title: CISD2 RBD-deleted replicate 1 eCLIP IP


title: CNBP RBD-deleted replicate 2 eCLIP IP

status: Public on Sep 20 2024

type: SRA

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

country: USA

institute: UCSD

description: CNBP_DEL.reproducible_enriched_windows.tsv.gz

library_source: transcriptomic

data_processing:
eCLIP data was analyzed using Skipper with default settings. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.
Assembly: hg38
Supplementary files format and content: Reproducible enriched peaks output by Skipper

molecule: total RNA

organism: Homo sapiens

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 5% CO2 and 37C.

extract_protocol: eCLIP experiments were performed as previously described using a V5 antibody (Bethyl A190-120A); see Blue et al. 2022 doi:10.1038/s41596-022-00680-z

treatment_protocol: V5-tagged zinc finger ORFs were transfected using Lipofectamine 3000 (Thermo Fisher). One 10cm dish was used for each biological replicate. After 72hr incubation, cells were UV crosslinked on ice at 400 mJoules/cm2 with 254 nm radiation. Cells were then scraped on ice and pelleted at °C, and the supernatant was discarded before the samples were snap-frozen and stored at -80°C. To minimize variability, all samples were prepared in two batches from the same thaw of cells.

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: CNBP RBD-deleted

tag: treatment

value: Bethyl A190-120A


title: ZNF593 RBD-deleted replicate 1 eCLIP IP

description: ZNF593_DEL.reproducible_enriched_windows.tsv.gz

value: ZNF593 RBD-deleted


title: ZNF277 endogenous eCLIP replicate 2 size-matched input

description: ZNF277_N.reproducible_enriched_windows.tsv.gz

value: ZNF277 endogenous


title: BRCA1 knockdown 2hr-chase replicate 3

data_processing:
Reads were aligned to hg38 using SlamDunk (v0.4.3) with inclusion of multi-mapping reads.
Assembly: hg38
Supplementary files format and content: C->T conversion counts within 3' UTR regions output by SlamDunk

molecule: polyA RNA

extract_protocol:
Total RNA was extracted with the Direct-Zol RNA miniprep kit (Zymo) with DTT added to the buffers.
RNA was alkylated using the SLAMseq kit per manufacturer’s instructions. Libraries were then prepared using the QuantSeq 3’ mRNA-seq Library Prep Kit for Illumina (Lexogen) and sequenced using the Novaseq 6000 platform (Illumina) to approximately 20M SE150 reads per sample.

treatment_protocol: HEK293T cells (3 biological replicates per knockdown, per timepoint) were transduced with lentivirus, puromycin-selected, and confirmed by qPCR. 4SU treatment and alkylation were performed using the SLAMseq Kinetics Kit, Catabolic Module (Lexogen). All steps were performed in the dark under a red light. Cells were treated with 10 uM 4SU for 24 hr with media changes every 8 hr. Then the media was replaced with fresh media containing 1 mM uridine. Cells were incubated for 0, 2, 4, or 8 hr in the presence of excess uridine. At the end of incubation, cells were immediately lysed using Trizol.


title: ZNF277 endogenous eCLIP replicate 1 size-matched input


title: ZNF277 endogenous eCLIP replicate 1 IP

value: Invitrogen PA5-55577


title: ZNF277 endogenous eCLIP replicate 2 IP


title: ZNF277 RBD-deleted replicate 2 eCLIP IP

description: ZNF277_DEL.reproducible_enriched_windows.tsv.gz

value: ZNF277 RBD-deleted


title: BRCA1 knockdown 8hr-chase replicate 2


title: ZNF593 RBD-deleted replicate 2 eCLIP IP


title: ZNF473 endogenous eCLIP replicate 1 IP

description: ZNF473_N.reproducible_enriched_windows.tsv.gz

value: ZNF473 endogenous

value: Thermo Fisher BS-12242R


title: ZNF473 endogenous eCLIP replicate 2 IP


title: ZNF473 endogenous eCLIP replicate 1 size-matched input


title: Activated primary spinal astrocytes#4

city: Winnipeg

first: Seyed Mojtaba

last: Hosseini

state: Manitoba

address: 745 Bannatyne Ave

country: Canada

institute: University of Manitoba

description: In vtiro

data_processing:
Data were processed using Galaxy workflow
Following QC, data were trimmed using Trimmomatic package
After trimming, transcripts were mapped to human genome hg38
Read counts were extracted and normalized using GenCount package in Galaxy workflow
Assembly: mm 10
Supplementary files format and content: txt file containing gene counts for all of the samples

source_name: Spinal primary astrocytes

growth_protocol: Astrocytes were cultured and matured in DMEM, 5% horse serum, 1% pen/strep and 1% L-glutamine

extract_protocol:
Cell lysate of astroyctes was kept in Trizol and RNA was extracted using ThermoFisher PureLink RNA mini kit
RNA libraries were generated using NEB kit by Genome Qubec

treatment_protocol: To activate astrocytes, they were treated with TNF-α+IL-1𝛽 (50ng/ml each) after one day of serum deprivation

value: Spinal primary astrocytes

value: Astrocytes

value: WT


title: Control primary spinal astroyctes #4

description: In vtiro

value: Control


title: Activated primary spinal astrocytes#1

description: In vtiro


title: Activated primary spinal astrocytes#2

description: In vtiro


title: Control primary spinal astroyctes #2

description: In vtiro


title: Control primary spinal astroyctes #3

description: In vtiro


title: Activated primary spinal astrocytes#3

description: In vtiro


title: BRCA1 knockdown 0hr-chase replicate 2


title: Control primary spinal astroyctes #1

description: In vtiro


title: Activated NPC-derived astrocytes#3

description: In vtiro

source_name: Differentiated from NPCs

value: Differentiated from NPCs


title: ZNF277 RBD-deleted replicate 1 eCLIP IP


title: Activated NPC-derived astrocytes#2

description: In vtiro


title: Activated NPC-derived astrocytes#1

description: In vtiro


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep3

city: Glasgow

first: Louisa

last: Iselin

state: Lanarkshire

address: 464 Bearsden Road

country: United Kingdom

institute: University of Glasgow

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed (Je Suite) and adapters trimmed (Cutadapt).
Reads were aligned to a combined human (GRCh38) and SINV (pT7-SVwt) genome annotation using STAR.
Crosslink position and counts were extracted using Bedtools.
HTSeq-clip was used to generate a sliding window annotation of the human and SINV genome (50nt window, 20nt step size) and calculate the frequency of crosslink truncation sites within each window.
DEW-Seq was then used to calculate the differential enrichment of each window relative to size matched input control samples, with a cut-off of 2 log2 fold change and 0.01 adjusted p-value.
Assembly: GRCh38 (ENSEMBL Release 106), pT7-SVwt
Supplementary files format and content: A count matrix derived from HTSeq-clip displaying signal within each 50nt sliding window across the genome. Each column represents a single sample. This matrix is used as input to DEW-Seq for identifying binding sites.

