title: BAL_MA1092_post_Batch2

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

data_processing:
Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of 30 (Galaxy FASTQ Trimmer tool v1.0.0). FastqMcf (v1.1.2) was used to remove adapter sequences.
Reads were aligned using the STAR aligner (v2.4.2) with the GRCh38 reference genome and gene annotations from ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1).
Libraries were quality filtered by median coefficient of variation (CV) coverage < 0.65, duplicate mapped reads > 0.8, total aligned sequences > 1 million, and the first two principal components
Counts were normalized for RNA composition using the trimmed mean of M-values normalization method, filtered to protein coding genes with at least 1 count per million (CPM) in at least 10% of samples, and converted to log2 CPM with quality weights using voom in R (v4.0.2)
Genome_build: hg38
Supplementary_files_format_and_content: CSV: normalized counts in genes (ENSEMBL ID) for each sample (library ID)

source_name: Bronchoalveolar lavage

extract_protocol:
Total RNA was extracted from BAL cell pellets (N = 22) using QIAshredder homogenizer columns followed by RNeasy purification using manufacturer’s instructions (QIAGEN). RNA quality and concentration were assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific).
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 5 million reads per sample.

treatment_protocol: Segmental allergen bronchial provocation (SABP) was used to provoke airway inflammation and retrieve airway cells.

tag: disease state

value: Asthma

value: Bronchoalveolar lavage

tag: visit

value: post

tag: donor

tag: batch

tag: pass-filter

value: FALSE


title: BAL_MA1092_pre_Batch2

status: Public on Aug 01 2023

type: SRA

state: WA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: pre


title: FHL1_B_ChEC-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

library_source: genomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a bigwig format and contains spike-in normalized signal per base pair.
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 FHL1-MNase::TRP1

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or SM, Raffinose or Galactose.

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 FHL1-MNase::TRP1


title: ChIPseq_Input_H929_rep1

city: London

first: Nikolaos

last: Trasanidis

address: Hammersmith Campus, Commonwealth Building, 4th Floor,, Du Cane Road, Imperial College London

department: Department of Immunology and Inflammation,

country: United Kingdom

institute: Imperial College London

description:
ChIPseq_MAF_H929_rep1_regions.bed
ChIPseq_MAF_H929_rep1_signal.bw

data_processing:
Bcl2Fastq (v2.20) software used for basecalling.
ChIP-seq analysis: Alignment was performed with bowtie2 against the hg38/GRCh38 genome. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling (ChIP versus Input)  was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. Bedtools was used to operate on genomic regions (union, intersections, etc.).
RNA-seq analysis: Alignment was performed using STAR (2.5.3a) against hg38/GRCh3 genome. The “Rsubread” Bioconductor package was used to obtain gene-level read counts. The “DESeq2” Bioconductor package was used for data normalization and differential expression analysis across different conditions of knock-down experiments in each cell line.
ATAC-seq analysis:  Alignment was performed with bowtie2 against the hg38/GRCh38 genome. Trimming was performed using TrimGalore. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. DESeq2 and ODIN were used for differential ATAC-seq analysis across conditions and treatments. Bedtools was used to operate on genomic regions (union, intersections, etc.).
Assembly: GRCh38
Supplementary files format and content: bedfile
Supplementary files format and content: BigWig
Supplementary files format and content: raw counts

extract_protocol: NEBNext Ultra II ChIP-seq Library Prep Master Mix (NEB)

tag: cell type

value: Multiple myeloma cell line

tag: cell line

tag: treatment

value: no treatment

tag: antibody

value: Input


title: EPL1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 EPL1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 EPL1-MNase::TRP1


title: BAL_MA1024_pre_Batch2

value: TRUE


title: ChIPseq_Input_MM1S_rep2

description:
ChIPseq_MAF_MM1S_rep1n2_regions.bed
ChIPseq_MAF_MM1S_rep1n2_signal.bw


title: BAL_MA1022_post_Batch2


title: BAL_MA1022_pre_Batch2


title: FKH1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 FKH1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 FKH1-MNase::TRP1


title: EPL1_B_ChEC-seq


title: ChIPseq_MAF_MM1S_rep2

value: anti-MAF


title: FHL1_C_ChEC-seq


title: ChIPseq_MAF_MM1S_rep1


title: BAL_MA1080_post_Batch1


title: BAL_MA1086_post_Batch2


title: BAL_MA1024_post_Batch2


title: ERT1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ERT1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ERT1-MNase::TRP1


title: FHL1_A_ChEC-seq


title: BAL_MA1092_pre_Batch1


title: FKH1_B_ChEC-seq


title: BAL_MA1067_pre_Batch1


title: ERT1_B_ChEC-seq


title: BAL_MA1086_pre_Batch2


title: BAL_MA1080_pre_Batch1


title: ERT1_A_ChEC-seq


title: BAL_MA1092_post_Batch1


title: EPL1_A_ChEC-seq


title: BAL_MA1086_post_Batch1


title: ECM22_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ECM22-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ECM22-MNase::TRP1


title: ECM5_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ECM5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ECM5-MNase::TRP1


title: ECM22_B_ChEC-seq


title: ECM22_C_ChEC-seq


title: BAL_MA1067_post_Batch1


title: EAF6_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 EAF6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 EAF6-MNase::TRP1


title: ECM5_C_ChEC-seq


title: EAF6_C_ChEC-seq


title: ECM5_B_ChEC-seq


title: BAL_MA1086_pre_Batch1

value: Asthma


title: EAF5_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 EAF5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 EAF5-MNase::TRP1


title: BAL_MA1072_pre_Batch1

value: Bronchoalveolar lavage


title: BAL_MA1083_pre_Batch1


title: BAL_MA1083_post_Batch1

value: post


title: BAL_MA1063_pre_Batch1

value: pre


title: EAF6_A_ChEC-seq


title: BAL_MA1072_post_Batch1


title: EAF5_B_ChEC-seq


title: EAF1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 EAF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 EAF1-MNase::TRP1


title: EAF1_C_ChEC-seq


title: EAF5_A_ChEC-seq


title: BAL_MA1063_post_Batch1


title: BAL_MA1069_pre_Batch1


title: EAF1_B_ChEC-seq


title: BAL_MA1058_post_Batch1


title: BAL_MA1055_post_Batch1


title: BAL_MA1055_pre_Batch1


title: BAL_MA1058_pre_Batch1


title: DIG2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 DIG2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 DIG2-MNase::TRP1


title: DIG1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 DIG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 DIG1-MNase::TRP1


title: DIG2_C_ChEC-seq


title: DIG1_B_ChEC-seq


title: BAL_MA1069_post_Batch1


title: DIG1_A_ChEC-seq


title: DIG2_A_ChEC-seq


title: BAL_MA1042_post_Batch1


title: BAL_MA1049_post_Batch1


title: BAL_MA1042_pre_Batch1


title: BAL_MA1038_post_Batch1


title: DAL82_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 DAL82-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 DAL82-MNase::TRP1


title: DAL82_C_ChEC-seq


title: DAL81_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 DAL81-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 DAL81-MNase::TRP1


title: DAL82_A_ChEC-seq


title: DAL81_B_ChEC-seq


title: BAL_MA1028_pre_Batch1

value: TRUE


title: BAL_MA1038_pre_Batch1


title: DAL81_C_ChEC-seq


title: BAL_MA1024_post_Batch1


title: BAL_MA1028_post_Batch1


title: BAL_MA1025_pre_Batch1


title: BAL_MA1025_post_Batch1


title: DAL80_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 DAL80-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 DAL80-MNase::TRP1


title: CYC8_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CYC8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CYC8-MNase::TRP1


title: DAL80_C_ChEC-seq


title: BAL_MA1022_post_Batch1

value: FALSE


title: BAL_MA1049_pre_Batch1


title: CYC8_B_ChEC-seq


title: CYC8_A_ChEC-seq


title: BAL_MA1022_pre_Batch1


title: BAL_MA1013_post_Batch1


title: BAL_MA1013_pre_Batch1


title: BAL_MA1012_post_Batch1


title: CUP9_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CUP9-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CUP9-MNase::TRP1


title: CUP9_C_ChEC-seq


title: CUP9_A_ChEC-seq


title: BAL_MA1009_post_Batch1

source_name: Bronchoalveolar lavage


title: CUP2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CUP2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CUP2-MNase::TRP1


title: BAL_MA1024_pre_Batch1


title: DAL80_A_ChEC-seq


title: BAL_MA1009_pre_Batch1


title: BAL_MA1007_post_Batch1


title: CUP2_B_ChEC-seq


title: CST6_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CST6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CST6-MNase::TRP1


title: CUP2_A_ChEC-seq


title: BAL_MA1007_pre_Batch1

value: Asthma


title: BAL_MA1001_post_Batch1


title: BAL_MA1001_pre_Batch1


title: DYRK1A_shDYRK1A-6_HeLa

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

data_processing:
Mapping and counting of genomic reads was performed against human and fly genomes using STAR.
Those reads that could not be uniquely mapped to just one region were discarded.
For normalization, the size factor of each replicate was calculated according to exogenous Drosophila spike-in reads.
Differential gene expression was assessed by using the R package DESeq2 filtering genes that had >10 average normalized counts per million
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and antibiotics (100 U/ml penicillin and 100 mg/ml streptomycin). Cells were grown at 37ºC and in a 5% CO2 atmosphere

extract_protocol:
RNA was isolated using the RNeasy extraction kit following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cell transduction, the virus indicated was added to the medium with the cells in suspension, and replaced with fresh complete DMEM 24 h after infection and seeding. Selection of infected cells was performed by adding 1.25 mg/ml of puromycin (Sigma) for 48-72 h, and cells were allowed to recover in the absence of puromycin for 24 h.

