title: lytic_LCL_input1

value: LCL

value: Treated with TPA and Butyric acidand  IP with IgG antibody


title: 4_NR4A1

status: Public on Mar 22 2023

type: SRA

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

description: HYNLFDSXY_104400-001-014_GACGAACT-TCGCATTG

library_source: genomic

data_processing:
Quality check of the raw sequencing reads was performed using the FastQC tool.
Sequencing reads were mapped against the reference genome GRCh38.p13 built from the human genome (NCBI) using bowtie2
Peaks were called using MACS2, by comparing the IP samples to their matched input samples in paired end mode (BAMPE).
After calling, peaks from ENCODE blacklist regions and X- and Y-chromosome peaks were filtered out to reduce noise and exclude sex-specific peaks.
Peaks were annotated to the nearest genes using the ChIPseeker Bioconductor/R package. Peaks were considered to be associated to a gene when they were annotated within a 10kb range (up- or downstream) to the gene transcription start site (TSS).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: peak text files and bed files

molecule: genomic DNA

organism: Homo sapiens

source_name: CD1c+ DCs

growth_protocol: CD1c+ cDCs were isolated from PBMCs obtained from healthy donor buffy coats using the MACS human CD1c dendritic cell isolation kit. 1.5×106 freshly isolated cDCs were cultured overnight in RPMI 1640 medium with GlutaMAX™ (Life Technologies), supplemented with 10% heat inactived fetal bovine serum (Biowest) and 1% penicillin streptomycin (Life Technologies).

extract_protocol:
After culture, cDCs were washed with PBS and crosslinked using the truChIP® Ultra-Low Chromatin Shearing Kit (Covaris), according to the manufacturer’s instructions. Chromatin shearing was performed using AFA Fiber Pre-Slit Snap-Cap microTUBEs (Covaris) by sonication (peak incident power: 105, duty factor: 2%, cycles per burst: 200, treatment time: 12 minutes) on the Covaris S220 focused ultrasonicator (Woburn, MA, USA). After shearing, the chromatin was transferred into pre-chilled microcentrifuge tubes and centrifuged at 10.000 x g, 4˚C for 5 minutes to pellet insoluble material, and the chromatin was stored at -20˚C for downstream processing. Chromatin immunoprecipitation was performed with 3µg anti-NR4A1 (NB100-56745, Novusbio), anti-NR4A2 (NB110-40415, Novusbio) or anti-NR4A3 (NLS2341, Novusbio) antibodies, using the low cell ChIP-seq kit (Active Motif), according to the manufacturer’s instructions. For all conditions, 10% of the input chromatin was removed prior to addition of the antibodies and used to normalize the amount of immunoprecipitated DNA (input control). Following immunoprecipitation, ChIP DNA was de-crosslinked in the presence of NaCl and Proteinase K (Active Motif) in a thermocycler at 65°C overnight, and DNA was extracted by penol:chloroform:isoamylalcohol precipitation and dissolved in Low-EDTA TE buffer (Active Motif).
ChIP-seq libraries were generated by GenomeScan (Leiden, the Netherlands) with the NEBNext® Ultra II DNA Library Prep kit (Illumina), and were sequenced using Illumina NovaSeq 6000 generating ~20 million 150bp paired ended reads for each sample.

treatment_protocol: Cells were either left untreated or treated with TLR7/8 agonist R848 (Resiquimod, 100ng/mL, Invivogen) overnight.

tag: cell type

value: CD1c+ dendritic cell

tag: tissue

value: Periperal blood

tag: replicate

tag: treatement

value: R848 stimulated

tag: chip antibody

value: anti-NR4A1 (NB100-56745, Novusbio)


title: 6_Input

description: H3HCVDRXY_104400-001-021_TACCTGCA-TGATGTCC

value: Input control


title: 4_NR4A2

description: H3HCVDRXY_104400-001-015_TCCACGTT-GTTCAACC

value: anti-NR4A2 (NB110-40415, Novusbio)


title: eaSSc_MT2032 [MT2.032]

library_source: transcriptomic

data_processing:
Quality filtering according to the BGI pipeline
Reads were aligned to the GrCh38 reference human genome and the homo sapiens transcriptome (Ensembl, version 79), using the STAR aligner
Summed exon read counts per gene were calculated using the Python package HTSeq, using annotations from the GrCh38 built from the human genome
Between lane normalization using the upper quartile normalization method was performed using the Bioconductor/R package EDAseq
To account for batch effects arising from the inclusion of samples from different geographic locations (The Netherlands and Italy), we applied the generalized linear model from the Bioconductor/R package RUVseq using the RUVr function for k = 2 factors of unwanted variation
Differential expression analysis was performed using the negative binomial distribution-based method implemented in DESeq2 on the normalized summed exon read counts per gene
Normalized gene expression levels were converted variance stabilised data (VSD), calculated according to DESeq2 instructions
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab delimited .txt files include counts and normalized expression values (VSD) for each sample.

molecule: total RNA

source_name: CD1c+ cDCs

extract_protocol:
Human CD1c+ dendritic cells were purified from heparinised whole blood of SSc patients and matched healthy donors after centrifugation over Ficoll-Paque gradient. Briefly,  CD1c+ dendritic cells were purified from PBMCs using the anti-BDCA1 microbeads (Miltenyi Biotec), on the autoMACs Pro Separator (Miltenyi Biotec) according to manufacturer’s protocol. Cells were lysed in RLTplus buffer (Qiagen) containing 1% (v/v) beta-mercaptoethanol (Sigma). Total RNA was purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. DNAse treatment (RNAse Free DNase I set, Qiagen) on column was performed.
RNA-Seq libraries were prepared using the TruSeq Stranded kit (Illumina, San Diego, CA, USA) after poly (A) capture, according to the manufacturer’s instructions. Libraries were sequenced on the HiSeq 2000 system (Illumina), using 100bp paired-end reads.

value: CD1c+ cDCs

value: Peripheral blood

tag: disease state

value: early systemic sclerosis

tag: location

value: Milan

tag: seks

value: Female


title: lytic_AKV_input1

city: Philadelphia

first: Erle

middle: S

last: Robertson

state: PA

address: 3610 Hamilton Walk

country: USA

institute: Otorhinolaryngology-Head and Neck Surgery Perelman School of Medicine

data_processing:
Quality control using fastqc version 0.11.5
Mapped to GRCh38 whole genome using STAR2.7.6a with parameters --runThreadN 4
Peaks calling using MACS3
Count the number of reads mapped to each gene using htseq-count version 0.12.4
Assembly: GRCh38
Supplementary files format and content: Narrow peaks for each group of sample
Supplementary files format and content: Table with raw gene counts for every gene in every sample

growth_protocol: LCL and AKATA cells were maitained in RPMI supplemented with 10% BGS and 1% antibiotics and maintained at 37 degree Celcius and maintained at a optimal concentration of 0.4 million/ml

extract_protocol:
EBV positive cells were induced to lytic reactivation by using TPA (20 ng/ml) and Butyric acid (3 mM) for 30 h induction.
RNAs were isolated and immune precipitated with m6A specific antibodies or with control IgG and the library was prepared using TrueSeq standard LT  RNA preparation kit

treatment_protocol: LCL and AKATA cells were induced with TPA and BA for 30 h for lytic reactivation

value: Lymphoid tissue

tag: cell line

value: AKATA

value: B cells

tag: genotype

value: Wild type

tag: treatment


title: eaSSc_MT2017 [MT2.017]


title: LCL_input1

value: LCL

value: Untreated IP with Control IgG specific antibody


title: Day1, 18m, 20%surfacePAR, insitu, biolrep3

city: OLD BRIDGE

first: Benjamin

last: Diaz

state: New Jersey

address: K12B Pine Tree Boulevard

department: Department of Biochemistry and Microbiology

institute: Rutgers University

description: Marine phytoplankton community <0.8 µm diameter

data_processing:
Supplementary files format and content: Only data from in situ samples were analyzed with differential expression, however our intial plan was to use incubation samples as well, so the asssembly was done with the incubated samples as well.
The set of transcripts belonging to the most abundant autotrophic phyotplankton genera present (Minutocellus, Chaetoceros, Thalassiosira, Extubocellulus, Fragilariopsis, Bathycoccus, Micromonas, Ostreococcocus) was subset before performing differential expression analysis.
Supplementary files format and content: DeSeq2 output of each genera analyzed with the comparisons made in the paper is presented in "Deseqoutputbygenera.xlsx" (using the column 'Sample number correspong to Fig. 1': "1V2", "1V3", "2V3", "4V6","2V5","3V6","4V6","5V6","4V5" as well as the comparisons used for Fig. 8a, "Shallow vs. Deep" , which is 1, 2, 3 vs. 4)
The raw reads from all samples were searched for sequencing adapters and low-quality nucleotides which were trimmed using CLC Genomic Workbench.
Protein coding regions within the metatranscriptome assembly were predicted with TransDecoder
To reduce redundancy in the metatranscriptome, the predicted coding regions were clustered at 95% identity using CD-HIT(37) which resulted in 2 053 751 sequences
Trimmed reads from each sample were then mapped to the assembly with CLC Workbench, and only uniquely mapped reads were counted.
Contigs with less than 50 total mapped reads across all samples were filtered out resulting in 673 142 contigs that were used for downstream analysis
Functional annotations were identified using EggNOG
Translated protein sequences were assigned phylogeny by using DIAMOND (v. 2.0.11, ultra-sensitive mode) against a custom database of MetaEuk, MaTOU, MMETSP, and Uniref100 (May 2020).  The highest bitscore matching to an organism was used, with a lower bitscore cutoff of 50.
The trimmed reads were assembled using Trinity yielding 11 046 104 contigs
Assembly: (no reference genomes used)
Supplementary files format and content: Count matrix of read counts for all samples are presented in "CountMatrixsamples.xlsx"
Supplementary files format and content: TPM of samples from the count matrix are presented in "TPMallsamples.xlsx"
Supplementary files format and content: Translated protein sequences are presented in "Aaseqs.fasta"

molecule: polyA RNA

organism: phytoplankton metagenome

source_name: Marine phytoplankton community <0.8 um diameter

extract_protocol:
RNA was extracted with Trizol kit from frozen 0.8 µm filters, without modifications.
PolyA-enriched messenger RNA was reverse transcribed using Invitrogen SuperScript II Reverse Transcriptase at the Rutgers Genome Cooperative. Libraries were prepared from this cDNA (TruSeq RNA Library Prep Kit v2.)

treatment_protocol: For incubated samples, seawater from the same depths as in situ samples was also emptied directly into acid-washed, 9 L bottles and placed in on-deck incubators, which were continuously circulated with surface water to maintain ambient temperatures and covered with neutral density screening to simulate 40, 20, and 1% surface irradiance.