growth_protocol: 10x106 HEK293 TRIM25 WT, TRIM25-m3, and TRIM25-m9 cells were seeded in 6 sets of 10 cm dishes and incubated for 24 h.

extract_protocol:
Cells were washed with PBS 1x, and UV irradiated with 300 mJ/cm2 at 254 nm. Cells were then lysed in 1 ml RIPA buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% wt/vol Na deoxycholate and 0.2 mM AEBSF).
Libraries were constructed using iCLIP2 procotol (https://doi.org/10.1016/j.ymeth.2019.10.003)

treatment_protocol: Three cell sets per cell line were then infected with 3 MOI of SINV for 9 hours.

value: SINV infection (9h, MOI 3)


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep1


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep2


title: ZNF473 endogenous eCLIP replicate 2 size-matched input


title: Control NPC-derived astrocytes#3

description: In vtiro


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep2


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep1


title: Control NPC-derived astrocytes#2

description: In vtiro


title: Control NPC-derived astrocytes#1

description: In vtiro


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep2


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25, Mock infected, rep3

value: Mock infection


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25, Mock infected, rep2


title: V5_50_to_125 replicate 1 size-matched input

data_processing:
*library strategy: eCLIP-seq
eCLIP data was analyzed using Skipper with default settings. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.
Assembly: hg38
Supplementary files format and content: Reproducible enriched peaks output by Skipper


title: V5_25_to_100 replicate 2 size-matched input


title: V5_75_to_150 replicate 2 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25, Mock infected, rep1


title: V5_25_to_100 replicate 1 size-matched input


title: V5_150_to_225 replicate 2 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep3


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep3


title: V5_150_to_225 replicate 1 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep1


title: V5_50_to_125 replicate 2 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP immunoprecipiated for TRIM25, Mock infected, rep2


title: V5_125_to_225 replicate 2 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep2


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep3


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep2


title: ZNF473 RBD-wild type replicate 2 eCLIP IP

description: ZNF473_WT.reproducible_enriched_windows.tsv.gz

value: ZNF473 RBD-wild type


title: V5_100_to_225 replicate 1 size-matched input

value: Human embryonic kidney


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep3


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M3) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep1


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (M9) add-back, iCLIP immunoprecipiated for TRIM25, Mock infected, rep1


title: V5_100_to_225 replicate 2 size-matched input


title: V5_125_to_225 replicate 1 size-matched input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP size matched input for TRIM25,  SINV infected (9h), rep1


title: V5_75_to_150 replicate 1 size-matched input


title: ZNF473 RBD-wild type replicate 1 eCLIP input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep2


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, Mock infected, rep2


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep1


title: ZNF473 RBD-wild type replicate 2 eCLIP input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, SINV infected (9h), rep3


title: ZNF473 RBD-deleted replicate 1 eCLIP IP

description: ZNF473_DEL.reproducible_enriched_windows.tsv.gz

value: ZNF473 RBD-deleted


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, Mock infected, rep3


title: ZNF473 RBD-deleted replicate 2 eCLIP IP

value: Bethyl A190-120A


title: ZNF473 RBD-deleted replicate 2 eCLIP input


title: HEK293-FRT-TRIM25KO TRIM25-FLAG (WT) add-back, iCLIP immunoprecipiated for TRIM25, Mock infected, rep1


title: ZNF473 RBD-deleted replicate 1 eCLIP input


title: Spheroids, IL11_IL11Rec_VEGF_2

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

data_processing:
NextSeq 2000 Control Software (NCS) v1.2.0.36376
STAR (Galaxy Version 2.7.5b) for aligning
FeatureCounts (Galaxy Version 1.6.4) for assigning reads to genes
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Spheroids

growth_protocol: HUVECs were grown to confluence. Endothelial spheroids were formed in a hanging drop and embedded in a collagen gel. Treatment was applied to the top of the gel and incubated for 17 hrs. The treatment was removed before lysing.

extract_protocol:
RNA was harvested using the RNeasy MinElute spin columns (RNeasy Micro Kit, QIAGEN, Hilden, Germany) including proteinase K digestion step
SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Cat#: 634893, Takara), Illumina Nextera XT Sample Preparation Guide (Cat#: FC-131-1024, Illumina)

treatment_protocol: VEGF, IL-11+VEGF, sIL-11R+VEGF, IL-11+sR+VEGF

tag: tissue

value: Spheroids

value: HUVECs


title: Spheroids, IL11_IL11Rec_VEGF_1


title: V5_75_to_150 replicate 2 eCLIP

description: V5_75_to_150.reproducible_enriched_windows.tsv.gz


title: ZNF473 RBD-wild type replicate 1 eCLIP IP


title: Spheroids, IL11_IL11Rec_VEGF_3


title: V5_75_to_150 replicate 1 eCLIP


title: V5_50_to_125 replicate 2 eCLIP

description: V5_50_to_125.reproducible_enriched_windows.tsv.gz


title: Spheroids, IL11Rec_VEGF_2


title: V5_50_to_125 replicate 1 eCLIP


title: Spheroids, IL11_VEGF_1


title: V5_25_to_100 replicate 2 eCLIP

description: V5_25_to_100.reproducible_enriched_windows.tsv.gz


title: V5_25_to_100 replicate 1 eCLIP


title: Spheroids, IL11_VEGF_3


title: V5_150_to_225 replicate 2 eCLIP

description: V5_150_to_225.reproducible_enriched_windows.tsv.gz


title: Spheroids, IL11Rec_VEGF_1


title: V5_125_to_225 replicate 2 eCLIP

description: V5_125_to_225.reproducible_enriched_windows.tsv.gz


title: V5_125_to_225 replicate 1 eCLIP


title: Spheroids, VEGF_2

value: VEGF


title: Spheroids, VEGF_1


title: Spheroids, VEGF_3


title: R3

city: Beijing

first: Rongni

last: Li

state: beijing

address: 18 Jiaomen Road, Fengtai District, Beijing

department: Fisheries Science Institute

country: China

institute: Beijing Academy of Agriculture and Forestry Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for more than 2 Ns, more than half of the base’s qualities were less than 10 and reads with less than 20 bp ,and the adapters from all reads, then mapped to Sscrofa10.2.72 whole genome using bowtie v0.12.5 and Tophat (version:2.0.9) and two mismatches were allowed for 100 bp reads in each alignment.
Numbers of fragment reads per kilobase of exon region in a gene per million mapped reads (FPKM) analyzed by Cufflink (version: 2.1.1) were used as the value of normalized gene expression
Differential expression analyses of four comparsion groups (TH vs.YH, TH vs.TL, YH vs.YL and TLvs.YL.) were performed using the DESeq R package (1.10.1)
Assembly: Sscrofa10.2.72
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Carassius auratus