value: HeLa

tag: tissue source

value: Cervix

value: Adenocarcinoma

value: Infected with shDYRK1A


title: CRZ1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CRZ1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CRZ1-MNase::TRP1


title: DYRK1A_shDYRK1A-4_HeLa


title: CST6_B_ChEC-seq


title: CRZ1_C_ChEC-seq


title: CST6_A_ChEC-seq


title: CRZ1_B_ChEC-seq


title: COM2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 COM2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 COM2-MNase::TRP1


title: COM2_B_ChEC-seq


title: COM2_A_ChEC-seq


title: BAL_MA1012_pre_Batch1

value: Bronchoalveolar lavage

value: pre


title: DYRK1A_shControl-3_HeLa

value: Infected with shControl


title: DYRK1A_shControl-2_HeLa


title: DYRK1A_shControl-1_HeLa


title: CHA4_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CHA4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CHA4-MNase::TRP1


title: shDYRK1A-1C

data_processing:
Mapping and counting of genomic reads was performed against human and fly genomes using STAR.
Those reads that could not be uniquely mapped to just one region were discarded.
For normalization, the size factor of each replicate was calculated according to exogenous Drosophila spike-in reads.
Differential gene expression was assessed by using the R package DESeq2  filtering genes that had >10 average normalized counts per million
Genome_build: hg38 for human reads, dm3 for drosophila reads
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: T98G cells

treatment_protocol: For spike-in normalization, equal number of T98G cells for each condition were mixed with a fixed number of Drosophila melanogaster Kc167 cells. For cell transduction, the virus indicated was added to the medium with the cells in suspension, and replaced with fresh complete DMEM 24 h after infection and seeding. Selection of infected cells was performed by adding 1.25 mg/ml of puromycin (Sigma) for 48-72 h, and cells were allowed to recover in the absence of puromycin for 24 h.

value: Brain

value: Glioblastoma


title: CHA4_C_ChEC-seq


title: shDYRK1A-1B


title: CHA4_A_ChEC-seq


title: shDYRK1A-1A


title: CBF1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CBF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CBF1-MNase::TRP1


title: CBF1_C_ChEC-seq


title: CAT8_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CAT8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CAT8-MNase::TRP1


title: CBF1_A_ChEC-seq


title: DYRK1A_shDYRK1A-5_HeLa


title: shControl-1B


title: shControl-1A


title: CAT8_B_ChEC-seq


title: RNAPOL2-ChIP

data_processing:
Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference (or to the mm9 mouse genome reference) using Bowtie and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38 or mm9
Supplementary_files_format_and_content: peak text files and bigwig files

growth_protocol: Human cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and antibiotics (100 U/ml penicillin and 100 µg/ml streptomycin). mESCs were maintained in 0.1% gelatin (Millipore ES-006-B)-coated plates mESC medium, which consisted of DMEM supplemented with 15% FBS, L– glutamine (2 mM), penicillin (100 U/ml), streptomycin (100 µg/ ml), sodium pyruvate (1 mM), non-essential amino acid (NEAA) (0,1 mM), 2-mercaptoethanol (0,5 mM) and ESGRO mLif (1000 U/ml).

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
DNA libraries were generated by using the OvationÒ Ultralow Library System V2 (NuGEN) following the manufacturer’s instructions. To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition.

treatment_protocol: For cell transduction, the virus was added to the medium with the cells in suspension, and replaced with fresh complete DMEM 24 h after infection and seeding. Selection of infected cells was performed by adding 1.25 mg/ml of puromycin (Sigma) for 48-72 h, and cells were allowed to recover in the absence of puromycin for 24 h.

value: Brain-Glioblastoma

tag: chip antibody

value: RNAPOLII (Cell Signaling, 14958)

value: untreated


title: ZBTB33/KAISO-ChIP

value: KAISO(6F8, Santa Cruz, sc-23871)


title: CAD1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 CAD1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 CAD1-MNase::TRP1


title: CAD1_A_ChEC-seq


title: CAT8_A_ChEC-seq


title: CAD1_B_ChEC-seq


title: DYRK1A-ChIP, HeLa

source_name: HeLa

value: HeLa

value: Cervix-Carcinoma

value: DYRK1A (Abcam, ab69811)


title: shControl-1C


title: DYRK1A-ChIP, U2OS

value: Bone-Osteosarcoma


title: DYRK1A-ChIP, shDYRK1A

value: Infected with shDYRK1A


title: DYRK1A-ChIP, shControl


title: BUR6_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 BUR6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 BUR6-MNase::TRP1


title: DYRK1A-ChIP, T98G


title: BUR6_A_ChEC-seq


title: BMH1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 BMH1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 BMH1-MNase::TRP1


title: PAR-CLIP_RNAPII_4SU_r1

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description:
Sample 3
RNAPII bound RNA

data_processing:
Adaptor trimming, custom python script (Sequence TCGTATGCCGTCTTCTGCTTGT)
Genomic alignment with bowtie 0.12.7 --sam -n 1 -l 20 -m 100 --best
Sam to bam conversion, samtools 0.1.19 samtools view -b -S
Sort and index, samtools 0.1.19 samtools sort, samtools index
Binding cluster calling, wavClusteR 1.99.2, R 3.1.0, left and right prob. 0.9 (0.6 both for 6SG), min. coverage 10, method is mrn with treshhold 2
Genome_build: HG19
Supplementary_files_format_and_content: Stranded BED-File of detected binding clusters, scores are mean read coverage across the cluster

source_name: HEK293T T-Rex cells

growth_protocol: DMEM  suppl. with 10% FCS and 5 µM Glutamine

extract_protocol:
300e6 HEK293T cells with overnight 4SU incubation were washed once in cold PBS and crosslinked at 365nm and a total energy of 0.15 J/cm2. Cells were scraped and resuspended in cold PBS. After centrifugation at 500 rcf for 5 minutes, pellet was resuspended in lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 5 mM CaCl2, 1 % NP-40) and incubated 15 minutes on ice. Lysate was treated with 20 U/mL Fermentas RNase T1 and 15 U/mL Fermentase RNase free DNase I for 15 minutes at RT and then sonicated for 15 cycles (30 sec on / off) on a Diagenode Bioruptor on high. Lysate was cleared at 21’000 rcf and 4 °C for 10 minutes. IP was performed for 3 hours with 100 uL streptavidin magnetic myONE T1 beads (Thermo Fisher). Beads were washed 3 times in lysis buffer and treated with RNase T in 100 uL at 20 U/uL for 15 minutes at RT. After three more lysis buffer and two dephosphorylation buffer washes (50 mM Tris-HCl pH 7.9, 100 mM NaCl, 10 mM MgCl2) RNA was dephosphorylated at 37 °C in 100 uL NEB buffer 3 with 0.5 U / uL CIP for 10 minutes. 500 uL lysis buffer were added for beads to rebind during 10 minutes on ice. Three more lysis buffer washes and two PNK-buffer (70 mM Tris-HCl, pH 7.6, 10 mM MgCl2) washes were followed by phosphorylation with radioactive 32P at 37 °C in 100 uL of PNK buffer with 5 mM DTT, 17 nM (10 uCi) 32P-ATP and 0.5 U/uL PNK. After 30 minutes 5 uM normal ATP were added for additional 5 minutes. 1 mL of lysis buffer was added and beads are allowed to rebind during 10 minutes on ice. Beads were washed 5 times with lysis buffer, boiled in SDS-DTT solution and run on a NuPage Novex 4-12 % bis-tris gel for 1.5 hours at 150 V in MOPS buffer. Gel was imaged for 30 minutes with a phosphorimaging cassette and bands of interest excised. Elution of Protein-RNA complex was performed three times in 400 uL MOPS buffer using d-tube dialyzer midi MWCO 3.5 kDa each for 1 hours at 100 V and 5 minutes at 100 V reversed polarity. All subsequent steps were carried out exactly as described Hafner M. et al 2010.
Library was prepared similary to Illumina small RNA protocol. We adhered to Hafner et al 2010.