tag: depth (m)

tag: time (days)

tag: mixed layer_depth_at_sampling_(m)

value: In situ

tag: sample number_corresponding_to_fig._1

value: Sample 2


title: Day1, 5m, 40%surfacePAR, insitu, biolrep1

value: Marine phytoplankton community <0.8 um diameter

value: Sample 1


title: 3_NR4A3

description: HYNLFDSXY_104400-001-012_GACGTCAT-TCAACTGG

value: CD1c+ dendritic cell

value: Periperal blood

value: unstimulated

value: anti-NR4A3 (NLS2341, Novusbio)


title: eaSSc_MT2014 [MT2.014]

value: CD1c+ cDCs

value: Peripheral blood

value: early systemic sclerosis


title: AKV_IP1

value: Lymphoid tissue

value: Untreated IP with M6A specific antibody


title: eaSSc_5 [X5]

value: Utrecht

value: Female


title: 3_NR4A2

description: HYNLFDSXY_104400-001-011_GGAGGAAT-AACCGTTC

value: anti-NR4A2 (NB110-40415, Novusbio)


title: eaSSc_38 [X38]

value: Rotterdam

value: Male


title: eaSSc_8 [X8]


title: 18_HFD_10

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
FastQC (default parameters) was used to verify the quality of the reads. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.6.0a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.6.0a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene counts for each alignment were analyzed for differentially expressed genes using the R package DESeq2 (version 1.34.0) (Love et al., 2014). A threshold of 1 log2 fold change and adjusted P value smaller than 0.05 were considered when identifying the differentially expressed genes.
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 4.2.2) package was then used to perform various Enrichment Analysis on the obtained results.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

organism: Mus musculus

source_name: epcam+ cells

growth_protocol: C57BL/6JRj (25 g, 8 weeks old) mice were obtained from Janvier Labs.

extract_protocol:
RNA was harvested using RNeasy micro kit (QIAGEN). Around 40 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 Ultra Low Input RNA Sample Library Construction Protocol
BGISEQ-500 Ultra Low Input RNA Sample Library Construction Protocol

treatment_protocol: C57BL/6JRj (25 g, 8 weeks old; Janvier-Labs) mice were fed with CD (SAFE® 150) and HFD (RD12492i) for fifteen weeks. Fifteen weeks later, mice underwent necropsy to collect livers. BECs were sorted from the livers after digestion with a solution of collagenase and dispase (0.125 mg/ml each) by using FACS.

tag: strain

tag: age (weeks)

tag: tratment

value: HFD

value: epcam+ cells


title: eaSSc_7 [X7]

tag: cell type

tag: tissue


title: AKV_input1

value: AKATA

value: B cells

value: Wild type

value: Untreated IP with Control IgG specific antibody


title: 17_HFD_9


title: 15_HFD_7


title: 3_NR4A1

description: HYNLFDSXY_104400-001-010_AGGATAGC-AACCTTGG

value: CD1c+ dendritic cell

value: Periperal blood

tag: replicate

tag: treatement

value: unstimulated

value: anti-NR4A1 (NB100-56745, Novusbio)


title: 4_Input

description: H3HCVDRXY_104400-001-013_CCGCTTAA-ACGATGAC

value: R848 stimulated

tag: chip antibody

value: Input control


title: LCL_IP1

value: Lymphoid tissue

value: LCL

value: Untreated IP with M6A specific antibody


title: 3_Input

description: H2GNHDSX2_104400-001-009_TCCTCATG-AGGTGTAC


title: 2_NR4A3

description: H3HCVDRXY_104400-001-008_ATCTGACC-AAGTCGAG

value: anti-NR4A3 (NLS2341, Novusbio)


title: 12_HFD_3


title: 2_NR4A2

description: H3HCVDRXY_104400-001-007_CTTAGGAC-CAGTGAAG

value: anti-NR4A2 (NB110-40415, Novusbio)


title: 11_HFD_2

value: HFD


title: hTSC, Control, KD, rep3

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

data_processing:
Paired-end reads were aligned to human transcript (hg38) using Salmon mapper  (v1.8.0)
Expression levels of each gene were calculated using R library tximport as transcripts per million (TPM). The read counts were quantified and normalized by median of ratio method and differentially expressed genes (DEGs) were obtained with the selection criteria of P-adjusted value < 0.01 and fold change > 2 using the R package DESeq2 (v1.30.1).
Assembly: hg38

source_name: Placenta

extract_protocol:
Total RNAs were extracted using the RNeasy plus mini kit following the manufacturer’s instructions. RNA-seq libraries were generated with 500 ng of total RNA using NEB Next Ultra II RNA Library prep kit (NEB, E7770) following the manufacturer’s protocol.
mRNAs were enriched from total RNAs with Magnetic mRNA Isolation Kit (oligo(dT) beads) (NEB, E7490), and then cDNAs were synthesized using random primers. cDNAs were purified by NEBNext Sample Purification Beads (NEB, E7767). End prep reactions were performed followed by ligation with a sample-specific adaptor and index.

value: Placenta

value: Human trophoblast stem cells


title: 2_Input

description: H2GNHDSX2_104400-001-005_GAATCCGT-TGGAGTTG


title: Day1, 5m, 40%surfacePAR, insitu, biolrep2

value: Marine phytoplankton community <0.8 um diameter

value: In situ

value: Sample 1


title: hTSC, Control, KD, rep2


title: eaSSc_28 [X28]

value: CD1c+ cDCs

value: Peripheral blood

tag: disease state

value: early systemic sclerosis

tag: location

value: Utrecht

value: Male


title: 7_CD_8

value: CD

value: epcam+ cells


title: 16_HFD_8


title: eaSSc_18 [X18]

tag: seks

value: Female


title: 2_NR4A1

description: H3HCVDRXY_104400-001-006_CATGAGCA-GCAAGATC

value: CD1c+ dendritic cell

value: Periperal blood

value: R848 stimulated

value: anti-NR4A1 (NB100-56745, Novusbio)


title: HC_MT2097 [MT2.097]

value: Healthy control

value: Milan


title: hTSC, TFAP2C, KD, rep2

value: Placenta

tag: cell line

value: Human trophoblast stem cells


title: 10_HFD_1

value: HFD


title: hTSC, Control, KD, rep4


title: hTSC, Control, KD, rep1


title: HC_MT2092 [MT2.092]

value: CD1c+ cDCs


title: 6_CD_7


title: 1_NR4A3

description: HYNLFDSXY_104400-001-004_GTAACCGA-GGTGTCTT

value: unstimulated

value: anti-NR4A3 (NLS2341, Novusbio)


title: hTSC, TFAP2C, KD, rep1


title: HC_MT2078 [MT2.078]

value: Peripheral blood


title: HC_MT2075 [MT2.075]


title: hTSC, TEAD4, KD, rep1


title: 1_NR4A1

description: HYNLFDSXY_104400-001-002_AGACCTTG-GCACGTAA


title: 1_Input

description: H3HCVDRXY_104400-001-001_TCGGATTC-TAGTTGCG

value: Input control


title: 3_CD_3

value: CD


title: 2_CD_2

value: epcam+ cells


title: HC_MT2073 [MT2.073]

value: Female


title: hTSC, MAFK, KD, rep2


title: 1_CD_1


title: HC_MT2071 [MT2.071]


title: hTSC, MAFK, KD, rep1


title: AP4: Peri-Lesion4 after NBUVB treatment

city: Bangkok

first: Pinyadapat

last: Vacharanukrauh

address: Sutthisan vinitchai

country: Thailand

institute: CICM Thammasat university,

description: test

data_processing:
The quality control of the sequenced raw reads was analyzed using FastQC program.
The low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed using Trimmomatic program
Trimmed reads are mapped to reference genome (UCSC hg19) with HISAT2, splice read mapping through Bowtie2 aligner.
Transcript is assembled by StringTie with aligned reads.
Gene differential expression analysis was performed with edgeR Bioconductor statistical library version 3.81,2 on RStudio.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: .xlsx.  The content contains TranscriptID, GeneID, GeneSymbol and score represent raw reads count

source_name: Lesional psoriasis

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Ambion) in accordance with the manufacturer’s instruction.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E
TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: NB-UVB phototherapy

value: peri-lesional psoriasis

tag: treatment

value: After NBUVB treatment


title: AP3: Peri-Lesion3 after NBUVB treatment

description: test


title: nts_3

city: shenyang

first: jun

last: zhang

address: liaoning

country: China

institute: Shenyang Agricultural University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Phaseolus vulgaris v2.1(https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1)

organism: Phaseolus vulgaris

source_name: the top stems

growth_protocol: The seeds of A18 and nts were directly seeded in a round nutrient pot with a diameter of 13. The culture environment was 25 ℃ and photcycle was 14h/10h (day and night).

extract_protocol:
Plants were grown until the first flowering stage, samples were taken when the apical stems of mutant nts differed significantly from those of wild-type A18, and frozen in liquid nitrogen.
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: the top stems

tag: genotype

value: nts


title: nts_2


title: hTSC, GATA2, KD, rep2


title: AP1: Peri-Lesion1 after NBUVB treatment

description: test


title: HC_MT2033 [MT2.033]

value: Healthy control


title: HC_69M [X69M]

value: Utrecht


title: hTSC, GATA2, KD, rep1

value: Placenta


title: nts_1


title: HC_65M [X65M]


title: hTSC, FOS, KD, rep2

value: Human trophoblast stem cells


title: 1_NR4A2

description: HYNLFDSXY_104400-001-003_GTCGTTAC-GCTTAGCT

value: CD1c+ dendritic cell

value: Periperal blood

value: anti-NR4A2 (NB110-40415, Novusbio)


title: A18_3

value: A18 wild-type


title: hTSC, TEAD4, KD, rep2


title: hTSC, FOS, KD, rep1


title: HC_31 [X31]

value: CD1c+ cDCs

value: Peripheral blood

value: Male


title: BP4: Peri-Lesion4 before NBUVB treatment

description: controls

value: Before NBUVB treatment


title: HC_63M [X63M]

value: Female


title: BP3: Peri-Lesion3 before NBUVB treatment

description: controls

value: peri-lesional psoriasis


title: A18_1


title: A18_2


title: AL4: Lesion4 after NBUVB treatment

description: test

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Ambion) in accordance with the manufacturer’s instruction.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

value: Lesional psoriasis

value: After NBUVB treatment


title: HC_29 [X29]


title: hTSC, Input, rep2

description: Chromatin IP against Input

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to human hg38 genome using Bowtie 2.4.5
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in human TSCs. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E7370L ) following by manufacturer’s instructions.

tag: antibody

value: Input


title: hTSC, Input, rep1

description: Chromatin IP against Input


title: SCF5

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Library strategy: WGS
The DNA libraries were sequenced using Illumina’s NovaSeq 6000 using Novaseq S4 cartridge (Novogene, Singapore).
The average coverage was 25X and was uniformly distributed. Whole genome sequence reads were aligned to the chicken reference genome draft (version GRCg6a) using Bowtie2 (22388286) 40.
Segmental copy number variation and aneuploidy were predicted by AneuFinder with default parameters using two size bin length of 15Kbp and 1Mbp, respectively.
Heatmap and dendrograms were plotted using R.
Genome_build: chicken reference genome draft (version GRCg6a)

organism: Gallus gallus

source_name: Spontaneously Immortalized, anchorage-independent , chicken embryonic fibroblast

extract_protocol:
Genomic DNA was extracted from FMT-SCF-1 to 5 using Quick-DNA™ MicroPrep Zymo-spin IC columns (ZR-D3021, Zymo research, Irvine CA) according to the manufacturer’s instructions. DNA was dehydrated on GenTegra DNA tubes and shipped to Syntezza (Jerusalem, Israel) for library preparation.
Library was construsted using Celero DNA library prep kit (Tecan Genomics),  according to the manufacturer’s instructions.