source_name: eye

extract_protocol:
Eyes were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: eye

tag: group

value: celestial-eye


title: V5_100_to_225 replicate 1 eCLIP

description: V5_100_to_225.reproducible_enriched_windows.tsv.gz


title: Spheroids, IL11Rec_VEGF_3


title: V5_150_to_225 replicate 1 eCLIP


title: ZNF800 replicate 2 eCLIP

description: ZNF800.reproducible_enriched_windows.tsv.gz


title: C3

value: normal eyes


title: R2\


title: ZNF706 replicate 2 eCLIP

description: ZNF706.reproducible_enriched_windows.tsv.gz


title: Spheroids, IL11_VEGF_2


title: C2


title: ZNF706 replicate 1 eCLIP


title: C1


title: ZNF593 replicate 2 eCLIP

description: ZNF593.reproducible_enriched_windows.tsv.gz


title: Piezo1 KO OCY454 D28 Rep2

city: Boston

first: Yizhong

last: Hu

state: MA

address: 190 Longwood Ave.

institute: Harvard School of Dental Medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

organism: Mus musculus

growth_protocol: WT and Piezo1 KO OCY454 cells were maintained at 33C in 10%FBS, 1% anti-anti in alpha-MEM. Differentiation was induced by switching to 37C.

extract_protocol:
RNA was isolated from cells grown in 12-well plates using Qiazol according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

value: osteoblast/osteocyte

value: Piezo1 knock out

value: osteocyte dfiferentiation D28


title: ZNF593 replicate 1 eCLIP


title: Piezo1 KOOCY454 D28 Rep1


title: ZNF574 replicate 2 eCLIP

description: ZNF574.reproducible_enriched_windows.tsv.gz


title: Piezo1 KO OCY454 D14 Rep2

value: osteocyte dfiferentiation D14


title: V5_100_to_225 replicate 2 eCLIP


title: ZNF574 replicate 1 eCLIP


title: Piezo1 KO OCY454 D14 Rep1


title: ZNF473 replicate 2 eCLIP

description: ZNF473.reproducible_enriched_windows.tsv.gz


title: ZNF473 replicate 1 eCLIP


title: ZNF317 replicate 2 eCLIP

description: ZNF317.reproducible_enriched_windows.tsv.gz


title: Piezo1 KO OCY454 D1 Rep1

value: osteocyte dfiferentiation D1


title: ZNF317 replicate 1 eCLIP


title: WT OCY454 D28 Rep2

value: WT


title: WT OCY454 D28 Rep1


title: ZNF277 replicate 2 eCLIP

description: ZNF277.reproducible_enriched_windows.tsv.gz


title: ZNF277 replicate 1 eCLIP


title: WT OCY454 D1 Rep2


title: WT OCY454 D14 Rep1


title: ZNF22 replicate 1 eCLIP

description: ZNF22.reproducible_enriched_windows.tsv.gz


title: [BT-20]-[3D]-[rep2]

type: RNA

city: Ciudad de México

first: Mercedes

last: Olvera-Valencia

state: Mexico

address: San Fernando

department: Investigación básica

country: Mexico

institute: Instituto Nacional de Cancerología

description: Gene expression data from MDA-MB-231 cell line growing in 3D cell culture

hyb_protocol: Apply the hybridization solution by Human Clariom D microarray containing the labeled cRNA to the microarray. Incubate at a temperature of  45°C,  60 rpm within for 16 hours to allow the cRNA to bind to the complementary probes on the microarray.

scan_protocol: To scan, we used a fluorescence scan.

data_processing: We process the data by the Transcriptome Analysis Console (TAC) by Affymetrix

label: Biotin-labeled cRNA

source_name: MDA-MB-231, 3D cell culture

label_protocol: The biotin-labeled cRNA was briefly done by converting RNA to cDNA using T7 as a promoter. Then, we use T7 RNA polymerase to transcribe the cDNA into biotin-labeled cRNA, incorporating biotin-labeled ribonucleotides. We purify the biotin-labeled cRNA to remove unincorporated nucleotides and enzymes (Biotin-11-CTP and Biotin-16-UTP) and finally, we fragment the biotin-labeled cRNA to enhance hybridization efficiency.

growth_protocol: both cell lines were grown in DMEM-F12 culture medium under CO2 conditions and at 37 degrees

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

treatment_protocol: For 3D cultures, the cells were grown within Matrigel diluted in DMEM-F12

tag: culture method

value: TNBC cell line in tridimensional cell culture


title: [BT-20]-[3D]-[rep1]


title: ZNF22 replicate 2 eCLIP


title: WT OCY454 D14 Rep2


title: WT OCY454 D1 Rep1


title: ZNF2 replicate 2 eCLIP

description: ZNF2.reproducible_enriched_windows.tsv.gz


title: [MDA-MB-231]-[3D]-[rep1]

description: Gene expression data from BT-20 cell line growing in 3D cell culture

source_name: BT-20, 3D cell culture


title: [MDA-MB-231]-[3D]-[rep2]


title: Piezo1 KO OCY454 D1 Rep2


title: ZMAT3 replicate 2 eCLIP

description: ZMAT3.reproducible_enriched_windows.tsv.gz


title: ZFP36L1 replicate 2 eCLIP

description: ZFP36L1.reproducible_enriched_windows.tsv.gz


title: [BT-20]-[2D]-[rep1]

description: Gene expression data from BT-20 cell line growing in 2D cell culture

source_name: BT-20, 2D cell culture

value: TNBC cell line in bidimensional cell culture


title: [BT-20]-[2D]-[rep3]


title: [MDA-MB-231]-[2D]-[rep2]

description: Gene expression data from MDA-MB-231 cell line growing in 2D cell culture

source_name: MDA-MB-231, 2D cell culture


title: ZFP36L1 replicate 1 eCLIP

value: Human embryonic kidney


title: [MDA-MB-231]-[2D]-[rep1]


title: ZC3H3 replicate 2 eCLIP

description: ZC3H3.reproducible_enriched_windows.tsv.gz


title: [MDA-MB-231]-[2D]-[rep3]


title: ZMAT3 replicate 1 eCLIP


title: ZNF2 replicate 1 eCLIP


title: [BT-20]-[2D]-[rep2]


title: ZC3HAV1 replicate 2 eCLIP

description: ZC3HAV1.reproducible_enriched_windows.tsv.gz


title: HCT116, N_12, rep2

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

institute: Jiangsu Ocean University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: N_12_gene counts.csv

source_name: Colon Cancer

growth_protocol: HCT116 cells were cultured in MC5A supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without N_12 for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Colon Cancer

value: Human Colon Cancer Cell


title: HCT116, DMSO, rep2

value: DMSO


title: ZMAT5 replicate 1 eCLIP

description: ZMAT5.reproducible_enriched_windows.tsv.gz

value: Bethyl A190-120A


title: U2AF1 replicate 1 eCLIP

description: U2AF1.reproducible_enriched_windows.tsv.gz


title: TRIM55 replicate 2 eCLIP

description: TRIM55.reproducible_enriched_windows.tsv.gz


title: ZC3H3 replicate 1 eCLIP


title: post-treatment, polyI:C, Placebo NT274

city: Perth

first: Niamh

last: Troy

address: Perth Children's Hospital, 15 Hospital Avenue Nedlands

country: Australia

institute: Telethon Kids Institute

description:
post-treatment, polyI:C, Placebo
post-treatment, polyI:C, Placebo

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer.
the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (filtered and normalised data)

source_name: PBMC

growth_protocol: PBMC isolation and storage as per standard protocols

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBMC cultured in vitro with LPS, PolyI:C or unstimulted controls for 24 hours.