treatment_protocol: Cells were grown overnight in the presence of 100 uM 4-SU

value: HEK293T T-Rex

tag: transgene

tag: rip antibody/reagent

value: aRNAPII ctd - abcam ab817


title: BMH1_B_ChEC-seq


title: BMH1_A_ChEC-seq


title: PAR-CLIP_PHC1_r2

description:
Sample 2
PHC1 bound RNA

data_processing:
Adaptor trimming, custom python script (Sequence TCGTATGCCGTCTTCTGCTTGT)
Genomic alignment with bowtie 0.12.7 --sam -n 1 -l 20 -m 100 --best
Sam to bam conversion, samtools 0.1.19 samtools view -b -S
Sort and index, samtools 0.1.19 samtools sort, samtools index
Binding cluster calling, wavClusteR 2.2.0, R 3.2.2, prob. given by bayes, min. coverage 10, method is mrn with treshhold 2
Genome_build: HG19
Supplementary_files_format_and_content: Stranded BED-File of detected binding clusters, scores are mean read coverage across the cluster

growth_protocol: DMEM  suppl. with 10% FCS and 5 µM Glutamine, 100 µg / mL Hygromycin

value: Streptavidin Dynabeads MyOne T1


title: PAR-CLIP_PHC1_r1

description:
Sample 1
PHC1 bound RNA


title: BUR6_C_ChEC-seq


title: BAS1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 BAS1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 BAS1-MNase::TRP1


title: BAS1_B_ChEC-seq


title: BAS1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with validation library, parenchyma, rep R1

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

country: Germany

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

description: Column names: R2Blood, R3Blood, R2Meninges, R3Meninges, R2Parenchyma, R3Parenchyma, R2Spleen, R3Spleen, R1Blood, R1Meninges, R1Parenchyma, R1Spleen

data_processing:
The Galaxy platform was used for data analysis. For raw fastq files, Je-Demultiplex-Illu was used for de-multiplexing, followed by Cutadapt and Trimmomatic to get the 20bp sgRNA sequence.
Counts were then obtained with MAGeCK (version 0.5.7.1+) count. Normalization across samples was conducted in R (version 4.0.0+) after a 50 raw count threshold using the geometric mean per sgRNA for normalization, and sgRNAs with fewer than 50 counts in more than two replicates of the same tissue were discarded altogether.
The MAGeCK test was run without normalization or zero removal, and otherwise default parameters on Galaxy, giving the information of control Non-Targeting sgRNA for noise correction.
All further data processing was done with R.
Tab-delimited txt file of geometric mean R normalized sgRNA counts
Tab-delimited txt file of raw sgRNA counts from MAGeCK counts

organism: Rattus norvegicus

source_name: Sorted CD4+ T-MBP cells from parenchyma

growth_protocol: Cells were transferred to Lewis rats three days before isolation. Prior to transfer, cells were kept in TCGF (complete DMEM supplemented with 10 % Horse serum and 2 % of PMA-stimulated EL4IL2 cell culture supernatant and 1 % Pen/Strep) for four days to expand the number of T cells. Then, the T cells were restimulated for two days with 50 Gy irradiated thymocytes in complete DMEM supplemented with 1 % rat serum and 10 µg/ml MBP, and the library was transduced by retroviral infection ontp Nycoprep purified T-MBP cells. For four days after transduction, T cells were kept in 0.5 ug/ml puromycin to select for infected cells. Cells were restimulated and transferred on the second day after restimulation

extract_protocol:
The spinal cord parenchyma was dissected and homogenized by passing through a metal strainer. Lymphocytes were isolated using a 30%/64% Percoll gradient and centrifugation at 1200g, room temperature for 30min with mild acceleration and brake. Lymphocytes were collected from the interface. BFP+ T cells were FACS sorted
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: Sorted CD4+ T-MBP cells from parenchyma

value: Validation screen KO

tag: strain

value: Lewis rat

tag: time

value: day 3 post transfer


title: AZF1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 AZF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 AZF1-MNase::TRP1


title: PAR-CLIP_RNAPII_6SG_r1

description:
Sample 4
RNAPII bound RNA

extract_protocol:
300e6 HEK293T cells with overnight 6SG incubation were washed once in cold PBS and crosslinked at 365nm and a total energy of 0.15 J/cm2. Cells were scraped and resuspended in cold PBS. After centrifugation at 500 rcf for 5 minutes, pellet was resuspended in lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 5 mM CaCl2, 1 % NP-40) and incubated 15 minutes on ice. Lysate was treated with 20 U/mL Fermentas RNase T1 and 15 U/mL Fermentase RNase free DNase I for 15 minutes at RT and then sonicated for 15 cycles (30 sec on / off) on a Diagenode Bioruptor on high. Lysate was cleared at 21’000 rcf and 4 °C for 10 minutes. IP was performed for 3 hours with 100 uL streptavidin magnetic myONE T1 beads (Thermo Fisher). Beads were washed 3 times in lysis buffer and treated with RNase T in 100 uL at 20 U/uL for 15 minutes at RT. After three more lysis buffer and two dephosphorylation buffer washes (50 mM Tris-HCl pH 7.9, 100 mM NaCl, 10 mM MgCl2) RNA was dephosphorylated at 37 °C in 100 uL NEB buffer 3 with 0.5 U / uL CIP for 10 minutes. 500 uL lysis buffer were added for beads to rebind during 10 minutes on ice. Three more lysis buffer washes and two PNK-buffer (70 mM Tris-HCl, pH 7.6, 10 mM MgCl2) washes were followed by phosphorylation with radioactive 32P at 37 °C in 100 uL of PNK buffer with 5 mM DTT, 17 nM (10 uCi) 32P-ATP and 0.5 U/uL PNK. After 30 minutes 5 uM normal ATP were added for additional 5 minutes. 1 mL of lysis buffer was added and beads are allowed to rebind during 10 minutes on ice. Beads were washed 5 times with lysis buffer, boiled in SDS-DTT solution and run on a NuPage Novex 4-12 % bis-tris gel for 1.5 hours at 150 V in MOPS buffer. Gel was imaged for 30 minutes with a phosphorimaging cassette and bands of interest excised. Elution of Protein-RNA complex was performed three times in 400 uL MOPS buffer using d-tube dialyzer midi MWCO 3.5 kDa each for 1 hours at 100 V and 5 minutes at 100 V reversed polarity. All subsequent steps were carried out exactly as described Hafner M. et al 2010.
Library was prepared similary to Illumina small RNA protocol. We adhered to Hafner et al 2010.

treatment_protocol: Cells were grown overnight in the presence of 100 uM 6-SG


title: Rat CD4+ T-MBP cells with validation library, meninges, rep R2

source_name: Sorted CD4+ T-MBP cells from meninges

extract_protocol:
Leptomeninges of the spinal cord were dissected and homogenized by passing through a metal strainer. BFP+ T cells were FACS sorted
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: Sorted CD4+ T-MBP cells from meninges


title: Rat CD4+ T-MBP cells with validation library, spleen, rep R3

source_name: Sorted CD4+ T-MBP cells from spleen

extract_protocol:
The spleen was dissected and homogenized by passing through a metal strainer. Erythrocytes were removed by treating with ACK buffer for 3 min on ice and CD4+ T cells were enriched using the EasySep™ Rat CD4+ T Cell Isolation Kit (StemCell technologies). BFP+ Tcells were FACS sorted
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: Sorted CD4+ T-MBP cells from spleen


title: AZF1_B_ChEC-seq


title: Rat CD4+ T-MBP cells with validation library, spleen, rep R2


title: AZF1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with validation library, meninges, rep R1


title: ASG1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ASG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ASG1-MNase::TRP1


title: Rat CD4+ T-MBP cells with validation library, spleen, rep R1


title: ASG1_C_ChEC-seq


title: ASG1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with validation library, parenchyma, rep R3