treatment_protocol: Primary fibroblasts were passaged regularly, recording changes in doubling time and morphology as cells underwent senescence (crisis) and breakthrough (immortalization). Cells were considered to be immortalized once the culture showed stable morphology and doubling time following at least 120 population doublings from isolation. Immortalized lines were expanded and cryopreserved in four immortalized-cell banks labeled HUN-CF. Suspension culture of immortalized chicken fibroblasts Fibroblasts spheroids were created using Aggrewell 400 according to the manufacturer’s directions. Briefly, 1.2x106 spontaneously immortalized fibroblasts were seeded in DMEM with 10% FBS at a density of 3,867 cells per microwell for 48 hrs. Spheroids were then gently detached and transferred to a low-attachment 10 cm petri dish, in culture media supplemented with 0.1% Pluronic F-68. Spheroids were mechanically disturbed daily for 4 consecutive days by vigorous pipetting. Spheroids were transferred to baffled shaker flasks on day 7 and cultured in a humified shaker incubator at 39°C, 5% CO2 and 80 RPM in DMEM10 culture media supplemented with 0.1% Pluronic F-68. Large cellular aggregates were broken down by TrypLE™ digestion each week, and cells reseeded at a density of 200,000 cells/mL. Suspension cultures were counted and diluted back to initial density 2-3 times a week. Following 30 days of culture, the shaker speed was increased to 100 RPM leading to aggregate breakdown and single-cell suspensions developing for 60 days. Cells were considered anchorage-independent once culture showed stable doubling time and viability above 94%. Anchorage-independent cell lines were expanded and cryopreserved in  master-cell banks labeled FMT-SCF.

tag: breed

value: Israeli Baladi

value: Spontaneously Immortalized chicken embryonic fibroblast

value: anchorage-independent


title: BP1: Peri-Lesion1 before NBUVB treatment

description: controls


title: AL1: Lesion1 after NBUVB treatment

description: test


title: hTSC, TFAP2C, ChIPseq, rep2

description: Chromatin IP against TFAP2C

value: Placenta

value: Human trophoblast stem cells


title: SCF4


title: BL3: Lesion2 before NBUVB treatment

description: controls


title: SCF3


title: Wild-type3

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

data_processing:
Sequence reads were trimmed for low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCm39 using subread.
Read quantification was performed by featureCounts.
Genes with low counts (< 75 in at least 2 samples of any group) were filtered out and normalization was performed by TMM.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Adult testis

extract_protocol:
Total RNA was extracted from testes using TRIzol reagent and then treated with Dnase for 1 h.
RNA libraries were prepared using the TruSeq RNA kit from Illumina (NEB, USA) according to the manufacturer’s recommendations.

value: Adult testis

value: WT


title: SCF2

value: Broiler Ross 308


title: hTSC, TFAP2C, ChIPseq, rep1

description: Chromatin IP against TFAP2C


title: SCF1


title: hTSC, TEAD4, ChIPseq, rep2

description: Chromatin IP against TEAD4


title: Wild-type4


title: BL1: Lesion1 before NBUVB treatment

description: controls


title: Iqch knockout 4

value: Iqch-/-


title: hTSC, MAFK, ChIPseq, rep2

description: Chromatin IP against MAFK

value: MAFK


title: BL4: Lesion3 before NBUVB treatment

description: controls


title: hTSC, TEAD4, ChIPseq, rep1

description: Chromatin IP against TEAD4


title: Iqch knockout 2


title: PROseq_exp2_NELFeKD_FP_10min_rep2

city: Ithaca

first: Michael

last: DeBerardine

state: NY

address: 426 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Adapter trimming using cutadapt v1.18 (--nextseq-trim 10 --minimum-length 15 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC).
Alignment to rDNA repeats using bowtie2 (--very-sensitive) to count and remove ribosomal RNA reads.
Alignment using bowtie2 (--very-sensitive) to a custom-made “combined” genome containing both dm6 and mm10 chromosomes, but where mm10 chromosomes have been masked for sites that Drosophila S2 cell PRO-seq (without spike-in) (Duarte et al. 2016, PMID: 27492368) can erroneously align uniquely.
R/Bioconductor package BRGenomics v1.4.0 used to process bam files to count and remove spike-in (mm10) reads and to generate and export bigWig coverage tracks made from only the 3’ most base before the run-on position. Spike-in normalization from BRGenomics uses the replicate-specific “batch normalization” approach, with units in relative reads per million (RRPM) (“method = SRPMC”).
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files of stranded, single-base resolution coverage data based on the second-most 3' base in the original RNA insert (the last base incorporated before the run-on). Scores are read counts, with minus strand scores negated. Normalized files in units RRPM (see processing steps/manuscript).
Library strategy: PRO-seq

organism: Drosophila melanogaster

growth_protocol: Drosophila melanogaster S2 cells grown at 26˚C in M3+BPYE with 10% FBS

extract_protocol:
S2 cells (with spike-in mouse embryonic fibroblasts) were permeabilized following the PRO-seq protocol in Mahat et al. 2016 (PMID: 27442863), with all steps performed within a cold room (4˚C), with cells kept on ice between handling, and all centrifugation steps at 4˚C. Cells were first spun and resuspended in 5 mL Wash Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 150 mM sucrose; 5 mM MgCl2; 0.5 mM CaCl2; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche cOmplete); 20 units Superase-In RNase inhibitor) before being resuspended in Permeabilization Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 250 mM sucrose; 5 mM MgCl2, 1 mM EGTA; 0.05% Tween-20; 0.1% Nonidet P-40 substitute; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche); 20 units Superase-In) and left on ice for 5 minutes. Cell permeability was assessed >99% under a microscope in the presence of 0.2% Trypan Blue. Permeabilized cells were then washed twice in 5 mL Wash Buffer before being resuspended in 220 µL Storage Buffer (50 mM Tris-Cl pH 8.3; 40% glycerol; 5 mM MgCl2; 0.1 mM EDTA; 0.5 mM DTT) which was divided between 2 aliquots (~9 million cells each) and flash frozen in liquid nitrogen before storage at -80˚C.
PRO-seq was performed as in Mahat et al. 2016 (PMID: 27442863), but for the time-course experiments, a 3’ adapter containing an in-line library-specific barcode (5’-/5Phos/GNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC-/Inverted dT/-3’) which allows libraries to be pooled following the 3’ adapter ligation to reduce the number of samples being handled for all steps downstream.

treatment_protocol: 15 million S2 cells were seeded in 15 mL of FBS-free media, and dsRNA was added at 10 µg/mL for a 45 min pre-incubation, after which 15 mL media with 20% FBS was added (for a final 10% FBS). After 2 days, the dsRNA treatment procedure was repeated, and cells were grown another 2 days. Cells from 2 identically treated T150 flasks were combined, and a sample was taken for spectrophotometric counting (OD600). 38.75 million cells for each dsRNA treatment were divided between 2 tubes for treatment with either DMSO or 500 nM Flavopiridol at 26˚C for the time indicated. Treatments were abruptly stopped by inserting the tubes into ice. Cells were pelleted (4˚C spin at 1000 x g for 5 min) and resuspended in ice-cold PBS. An estimated 8 x 10e4 mouse embryonic fibroblasts (roughly 1:250 ratio to S2 cells) were added as an exogenous spike-in control for normalization.

tag: dsrna

value: NELF-E

tag: treatment drug

value: Flavopiridol (500 nM)

tag: treatment time

value: 10 min


title: hTSC, MAFK, ChIPseq, rep1

description: Chromatin IP against MAFK


title: PROseq_exp2_NELFeKD_FP_20min_rep1

value: 20 min


title: PROseq_exp2_NELFeKD_FP_20min_rep2


title: hTSC, GATA2, ChIPseq, rep2

description: Chromatin IP against GATA2


title: Iqch knockout 3


title: Iqch knockout 1


title: hTSC, GATA2, ChIPseq, rep1

description: Chromatin IP against GATA2


title: Wild-type2


title: PROseq_exp2_NELFeKD_FP_10min_rep1


title: Wild-type1


title: Human T10, small RNA

city: Baltimore

first: Brittney

last: Williams

state: Maryland

address: 22 South Greene St, S11C00

department: Anesthesiology

institute: University of Maryland Baltimore

data_processing:
Raw reads and counts were determined for small RNA
Normalization was performed using cel-mir-39-spike in for human and mouse samples and counts were averaged across all human and mouse samples, respectively
A normilization factor for cel-mir-39-spike was calculated within each individual sample and then applied to the raw read count to generate the processed files
Supplementary files format and content: .txt files for small RNA species for each sample

source_name: Plasma

extract_protocol:
RNA was isolated using Trizol LS from 100 µl of cell-free plasma and was analyzed by an Agilent 2100 Bioanalyzer with the Small RNA kit
Libraries were sequenced on an Illumina HiSeq2500 using six microliters of each RNA solution and used for small RNA sequencing library preparation.
small RNAseq, Library creation using  Norgen Biotek Small RNA Library Prep Kit for miRNA and exceRpt small RNA-seq Pipeline (v4.6.2)

value: Plasma

value: Trauma


title: PROseq_exp2_NELFeKD_FP_05min_rep2

value: 5 min


title: hTSC, FOS, ChIPseq

description: Chromatin IP against FOS

value: FOS


title: hTSC, EP300, ChIPseq, rep2

description: Chromatin IP against EP300


title: Human T9, small RNA


title: PROseq_exp2_NELFeKD_FP_05min_rep1


title: hTSC, EP300, ChIPseq, rep1

description: Chromatin IP against EP300


title: Human T8, small RNA


title: PROseq_exp2_NELFeKD_DMSO_rep1

value: DMSO


title: Human T7, small RNA


title: Human T6, small RNA


title: PROseq_exp2_LacZKD_FP_20min_rep2

value: LacZ


title: L1207 H3K9ac rep1

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 1.18.61   and CASAVA 1.8.2.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0   with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: ChIPed DNA

growth_protocol: DMEM/F12 supplemented with 10% FBS

extract_protocol: Fixation in 10% Formaldehyde. ChIP using Active Motif High sensitivity ChIP kit

treatment_protocol: No treatment


title: L1207 H3K27ac rep1


title: PROseq_exp2_LacZKD_FP_20min_rep1


title: Human T5, small RNA


title: L1207 H3K4me1 rep1


title: Human T4, small RNA


title: Xinyan1_28℃_10d_rep3

type: RNA

city: Chongqing

first: Kexuan

last: Deng

address: Tiansheng

institute: Southwest University

description: Gene expression under normal condition

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Nicotiana tabacum

source_name: stem tip_28℃_10d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The seedling of two ﬂue cured tobacco varieties (Xingyan 1 and YunYan 85) grow in growth chamber.