tag: gender

tag: age at pre-treatment (days)


title: ZMAT5 replicate 2 eCLIP


title: U2AF1 replicate 2 eCLIP


title: HCT116, DMSO, rep1


title: post-treatment,  unstimulated control, Placebo NT272

description:
post-treatment,  unstimulated control, Placebo
post-treatment,  unstimulated control, Placebo


title: TRIM55 replicate 1 eCLIP


title: TF3C4 replicate 2 eCLIP

description: TF3C4.reproducible_enriched_windows.tsv.gz


title: ZC3HAV1 replicate 1 eCLIP


title: post-treatment, LPS, OM85 NT266

description:
post-treatment, LPS, OM85
post-treatment, LPS, OM85


title: WBP4 replicate 2 eCLIP

description: WBP4.reproducible_enriched_windows.tsv.gz


title: WBP4 replicate 1 eCLIP


title: TEX13A replicate 2 eCLIP

description: TEX13A.reproducible_enriched_windows.tsv.gz


title: post-treatment,  unstimulated control, OM85 NT265

description:
post-treatment,  unstimulated control, OM85
post-treatment,  unstimulated control, OM85


title: pre-treatment, polyI:C, OM85 NT264

description:
pre-treatment, polyI:C, OM85
pre-treatment, polyI:C, OM85


title: post-treatment, LPS, Placebo NT273

description:
post-treatment, LPS, Placebo
post-treatment, LPS, Placebo


title: pre-treatment, LPS, OM85 NT262

description:
pre-treatment, LPS, OM85
pre-treatment, LPS, OM85


title: SNRPC replicate 2 eCLIP

description: SNRPC.reproducible_enriched_windows.tsv.gz

value: SNRPC


title: pre-treatment, unstimulated control, OM85 NT261

description:
pre-treatment, unstimulated control, OM85
pre-treatment, unstimulated control, OM85


title: SALL4 replicate 2 eCLIP

description: SALL4.reproducible_enriched_windows.tsv.gz


title: post-treatment,  unstimulated control, Placebo NT259


title: RNF14 replicate 2 eCLIP

description: RNF14.reproducible_enriched_windows.tsv.gz


title: pre-treatment, polyI:C, Placebo NT258

description:
pre-treatment, polyI:C, Placebo
pre-treatment, polyI:C, Placebo


title: SNRPC replicate 1 eCLIP


title: SALL4 replicate 1 eCLIP


title: pre-treatment, unstimulated control, Placebo NT257

description:
pre-treatment, unstimulated control, Placebo
pre-treatment, unstimulated control, Placebo


title: RNF14 replicate 1 eCLIP


title: TF3C4 replicate 1 eCLIP


title: post-treatment, LPS, OM85 NT254


title: post-treatment,  unstimulated control, OM85 NT253


title: RBM5 replicate 1 eCLIP

description: RBM5.reproducible_enriched_windows.tsv.gz


title: RBM5 replicate 2 eCLIP


title: TEX13A replicate 1 eCLIP


title: R113A1 replicate 2 eCLIP

description: R113A1.reproducible_enriched_windows.tsv.gz


title: post-treatment, polyI:C, OM85 NT256

description:
post-treatment, polyI:C, OM85
post-treatment, polyI:C, OM85


title: pre-treatment, LPS, OM85 NT250


title: R113A1 replicate 1 eCLIP


title: PHF7 replicate 2 eCLIP

description: PHF7.reproducible_enriched_windows.tsv.gz


title: pre-treatment, unstimulated control, OM85 NT249


title: PHF7 replicate 1 eCLIP


title: post-treatment, polyI:C, Placebo NT260

description:
post-treatment, polyI:C, Placebo
post-treatment, polyI:C, Placebo


title: post-treatment, polyI:C, Placebo NT248


title: NANO2 replicate 1 eCLIP

description: NANO2.reproducible_enriched_windows.tsv.gz


title: post-treatment,  unstimulated control, Placebo NT245

description:
post-treatment,  unstimulated control, Placebo
post-treatment,  unstimulated control, Placebo


title: pre-treatment, polyI:C, Placebo NT244


title: MBNL1 replicate 2 eCLIP

description: MBNL1.reproducible_enriched_windows.tsv.gz


title: MBNL1 replicate 1 eCLIP


title: pre-treatment, unstimulated control, Placebo NT241


title: MAZ replicate 2 eCLIP

description: MAZ.reproducible_enriched_windows.tsv.gz

value: MAZ


title: pre-treatment, LPS, Placebo NT242

description:
pre-treatment, LPS, Placebo
pre-treatment, LPS, Placebo


title: MAZ replicate 1 eCLIP


title: post-treatment, LPS, Placebo NT246

description:
post-treatment, LPS, Placebo
post-treatment, LPS, Placebo


title: post-treatment, polyI:C, OM85 NT232


title: LN28B replicate 2 eCLIP

description: LN28B.reproducible_enriched_windows.tsv.gz


title: IGHMBP2 replicate 2 eCLIP

description: IGHMBP2.reproducible_enriched_windows.tsv.gz


title: pre-treatment, LPS, OM85 NT226

description:
pre-treatment, LPS, OM85
pre-treatment, LPS, OM85


title: pre-treatment, polyI:C, OM85 NT228

description:
pre-treatment, polyI:C, OM85
pre-treatment, polyI:C, OM85


title: IGHMBP2 replicate 1 eCLIP


title: post-treatment, LPS, OM85 NT230

description:
post-treatment, LPS, OM85
post-treatment, LPS, OM85


title: HCT116, N_12, rep1


title: pre-treatment, polyI:C, OM85 NT252


title: LN28B replicate 1 eCLIP


title: GIN1 replicate 2 eCLIP

description: GIN1.reproducible_enriched_windows.tsv.gz


title: NANO2 replicate 2 eCLIP


title: post-treatment, LPS, OM85 NT222


title: GIN1 replicate 1 eCLIP


title: post-treatment, polyI:C, OM85 NT268


title: G2E3 replicate 2 eCLIP

description: G2E3.reproducible_enriched_windows.tsv.gz


title: post-treatment,  unstimulated control, OM85 NT221

description:
post-treatment,  unstimulated control, OM85
post-treatment,  unstimulated control, OM85