title: Rat CD4+ T-MBP cells with validation library, meninges, rep R3


title: Rat CD4+ T-MBP cells with validation library, parenchyma, rep R2


title: ARR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ARR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ARR1-MNase::TRP1


title: Rat CD4+ T-MBP cells with validation library, blood, rep R2

source_name: Sorted CD4+ T-MBP cells from blood

extract_protocol:
Blood was drawn by heart puncture into a heparinized syringe. Lymphocytes were isolated from blood by a Nycoprep gradient. First, the blood was diluted with an equal volume of PBS and overlaid onto Nycoprep. After centrifugation at 800 g, room temperature for 30 min with mild acceleration and brake, lymphocytes were collected from the interface. BFP+ T cells were FACS sorted.
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: Sorted CD4+ T-MBP cells from blood


title: Rat CD4+ T-MBP cells with validation library, blood, rep R3


title: ARR1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with validation library, blood, rep R1


title: ARO80_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ARO80-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ARO80-MNase::TRP1


title: Rat CD4+ T-MBP cells with GW library, culture, rep R3

description: Column names: R3Blood, R3Culture, R3Meninges, R3Parenchyma, R3Spleen, R2Blood, R2Meninges, R2Parenchyma, R2Spleen, R1Parenchyma, R1Spleen, R1Blood, R1Meninges, R1Plasmid, R1Culture

source_name: CD4+ T-MBP cells

extract_protocol:
Cells were collected from the cell culture and purified with a Nycoprep gradient to enrich for T cells
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: CD4+ T-MBP cells

value: GW screen KO

value: day 2 post restimulation


title: ARO80_A_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, culture, rep R1


title: ARO80_B_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, parenchyma, rep R1

source_name: Lymphocytes

extract_protocol:
The spinal cord parenchyma was dissected and homogenized by passing through a metal strainer. Lymphocytes were isolated using a 30%/64% Percoll gradient and centrifugation at 1200g, room temperature for 30min with mild acceleration and brake. Lymphocytes were collected from the interface.
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: Lymphocytes


title: Rat CD4+ T-MBP cells with GW library, meninges, rep R3

extract_protocol:
Leptomeninges of the spinal cord were dissected and homogenized by passing through a metal strainer
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).


title: ARG80_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ARG80-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ARG80-MNase::TRP1


title: AFT2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 AFT2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 AFT2-MNase::TRP1


title: ARR1_B_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, meninges, rep R1


title: AFT2_B_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, spleen, rep R3

source_name: CD4+ T cell enriched lymphocytes

extract_protocol:
The spleen was dissected and homogenized by passing through a metal strainer. Erythrocytes were removed by treating with ACK buffer for 3 min on ice and CD4+ T cells were enriched using the EasySep™ Rat CD4+ T Cell Isolation Kit (StemCell technologies)
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: CD4+ T cell enriched lymphocytes


title: ADR1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ADR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ADR1-MNase::TRP1


title: Rat CD4+ T-MBP cells with GW library, spleen, rep R2

value: Lewis rat


title: Rat CD4+ T-MBP cells with GW library, parenchyma, rep R3

value: day 3 post transfer


title: AFT2_A_ChEC-seq


title: ARG80_C_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, parenchyma, rep R2


title: Rat CD4+ T-MBP cells with GW library, blood, rep R2

extract_protocol:
Blood was drawn by heart puncture into a heparinized syringe. Lymphocytes were isolated from blood by a Nycoprep gradient. First, the blood was diluted with an equal volume of PBS and overlaid onto Nycoprep. After centrifugation at 800 g, room temperature for 30 min with mild acceleration and brake, lymphocytes were collected from the interface
Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).


title: ADR1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, meninges, rep R2


title: ARG80_A_ChEC-seq


title: ADF1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ADF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ADF1-MNase::TRP1


title: ADF1_B_ChEC-seq


title: ADR1_C_ChEC-seq


title: ADF1_A_ChEC-seq


title: Rat CD4+ T-MBP cells with GW library, spleen, rep R1


title: Rat CD4+ T-MBP cells with GW library, blood, rep R3


title: ACA1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ACA1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ACA1-MNase::TRP1


title: ACA1_C_ChEC-seq


title: ACA1_A_ChEC-seq


title: Reporter Plasmid Library Maxiprep from E. coli, R1

city: Stanford

first: Meng

last: Zhang

state: California

address: 443 Via Ortega

institute: Stanford

description: Plasmid DNA isolated from E.coli by Maxiprep

library_source: other

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina), and then evaluated for quality control (QC) with FastQC.
Fastq files were then converted to Fasta files using the FASTX-Toolkit. Fasta files were trimmed to remove shared linker sequence and to retain regions in each read with high quality (Phred Score > 25.75 as determined by FastQC).
To map each NGS read to the library, we created a local blast database containing SHIELD library sequences, and used the BLAST+ 2.7.1. module to perform alignment analysis of NGS data against library database.
For post-alignment data processing, we first removed duplicates (i.e., one read being mapped to multiple library sequences) and kept only one alignment with the highest bitscore (lowest e-vaule) for each read. In addition, we removed alignments with more than 3 mismatches, or more than 3 gaps, or with a total mapped length less than the maximum possible minus 10 nucleotides.
Assembly: n.a.
Supplementary files format and content: Tab-delimited text file including raw counts for each DNA element in the library

molecule: other

organism: synthetic construct

growth_protocol: HCT116 cells were maintained following ATCC recommended guidelines

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA Mini Kit (Invitrogen #182001) following manufacturer's protocol
NGS library was prepared following Illumina's Metagenomic Sequencing Library Preparation protocol to add sequencing indexes by 2-step PCR
Amplicon sequencing to determine the relative abundace of barcoded DNA

tag: sample type

value: Reporter Plasmid Library


title: ZAP1_DMSO_A_S7_RNA-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ZAP1-3xV5 IAA7::URA3

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ZAP1-3xV5 IAA7::URA3


title: ZAP1_3IAA_B_S11_RNA-seq


title: ZAP1_3IAA_A_S10_RNA-seq


title: Rat CD4+ T-MBP cells with GW library, blood, rep R1


title: Reporter Plasmid Library Maxiprep from E. coli, R2


title: ZAP1_DMSO_C_S9_RNA-seq


title: ZAP1_3IAA_C_S12_RNA-seq


title: May_6dpf_DS1_rep4

city: Milwaukee

first: Rebecca

last: Klaper

state: WI

address: 600 E Greenfield

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

data_processing:
quality-assessed using FastQC v0.11.5
sequencing adapters were clipped using Cutadapt v1.18
pseudoaligned and sample-quantified against the GRCz11 Ensembl release of the zebrafish reference transcriptome using Kallisto v0.45.0
Genome_build: GRCz11 Ensembl zebrafish transcriptome
Supplementary_files_format_and_content: estimated counts, tsv text

organism: Danio rerio

source_name: larvae

growth_protocol: embryo density at 20 per 50 mL petri dish, 14:10-hour light/dark cycle, 27C, no feeding

extract_protocol:
Flash-frozen (liquid nitrogen) larvae were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos at 6 hours post-fertilization were exposed to streamwater samples for 3 and 6 days. In each petri dish (5 replicates), 20 embryos were submerged in 30 mL of stream water taken from grab samples collected at three sites along an effluent-dominated stream: (1) at the effluent oufall, (2) 100 meters above the outfall, and (3) 100 meters below the outfall.