extract_protocol: Total RNA was extracted from 100 mg of tobacco stem tips using Trizol (Invitrogen, Gaithersburg, MD, USA).

treatment_protocol: The seedling of two ﬂue cured tobacco varieties (Xingyan 1 and YunYan 85) with six true-leaf were grown at 28°C and 12°C for 10 days in growth chamber.

tag: cultivar

value: stem tips

tag: period

value: Flower bud differentiation


title: L1207 H3K27me3 rep1


title: PROseq_exp2_NELFeKD_DMSO_rep2


title: PROseq_exp2_LacZKD_FP_10min_rep1


title: L1207 H3K9me3 rep1


title: Xinyan1_12℃_10d_rep1

description: Gene expression under cold stress

source_name: stem tip_12℃_10d

tag: tissue


title: Sinoatrial Node Sample Pool 3

city: Chapel Hill/ 27599

last: Bressan

state: NC

address: 100 Mason Farm Rd

department: Cell Biology and Physiology

institute: University of North Carolina Chapel Hill

data_processing:
The quality control and alignment were done in the Linux environment on the UNC Longleaf server.
The ends of the FASTA files were run through Trimmomatic using the recommended settings.
The FASTA files were aligned to the Gallus gallus GRCg6a genome downloaded from the NCBI ensemble genome. The samtools package was used to convert SAM files to BAM files.
The gene count matrix was created using the FeatureCounts package.
Files were then exported from the Linux environment were DESEQ analysis was compelted in R
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file providing gene counts per sample

source_name: sinoatrial node

growth_protocol: Gallus gallus eggs were incubated to HH stage 35 (~6.5 days at 37C in a humidified incubator)

extract_protocol:
RNA was extracted using a TRIzol/chloroform protocol followed by column purification using a Monarch Total RNA miniprep Kit
Library construction was preformed using the Illumina NextSeq High Output kitv2.5 according to manufacturer's protocols

value: sinoatrial node


title: PROseq_exp2_LacZKD_FP_05min_rep2


title: L1207 H3K4me3 rep1


title: Xinyan1_28℃_10d_rep1

description: Gene expression under normal condition


title: Sinoatrial Node Sample Pool 2


title: L1207 Input rep1


title: Xinyan1_12℃_10d_rep3

description: Gene expression under cold stress


title: Xinyan1_12℃_10d_rep2

description: Gene expression under cold stress


title: Human T1, small RNA


title: Sinoatrial Node Sample Pool 1


title: L1207 CTCF

value: CTCF


title: Xinyan1_28℃_10d_rep2

description: Gene expression under normal condition


title: Yunyan85_12℃_10d_rep3

description: Gene expression under cold stress


title: Yunyan85_12℃_10d_rep2

description: Gene expression under cold stress


title: Yunyan85_12℃_10d_rep1

description: Gene expression under cold stress


title: Yunyan85_28℃_10d_rep3

description: Gene expression under normal condition


title: PROseq_exp2_LacZKD_FP_10min_rep2


title: PROseq_exp2_LacZKD_DMSO_rep1


title: Human T3, small RNA


title: Atrial Sample Pool 3

source_name: Atria

value: Atria


title: Stationary_Anaerobic_R3

city: Stanford

first: Denise

last: Monack

state: Ca

address: 299 Campus Drive, Fairchild Building D331

department: Microbiology and Immunology

institute: Stanford University

description:
B15
Wildtype SL1344
mRNA

data_processing:
Nf-core-RNA-SEQ, QC, trimgalore, clean reads aligned to WT SL1344 full genome, HiSatt2 as aligner.
Assembly: WT SL1344
Supplementary files format and content: processed_data_gene_counts.xls: Excel sheet of raw gene counts.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Culture

extract_protocol:
RNA from cecal contents and feces was extracted using the QIAGEN RNeasy PowerMicrobiome Kit following manufacturer’s instructions. RNA from liquid cultures was extracted with the QIAGEN RNeasy Mini Kit following the QIAGEN supplementary protocol: purification of total RNA from bacteria.
RNA libraries were prepared using the Illumina stranded total RNA prep ligation with ribo-zero plus kit. rRNA from mice was depleted prior to library construction and confirmed with Agilent Bioanalyzer Prokaryote Total RNA Pico. No experimental rRNA removal was used for the in vitro samples. RNA integrity was confirmed with Agilent Bioanalyzer Prokaryote Total RNA Pico.
In vivo and in vitro libraries underwent quality control by Novogene Corporation Inc. Pulled in vivo and in vitro libraries were loaded onto separate lanes of the S4 flow cell and sequenced on an Illumina NovaSeq 6000 and were run using the PE150 strategy. Data were unequally shared, 10.11G raw data (100.4 million paired reads) for each in vivo sample and 4.5G raw data (15 million paired reads) for each in vitro sample.

value: Culture

tag: sample type

value: in vitro

value: Wildtype

tag: condition

value: stationary anerobic in LB


title: Atrial Sample Pool 2


title: L1207 H3K9ac rep2


title: Human T2, small RNA


title: Atrial Sample Pool 1


title: L1207 H3K4me1 rep2


title: PROseq_exp2_LacZKD_FP_05min_rep1

value: Flavopiridol (500 nM)


title: Log_Anaerobic_R2

description:
B11
Wildtype SL1344
mRNA

value: log anerobic in LB


title: Yunyan85_28℃_10d_rep1

description: Gene expression under normal condition


title: Yunyan85_28℃_10d_rep2

description: Gene expression under normal condition


title: PROseq_exp2_LacZKD_DMSO_rep2

value: 20 min


title: PROcap_LacZKD_noTAP

data_processing:
Adapter trimming using cutadapt v1.18 (--nextseq-trim 10 --minimum-length 15 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC).
Alignment to rDNA repeats using bowtie2 (--very-sensitive) to count and remove ribosomal RNA reads.
Alignment using bowtie2 (--very-sensitive) to a custom-made “combined” genome containing both dm6 and mm10 chromosomes, but where mm10 chromosomes have been masked for sites that Drosophila S2 cell PRO-seq (without spike-in) (Duarte et al. 2016, PMID: 27492368) can erroneously align uniquely.
R/Bioconductor package BRGenomics v1.4.0 used to process bam files to remove spike-in (mm10) reads and to generate and export bigWig coverage tracks made from only the 5’ most base.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files of stranded, single-base resolution coverage data based on the most 5' base in the original RNA insert. Scores are read counts, with minus strand scores negated.
Library strategy: PRO-cap

extract_protocol:
S2 cells (with spike-in mouse embryonic fibroblasts) were permeabilized following the PRO-seq protocol in Mahat et al. 2016 (PMID: 27442863), with all steps performed within a cold room (4˚C), with cells kept on ice between handling, and all centrifugation steps at 4˚C. Cells were first spun and resuspended in 5 mL Wash Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 150 mM sucrose; 5 mM MgCl2; 0.5 mM CaCl2; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche cOmplete); 20 units Superase-In RNase inhibitor) before being resuspended in Permeabilization Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 250 mM sucrose; 5 mM MgCl2, 1 mM EGTA; 0.05% Tween-20; 0.1% Nonidet P-40 substitute; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche); 20 units Superase-In) and left on ice for 5 minutes. Cell permeability was assessed >99% under a microscope in the presence of 0.2% Trypan Blue. Permeabilized cells were then washed twice in 5 mL Wash Buffer before being resuspended in 220 µL Storage Buffer (50 mM Tris-Cl pH 8.3; 40% glycerol; 5 mM MgCl2; 0.1 mM EDTA; 0.5 mM DTT) which was divided between 2 aliquots (~9 million cells each) and flash frozen in liquid nitrogen before storage at -80˚C.
PRO-cap libraries were prepared as in Mahat et al. 2016 (PMID: 27442863), but prior to enzymatic removal of the nascent RNA 5’ cap, the PRO-cap sample was split into two tubes. One tube received enzymatic treatment with tobacco acid pyrophosphatase (TAP; EpiCentre T19500, now discontinued) to remove the 5’ cap structure, while the other received only reaction buffer, lacking TAP, and thus serves as a measurement of remaining background (uncapped) signal (Kruesi et al. 2013, PMID: 23795297). The remainder of the library preparation was performed identically for control and experimental PRO-cap samples.

treatment_protocol: 15 million S2 cells were seeded in 15 mL of FBS-free media, and dsRNA was added at 10 µg/mL for a 45 min pre-incubation, after which 15 mL media with 20% FBS was added (for a final 10% FBS). After 2 days, the dsRNA treatment procedure was repeated, and cells were grown another 2 days. Cells were counted using spectrophotometry (OD600), pelleted (4˚C spin at 1000 x g for 5 min) and resuspended in ice-cold PBS. An estimated 8 x 10e4 mouse embryonic fibroblasts (roughly 1:250 ratio to S2 cells) were added as an exogenous spike-in control for normalization.


title: L1207 H3K27me3 rep2


title: PROcap_LacZKD


title: L1207 H3K9me3 rep2


title: Log_Anaerobic_R1

description:
B10
Wildtype SL1344
mRNA


title: Stationary_Aerobic_R3

description:
B9
Wildtype SL1344
mRNA

value: stationary aerobic in LB


title: RNAseq_exp1_NELFeKD_DMSO_rep2

data_processing:
Adapter trimming and UMI extraction using fastp v0.20.0 (--trim_poly_g --trim_poly_x --umi --umi_loc read1 --umi_len 6 --overrepresentation_analysis --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA).
Alignment using STAR v2.7.3a (--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000) to a custom-made “combined” genome containing both dm6 and mm10 chromosomes, but where mm10 chromosomes have been masked for sites that Drosophila S2 cell PRO-seq (without spike-in) (Duarte et al. 2016, PMID: 27492368) can erroneously align uniquely.
Removal of PCR duplicates using umi_tools v1.0.0, with option (--umi-separator=:) to match fastp default UMI extraction format.
R/Bioconductor package BRGenomics v1.4.0 used to process bam files to count and remove spike-in (mm10) reads, and to export bedGraph files of the full-length reads. Spike-in normalization from BRGenomics uses the replicate-specific “batch normalization” approach, with units in relative reads per million (RRPM) (“method = SRPMC”).
Genome_build: dm6
Supplementary_files_format_and_content: bedGraph files contain the full span of uniquely aligned reads, with one line for each exact mapped read insert (exact same 5' and 3'), and scores show number of reads with that exact inserts. Minus strand files have scores negated. Normalized files in units RRPM (see processing steps/manuscript).

extract_protocol:
RNA was extracted from the same S2 cell material (with mouse embryonic fibroblasts spiked-in) used for the PRO-seq libraries. For each condition, ~1.9 million S2 cells were used, and total RNA was extracted using TRIzol LS followed by ethanol precipitation and DNase treatment (1hr @ 37˚C with 2U DNase I), followed by a second TRIzol LS extraction and ethanol precipitation. RNA was quantified using Qubit RNA BR assay.
400 ng of total RNA was used for RNA-seq library preparation using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) (Lexogen A01172), which uses oligo-dT to prime for first strand synthesis and random priming for second strand synthesis (which is followed by single-ended sequencing in the forward/sense direction of the mRNA). cDNA was prepared using the manufacturer’s instructions. The manufacturer’s UMI Second Strand Synthesis Module was used to add UMIs for detection of PCR duplicates. Final libraries were PCR amplified (12 cycles) and quantified using the Qubit dsDNA HS assay.