title: pre-treatment, polyI:C, OM85 NT220


title: FUS replicate 2 eCLIP

description: FUS.reproducible_enriched_windows.tsv.gz

value: FUS


title: G2E3 replicate 1 eCLIP


title: pre-treatment, LPS, OM85 NT218


title: ERI2 replicate 2 eCLIP

description: ERI2.reproducible_enriched_windows.tsv.gz


title: pre-treatment, unstimulated control, OM85 NT217

description:
pre-treatment, unstimulated control, OM85
pre-treatment, unstimulated control, OM85


title: FUS replicate 1 eCLIP


title: post-treatment, LPS, Placebo NT214


title: ERI2 replicate 1 eCLIP


title: pre-treatment, unstimulated control, OM85 NT225


title: CTCF replicate 2 eCLIP

description: CTCF.reproducible_enriched_windows.tsv.gz

value: CTCF


title: CTCF replicate 1 eCLIP


title: pre-treatment, LPS, Placebo NT210


title: pre-treatment, polyI:C, Placebo NT212

description:
pre-treatment, polyI:C, Placebo
pre-treatment, polyI:C, Placebo


title: CPSF4 replicate 2 eCLIP

description: CPSF4.reproducible_enriched_windows.tsv.gz


title: pre-treatment, unstimulated control, Placebo NT209

description:
pre-treatment, unstimulated control, Placebo
pre-treatment, unstimulated control, Placebo


title: post-treatment, polyI:C, OM85 NT224

description:
post-treatment, polyI:C, OM85
post-treatment, polyI:C, OM85


title: post-treatment, polyI:C, Placebo NT208

description:
post-treatment, polyI:C, Placebo
post-treatment, polyI:C, Placebo


title: CPSF4 replicate 1 eCLIP


title: CPS4L replicate 2 eCLIP

description: CPS4L.reproducible_enriched_windows.tsv.gz


title: CNOT4 replicate 2 eCLIP

description: CNOT4.reproducible_enriched_windows.tsv.gz


title: R1

value: eye

value: celestial-eye


title: CPS4L replicate 1 eCLIP


title: CNBP replicate 2 eCLIP

description: CNBP.reproducible_enriched_windows.tsv.gz

value: CNBP


title: CNOT4 replicate 1 eCLIP


title: pre-treatment, LPS, Placebo NT202

description:
pre-treatment, LPS, Placebo
pre-treatment, LPS, Placebo


title: CNBP replicate 1 eCLIP


title: pre-treatment, unstimulated control, Placebo NT201


title: CISD2 replicate 2 eCLIP

description: CISD2.reproducible_enriched_windows.tsv.gz


title: post-treatment, LPS, Placebo NT206

description:
post-treatment, LPS, Placebo
post-treatment, LPS, Placebo


title: post-treatment,  unstimulated control, Placebo NT213

description:
post-treatment,  unstimulated control, Placebo
post-treatment,  unstimulated control, Placebo


title: post-treatment, polyI:C, OM85 NT200


title: CISD1 replicate 1 eCLIP

description: CISD1.reproducible_enriched_windows.tsv.gz


title: post-treatment, LPS, OM85 NT198

description:
post-treatment, LPS, OM85
post-treatment, LPS, OM85


title: pre-treatment, polyI:C, OM85 NT196

description:
pre-treatment, polyI:C, OM85
pre-treatment, polyI:C, OM85


title: CISD1 replicate 2 eCLIP


title: CISD2 replicate 1 eCLIP


title: post-treatment,  unstimulated control, OM85 NT197

description:
post-treatment,  unstimulated control, OM85
post-treatment,  unstimulated control, OM85


title: BRCA1 replicate 1 eCLIP

description: BRCA1.reproducible_enriched_windows.tsv.gz


title: post-treatment, polyI:C, Placebo NT192


title: BRCA1 replicate 2 eCLIP


title: ZNF800 replicate 1 eCLIP

description: ZNF800.reproducible_enriched_windows.tsv.gz


title: post-treatment, LPS, Placebo NT190


title: APEX2 replicate 2 eCLIP

description: APEX2.reproducible_enriched_windows.tsv.gz


title: pre-treatment, polyI:C, Placebo NT204

description:
pre-treatment, polyI:C, Placebo
pre-treatment, polyI:C, Placebo


title: APEX2 replicate 1 eCLIP


title: ZNF800 replicate 2 Cut&Run

library_source: genomic

data_processing:
*library strategy: Cut&Run
Data analysis was performed using a modified version of CUT&RUNTools 2.0. Adapters were trimmed using Trimmomatic (v0.36), followed by a second round of trimming to remove any remaining adapter overhang sequences not removed due to fragment read-through. Reads were aligned to hg38 using bowtie2 (v2.3.5.1) using preset “--very-sensitive-local,” minimum fragment length 10, and maximum fragment length 700. After removing PCR duplicates with Picard (v0.1.8), peaks were called using MACS2 (v2.2.7.1) on the default narrowPeak setting using the same-batch V5 mock IP sample as a normalization control.
Assembly: hg38
Supplementary files format and content: narrowPeak files (q<0.05) output by MACS2

molecule: genomic DNA

extract_protocol: After 48hr incubation, Cut&Run was performed using the CUTANA Cut&Run kit (Epicypher) with the non-crosslinking protocol. A validated V5 antibody (Bethyl A190-120A) was used for Cut&Run immunoprecipitation. Libraries were sequenced using the Novaseq 6000 platform (Illumina) to approximately 10M paired-end reads per sample.

treatment_protocol: HEK293T cells were transfected with V5-tagged ZFP plasmids using Lipofectamine 3000 (Thermo Fisher), along with un-transfected samples as a mock IP negative control. One well of a 12-well plate was used for each biological replicate.