value: wild type

value: whole larvae

tag: month of water samples used for exposure

value: May

tag: stream site full name

value: 100 m downstream of effluent outfall

tag: stream site short name

tag: exposure duration

value: 6 days

tag: exposure, age at start

value: 6 hours post-fertilization


title: May_6dpf_DS1_rep5

tag: genotype

tag: tissue


title: May_6dpf_DS1_rep2


title: May_6dpf_DS1_rep1


title: May_6dpf_DS1_rep3


title: YRR1_DMSO_C_S51_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YRR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YRR1-3xV5 IAA7::URA3


title: YRR1_DMSO_A_S49_RNA-seq


title: YRR1_DMSO_B_S50_RNA-seq


title: YRR1_3IAA_C_S54_RNA-seq


title: YRR1_3IAA_B_S53_RNA-seq


title: May_6dpf_Effluent_rep4

value: WWTP effluent outfall

value: Effluent


title: YRM1_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YRM1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YRM1-3xV5 IAA7::URA3


title: ZAP1_DMSO_B_S8_RNA-seq


title: May_6dpf_Effluent_rep5


title: YRR1_3IAA_A_S52_RNA-seq


title: YRM1_DMSO_A_S19_RNA-seq


title: May_6dpf_Effluent_rep2


title: May_6dpf_Effluent_rep3


title: May_6dpf_Effluent_rep1


title: May_6dpf_US1_rep2

value: 100 m upstream of effluent outfall


title: YRM1_3IAA_B_S23_RNA-seq


title: May_6dpf_US1_rep1


title: May_6dpf_US1_rep4


title: YNR063W_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YNR063W-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YNR063W-3xV5 IAA7::URA3


title: YRM1_DMSO_B_S20_RNA-seq


title: YRM1_3IAA_A_S22_RNA-seq


title: May_3dpf_DS1_rep4

value: 3 days


title: YNR063W_DMSO_B_S26_RNA-seq


title: YNR063W_3IAA_B_S29_RNA-seq


title: YNR063W_DMSO_A_S25_RNA-seq


title: May_3dpf_DS1_rep5


title: YNR063W_3IAA_C_S30_RNA-seq


title: May_3dpf_DS1_rep1


title: May_3dpf_Effluent_rep4


title: May_6dpf_US1_rep3


title: May_3dpf_DS1_rep2


title: YRM1_3IAA_C_S24_RNA-seq


title: YKL222C_DMSO_A_S25_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YKL222C-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YKL222C-3xV5 IAA7::URA3


title: May_3dpf_Effluent_rep3


title: YKL222C_DMSO_C_S27_RNA-seq


title: May_3dpf_Effluent_rep2


title: May_3dpf_DS1_rep3


title: YKL222C_DMSO_B_S26_RNA-seq


title: May_3dpf_Effluent_rep1


title: YKL222C_3IAA_A_S28_RNA-seq


title: YKL222C_3IAA_B_S29_RNA-seq


title: YKL222C_3IAA_C_S30_RNA-seq


title: May_3dpf_US1_rep5


title: May_3dpf_US1_rep4


title: YAP6_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YAP6-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YAP6-3xV5 IAA7::URA3


title: YAP6_DMSO_C_S15_RNA-seq


title: YAP6_3IAA_A_S16_RNA-seq


title: May_3dpf_Effluent_rep5


title: May_3dpf_US1_rep2


title: Jan_6dpf_DS1_rep4

value: January


title: YNR063W_3IAA_A_S28_RNA-seq


title: YAP6_DMSO_A_S13_RNA-seq


title: May_3dpf_US1_rep3


title: Jan_6dpf_DS1_rep3


title: Jan_6dpf_DS1_rep5


title: Jan_6dpf_DS1_rep2


title: YAP5_DMSO_B_S8_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YAP5-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YAP5-3xV5 IAA7::URA3


title: YAP5_3IAA_A_S10_RNA-seq


title: YAP5_DMSO_A_S7_RNA-seq


title: Jan_6dpf_Effluent_rep4

value: wild type


title: YAP5_3IAA_C_S12_RNA-seq


title: Jan_6dpf_Effluent_rep3

value: whole larvae


title: YAP6_3IAA_B_S17_RNA-seq


title: Jan_6dpf_DS1_rep1


title: Jan_6dpf_Effluent_rep2


title: Jan_6dpf_Effluent_rep5


title: YAP1_DMSO_A_S55_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 YAP1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 YAP1-3xV5 IAA7::URA3


title: YAP5_3IAA_B_S11_RNA-seq


title: YAP6_3IAA_C_S18_RNA-seq


title: YAP1_3IAA_C_S60_RNA-seq


title: YAP1_DMSO_C_S57_RNA-seq


title: Jan_6dpf_US1_rep3


title: YAP1_3IAA_A_S58_RNA-seq


title: YAP1_DMSO_B_S56_RNA-seq


title: May_3dpf_US1_rep1

value: May


title: Jan_6dpf_US1_rep2

value: 6 days


title: Jan_6dpf_US1_rep5

value: 6 hours post-fertilization


title: XBP1_DMSO_B_S50_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 XBP1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 XBP1-3xV5 IAA7::URA3


title: YAP5_DMSO_C_S9_RNA-seq


title: Jan_3dpf_DS1_rep5

value: 100 m downstream of effluent outfall


title: YAP1_3IAA_B_S59_RNA-seq


title: Jan_6dpf_US1_rep4


title: XBP1_DMSO_C_S51_RNA-seq


title: XBP1_3IAA_C_S54_RNA-seq


title: Jan_6dpf_Effluent_rep1

value: WWTP effluent outfall

value: Effluent


title: XBP1_3IAA_A_S52_RNA-seq


title: Jan_6dpf_US1_rep1

value: 100 m upstream of effluent outfall


title: Jan_3dpf_DS1_rep3


title: Jan_3dpf_DS1_rep4


title: XBP1_DMSO_A_S49_RNA-seq


title: WT_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 WT-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 WT-3xV5 IAA7::URA3


title: WT_DMSO_A_S43_RNA-seq


title: XBP1_3IAA_B_S53_RNA-seq


title: Jan_3dpf_DS1_rep2

value: 3 days


title: Jan_3dpf_Effluent_rep4


title: Jan_3dpf_Effluent_rep3


title: WT_3IAA_A_S46_RNA-seq


title: Jan_3dpf_Effluent_rep1


title: Jan_3dpf_DS1_rep1


title: WT_DMSO_B_S44_RNA-seq


title: WHI5_DMSO_B_S44_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 WHI5-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 WHI5-3xV5 IAA7::URA3


title: Jan_3dpf_Effluent_rep5


title: WT_3IAA_C_S48_RNA-seq


title: WT_3IAA_B_S47_RNA-seq


title: Jan_3dpf_US1_rep4


title: Jan_3dpf_US1_rep3


title: WHI5_DMSO_C_S45_RNA-seq


title: Jan_3dpf_Effluent_rep2


title: GFP Neg, day 15, replicate 2, R2

tag: cell line

value: reporter DNA integrated at H1 landing pad


title: WHI5_DMSO_A_S43_RNA-seq


title: WHI5_3IAA_C_S48_RNA-seq


title: WHI5_3IAA_B_S47_RNA-seq


title: Jan_3dpf_US1_rep2

value: January


title: WHI5_3IAA_A_S46_RNA-seq


title: GFP Med, day 15, replicate 2


title: root, replicate 3 (sRNA-seq)

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
The reads were mapped to the Mikania micrantha using SOAP2 v2.21 (M4v0r1)
Bioinformatics analyses to categorize miRNA reads
Assembly: txt file, which has two columns: small RNA sequence, counts
Supplementary files format and content: GCA_009363875.1_ASM936387v1
Supplementary files format and content: txt file, which has two columns: small RNA sequence, counts

organism: Mikania micrantha

source_name: root

growth_protocol: Wild-type M. micrantha vines were collected from Shenzhen University (Lihu Campus) and cut into several branches with two stem nodes and a leaf on the apical side. Then the morphological base end was cultured in water under low light conditions for approximately 1 week. Plants with root lengths of approximately 4–5 cm were transferred to Hoagland liquid medium and grown in the growth room with daily cycles of 16 h/light and 8 h/dark at 24°C for 60 days.

extract_protocol:
Total RNA was extracted from M. micrantha flower, leaf, shoot apex, stem, and root tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. RNA integrity and concentration were determined with NanoDrop (Thermo Fisher, CA, USA).
SRNA libraries were constructed using the Next Multiplex Small RNA Library Prep kit (NEB, USA) following the manufacturer’s instructions

value: root


title: Jan_3dpf_US1_rep1

value: wild type


title: root, replicate 1 (sRNA-seq)


title: GFP Low, day 15, replicate 2


title: GFP Neg, day 15, replicate 2, R1


title: WAR1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 WAR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 WAR1-3xV5 IAA7::URA3


title: GFP High, day 15, replicate 2


title: GFP Med, day 15, replicate 1


title: stem, replicate 3 (sRNA-seq)

source_name: stem

value: stem


title: WAR1_DMSO_B_S38_RNA-seq


title: GFP High, day 15, replicate 1


title: root, replicate 2 (sRNA-seq)


title: GFP Low, day 15, replicate 1


title: stem, replicate 2 (sRNA-seq)


title: GFP High, day 3, replicate 2


title: GFP Low, day 3, replicate 2


title: WAR1_DMSO_A_S37_RNA-seq


title: WAR1_3IAA_C_S42_RNA-seq


title: GFP Med, day 3, replicate 2


title: stem, replicate 1 (sRNA-seq)


