suchitra

last: GOPINATH

address: NCR Biotech Science Cluster, 3rd Milestone,

country: India

institute: Translational Health Science and Technology Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 with default parameters
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using  Cufflinks from tuxedo pipeline (Trapnell et al, 2012) .
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values

source_name: UCT-derived MSCs_untreated

growth_protocol: Mesenchymal stem cells derived from umbilical cord tissue were grown in αMEM (Hyclone, cat- SH30568.FS) with 20%FBS, 2mM Sodium pyruvate and 4mM L-glutamine

extract_protocol:
RNA was isolated using TRIzol (SIGMA) and extracted using spin column purification from Direct-zol RNA miniprep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs isolated from human umbilical cord tissue (UCT) and grown in αMEM with 20% fetal bovine serum on Laminin and Collagen Type 1-coated tissue culture plates were switched to medium containing αMEM with 15% KnockOut Serum Replacement. After 24 hours, MSCs from each of the biological replicates were treated with 100nM vitamin D or vehicle control for 3 days, with fresh medium being added every day. This was followed by induction of myogenic differentiation in both vitamin D-treated and untreated samples by the addition of medium containing 5% horse serum, 0.1 µM dexamethasone, and 50 µM hydrocortisone. After 7 days, total RNA was isolated from vitamin D-treated and control samples by Trizol (SIGMA) and processed for RNA-seq.

value: umbilical cord tissue (UCT) derived mesenchymal stem cells (MSCs)

value: vehicle control for 3 days

tag: passages

value: 3 to 5


title: CD62

value: B


title: UCT25T25plusVitD

source_name: UCT-derived MSCs_VitD treated

value: 100nM vitamin D for 3 days


title: Def-SA-4


title: CD61

value: scr

value: A


title: CD53


title: TCRaKO_INFECTED_LY6GHIGH_3


title: CD57

value: C


title: Def-con-1

value: skin

value: Def cKO

value: Naive


title: CD56


title: TCRaKO_INFECTED_LY6GHIGH_2

value: Primary cells from spleen


title: WT-SA-6

value: WT

value: 8 weeks old

value: S. aureus infected


title: UCT24T24plusVitD


title: A2-con-1

value: Mrgpra2 dKO


title: CD68

value: bladder carcinoma


title: TCRaKO_INFECTED_LY6GHIGH_1

value: Neutrophils

value: TCRaKO

value: infected


title: UCT24T24minusVitD

value: umbilical cord tissue (UCT) derived mesenchymal stem cells (MSCs)

value: vehicle control for 3 days

value: 3 to 5


title: CD63

value: scr


title: CD55

value: A


title: CD51

value: C


title: WT-SA-5

value: skin


title: WT-SA-4


title: UCT15T15minusVitD


title: WT-SA-2


title: UCT15T15plusVitD

value: 100nM vitamin D for 3 days


title: CD50

value: B


title: CD49


title: UCT14T14plusVitD


title: WT-SA-1

value: WT


title: WT-SA-3

value: 8 weeks old


title: UCT14T14minusVitD


title: wtIDH1_rep3 [72861_TGACCA_S7_L001]

city: Ann Arbor

first: Maria

last: Castro

address: 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

data_processing:
The quality of the raw reads data was verified for each sample using FastQC  (version v0.11.3)
Tuxedo Suite for alignment and differential expression analysis (TopHat version 2.0.13, Bowtie version 2.2.1, Cufflinks/CuffDiff version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts from HTSeq for every gene and every sample

source_name: wtIDH1_tumor-infiltrating myeloid cells

extract_protocol:
Tumor was dissected and processed to obtain a single cell suspension. Immune cells were enriched by percoll purification. Myeloid cells were sorted by flow cytometry. Total RNA was isolated from the sorted tumor-infiltrating CD11b+ Gr-1+ cells using RNeasy Plus Mini Kit
RNA quality was assessed using a TapeStation (Agilent Technologies) following the manufacturer's recommended protocol. Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared using the Illumina TruSeq mRNA Sample Prep Kit v2 (Illumina, RS-122-2001, RS-122-2002). An amount of 0.1-3 μg of total RNA was converted to mRNA using polyA purification. The mRNA was then fragmented and copied into first-strand cDNA using reverse transcriptase and random primers. The 3’ ends of the cDNA were then adenylated and ligated to adapters. Each ligated adapter had a unique 6 nucleotide barcode to identify each sample, enabling multiple samples to be sequenced from each lane of a HiSeq flow cell (Illumina). The products were purified and enriched by PCR to create the final cDNA library. Libraries were checked for quality and quantity by TapeStation (Agilent Technologies) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems, KK4835) using the manufacturer's recommended protocols.