value: NELF-E

value: 10 min


title: L1207 H3K4me3 rep2


title: RNAseq_exp1_LacZKD_DMSO_rep2

value: DMSO


title: Stationary_Aerobic_R1

description:
B7
Wildtype SL1344
mRNA


title: L1207 Input rep2


title: RNAseq_exp1_NELFeKD_DMSO_rep1


title: L1207 H3K27ac rep2


title: Stationary_Anaerobic_R1

description:
B13
Wildtype SL1344
mRNA


title: Log_Aerobic_R2

description:
B5
Wildtype SL1344
mRNA

value: log aerobic in LB


title: RNAseq_exp1_LacZKD_DMSO_rep1

value: LacZ


title: Log_Aerobic_R3

description:
B6
Wildtype SL1344
mRNA


title: hNK16

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

description:
Cell isolation protocol: Non-parenchymal cells were isolated from whole liver explant using mechanical and enzymatic digestion. Briefly, small pieces of liver were minced and incubated at 37˚C for 2h in 0.05% Collagen type IV + 0.02% DNAse in RPMI. Cell suspension was washed twice with DNAse wash solution and washed a third time with RPMI medium.
Sorting staining protocol: Cells were then incubated at 4˚C at the dark with Fixable Viability Dyes-FITC, anti-CD45-APC, anti-CD3-PE.CF594, anti-CD56-V450, and anti-CD16-BV605. After wash, cells were resuspended in PBS+2% FBS and sorted using the BD FACSAria™ Fusion into 90% FBS solution at 4˚C. Sorted cells were centrifuge at 400xg for 5 min at 4°C, resuspended in 50µl of PBS with 0.04% BSA and cell number and viability were accessed by Countess II (Invitrogen).
Partitioning protocol: Cells were partitined using Next GEM Single Cell 3ʹ GEM Kit v3.1 (10x Genomics) according to manufacturer's instructions.

library_source: transcriptomic single cell

data_processing:
Illumina BCL files were de-multiplexed and converted to FASTQs using Cell Ranger mkfastq (version 5.0.1, 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
FASTQs were then used to quantify gene expression using Cell Ranger count (version 5.0.1) and the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: Position sorted BAMs, BAM indexes, and gene expression counts in 10X format (separate barcodes, features, and matrix files for each sample).

source_name: NK cells from subject 16

extract_protocol: Libraries were prepared using Next GEM Single Cell 3ʹ Library Kit v3.1 according to manufacturer's instructions.

tag: pathology

value: NASH

tag: cell type

value: NK


title: hNK15

source_name: NK cells from subject 15


title: PROseq_exp1_NELFeKD_FP_rep2

data_processing:
Removal of PCR duplicates using prinseq_lite v0.20.4 (-derep 1).
Adapter trimming using cutadapt (--cut 6 --nextseq-trim 10 --minimum-length 15 -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC).
Alignment to rDNA repeats using bowtie2 (--very-sensitive) to count and remove ribosomal RNA reads.
Alignment using bowtie2 (--very-sensitive) to a custom-made “combined” genome containing both dm6 and mm10 chromosomes, but where mm10 chromosomes have been masked for sites that Drosophila S2 cell PRO-seq (without spike-in) (Duarte et al. 2016, PMID: 27492368) can erroneously align uniquely.
R/Bioconductor package BRGenomics v1.4.0 used to process bam files to count and remove spike-in (mm10) reads and to generate and export bigWig coverage tracks made from only the 3’ most base before the run-on position. Spike-in normalization from BRGenomics uses the replicate-specific “batch normalization” approach, with units in relative reads per million (RRPM) (“method = SRPMC”). However, spike-in NFs modified for FP samples in experiment 1 due to a variance in adding spike-in (this approach validated in experiment 2, see manuscript).
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files of stranded, single-base resolution coverage data based on the second-most 3' base in the original RNA insert (the last base incorporated before the run-on). Scores are read counts, with minus strand scores negated. Normalized files in units RRPM (see processing steps/manuscript).
Library strategy: PRO-seq

extract_protocol:
S2 cells (with spike-in mouse embryonic fibroblasts) were permeabilized following the PRO-seq protocol in Mahat et al. 2016 (PMID: 27442863), with all steps performed within a cold room (4˚C), with cells kept on ice between handling, and all centrifugation steps at 4˚C. Cells were first spun and resuspended in 5 mL Wash Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 150 mM sucrose; 5 mM MgCl2; 0.5 mM CaCl2; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche cOmplete); 20 units Superase-In RNase inhibitor) before being resuspended in Permeabilization Buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 250 mM sucrose; 5 mM MgCl2, 1 mM EGTA; 0.05% Tween-20; 0.1% Nonidet P-40 substitute; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche); 20 units Superase-In) and left on ice for 5 minutes. Cell permeability was assessed >99% under a microscope in the presence of 0.2% Trypan Blue. Permeabilized cells were then washed twice in 5 mL Wash Buffer before being resuspended in 220 µL Storage Buffer (50 mM Tris-Cl pH 8.3; 40% glycerol; 5 mM MgCl2; 0.1 mM EDTA; 0.5 mM DTT) which was divided between 2 aliquots (~9 million cells each) and flash frozen in liquid nitrogen before storage at -80˚C.
PRO-seq was performed as in Mahat et al. 2016 (PMID: 27442863), but with a modified 3’ RNA adapter (5’-/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/Inverted dT/-3’) that contains a random 6-mer as a Unique Molecular Index (UMI) which is used to remove PCR duplicates. Note that this adapter is different from the one used in the time-course experiment (experiment 2).


title: Log_Aerobic_R1

description:
B4
Wildtype SL1344
mRNA


title: PROseq_exp1_NELFeKD_FP_rep1


title: RT112 H3K27ac rep1

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0   with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: RT112 H3K27ac

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol:
Fixation in 10% Formaldehyde. ChIP using Active Motif High sensitivity ChIP kit
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881,Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

tag: chip antibody


title: RT112 H3K4me1 rep1

source_name: RT112 H3K4me1


title: RT112 H3K9ac rep1

source_name: RT112 H3K9ac


title: RT112 H3K27me3 rep1


title: MidLog_Aerobic_R3

description:
B3
Wildtype SL1344
mRNA

value: mid log aerobic in LB


title: hNK14

source_name: NK cells from subject 14


title: MidLog_Aerobic_R2

description:
B2
Wildtype SL1344
mRNA


title: RT112 H3K9me3 rep1

source_name: RT112 H3K9me3


title: hNK13

source_name: NK cells from subject 13


title: PROseq_exp1_NELFeKD_DMSO_rep1


title: PROseq_exp1_NELFeKD_DMSO_rep2


title: 21dpi_Cecum_R4

description:
A21
Wildtype SL1344
mRNA

source_name: Cecum

value: Cecum

value: in vivo

tag: time

value: 21 days post infection


title: Stationary_Aerobic_R2

description:
B8
Wildtype SL1344
mRNA

value: Culture

value: in vitro

value: Wildtype


title: hNK12

source_name: NK cells from subject 12

value: PSC


title: 21dpi_Cecum_R3

description:
A19
Wildtype SL1344
mRNA


title: PROseq_exp1_LacZKD_FP_rep2

tag: cell line

value: Flavopiridol (500 nM)


title: RT112 Input rep1

source_name: RT112 Input


title: PROseq_exp1_LacZKD_FP_rep1


title: hNK11

source_name: NK cells from subject 11


title: RT112 CTCF

source_name: RT112 CTCF

value: CTCF


title: 21dpi_Feces_R5

description:
A24
Wildtype SL1344
mRNA

source_name: Feces

value: Feces


title: hNK10

source_name: NK cells from subject 10


title: PROseq_exp1_LacZKD_DMSO_rep2

value: 10 min


title: RT112 H3K27ac rep2


title: 21dpi_Base_Cecum_R2

description:
A14
Wildtype SL1344
mRNA


title: hNK8

source_name: NK cells from subject 8

value: HCV


title: 21dpi_Feces_R3

description:
A22
Wildtype SL1344
mRNA


title: hNK9

source_name: NK cells from subject 9


title: RT112 H3K9ac rep2


title: PROseq_exp1_LacZKD_DMSO_rep1

value: DMSO


title: HSC-1 siLINP1

city: Guangzhou

first: Xiaoting

last: Liang

state: Guangdong

address: School of Public Health, 1023 Shatai South Road, Southern Medical University, Baiyun District, Guangzhou city, Guangdong Province

department: school of public health

institute: southern medical university

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values for each Sample.

source_name: HSC-1 cells

growth_protocol: HSC-1 were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with siNC or siLINP1 with transfection reagent when the cells were about 70% confluency and then cells were incubate in non-serum DMEM at 37°C with 5% CO2 for 6 hour. After 6h change the medium with 10% serum DMEM and continuously incubate  24h.

tag: treatment


title: 21dpi_Feces_R4

description:
A23
Wildtype SL1344
mRNA

tag: genotype


title: RT112 H3K4me1 rep2


title: HSC-1 siNC

value: siNC


title: RT112 H3K4me3 rep1

source_name: RT112 H3K4me3


title: RT112 H3K27me3 rep2


title: hNK7

source_name: NK cells from subject 7


title: hNK6

source_name: NK cells from subject 6


title: RT112 H3K9me3 rep2


title: 21dpi_Base_Cecum_R1

description:
A13
Wildtype SL1344
mRNA


title: 21dpi_Base_Feces_R2

description:
A17
Wildtype SL1344
mRNA


title: GCN4 ko H2O2 30 R2

city: Buffalo

first: John

middle: C.

last: Panepinto

address: 955 Main Street Suite 5240

institute: University at Buffalo

data_processing:
Adapter sequences were trimmed and quality filtering performed using Cutadapt (-q 20 -m 1 -a AGATCGGAAGAG -A AGATCGGAAGAG).
Trimmed reads were then checked for quality using FastQC.
Reads were mapped to the genome using STAR aligner (--runThreadN 6 --runMode alignReads).
Transcipt counts were quantified usin RSEM. (-p 12)
Differential expression was determined using DeSeq2 in R.
Assembly: FungiDB-54_CneoformansH99
Supplementary files format and content: rsem counts

organism: Cryptococcus neoformans

growth_protocol: Cells were grown to midlog stage in YPD at 30 ˚C.

extract_protocol:
RNA was extracted using RNeasy kit  from QIAGEN, and Dnase treated using the QIAGEN on-column RNase free DNase kit.
Library prep was performed using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Indicated samples (H2O2) were treated with 1 mM H2O2 for 1 hour.