title: shoot apex, replicate 3 (sRNA-seq)

source_name: shoot apex

value: shoot apex


title: GFP Med, day 3, replicate 1


title: GFP Neg, day 3, replicate 1


title: shoot apex, replicate 2 (sRNA-seq)


title: GFP Low, day 3, replicate 1


title: WAR1_3IAA_A_S40_RNA-seq


title: patient12_B0_TCRbeta

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

data_processing:
Deep sequencing of the TCR beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Assembly: IMGT data base was used to identifiy TCR
Supplementary files format and content: txt files containing the list of TCR and their frequencies
Library strategy: TCR-seq

source_name: blood

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction and as described in Genolet et al., Cell Report Methods, 2013.
Libraries were prepare using targeted TCR amplification

value: blood

tag: cell type

value: peripheral blood mononuclear cell (PBMC)

tag: patient

value: pre-ACT


title: GFP High, day 3, replicate 1


title: VHR1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 VHR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 VHR1-3xV5 IAA7::URA3


title: WAR1_3IAA_B_S41_RNA-seq


title: WL-T-41

city: Newcastle Upon Tyne

first: Kirsty

middle: Jamie

last: McInnes

address: Kings road, newcastle university, newcastle upon tyne, NE1 7RU

institute: Newcastle University

data_processing:
Reads were aligned to the Brassica 95K Unigene, B. napus genome and Arabidopsis genome using TopHat v 2.1.12
Differential expression analysis was conducted with Cufflinks v 2.2.1
Arabidopsis gene annotations were assigned to the RNA-seq transcripts based on their sequence similarity to the Arabidopsis genome (TAIR10)
Functional analysis of the RNA-seq transcripts was carried out using the online bioinformatics resource, DAVID (the Database for Annotation, Visualization and Integrated Discovery)
Assembly: GCF_000001735.4

organism: Brassica napus

source_name: True Leaf Tissue

growth_protocol: Brassica napus plants were grown under 70 µmol m−2 s −1 white light for 21 days.

extract_protocol:
RNA was extracted from leaf tissue using TRIzol® Reagent (Life Technologies) following the manufacturer’s instructions with one minor modification: RNA precipitation was carried out overnight at 4 °C using pre-chilled isopropyl alcohol. DNase treatment of RNA was conducted using the DNA-free™ DNA removal kit (Life Technologies)
TruSeq™ RNA Sample Preparation kit

treatment_protocol: Plants were harvested 4 hours after exposure to one of the folowng treatments: 4 h irradiation with 3 µmol m−2 s−1 UV-B ('UVB-T') or 70 µmol m−2 s−1 white light in the absence of UV-B ('WL-T;' UV-B control); exogenous application of 4 mL 100 µM MeJA ('MJ-T;' MeJA treatment), 4 mL 0.01% ethanol and 0.01% UN65 ('EU-T;' MeJA control) or  4 mL distilled water ('MC-T;' MeJA control); 1h P. xylostella larvae herbivory ('Plut-T').

value: True Leaf Tissue

tag: treatment

value: UV-B Control


title: UVB-T-42

value: UV-B


title: WL-T-42


title: leaf, replicate 3 (sRNA-seq)

source_name: leaf

value: leaf


title: UVB-T-41


title: Plut-T-41

value: Plutella xylostella Herbivory


title: Plut-T-42


title: leaf, replicate 1 (sRNA-seq)


title: VHR1_DMSO_A_S31_RNA-seq


title: VHR1_DMSO_B_S32_RNA-seq


title: leaf, replicate 2 (sRNA-seq)


title: MC-T-42

value: Water MEJA Control


title: flower, replicate 2 (sRNA-seq)

source_name: flower

value: flower


title: VHR1_3IAA_B_S35_RNA-seq


title: VHR1_3IAA_A_S34_RNA-seq


title: VHR1_3IAA_C_S36_RNA-seq


title: MJ-T-41

value: Methyl jasmonate


title: EU-T-42

value: Ethanol MEJA Control


title: EU-T-41


title: flower, replicate 3 (sRNA-seq)


title: MC-T-41


title: flower, replicate 1 (sRNA-seq)


title: shoot apex, replicate 1 (sRNA-seq)


title: USV1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 USV1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 USV1-3xV5 IAA7::URA3


title: stem, replicate 3 (RNA-seq)

data_processing:
The raw reads were aligned to the Mikania micrantha using hisat2.
The raw counts of gene were generated by perl script.
Supplementary files format and content: GCA_009363875.1_ASM936387v1
Supplementary files format and content: tab-delimited text files include raw count of all genes for each Sample

extract_protocol:
Total RNA was extracted from M. micrantha flower, leaf, shoot apex, stem, and root tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. RNA integrity and concentration were determined with NanoDrop (Thermo Fisher, CA, USA).
RNA libraries for RNA-seq were constructed and sequenced by Berry Genomics Co., Ltd. (Beijing, China).


title: USV1_DMSO_B_S26_RNA-seq


title: stem, replicate 2 (RNA-seq)


title: MJ-T-42


title: WT_sal_rep4

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm39 reference genome using STAR and default parameters
Ensmebl v104 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method and differential gene expression conducted using LIMMA.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include VOOM adjusted cpms values for each Sample

organism: Mus musculus

source_name: Brown adipose

extract_protocol:
After 3 days, interscapular BAT of WT and Ucp1-/- mice was harvested, and total RNA extracted by using an RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Total RNA was assayed for quantity and quality with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries of coding and small non-coding RNAs were generated using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) as per standard protocol in the kit’s guide. A MiSeq micro test lane was run to check pool balance followed by 75 bp single-read sequencing on an Illumina HiSeq 2000 sequencer.

treatment_protocol: Mice were implanted with Alzet minipumps for the infusion of isoproterenol (60 mg/kg/day for 3 days)

value: Brown adipose

value: Wildtype

value: Saline


title: stem, replicate 1 (RNA-seq)

value: stem


title: WT_sal_rep2


title: USV1_3IAA_C_S30_RNA-seq


title: shoot apex, replicate 3 (RNA-seq)

value: shoot apex


title: WT_sal_rep3


title: shoot apex, replicate 2 (RNA-seq)


title: KO_sal_rep4


title: USV1_3IAA_B_S29_RNA-seq


title: KO_sal_rep2


title: shoot apex, replicate 1 (RNA-seq)


title: URC2_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 URC2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 URC2-3xV5 IAA7::URA3


title: USV1_3IAA_A_S28_RNA-seq


title: URC2_DMSO_B_S20_RNA-seq


title: root, replicate 3 (RNA-seq)

value: root


title: root, replicate 2 (RNA-seq)


title: KO_sal_rep1


title: URC2_DMSO_A_S19_RNA-seq


title: USV1_DMSO_A_S25_RNA-seq


title: sk2d, biological rep2

type: RNA

city: Chihuahua

first: Mercedes

last: Bermúdez

state: Chihuahua

address: Chihuahua

department: Dentistry

country: Mexico

institute: Universidad autónoma de Chihuahua

description: GENE EXPRESSION DATA FROM BIDIMENSIONAL CULTURE OF SKRB3 CELLS

hyb_protocol: The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, cDNA preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cRNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.

data_processing: For the subsequent analysis, Partek Genomic Suite v8.0 software was employed. All samples were normalized using the Robust Multiarray Average (RMA) method, which encompasses background correction, normalization, and calculation of expression values. Differential expression analysis was performed using one-way ANOVA. Differentially expressed genes (DE-mRNAs) were selected between the groups based on an absolute fold-change of 2, and the Benjamini and Hochberg false discovery rate [23] was applied to account for multiple hypothesis testing. Genes with an adjusted p-value < 0.01 were considered significant.

label: biotin

source_name: BIDIMENSIONAL CELL CULTURE

growth_protocol: The human cell line SKBR3 (SK-BR-3, HTB-30. ATCC, USA) derived from a patient with breast carcinoma Her2+ was grown in Dulbecco's modification of Eagle's minimal medium (DMEM/F-12) supplemented with 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin (Invitrogen, USA) at 37 °C, in a 5 % CO2 atmosphere