title: pre-treatment, LPS, OM85 NT194

description:
pre-treatment, LPS, OM85
pre-treatment, LPS, OM85


title: pre-treatment, polyI:C, Placebo NT188


title: ZNF706 replicate 2 Cut&Run


title: pre-treatment, unstimulated control, Placebo NT185

description:
pre-treatment, unstimulated control, Placebo
pre-treatment, unstimulated control, Placebo


title: pre-treatment, LPS, Placebo NT186


title: ZNF800 replicate 1 Cut&Run


title: ZNF706 replicate 1 Cut&Run


title: post-treatment,  unstimulated control, Placebo NT189


title: pre-treatment, unstimulated control, OM85 NT181

description:
pre-treatment, unstimulated control, OM85
pre-treatment, unstimulated control, OM85


title: ZNF593 replicate 1 Cut&Run


title: ZNF574 replicate 2 Cut&Run


title: ZNF593 replicate 2 Cut&Run


title: pre-treatment, polyI:C, OM85 NT182


title: ZNF473 replicate 2 Cut&Run


title: pre-treatment, polyI:C, OM85 NT178


title: post-treatment,  unstimulated control, OM85 NT179


title: ZNF473 replicate 1 Cut&Run


title: ZNF473 RBD-wild type replicate 2 Cut&Run

value: ZNF473 RBD-wild type


title: ZNF473 RBD-wild type replicate 1 Cut&Run


title: post-treatment, polyI:C, OM85 NT176

description:
post-treatment, polyI:C, OM85
post-treatment, polyI:C, OM85


title: pre-treatment, unstimulated control, OM85 NT193


title: post-treatment,  unstimulated control, OM85 NT173


title: post-treatment, LPS, OM85 NT174


title: ZNF473 RBD-deleted replicate 1 Cut&Run

value: ZNF473 RBD-deleted


title: ZNF473 RBD-deleted replicate 2 Cut&Run


title: post-treatment, polyI:C, OM85 NT184


title: ZNF317 replicate 2 Cut&Run


title: post-treatment,  unstimulated control, OM85 NT183


title: pre-treatment, unstimulated control, OM85 NT169


title: pre-treatment, LPS, OM85 NT170


title: ZNF2 replicate 2 Cut&Run


title: ZNF2 replicate 1 Cut&Run


title: post-treatment, LPS, OM85 NT166


title: post-treatment, polyI:C, OM85 NT168


title: ZNF277 replicate 2 Cut&Run


title: pre-treatment, polyI:C, OM85 NT172


title: pre-treatment, unstimulated control, OM85 NT177


title: ZNF277 replicate 1 Cut&Run


title: ZNF22 replicate 2 Cut&Run


title: pre-treatment, polyI:C, OM85 NT164


title: ZMAT5 replicate 2 Cut&Run


title: ZNF22 replicate 1 Cut&Run


title: pre-treatment, LPS, OM85 NT162


title: pre-treatment, unstimulated control, OM85 NT161


title: post-treatment, polyI:C, OM85 NT180


title: post-treatment, polyI:C, Placebo NT160

description:
post-treatment, polyI:C, Placebo
post-treatment, polyI:C, Placebo


title: post-treatment, LPS, Placebo NT158


title: ZMAT5 replicate 1 Cut&Run


title: ZFP36L1 replicate 2 Cut&Run


title: ZMAT3 replicate 2 Cut&Run


title: pre-treatment, polyI:C, Placebo NT156


title: pre-treatment, unstimulated control, Placebo NT153


title: ZC3H3 replicate 1 Cut&Run


title: post-treatment,  unstimulated control, Placebo NT157


title: ZFP36L1 replicate 1 Cut&Run


title: post-treatment,  unstimulated control, OM85 NT165


title: post-treatment, polyI:C, OM85 NT152


title: post-treatment, LPS, OM85 NT150


title: WBP4 replicate 1 Cut&Run


title: WBP4 replicate 2 Cut&Run


title: post-treatment,  unstimulated control, OM85 NT149


title: V5 Mock IP 2 Cut&Run

value: V5 Mock IP 2 Cut&Run


title: post-treatment, polyI:C, Placebo NT144


title: V5 Mock IP 1 Cut&Run

value: V5 Mock IP 1 Cut&Run


title: post-treatment, LPS, Placebo NT142


title: U2AF1 replicate 2 Cut&Run


title: ZMAT3 replicate 1 Cut&Run


title: pre-treatment, polyI:C, Placebo NT140


title: pre-treatment, LPS, Placebo NT138

description:
pre-treatment, LPS, Placebo
pre-treatment, LPS, Placebo


title: U2AF1 replicate 1 Cut&Run


title: TRIM55 replicate 2 Cut&Run


title: post-treatment, polyI:C, Placebo NT136


title: pre-treatment, unstimulated control, Placebo NT137


title: ZC3H3 replicate 2 Cut&Run


title: pre-treatment, LPS, Placebo NT154


title: TEX13A replicate 2 Cut&Run


title: TEX13A replicate 1 Cut&Run


title: SNRPC replicate 2 Cut&Run


title: post-treatment,  unstimulated control, Placebo NT133


title: pre-treatment, polyI:C, Placebo NT132


title: SNRPC replicate 1 Cut&Run


title: pre-treatment, LPS, Placebo NT130


title: SALL4 replicate 2 Cut&Run


title: pre-treatment, unstimulated control, Placebo NT129


title: RNF14 replicate 2 Cut&Run


title: post-treatment, polyI:C, OM85 NT128


title: post-treatment,  unstimulated control, Placebo NT141


title: ZNF574 replicate 1 Cut&Run


title: SALL4 replicate 1 Cut&Run


title: RNF14 replicate 1 Cut&Run


title: post-treatment, LPS, OM85 NT127


title: RNF113A replicate 2 Cut&Run


title: post-treatment,  unstimulated control, Placebo NT205


title: RBM5 replicate 2 Cut&Run


title: pre-treatment, LPS, OM85 NT122


title: post-treatment,  unstimulated control, OM85 NT125


title: TRIM55 replicate 1 Cut&Run


title: RNF113A replicate 1 Cut&Run


title: post-treatment, LPS, Placebo NT134


title: RBM5 replicate 1 Cut&Run


title: pre-treatment, unstimulated control, OM85 NT121


title: ZNF317 replicate 1 Cut&Run


title: PHF7 replicate 2 Cut&Run


title: post-treatment, LPS, Placebo NT118


title: PHF7 replicate 1 Cut&Run


title: Sample6

city: Shanghai

first: Yinglin

last: Han

address: 280 Chongqing South Road, Huangpu District

institute: Shanghai Jiao Tong University School of Medicine

description:
Sample6
LKO

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) (or DEGseq or PoissonDis) with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample.