tag: strain

tag: growth phase

value: Mid Log Culture


title: hNK5

source_name: NK cells from subject 5

value: Normal

value: NK


title: H99 H2O2 30 R2

source_name: Wildtype


title: 21dpi_Base_Feces_R1

description:
A16
Wildtype SL1344
mRNA


title: GCN4 ko 30 R2


title: RT112 H3K4me3 rep2


title: 14dpi_Cecum_R3

description:
A8
Wildtype SL1344
mRNA

value: Cecum

value: 14 days post infection


title: RT112 Input rep2


title: hNK3

source_name: NK cells from subject 3


title: PUF4 ko 30 R2


title: 14dpi_Cecum_R1

description:
A7
Wildtype SL1344
mRNA

value: in vivo


title: H99 30 R2


title: 14dpi_Feces_R4

description:
A12
Wildtype SL1344
mRNA


title: hNK1

source_name: NK cells from subject 1


title: GCN4 ko H2O2 30 R1


title: Inf_03

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to the cynomolgus reference genome (Macaca_fascicularis_5.0) using HISAT2 (v2.0.5) and quantified using FeatureCounts (v1.5.0-p3).
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

organism: Macaca fascicularis

source_name: aorta

extract_protocol:
RNA was extracted using Rneasy fibrous tissue mini kits (Qiagen, #74704). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA library prep kit for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Aortic samples were harvested from norma cynomolgus monkeys.

value: aorta

value: Baseline


title: Inf_02


title: Inf_04


title: H99 H2O2 30 R1

value: Wildtype


title: Inf_01


title: 14dpi_Feces_R3

description:
A10
Wildtype SL1344
mRNA


title: 14dpi_Base_Feces_R2

description:
A5
Wildtype SL1344
mRNA


title: Sup_04


title: GCN4 ko 30 R1


title: 14dpi_Base_Feces_R1

description:
A4
Wildtype SL1344
mRNA


title: Sup_03


title: PUF4 ko 30 R1


title: PlusAP_Input_BiolRep2

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description: With EGFR-Erbb2 dimerizer, input chromatin, replicate 2

data_processing:
Samples were demultiplexed with Bcl2fastq2 before analysis.
Read quality was assessed with FastQC (version 0.11.5), and reads were aligned to the human genome (GRCh38) using Bowtie2 (version 2.2.9) with default settings.  Only uniquely mapped and non-duplicated reads were selected for further analysis. Peaks were called using MACS2 (version 2.2.7.1) comparing immunoprecipitated chromatin with input chromatin using default settings.

source_name: B2B1 clone of MCF10A-5E

growth_protocol: Cells were plated at 12,500 cells/cm^2 in assay medium + 2% matrigel + 5 ng/ml EGF and refed after four days.

extract_protocol:
Cells were crosslinked with 37% methanol-stabilized formaldehyde at a final concentration of 1% for 10 min at room temperature.  Crosslinking was quenched with 0.125 M Glycine for 5 min at room temperature.  Cells were lysed with 300 µl lysis buffer (50 mM Tris-HCl [pH 8.0], 1% SDS, 5 mM EDTA, 10 µg/ml aprotinin, 10 µg/ml leupeptin, 1 µg/ml pepstatin, 1 mM PMSF).
Approximately 0.1–20 ng ChIP DNA was fragmented to a size range of 200 bp on a Covaris instrument for 2 mins using 15 µl microTUBE-15 AFA Beads Screw-cap.  Libraries were prepared with the NEBNext Ultra II DNA library preparation kit (New England Biolabs) and quantified by Qubit fluorimetry and quality controlled on a Bioanalyzer.

treatment_protocol: 0.5 µM AP21967 or 0.1% ethanol vehicle control for 24 hours

value: B2B1 clone of MCF10A-5E

value: Breast epithelial

value: Overlay culture, six days plus 0.5 uM AP21967 for 24 hours


title: PlusAP_EGFRGluGlu_BiolRep1

description: With EGFR-Erbb2 dimerizer,GluGlu ChIP, replicate 1


title: hNK4

source_name: NK cells from subject 4


title: PlusAP_NaiveIgG_BiolRep2

description: With EGFR-Erbb2 dimerizer, naïve IgG ChIP, replicate 2


title: Sup_02


title: H99 30 R1


title: Sup_01


title: hNK2

source_name: NK cells from subject 2


title: DS

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

institute: Institut Curie

description: paired-end Illumina Miseq (2x250bp)

data_processing:
Library strategy: Mobilome-seq
TEs generate extrachromosomal circular DNAs (eccDNAs) when they are active.  The sequencing of these eccDNAs by the mobilome sequencing was a  successfully method to identify active TEs (Lanciano et al., 2017). In  order to identify the effect of DDM1 knock down and a hydric stress on the  release of TE activity we used approximately 6   g of genomic DNA to perform  mobilome-seq libraries. eccDNAs were isolated and libraries were prepared  and sequenced following Lanciano et al., (2017). Bioinformatics was carried  out on the Populus tremula    alba genome (SPta717 v1.1) by using the same  pipelines as described in Lanciano et al., (2017). In order to obtain TE  database for Populus tremula    alba genome, we used the TE database based  on Populus trichocarpa genome (version 3.0). In brief, the sequencing reads  were first filtered against the mitochondria and chloroplast genomes before  being i) mapped against the P. tremula    alba reference genome using  Bowtie2, ii) mapped for split reads (SR) using segemehl software (Hoffmann  et al., 2014) and iii) de novo assembled using a5-miseq (Coil et al.,  2015). Given the range of variation of the DOC coverage, we assigned TE  families to four groups following Lanciano et al., (2017): The first group  was named    moderate or not active TEs (group    TE   )   , and comprised TEs with  a DOC ranging from 4 to 199X. The second group was named    active TEs     (group    TE+   ) and comprised TEs with a DOC ranging from 200-1999X. The  third group was named    very active TEs    (   TE++   ) and comprised TEs with a  DOC ranging from 2000 to 9999X. The fourth group was named    highly active  group    (   TE+++   ), and comprised TEs with a DOC ranging from 10000 to 51000X.
Supplementary_files_format_and_content: coverage data

organism: Populus tremula x Populus alba

source_name: meritem

extract_protocol:
Genomic DNA was extracted using CTAB protocol and extrachrosomal DNA was amplified as described in Lanciano et al, PLoS Genetics 2017.
Illumina NexteraXT

value: 717-1B4 clone

value: shoot apical meristem

value: RNAi ddm1 line 23

tag: stress

value: control


title: BT

description: paired-end Illumina Miseq (2x250bp)

value: RNAi ddm1 line 15

value: drought and rewatering


title: testis, dot1l_ko_scRNAseq

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: 150bp PE scRNA-seq from Dot1L cKO testes

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics).
Matrices were imported to R using Seurat 4.1.0 and conditions were combined into one Seurat object. Reads were filtered to exclude doublets, dying cells, or cells with high mitochondrial content. The filtered subset was log normalized and scaled, and linear dimensional reduction was performed  using PCA. The “RunUMAP()” function was used to generate Uniform Manifold Approximation and Projection (UMAP) objects for further analysis.
Clusters were associated with stages of spermatogenesis based on expression of key spermatogenic genes. Clusters that could not confidently be assigned an identity were removed and the data was normalized and scaled again.
The datasets were integrated using Harmony, and a final UMAP was generated for further analysis.
Assembly: mm10
Supplementary files format and content: index (.tsv), feature (.tsv), and matrix (.mtx) files

source_name: whole testis

extract_protocol:
Decapsulated testes were incubated in DMEM containing 0.75 mg/ml collagenase type IV (Gibco, 17104-019) for 10 mins at 37°C with occasional inversion. Equal volume of DMEM was added to the suspension of dissociated tubules before centrifuging at 400 xg for 5 mins at 4 °C. After removing the supernatant, the cell pellet was washed in DMEM and resuspended in 0.05% trypsin-EDTA (Gibco, 25200-056) for 10 mins incubation at room temperature. An equal volume of ice-cold DMEM+10%FBS was then added to the cell suspension before washing the pellet twice with media. The cell pellet was resuspended in DPBS (Sigma, D8537) containing 0.04% bovine serum albumin (sigma, A9647) and filtered through a 100 µm filter (Falcon, 22363549) then a 40 µm filter (Falcon, 352340) to generate a single cell suspension.
Single cell RNA-seq libraries were constructed from whole dissociated testis samples using the Chromium Next GEM Single Cell 3’ GEM kit v3.1 (10x Genomics PN-1000121) according to the manufacturer’s instructions.
150 bp paired end

value: whole testis

value: Dot1L fl/delta; Ddx4-Cre+ (Dot1L cKO)


title: BS

description: paired-end Illumina Miseq (2x250bp)


title: MinusAP_EGFRGluGlu_BiolRep2

description: Without EGFR-Erbb2 dimerizer,GluGlu ChIP, replicate 2

value: Overlay culture, seven days


title: testis, control_scRNAseq

description: 150bp PE scRNA-seq from control testes

value: Dot1L fl/+; Cre- (control)


title: RM9-CBD-IL-12 #2 [scRNA-seq]

city: Seattle

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
The demultiplexing, barcoded processing, gene counting visulaizing and clustering were made using the Seurat v4 and SingleR v1.10.0.
Assembly: mm10
Supplementary files format and content: comma-separated values files

extract_protocol:
RNA was harvested using Purelink™ RNA Mini Kit (Thermo Scientific). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library was performed according to the manufacter’s instructions (10x Genomics Chromium platform).

value: Mouse prostate cells

value: CBD-IL-12 treated


title: PlusAP_Input_BiolRep1

description: With EGFR-Erbb2 dimerizer, input chromatin, replicate 1


title: Dsc_04

value: aorta

value: Baseline


title: Dsc_03


title: AT

description: paired-end Illumina Miseq (2x250bp)

value: WT


title: RM9-CBD-IL-12 #1 [scRNA-seq]


title: PlusAP_EGFRGluGlu_BiolRep2

description: With EGFR-Erbb2 dimerizer,GluGlu ChIP, replicate 2

value: B2B1 clone of MCF10A-5E

value: Breast epithelial


title: MinusAP_NaiveIgG_BiolRep2

description: Without EGFR-Erbb2 dimerizer, naïve IgG ChIP, replicate 2


title: MinusAP_Input_BiolRep2

description: Without EGFR-Erbb2 dimerizer, input chromatin, replicate 2


title: DT

description: paired-end Illumina Miseq (2x250bp)

value: 717-1B4 clone


title: AS

description: paired-end Illumina Miseq (2x250bp)

value: shoot apical meristem


title: Dsc_01


title: RM9-Vehicle #2 [scRNA-seq]

value: Vehicle treated

value: Vehicle control


title: Asc_04


title: RM9-Vehicle #1 [scRNA-seq]


title: PlusAP_NaiveIgG_BiolRep1

description: With EGFR-Erbb2 dimerizer, naïve IgG ChIP, replicate 1

value: Overlay culture, six days plus 0.5 uM AP21967 for 24 hours


title: MinusAP_NaiveIgG_BiolRep1

description: Without EGFR-Erbb2 dimerizer, naïve IgG ChIP, replicate 1


title: Asc_03


title: kidney IRI24h-TD

first: Liting

last: Chen

address: 1838 North Guangzhou Blvd.