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's instructions. The quantity and quality of total RNA were evaluated using Nanodrop (ThermoFisher Scientific, USA) and RNA integrity was assessed using agarose gel electrophoresis at 60 V, stained with GelRed 0.5 X, and visualized on a UV transilluminator

treatment_protocol: To obtain SKBR3 organoids, a standard On-Top protocol was used [3, 19], briefly, 24-well flat-bottom plates were coated with 150 μL of LDEV-free growth factor-reduced Geltrex (Gibco, USA) and incubated at 37 °C for 30 minutes to promote its gelation. Then, 4.2x104 cells were seeded and DMEM/F-12 supplemented medium was added to incubate for up to 5 days. The only modification was that the medium had no additional 5 % Geltrex as reported. Wells without Geltrex were used as a control (2D), maintaining the rest of the conditions. Similarly, a standard In-Gel protocol was used, briefly, the same number of cells were mixed with Geltrex pregel and then placed in 24-well flat-bottom plates before gelation.[27] Additionally, single cells were diluted to a density of 5x103 cells and placed into ultra-low attachment (ULA) 24-well plates and incubated under the same conditions to let the formation of cell spheroids. Cells were monitored at 72, 96, and 120 h to measure the number and size of spheres using ImageJ software in which regions of interest were surrounded manually around the entire organoid from a bright-field microscopy image, and then in the imageJ module ("Area Measurements of a Complex Object"), the surface area is calculated[28].

value: BREAST CANCER CELLS

tag: growth

value: bidimensional


title: sk3d, biological rep2

description: GENE EXPRESSION DATA FROM TRIDIMENSIONAL CULTURE OF SKRB3 CELLS

scan_protocol: The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, cDNA preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cRNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.

source_name: TRIDIMENSIONAL CELL CULTURE

value: tridimensional


title: WT_sal_rep1


title: sk2d, biological rep1

label_protocol: The hybridization for whole-genome transcriptome analysis was performed following the instructions provided by the manufacturer. Briefly, cDNA preparation and biotin labeling were carried out using the Affymetrix GeneChip WT Pico Kit. Subsequently, cRNA purification was performed using the Affymetrix magnetic bead protocol. Array processing was performed using the Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit. The arrays were incubated for 16 hours in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm. Fluorescence amplification was achieved by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was utilized to capture the fluorescence signal at a resolution of 3 μm after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray.


title: root, replicate 1 (RNA-seq)


title: GW library, plasmid

source_name: plasmid (not a cell)

extract_protocol: Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

value: plasmid (not a cell)


title: WT_iso_rep4

value: Isoproterenol


title: sk3d, biological rep1


title: leaf, replicate 3 (RNA-seq)

value: leaf


title: Y86D_rep3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq output file

molecule: polyA RNA

organism: Schizosaccharomyces pombe

extract_protocol:
hot acid phenol RNA purification protocol
Stranded polyA+ RNA Seq; RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: growth phase

value: log phase culture

tag: growth medium

value: YES medium

value: h- pla1-Y86D::kanMX


title: URC2_3IAA_C_S24_RNA-seq


title: WT_iso_rep3

tag: strain


title: URC2_3IAA_B_S23_RNA-seq


title: Y86D_rep2


title: leaf, replicate 2 (RNA-seq)


title: WT_iso_rep2


title: URC2_3IAA_A_S22_RNA-seq


title: Y86D_rep1


title: WT_rep3

value: h- pla1-WT::kanMX


title: KO_sal_rep3

value: Brown adipose


title: leaf, replicate 1 (RNA-seq)


title: flower, replicate 3 (RNA-seq)

value: flower


title: KO_iso_rep4


title: WT_rep2


title: UPC2_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 UPC2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 UPC2-3xV5 IAA7::URA3


title: flower, replicate 1 (RNA-seq)


title: WT_iso_rep1

value: Wildtype


title: UPC2_DMSO_B_S32_RNA-seq


title: UPC2_3IAA_C_S36_RNA-seq


title: KO_iso_rep3


title: flower, replicate 2 (RNA-seq)


title: KO_iso_rep2


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 12, culture 2

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

library_source: transcriptomic single cell

data_processing:
10X Chromium V3 Chemistry Single-cell RNA Seq
kallisto bustools pseudoalignment
log transformation and TPM normalization (Seurat R package)
PCA (Seurat R package)
UMAP and leiden clustering (Seurat R)
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_011764305.1
Supplementary files format and content: Log2(Transcripts per million (TPM) + 1) expression values (derived from kallisto bustools  for each gene (rows) in each single-cell (columns)

organism: Mustela putorius furo

source_name: Ferret airway epithelial cells cultured in air-liquid interface (ALI)

growth_protocol: Ferret tracheal airway basal stem cell were isolated using an enzymatic digestion method similar to previous reports (Lynch, T. J. et al, Stem Cells 2016; 34, 2758-2771). The cells were cultured in PneumaCult-Ex Plus media (Stem Cell Technologies) on plastic plates pre-coated with laminin enriched 804G-conditioned medium. For passaging, the cells were detached with Accutase (Stem Cell Technologies) and re-seeded at a 1:4 split on 804G coated plates as previously described52. For differentiation at ALI, ferret basal cells were seeded onto transwell membranes coated with 804G in PneumaCult-Ex Plus media for 24 hrs and then lifted to an ALI with PneumaCult-ALI medium (Stem Cell Technologies) placed only on the basal side of the transwell.

extract_protocol:
Fully differentiated ferret airway epithelia ALI cultures were dissociated using Accumax (Stem Cell Technologies) followed by DNase treatment. Cells were filtered through a 20 μMstrainer and pelleted in 0.04% BSA PBS at 500g for 10 min. Nonviable dead cells were removedby using MACS Dead Cell Removal Kit following 10X Genomics recommendations (DocumentCG00039).
Single cells were counted on a Thermo countess cell counter and 0.04% BSA/PBSwas added to achieve a targeted concentration of 1000 cells/μL. Ionocyte-enrichment wasperformed on OH-Tam treated FOXI1-CreERT2::ROSA-TG ALI cultures followed by FACSisolation of EGFP and Tomato positive cells. FACS isolated EGFP positive cells where thenmixed with Tomato positive epithelial cells to achieve ~10,000 total cells for 10x sequencing.The ratio of EGFP to Tomato positive cells varied for each experiment depending on the yield oflineage-labeled cells.
Sequencing libraries were generated by following 10X Genomicsrecommendations (Document CG000315). Briefly, single cells and reverse transcription mastermix were partitioned into Gel Beads in partitioning oil in the 10X Chromium controller. Afterreverse transcription, cDNA libraries were amplified and fragmentated, followed by adaptorligation and sample index PCR reaction. Libraries were sequenced on NovaSeq 6000 platform by the University of Iowa Genomics Division.

treatment_protocol: For scRNA-seq experiments, cultures were treated with OH-Tam during differentiation at ALI from day-1 to day-17 (media change every other day) and cells were harvested at 21 days of ALI. This was done since it gave rise to a greater number of EGFP+ cells in the cultures following full differentiation.

tag: time point

value: airway epithelial cells

tag: donor

value: Donor 12, culture 2


title: UPC2_DMSO_A_S31_RNA-seq


title: P-3

city: Jinan

first: Shuxian

last: Li

address: Jingshi 238 RD

institute: Maternal and Child Health Care Hospital of Shandong Province

data_processing:
The raw sequencing data was subjected to filtration using SOAPnuke in order to obtain clean reads. The clean reads were mapped to the reference genome using HISAT, and aligned to the assembled unique gene set using Bowtie2.
The gene expression was quantified utilizing the RNA-Seq by Expectation-Maximization (RSEM) algorithm, and differentially expressed genes (DEGs) were identified by the R-Bioconductor package DESeq2 with pre-set Q value﹤0.05 and |log2[Fold Change]|≥1.
KEGG enrichment analysis of annotated DEGs was performed using phyper based on Hypergeometric test, and the significance values of pathways were strictly threshold corrected by Q values (Q values≤0.05).
Gene Set Enrichment Analysis (GSEA) was performed on control and treatment groups based on KEGG database data.