source_name: Liver

extract_protocol:
RNA were extracted from liver tissue using Trizol method.
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: Liver

value: Zbtb7b LKO

value: fast for 24h


title: post-treatment, polyI:C, Placebo NT120


title: NANOS2 replicate 2 Cut&Run

value: Human embryonic kidney


title: pre-treatment, LPS, Placebo NT114


title: post-treatment,  unstimulated control, Placebo NT117


title: Sample5

description:
Sample5
LKO


title: pre-treatment, polyI:C, Placebo NT116


title: pre-treatment, unstimulated control, Placebo NT113


title: post-treatment, polyI:C, OM85 NT112


title: Sample3

description:
Sample3
WT


title: pre-treatment, polyI:C, OM85 NT124


title: post-treatment, LPS, OM85 NT110


title: post-treatment,  unstimulated control, OM85 NT109


title: Sample2

description:
Sample2
WT


title: post-treatment, LPS, OM85 NT102


title: pre-treatment, unstimulated control, OM85 NT105


title: post-treatment, polyI:C, OM85 NT104


title: Sample1

description:
Sample1
WT


title: MAZ replicate 2 Cut&Run


title: post-treatment,  unstimulated control, OM85 NT101


title: H2O2 2

city: Gangneung-si

first: Kyunghun

last: Min

state: Gangwon

address: 7 Jukheon-gil

department: Department of Plant Science

country: South Korea

institute: Gangneung-Wonju National University

data_processing:
Image analysis and base calling were performed using HiSeq Control Software (HCS). The raw sequence data (.bcl files) were converted to fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software, allowing one mismatch for index sequence identification.
The sequence data underwent quality profiling, adapter trimming, read filtering, and base correction using fastp, an all-in-one FASTQ preprocessor (DOI: 10.1093/bioinformatics/bty560).
Assembly: The high-quality paired-end reads were aligned to the C. albicans SC5314 genome (Candida Genome Database; Assembly 22) using HISAT2 (DOI: 10.1038/nmeth.3317). The resulting read alignments were assembled with StringTie (DOI: 10.1038/nprot.2016.095) to estimate transcript abundances.
Supplementary files format and content: Absolute mRNA abundance was expressed as fragments per kilobase of transcript per million mapped reads (FPKM). Differential gene expression analysis was conducted using the DESeq2 package (DOI: 10.1186/s13059-014-0550-8) from Bioconductor (DOI: 10.1186/gb-2004-5-10-r80) on R.

organism: Candida albicans

source_name: Yeast

growth_protocol: Cells were grown overnight in BYNB media containing 2% dextrose and uridine and then diluted via a 6-fold dilution series and incubated overnight. A cell culture in log phase was then diluted to 10^6 cells/mL and incubated until cell concentration was 10^7 cells/mL (about 7 h).

extract_protocol:
RNA was isolated from a frozen cell pellet containing 1x10^8 cells using the RNeasy Plus Universal Mini Kit, following the manufacturer’s guidelines (Qiagen, Germantown, MD). The RNA concentration was determined using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was checked with an Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA).
For sequencing, RNA samples were processed using the NEBNext Ultra II RNA Library Prep Kit for Illumina, adhering to the manufacturer’s protocol (NEB, Ipswich, MA). Briefly, mRNA was enriched with Oligo(dT) beads, fragmented at 94°C for 15 m, and used to synthesize cDNA. The cDNA fragments were end-repaired, adenylated at the 3’ ends, and ligated with universal adapters, followed by index addition and library amplification via limited-cycle PCR.
The sequencing libraries were validated using an Agilent TapeStation (Agilent Technologies), quantified using a Qubit 2.0 Fluorometer (Invitrogen), and assessed by quantitative PCR (KAPA Biosystems). The libraries were pooled, clustered on a single lane of a flowcell, and sequenced on an Illumina HiSeq instrument (4000 or equivalent) using a 2x150 bp Paired End (PE) configuration.

treatment_protocol: 10 mL of the cell cultures were added to 3, 15 mL tubes and H2O2 or t-BHP were then added to their respective cultures at a final concentration of 0.5 mM H2O2 or 0.5 mM t-BHP. The third tube received no oxidant and was used as a control. Cultures were incubated for 15 m before being spun down at 4˚C and washed with ice cold water. After the final spin, the supernatant was removed and cells were flash frozen with liquid nitrogen before being stored at -80˚C. Frozen cell pellets were submitted to Azenta (South Plainfield, NJ, USA) for RNA-sequencing.

value: Yeast

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm441

value: 0.5mM H2O2 for 15 m


title: H2O2 3

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm442


title: pre-treatment, LPS, OM85 NT106


title: pre-treatment, polyI:C, OM85 NT100


title: pre-treatment, unstimulated control, OM85 NT097


title: pre-treatment, LPS, OM85 NT098


title: Sample4

description:
Sample4
LKO


title: MAZ replicate 1 Cut&Run

value: MAZ

value: Bethyl A190-120A


title: NANOS2 replicate 1 Cut&Run


title: H2O2 1

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm440


title: MBNL1 replicate 2 Cut&Run


title: LIN28B replicate 1 Cut&Run


title: t-BHP 3

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm439

value: 0.5mM t-BHP for 15 m


title: post-treatment, LPS, Placebo NT094


title: pre-treatment, polyI:C, Placebo NT092


title: post-treatment, polyI:C, Placebo NT096


title: IGHMBP2 replicate 2 Cut&Run


title: MBNL1 replicate 1 Cut&Run


title: t-BHP 2

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm438


title: pre-treatment, LPS, Placebo NT090


title: IGHMBP2 replicate 1 Cut&Run


title: pre-treatment, unstimulated control, Placebo NT089


title: t-BHP 1

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm437


title: Control 3

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm436


title: LIN28B replicate 2 Cut&Run


title: GTF3C4 replicate 2 Cut&Run


title: post-treatment, polyI:C, OM85 NT088


title: post-treatment, LPS, OM85 NT086


title: pre-treatment, polyI:C, OM85 NT084


title: Control 2

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm435


title: post-treatment,  unstimulated control, OM85 NT085


title: GTF3C4 replicate 1 Cut&Run


title: pre-treatment, unstimulated control, OM85 NT081


title: GIN1 replicate 2 Cut&Run


title: pre-treatment, LPS, OM85 NT082


title: Control 1

value: ARG4/arg4d LEU2/leu2d HIS1/his1d URA3/ura3d::imm434 IRO1/iro1d::imm434


title: post-treatment,  unstimulated control, OM85 NT077


title: GIN1 replicate 1 Cut&Run


title: G2E3 replicate 2 Cut&Run


title: post-treatment, polyI:C, OM85 NT080


title: post-treatment,  unstimulated control, Placebo NT093


title: pre-treatment, unstimulated control, OM85 NT073


title: pre-treatment, LPS, OM85 NT074


title: etha_24h_1000µM_3

city: Castanet-Tolosan

first: Alice

last: DIOT

state: Occitanie

address: 24 Chem. de Borde Rouge

country: France

institute: LRSV

description: biol rep3

data_processing:
raw reads were trimmed with trimgalore
trimmed reads were mapped using STAR
raw read count was made using featurecounts
Assembly: Chasselas reference genome from Djari et al. 2024 (Djari A, Madignier G, Di Valentin O, Gillet T, Frasse P, Djouhri A, Hu G, Julliard S, Liu M, Zhang Y, Regad F. 2024. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proceedings of the National Academy of Sciences, 121(23), e2403750121.)
Supplementary files format and content: tab-delimited text includes raw count per sample

organism: Vitis vinifera

source_name: 3-week-old callus

growth_protocol: Cells from the berry of Vitis vinifera L. cv. Gamay Fréaux were sub-cultured in 55x15 mm Petri dishes using a previously published method (Triantaphylidès et al., 1993). Parafilm was wrapped around the plates to prevent the medium and the calli from drying out. The plates were placed in a climatic chamber under constant conditions with a day/night photoperiod of 16h/ 8h, a temperature of 25°C/ 20°C and a light intensity of 150 μmol/m2/s. Plates were moved every day within the chamber to ensure homogenous growth conditions.