tag: strain background

value: Wild type IDH1

tag: celltype

value: Myeloid cell (CD11b+ Gr-1+)

value: TME


title: mIDH1_rep2 [72865_GGCTAC_S10_L001]

source_name: mIDH1_tumor-infiltrating myeloid cells

value: Mutant IDH1


title: CD45

value: bladder carcinoma

tag: cell line


title: wtIDH1_rep2 [72860_TTAGGC_S6_L001]


title: CD44


title: wtIDH1_rep1 [72858_CGATGT_S5_L001]


title: UCT12T12plusVitD

tag: cell type

tag: treatment


title: WT-con-5

tag: age

value: Naive


title: mIDH1_rep3 [72867_GCCAAT_S12_L001]


title: CD43


title: Ubr1-4

city: Fuzhou

first: Dingyi

last: Wang

state: None Selected

address: Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China

institute: Fujian Normal University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.

organism: Beauveria bassiana

source_name: blastospore

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARSEF 2860

value: 13 hours

value: ubr1-deletion strain


title: Ubr1-2


title: WT-con-4


title: CD38

value: No


title: WT-con-2


title: WT-con-3


title: mIDH1_rep1 [72864_TAGCTT_S9_L001]


title: Ubr1-1


title: CD39


title: WT-3

value: wild type


title: Input_T24_donor3

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Reads were aligned to hg38 reference genome using Bowtie2
For each condition, peaks were called independently for each of the three donors using HOMER on the aligned reads with FDR < 0.1.
Peaks detected by both two callers were kept and labeled by the peak names generated by HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig. H3K27me3 coverage; tab-delimited, JMJD3 peaks.

source_name: peripheral blood of healthy donors

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: naive CD4 T cells

tag: antibody

value: input


title: WT-2


title: plus Th17 Adcy10-/- rep 3

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were aligned to the mouse genome (mm9) using STAR_2.4.0f1 with default parameters, and SAMTOOLS v0.1.19 was used for sorting and indexing reads. CuffLinks was then used to calculate normalized expression levels (FPKM; Fragments Per Kilobase of transcripts per Million reads) Counts were calculated using htseq-count
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: T cells

extract_protocol:
RNA was isolated according to specifications of the RNA Easy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spleens or lymph nodes from male Adcy10-/- and wild type C57Bl/6 mice age 8-10 weeks were excised and mechanically disrupted to obtain single cell suspensions.  Cells were treated with a red blood cell lysis buffer (155 mM Ammonium chloride, 10 mM sodium bicarbonate, 0.1 mM EDTA in PBS pH 7.4) for two minutes and enriched for CD4+ T cells using a magnetic bead negative selection (Miltenyi).  T cells were cultured in 96-well plates coated the night before with 200 uL of 10 µg/mL anti-CD3 antibody (BD biosciences) in IMDM modified with 1% sodium pyruvate, 1% L-glutamine, 1% pen/strep, and 10% FBS (Thermo Fischer), in the presence of 2 µg/mL anti-CD28 antibody (BD biosciences), 20 ng/mL recombinant mouse IL-1β (Miltenyi), 25 ng/mL IL-6 (Miltenyi), and 20 ng/mL IL-23 (R&D Systems). Media was also supplemented with 1 µg/mL anti-IFNγ antibody (Thermo Fisher) and 1 µg/mL anti IL-4 antibody (Thermo Fisher) to inhibit Th1 and Th2 polarization, respectively.  Cells were used as follows for different analyses. After 18 hours in culture, cells were collected for RNA sequencing.

value: baseline media + polarizing cytokines

value: 8-10 weeks


title: CD37

tag: sirna

value: A


title: Input_T24_donor2


title: WT-1


title: WT-con-1

value: skin

value: WT

value: 8 weeks old


title: WT-con-6


title: UCT12T12minusVitD

value: umbilical cord tissue (UCT) derived mesenchymal stem cells (MSCs)

value: vehicle control for 3 days

value: 3 to 5