extract_protocol:
1 Tissue Sample Fragmentation and Lysis
1.1 Grinding Machine
1.1.1 Transfer appropriate sample to corresponding grinding tube,
1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min
1.2 Liquid Nitrogen Grinding and Crushing
1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube.
1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.
Stand flat for 5 min for the fully lysis of tissue cells.
1.3 Cell Sample Lysis
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells)
2 Sample Purification
2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃.
2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；
2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity).
2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h.
2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting.
2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。
2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min.
2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: placental trophoblast

value: WT


title: KO_iso_rep1


title: UPC2_3IAA_B_S35_RNA-seq


title: WT_rep1


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 11, culture 2

value: Donor 11, culture 2


title: HKO3

city: Beijing

first: Huan

last: Wang

address: Yongan RD

institute: Capital Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

extract_protocol:
RNA was harvested by TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Pld1 knockdown

value: high fat diet


title: P-2


title: UPC2_3IAA_A_S34_RNA-seq


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 10, culture 2

value: Donor 10, culture 2


title: P-1


title: HKO2


title: UGA3_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 UGA3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 UGA3-3xV5 IAA7::URA3


title: UGA3_DMSO_B_S44_RNA-seq


title: HKO1


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 9, culture 2

value: Donor 9, culture 2


title: CON-3

value: no


title: NKO3

value: normal chow diet


title: CON-1


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 12

value: Donor 12


title: NKO2


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 11

value: Donor 11


title: UGA3_3IAA_C_S48_RNA-seq


title: MDP1_#2 cKD  Day14  biol rep 3

city: Niigata

first: Shaban

middle: Amina

last: Kaboso

address: Asahimachi-Dori 1-757l, Chuo

department: Bacteriology

country: Japan

institute: Niigata University

description: VC-MDP1_#2 cKD_day14.csv

data_processing:
Mapped forward.fastq and reverse.fastq to Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa with default settings using BWA
Counted the number of reads in featureCounts in pair-end mode
Calculated significant differences between gene expression with DESeq2
Assembly: Mycobacterium_bovis_bcg.ASM70565v1.dna.nonchromosomal.fa
Supplementary files format and content: CSV format calculated by DESeq2

organism: Mycobacterium tuberculosis variant bovis

source_name: BCG Tokyo 172

growth_protocol: BCG cultures were grown in 7H9/ADC containing 20 µg/ml kanamycin and 50 µg/ml hygromycin as standing cultures at 37 degrees celcius.

extract_protocol:
RNA was harvested using Direct-Zol RNA MiniPrep kit (Zymo research) following manufacturer's protocol
cDNA sample was randomly fragmented followed by 5' and 3' adapta ligation. Alternatively  "tagmentation" was done to combine the fragmentation and ligation in a single more efficient step. Adapter-ligated fragments were then PCR amplified and gel purified

treatment_protocol: For induction and maintainance of sgRNA and dcas9 expression the cultures were supplimented with Anhydrotetracycline at a final concentration of 200ng/ml every 48 hrs

value: BCG Tokyo 172

value: Anhydrotetracycline 200ng/ml every 48 hours

value: hupB_#2 conditional knockdown

tag: time

value: Day 14


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 10

value: airway epithelial cells

value: Donor 10


title: CON-2

value: placental trophoblast

value: WT


title: UGA3_DMSO_A_S43_RNA-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

institute: Fred Hutchinson Cancer Center


title: MDP1_#2 cKD  Day14  biol rep 2

description: VC-MDP1_#2 cKD_day14.csv


title: FOXI1-CreERT2::ROSA-TG ferret airway epithelial cells - Donor 9

value: Donor 9


title: HFD3

value: Liver

value: high fat diet


title: MDP1_#2 cKD  Day14  biol rep 1

description: VC-MDP1_#2 cKD_day14.csv


title: UGA3_3IAA_A_S46_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 UGA3-3xV5 IAA7::URA3


title: NKO1

value: Pld1 knockdown


title: MDP1_#1 cKD  Day14  biol rep 3

description: VC-MDP1_#1 cKD_day14.csv

value: hupB_#1 conditional knockdown


title: HFD2


title: FOXI1-KO ferret airway epithelial cells - Donor 8

value: Donor 8


title: TYE7_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 TYE7-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 TYE7-3xV5 IAA7::URA3


title: TYE7_DMSO_B_S38_RNA-seq


title: UGA3_3IAA_B_S47_RNA-seq


title: FOXI1-KO ferret airway epithelial cells - Donor 7

value: Donor 7


title: FOXI1-KO ferret airway epithelial cells - Donor 6

value: Donor 6


title: MDP1_#1 cKD  Day14  biol rep 2

description: VC-MDP1_#1 cKD_day14.csv

value: BCG Tokyo 172

value: Anhydrotetracycline 200ng/ml every 48 hours


title: NC2

value: normal chow diet


title: HFD1


title: Wild-type ferret airway epithelial cells - Donor 4

value: Wild Type

value: airway epithelial cells

value: Donor 4


title: NC3

value: WT


title: Blood, C27

type: genomic

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: methylation profiling using bisulfite conversion

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Genome-wide methylation analysis was performed by the Illumina Infinium methylation Epic array on bisulfite converted DNA extracted from the three tissues of the patient. Data were analyzed using R version 4.1.0. Beta values (Bvalues) were derived from “idat” files by the “champ.load” module of the “ChAMP” R package (v.2.22.0), with quality control options set as default and array type as “EPIC.” To adjust the Bvalues of type 2 probes, we applied BMIQ normalization with the default options for array type as “EPIC.”

label: Cy5 and Cy5

source_name: Blood

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

value: peripheral blood lymphocytes

tag: gender

value: F

tag: condition

value: Control

tag: age


title: TYE7_DMSO_A_S37_RNA-seq

address: 1100 FAIRVIEW AVE N


title: FOXI1-KO ferret airway epithelial cells - Donor 5

value: Donor 5


title: NC1

value: Liver


title: TYE7_3IAA_B_S41_RNA-seq


title: VC  Day14  biol rep 3

description: VC-MDP1_#1 cKD_day14.csv

value: Day 14


title: Blood, C26

label: Cy5 and Cy4

value: M


title: TYE7_3IAA_C_S42_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 TYE7-3xV5 IAA7::URA3


title: MDP1_#1 cKD  Day14  biol rep 1

description: VC-MDP1_#1 cKD_day14.csv

value: hupB_#1 conditional knockdown


title: Blood, C29

label: Cy5 and Cy7


title: Wild-type ferret airway epithelial cells - Donor 3

value: Donor 3


title: Wild-type ferret airway epithelial cells - Donor 2

value: Donor 2


title: Blood, P48

label: Cy5 and Cy3


title: TEC1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 TEC1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 TEC1-3xV5 IAA7::URA3


title: Blood, C28

label: Cy5 and Cy6


title: P50-1

city: Nanjing

first: Boshi

last: Yu

state: Please choose a State

address: No. 123 Tian Fei Xiang, Mo Chou Road, Nanjing 210004, Jiangsu Province, China

department: Pediatrics

institute: Womenʼs Hospital of Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and count values for each Sample

growth_protocol: The P19 cells were cultured in a complete α-MEM medium (Gibco, containing 10% fetal bovine serum, 100U/ml penicillin and 100mg/L streptomycin) and cultured in a 5%CO2 incubator at 37 ℃

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The P19 cells were treated with peptide PDTLN1

value: peptide PDTLN1


title: VC  Day14  biol rep 1

description: VC-MDP1_#1 cKD_day14.csv

value: BCG Tokyo 172

value: Anhydrotetracycline 200ng/ml every 48 hours


title: MDP1_#2 cKD  Day7  biol rep 3

description: VC-MDP1_#2 cKD_day7.csv

value: hupB_#2 conditional knockdown

value: Day 7


title: Wild-type ferret airway epithelial cells - Donor 1

value: Wild Type

value: airway epithelial cells

value: Donor 1


title: MRSL_Control

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 295 Duck Pond Dr

institute: Virginia Tech

description: Clariom S Affymetrix and ThermoFisher

hyb_protocol: Performed by ThermoFisher ClariomS services

data_processing: CHP data provided by ThermoFisher ClariomS services. Researchers analysed data using the Transcriptome Analysis Console (ThermoFisher, Applied Biosystems)

label: Biotin

source_name: Mouse RNA MRSL control from Thermo Fisher

growth_protocol: 4T1 cells (4T1, 4T1OE, or 4T1OE-CTL) were injected into a singular mammary fat pad in the mouse. After the tumor had grown, tumors were collected following euthanasia and flash frozen.

extract_protocol: Qiagen Rneasy extraction kit per manufacturer's protocols

tag: mouse genotype

tag: 4t1 cell line


title: Control-3

value: none (control)


title: VC  Day14  biol rep 2

description: VC-MDP1_#1 cKD_day14.csv

tag: genotype

value: WT


title: P50-3

tag: cell line


title: TYE7_3IAA_A_S40_RNA-seq

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.


title: TEC1_DMSO_A_S31_RNA-seq


title: MDP1_#2 cKD  Day7  biol rep 1

description: VC-MDP1_#2 cKD_day7.csv


title: Control-2


title: Control-1


title: P50-2


title: MDP1_#1 cKD  Day7  biol rep 3

description: VC-MDP1_#1 cKD_day7.csv


title: TEC1_3IAA_B_S35_RNA-seq