department: Division of Nephrology

institute: Nanfang Hospital, Southern Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 50%;
 Cell Gene Number < 10000;
 Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: tdT+ single cell suspension from kidney underwent IRI 24h

extract_protocol:
Tissues were dissociated to single cell.
RNA libraries were generated by BD Rhapsody single cell RNA-seq and prepared for sequencing using standard Illumina protocols
scRNA-seq

value: kidney

value: IRI 24h

value: TdT+ cells (mainly podocytes and WT1+ PECs)


title: kidney IRI24h-TDN

source_name: single cell suspension from kidney underwent IRI 24h

value: renal cell mixture (TdT+ cells were enriched)


title: MinusAP_Input_BiolRep1

description: Without EGFR-Erbb2 dimerizer, input chromatin, replicate 1

value: Overlay culture, seven days


title: kidney sham

source_name: single cell suspension from kidney underwent sham surgery

value: sham surgery


title: Dsc_02


title: Asc_02


title: A549 parental rep2

city: Kuopio

first: Anna-Liisa

last: Levonen

state: Savonia region

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Nextseq500 base calling
Hisat2 for alignment with hg19
Raw counts with Homer -condensed
Generation of counts with Homer analyzeRepeats.pl rna hg19 -noadj -condenseGenes -count gene
Genome_build: hg19
Supplementary_files_format_and_content: A549_counts.txt (raw counts for A549 mock, knockout and parental)
Supplementary_files_format_and_content: IFNy_A549_counts.txt (raw counts for A549 mock and knockout +/- IFN-gamma (10 and 100 ng/ml))

source_name: A549 parental

growth_protocol: DMEM + 10 % p/s & 1% FBS. Seeded before confluency

extract_protocol:
Roche High Pure RNA Isolation Kit
Standard Illumina RNA

treatment_protocol: IFN-gamma of 10/ml ng or 100 ng/ml for 48h

value: lung adenocarcinoma

value: NA, no IFN-gamma

value: parental


title: A549 parental rep1


title: cml24-2_Tre_1

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

data_processing:
The isolated total RNA samples were treated with DNase I to degrade any possible DNA contamination and enriched using oligo(dT) magnetic beads, the purified target RNA was fragmented and the transcription was reversed to double-strand cDNA (dscDNA) by using N6 random primer.
The dscDNA was end repaired with phosphate at 5’ end and stickiness ‘A’ at 3’ end, then ligate and adaptor with stickness ’T’ at 3’ end to the dscDNA.
The ligation product was amplified with two specific primers and the PCR product was denatured by heat.
The single strand DNA was cyclized by splint oligo and DNA ligase, sequencing were performed on prepared library. The primary sequencing data, called as raw reads, was subjected to quality control and was filtered into clean reads.
The gene expression levels were calculated using RSEM according to Li and Dewey (2011), and the NOISeq method (Tarazona et al., 2011) was used to screen the differentially expressed genes (DEGs) within samples. The absolute values of the log2(fold change) ≥ 2 and the divergence probability ≥0.8 were used as thresholds to identify significant DEGs. The functional categories of the DEGs were BLASTed against the non redundant GenBank, KEGG Pathway, and UniProt protein databases by the Gene Ontology annotation. The cluster 3.0 program was used to perform the cluster analysis of DEGs,and Java TreeView was used to view the clustering results generated by Cluster 3.0
Genome_build: The clean raw reads with high-quality sequences were mapped to reference sequences and then the downstream analysis including gene expression, Gene Ontology (GO) enrichment analysis, KEGG pathway enrichment analysis, cluster analysis, etc. was performed.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: roots_with Al

growth_protocol: The seedlings were pre-grown in nutrient solution for 6 d at pH5.0 in a growth chamber with a 16/8 h light/dark cycle at 22 oC.

extract_protocol:
The total RNA was isolated using the RNeasy PlantMini Kit (Qiagen) following the manufacturer’s protocol.
RNAseq analysis was performed by BGI Tech (Shenzhen, China) via BGISEQ-500 RNA-Seq platform.

treatment_protocol: Approximately 500 seedlings (6-d-old) of both the wild-type Col and cml24-2 mutant line were exposed to a nutrient solution containing 0 or 10 μM AlCl3 (pH5.0). After 6 h, the roots were sampled for RNA isolation.

value: roots

tag: age

value: six-days

value: with Al

value: cml24-2 mutant


title: Asc_01

value: aorta

value: Baseline


title: LmESAT_C7_40hr

city: New York

first: Herman

last: Gudjonson

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

description:
LmESAT_C7_CD4_T_cell_metadata_11403x11.tsv.gz
LmESAT_C7_CD4_T_counts_normalized_11403x12044.tsv.gz
LmESAT_C7_CD4_T_counts_imputed_11403x12044.tsv.gz
LmESAT_C7_CD4_T_LmESAT_C7_40hr_raw_counts.tsv.gz

data_processing:
Single-cell RNA seq samples were individually processed using the SEQC v0.2.1 pipeline (Azizi et al., 2018) using the package provided mm38 mouse genome reference and default parameters for the 10X platform. The SEQC pipeline performs read alignment, multi-mapping read resolution, as well as cell barcode and UMI correction to generate a (cells x genes) count matrix. The pipeline filters empty droplets from true cells based on total molecule counts, filters cells with >20% mitochondrial molecule fraction and filters cells with low library complexity. Data from D7 gp66:I-Ab+ single-cell TCR-seq were individually processed with the CellRanger (v3.1.0) 5’ RNA-seq and V(D)J pipeline, aligned to mm10-3.0.0 for genomic libraries and vdj_GRCm38_alts_ensembl-3.1.0 for TCR libraries. For each sample, an additional library size filter was used to remove any remaining low quality cell libraries. Genes that were expressed in more than 10 cells were retained for further analysis.
The filtered count matrix was normalized for library size. This normalized matrix was then multiplied by the median of the total molecule count across all cells for numerical stability and log2 transformed with a pseudocount of 0.1 for downstream analysis.
To perform an integrated analysis of naïve CD4 T cell samples, we selected the top 1000 highly variable genes based on normalized dispersion. We then batch corrected expression in naïve CD4 T cell samples using mnnCorrect (Haghverdi et al., 2018).
For naïve C7 and LmESAT C7 timecourse samples, we enhanced connectivity between time-adjacent using the data integration technique Harmony (github.com/dpeerlab/Harmony).
Phenograph was used to cluster PCA reduced expression data for cell type identification. Imputed gene expression was calculated using MAGIC (van Dijk et al., 2018). Putative cell doublets were identified using Scrublet (Wolock et al., 2019) and removed from further analysis.
Genome_build: mm38
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts generated by the SEQC or CellRanger pipeline for each sample, library-size normalized log2-transformed counts for each experiment, MAGIC imputed gene expression data for each experiment and associated cell metadata containing per-cell annotations as presented in the publication.
Supplementary_files_format_and_content: naive_CD4_T_cell_metadata_28146x12.tsv: cell metadata
Supplementary_files_format_and_content: naive_CD4_T_counts_normalized_28146x11488.tsv: normalized abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_counts_imputed_28146x11488.tsv: imputed abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_B6_Naive_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_C7_Naive_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_C7_Naive_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_SMARTA_Naive_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_SMARTA_Naive_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_cell_metadata_11403x11.tsv: cell metadata
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_counts_normalized_11403x12044.tsv: normalized abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_counts_imputed_11403x12044.tsv: imputed abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_16hr_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_16hr_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_40hr_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_cell_metadata_2964x16.tsv: cell metadata
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_counts_normalized_2964x10857.tsv: normalized abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_counts_imputed_2964x10857.tsv: imputed abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_raw_contig_annotations.tsv: raw TCR contig annotations
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_cell_metadata_2717x16.tsv: cell metadata
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_counts_normalized_2717x10573.tsv: normalized abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_counts_imputed_2717x10573.tsv: imputed abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_raw_contig_annotations.tsv: raw TCR contig annotations

source_name: spleen

extract_protocol:
Splenic CD4+ T cells were enriched with the CD4 T cell negative isolation kit (Miltenyi). Cells were incubated with anti-CD16/32 in sorting buffer (2% FBS in PBS) for 10 min at 4°C to block binding to Fc receptors. Extracellular antigens were stained for 30 min at 4°C in sorting buffer. Cells were washed and resuspended in sorting buffer with SYTOX blue (Invitrogen) for exclusion of dead cells. Cells were sorted into cRPMI, pelleted and resuspended in RPMI-2% FBS.
scRNA-seq of FACS-sorted cell suspensions was performed on the Chromium instrument (10X Genomics) following the user guide manual (CG00052 Rev E) and using Single Cell 3’ Reagent Kit (v2). Each sample, containing approximately 8000 cells at a final dilution of 66–70 cells/µl, was encapsulated and barcoded following the manual. Viability was 82-85% for samples containing naïve cells, and 80-99% for samples containing effector cells, as confirmed with 0.2% (w/v) Trypan Blue staining. The encapsulated cells were lysed, and following reverse transcription, the barcoded cDNA was purified with DynaBeads and amplified by 14 cycles of PCR: 98 ̊C for 180 s, 12x (98 ̊C for 15 s, 67 ̊ C for 20 s, 72 ̊C for 60 s), and 72 ̊C for 60 s. 50 ng of PCR-amplified barcoded cDNA was fragmented with the reagents provided in the kit, purified with SPRI beads, and the resulting DNA library was ligated to the sequencing adapter followed by indexing PCR: 98 ̊C for 45 s; 12 cycles of (98 ̊C for 20 s, 54 ̊C for 30 s, 72 ̊C for 20 s), and 72 ̊C for 60 s. The final DNA library was double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). Sequencing depth for naïve cell samples was between 65-85 million reads per sample (9.660 reads per cell), and for effector cells 175-240 million reads per sample (57.150 reads per cell).

treatment_protocol: 3 x 10^6 naïve CD4+CD25–CD44loCD62LhiV11+V10+ C7 T cells, sorted from a pool of 2 spleens, were adoptively transferred into congenic CD45.2+ C57Bl/6 mice. Mice were injected intravenously with 1 x 10^7 colony forming units (CFU) of L. monocytogenes-ESAT 18 h later. Spleens were harvested 16 h (two replicates) and 40 h post infection.

value: C7 tgTCR

tag: purification

value: 40hr post Lm-ESAT infection


title: MinusAP_EGFRGluGlu_BiolRep1

description: Without EGFR-Erbb2 dimerizer,GluGlu ChIP, replicate 1

value: B2B1 clone of MCF10A-5E

value: Breast epithelial


title: LmESAT_C7_16hr_2

description:
LmESAT_C7_CD4_T_cell_metadata_11403x11.tsv.gz
LmESAT_C7_CD4_T_counts_normalized_11403x12044.tsv.gz
LmESAT_C7_CD4_T_counts_imputed_11403x12044.tsv.gz
LmESAT_C7_CD4_T_LmESAT_C7_16hr_2_raw_counts.tsv.gz

value: 16hr post Lm-ESAT infection


title: A549 NRF2 KO rep3

source_name: A549 NRF2 KO

value: sgNRF2, no IFN-gamma

value: NRF2 KO


title: A549 parental rep3


title: cml24-2_Con_2

source_name: roots_without Al

value: without Al


title: cml24-2_Con_1


title: cml24-2_Tre_2


title: LmESAT_C7_16hr_1

description:
LmESAT_C7_CD4_T_cell_metadata_11403x11.tsv.gz
LmESAT_C7_CD4_T_counts_normalized_11403x12044.tsv.gz
LmESAT_C7_CD4_T_counts_imputed_11403x12044.tsv.gz
LmESAT_C7_CD4_T_LmESAT_C7_16hr_1_raw_counts.tsv.gz


title: A549 NRF2 KO rep2

value: lung adenocarcinoma


title: A549 NRF2 KO rep1


title: Naïve_Smarta_2

description:
naive_CD4_T_cell_metadata_28146x12.tsv.gz
naive_CD4_T_counts_normalized_28146x11488.tsv.gz
naive_CD4_T_counts_imputed_28146x11488.tsv.gz
naive_CD4_T_SMARTA_Naive_2_raw_counts.tsv.gz

value: Smarta tgTCR

value: steady state


title: Naïve_Smarta_1

description:
naive_CD4_T_cell_metadata_28146x12.tsv.gz
naive_CD4_T_counts_normalized_28146x11488.tsv.gz
naive_CD4_T_counts_imputed_28146x11488.tsv.gz
naive_CD4_T_SMARTA_Naive_1_raw_counts.tsv.gz


title: WT_Tre_2

value: roots

value: wild type


title: outer medulla ethylene glycol-induced nephrolithiasis

city: Sendai

first: Takuo

last: Hirose

state: Miyagi

address: 1-15-1 Fukumuro Miyagino

department: Department of Nephrology and Endocrinology

country: Japan

institute: Tohoku Medical and Pharmaceutical University

hyb_protocol: Microarray was performed at Filgen according to manufacturer's protocol for Affymetrix Clariom S Arrays.

data_processing: RMA

label: biotin

organism: Rattus norvegicus

source_name: renal outer medulla

growth_protocol: Rats were housed in environmentally controlled rooms under a 12-h light/dark cycle, and had free access to a pelleted diet and water.

extract_protocol: The kidneys were isolated after 2 weeks treatment, divided into the cortex and outer medulla, and preserved in RNA Later. Total RNA from the rat renal cortex and outer medulla was isolated by a guanidinium thiocyanate-phenol-chloroform extraction method and purified using a silica column with an on-column DNase I treatment.

treatment_protocol: The renal stone was induced by ethylene glycol and alfacalcidol for 2 weeks.

value: Sprague-Dawley

value: renal outer medulla

value: ethylene glycol-induced nephrolithiasis

tag: Sex

value: male

value: 10 week-old


title: outer medulla ethylene glycol-induced nephrolithiasis with phlorizin treatment

scan_protocol: Microarray was performed at Filgen according to manufacturer's protocol for Affymetrix Clariom S Arrays.


title: bulk_wing_discs_Xrp1_S_2_2

city: Leuven

first: Stein

last: Aerts

state: Flemish-Brabant

address: Herestraat 49

department: Department of Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
Sequencing data were mapped using STAR with default parameters and no multimapping reads (outFilterMultimapNmax = 1) on FlyBase r6.35 reference genome (sjdbOverhang = 99, genomeSAindexNbases = 12)
Gene counts were obtained using htseq-count with default parameters on gene symbols GFF file (r6.35)
Assembly: dm6
Supplementary files format and content: HTSeq-count output for each RNA sample (control and Xrp1-S) comprising gene count information as TSV format.

source_name: wing imaginal disc

growth_protocol: Larvae were raised at 22 oC and shifted to 29°C on day 7 AEL

extract_protocol:
Wing imaginal discs (120 WDs for rnts>, 160 WDs for rnts>Xrp1-S) were dissected 48h later in PBS and flash-frozen in liquid nitrogen. Total RNA was isolated according to standard TRI Reagent protocol (Sigma Aldrich, #T9424), followed by DNase I treatment (Invitrogen, #AM2238) and repurification as described in (Mundorf and Uhlirova, 2016)
RNAseq libraries were prepared according to TruSeq stranded mRNA sample preparation guide (Illumina)

treatment_protocol: Expression of the Xrp1 short isoforn was induced by temperature shift from 22 to 29°C

value: wing imaginal disc

tag: developmental stage

value: third instar larvae

value: epithelial and mesenchymal cells

value: UAS-mCD8-ChRFP, UAS-Xrp1-S, rn-Gal4, tub-Gal80ts

value: Xrp1-S induction


title: cortex ethylene glycol-induced nephrolithiasis with phlorizin treatment

source_name: renal cortex

label_protocol: Microarray was performed at Filgen according to manufacturer's protocol for Affymetrix Clariom S Arrays.

tag: tissue

value: renal cortex


title: cortex control with phlorizin treatment

value: control with phlorizin treatment


title: Naïve_C7_2

description:
naive_CD4_T_cell_metadata_28146x12.tsv.gz
naive_CD4_T_counts_normalized_28146x11488.tsv.gz
naive_CD4_T_counts_imputed_28146x11488.tsv.gz
naive_CD4_T_C7_Naive_2_raw_counts.tsv.gz

value: C7 tgTCR


title: outer medulla control with phlorizin treatment


title: cortex control

value: control


title: cortex ethylene glycol-induced nephrolithiasis


title: A549 mock rep 3

source_name: A549 mock

value: lung adenocarcinoma

value: scramble sgRNA, no IFN-gamma

value: mock


title: Naïve_C7_1

description:
naive_CD4_T_cell_metadata_28146x12.tsv.gz
naive_CD4_T_counts_normalized_28146x11488.tsv.gz
naive_CD4_T_counts_imputed_28146x11488.tsv.gz
naive_CD4_T_C7_Naive_1_raw_counts.tsv.gz

value: steady state


title: A549 mock rep 1


title: WT_Con_2

value: roots

value: six-days

value: without Al

value: wild type


title: bulk_wing_discs_Rn1_2_ctrl

value: wing imaginal disc

value: rnts>; UAS-mCD8-ChRFP, rn-Gal4, tub-Gal80ts


title: Naïve_B6

description:
naive_CD4_T_cell_metadata_28146x12.tsv.gz
naive_CD4_T_counts_normalized_28146x11488.tsv.gz
naive_CD4_T_counts_imputed_28146x11488.tsv.gz
naive_CD4_T_B6_Naive_raw_counts.tsv.gz


title: bulk_wing_discs_Rn1_1_ctrl

value: third instar larvae

value: epithelial and mesenchymal cells


title: outer medulla control

value: Sprague-Dawley

value: renal outer medulla

value: male

value: 10 week-old


title: A549 mock rep 2


title: WT_Con_1


title: bulk_wing_discs_Xrp1_S_2_1

value: UAS-mCD8-ChRFP, UAS-Xrp1-S, rn-Gal4, tub-Gal80ts

value: Xrp1-S induction


title: Participant 35, No-stress session, Time 1

status: Public on Mar 21 2023

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building, Penn State University

institute: Penn State University

data_processing:
Raw reads were preprocessed using BBDuk (version 38.87) for quality trimming (minimum read lengths: 25bp, maximum read lengths: 70bp, quality-trim of Q10 using the Phred algorithm), polyA trimming and read decontamination.
Reads were aligned to the human reference genome (GRCh38) using STAR (version 2.7.9a).
Read counts were generated using featureCounts (version 2.0.1) excluding multimapping reads. “ID” and “gene” were the feature specifications used for –g and –t flags, respectively.
After reads were quantified, edgeR (version 3.38.2) was used to calculate counts per million (CPM) values for each gene. Genes that had a CPM value higher than 1 in 200 or more samples (13,381 genes) were kept, and all other genes were excluded. After filtering out lowly expressed genes, the original count matrices were normalized using the TMM method.
Batch correction was performed using the ComBat function in SVA (version 3.44.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes filtered log2-CPM TMM normalized values for all samples.

source_name: PBMC

extract_protocol:
Whole blood samples were repeatedly collected via an IV catheter into the antecubital vein. Blood samples collected in 10mL EDTA tubes were immediately centrifuged for 10min at 1500g prior to collection of plasma. Peripheral blood mononuclear cells (PBMCs) were then isolated through density-gradient centrifugation using Ficoll. 1 ug of total RNA per sample was extracted using QIAamp RNA Blood Mini Kit (Qiagen) and samples were delivered to Penn State College of Medicine’s Genomic Facility where RNA quality was verified using the Agilent Bioanalzyer, followed by library construction.
Library preparation was done using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) supplemented with UMI (unique molecular index) as per the manufacturer’s instructions.

value: PBMC

value: Female

tag: ela status

value: ELA

tag: session

value: No-stress


title: Participant 35, Stress session, Time 4

value: Stress


title: Participant 35, Stress session, Time 3


title: Participant 35, Stress session, Time 2


title: Participant 35, No-stress session, Time 4


title: Participant 35, Stress session, Time 1


title: Participant 35, No-stress session, Time 2


title: Participant 34, Stress session, Time 3

value: Control


title: Participant 34, Stress session, Time 4


title: WT_Tre_1

value: roots

value: six-days

value: with Al

value: wild type


title: Participant 34, Stress session, Time 1


title: Participant 34, No-stress session, Time 1


title: Participant 34, No-stress session, Time 2


title: Participant 34, No-stress session, Time 4


title: Participant 33, Stress session, Time 3


title: Participant 33, No-stress session, Time 3


title: Participant 33, Stress session, Time 2


title: Participant 33, No-stress session, Time 2


title: Participant 33, No-stress session, Time 1


title: Participant 33, Stress session, Time 1


title: Participant 34, Stress session, Time 2


title: Participant 33, No-stress session, Time 4


title: Participant 33, Stress session, Time 4


title: Participant 32, Stress session, Time 2


title: Participant 32, Stress session, Time 1


title: Participant 32, Stress session, Time 3


title: Participant 32, Stress session, Time 4


title: Participant 35, No-stress session, Time 3


title: Participant 34, No-stress session, Time 3


title: Participant 31, Stress session, Time 3


title: Participant 31, Stress session, Time 4


title: Participant 31, No-stress session, Time 4


title: Participant 32, No-stress session, Time 3


title: Participant 32, No-stress session, Time 4


title: Participant 32, No-stress session, Time 2


title: Participant 32, No-stress session, Time 1


title: Participant 31, Stress session, Time 1


title: Participant 31, No-stress session, Time 2


title: Participant 31, No-stress session, Time 1


title: Participant 31, No-stress session, Time 3


title: Participant 31, Stress session, Time 2


title: Participant 30, No-stress session, Time 3


title: Participant 30, No-stress session, Time 2


title: Participant 30, No-stress session, Time 1


title: Participant 30, No-stress session, Time 4


title: Participant 30, Stress session, Time 1


title: Participant 30, Stress session, Time 4


title: Participant 30, Stress session, Time 2


title: Participant 29, Stress session, Time 3


title: Participant 29, Stress session, Time 2


title: Participant 29, Stress session, Time 1


title: Participant 29, Stress session, Time 4