extract_protocol:
Liquid nitrogen frozen callus samples were first homogenised to powder. Total RNA from individual calli was extracted using 160 mg of frozen powder with the Promega ReliaPrep™ RNA Tissue Miniprep System kit (Promega, France, Ref. Z6112) following the Promega - ReliaPrep™ RNA Tissue Miniprep System protocol, optimized for RNA extractions of grapevine cell cultures. Then, RNAs underwent DNAse treatment with the Invitrogen™ ezDNase™ Enzyme kit to remove genomic DNA contamination from RNA preparations, following the ezDNase™ Enzyme kit protocol. For each sample, quantity and purity were first assessed by measuring the optical density at 260 nm and 280 nm and with a 1% (w/v) gel electrophoresis. Then, for each sample, RNA Integrity Number (RIN) was measured using an Agilent 2100 Bioanalyzer System microfluidic on-chip capillary electrophoresis device, following the RNA 6000 Nano kit protocol (Agilent Technologies, Germany). Samples with a RIN > 8.8 were selected and then aliquoted to obtain 20 μL RNA samples at 50 ng/μL.
mRNAs were sequenced by Illumina NovaSeq 6000 sequencing system with 2 × 150 bp paired-end sequences.The RNA libraries were constructed following the manufacturer's protocol.

treatment_protocol: Three-week-old cell cultures were treated with either 100 µL of a control solution (fresh growth medium) or with 100 µL of a fresh growth medium containing 1 mM EtOH and then placed back in their culture chamber for either 6 hours or 24 hours. Growth culture medium for this treatment purpose was prepared without agar.

value: 3-week-old callus

tag: cultivar

value: cv. Gamay Freaux var. Teinturier

value: 1 mM EtOH, 24h after treatment


title: etha_6h_0mM_4

description: biol rep4

value: Control, 6h after control treatment


title: G2E3 replicate 1 Cut&Run

value: Human embryonic kidney


title: post-treatment, LPS, Placebo NT070


title: FUS replicate 2 Cut&Run

value: FUS


title: etha_24h_1000µM_1

description: biol rep1


title: post-treatment,  unstimulated control, Placebo NT069


title: FUS replicate 1 Cut&Run


title: pre-treatment, LPS, Placebo NT066


title: etha_24h_0µM_4

description: biol rep3

value: Control, 24h after control treatment


title: etha_24h_1000µM_2

description: biol rep2


title: pre-treatment, polyI:C, Placebo NT068


title: etha_24h_0µM_3

description: biol rep2


title: post-treatment, LPS, OM85 NT078


title: post-treatment, LPS, Placebo NT062


title: pre-treatment, unstimulated control, Placebo NT065


title: ERI2 replicate 1 Cut&Run


title: etha_24h_0µM_2

description: biol rep1


title: pre-treatment, LPS, Placebo NT058


title: post-treatment, polyI:C, Placebo NT064


title: pre-treatment, polyI:C, Placebo NT060


title: pre-treatment, unstimulated control, Placebo NT057


title: CTCF replicate 2 Cut&Run

value: CTCF


title: pre-treatment, polyI:C, OM85 NT076


title: etha_6h_1mM_4

description: biol rep3

value: 1 mM EtOH, 6h after treatment


title: CTCF replicate 1 Cut&Run

value: Bethyl A190-120A


title: post-treatment, polyI:C, Placebo NT056


title: etha_6h_1mM_3

description: biol rep2


title: post-treatment, polyI:C, Placebo NT072


title: CPSF4 replicate 2 Cut&Run


title: post-treatment, LPS, Placebo NT054


title: post-treatment,  unstimulated control, Placebo NT053


title: pre-treatment, LPS, Placebo NT050


title: ERI2 replicate 2 Cut&Run


title: etha_6h_0mM_3

description: biol rep3


title: CPSF4L replicate 2 Cut&Run


title: pre-treatment, unstimulated control, Placebo NT049


title: post-treatment, LPS, Placebo NT046


title: CPSF4 replicate 1 Cut&Run


title: etha_6h_0mM_2

description: biol rep2


title: post-treatment,  unstimulated control, Placebo NT045


title: etha_6h_0mM_1

description: biol rep1


title: pre-treatment, polyI:C, Placebo NT044


title: CPSF4L replicate 1 Cut&Run


title: pre-treatment, LPS, Placebo NT042


title: CNOT4 replicate 2 Cut&Run


title: post-treatment, polyI:C, OM85 NT040


title: CNOT4 replicate 1 Cut&Run


title: post-treatment,  unstimulated control, OM85 NT037


title: pre-treatment, polyI:C, OM85 NT036


title: post-treatment, LPS, OM85 NT038


title: BPS-8A

city: Chengdu

first: Man

last: Zhu

state: Sichuan

address: No. 4, Section 2, Jianshe North Road, Chenghua District, Chengdu City, Sichuan, China

department: School of Medicine

institute: University of Electronic Science and Technology of China

data_processing:
SOAPnuke v1.5.6
Sequence reads for adaptor sequence/low-quality sequence/unknown base ('N' base) using SOAPnuke software. Low-Quality limit (base quality less than or equal to 15):20%, unknown base limit: 5%.
Clean sequence reads analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
The clean data were aligned to the reference genome using HISAT2 (v2.1.0) and  aligned to the gene set using Bowtie2.
Expression level of gene was calculated by RSEM (v1.3.1). The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: tab-delimited text included FPKM values for each sample

source_name: brown adipose tissue

extract_protocol:
RNA was harvested using TRIzol reagent. 1.0μg of total RNA was used for the construction of sequencing libraries
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized doublestranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: brown adipose tissue

value: BPS


title: BPS-5A


title: CNBP replicate 2 Cut&Run

value: CNBP


title: pre-treatment, unstimulated control, OM85 NT033


title: CNBP replicate 1 Cut&Run


title: pre-treatment, LPS, OM85 NT034


title: BPS-6A


title: etha_6h_1mM_2

description: biol rep1


title: pre-treatment, polyI:C, Placebo NT052


title: post-treatment, polyI:C, Placebo NT032


title: post-treatment,  unstimulated control, Placebo NT029


title: post-treatment, LPS, Placebo NT030


title: BPS-3A


title: pre-treatment, polyI:C, Placebo NT028


title: CISD2 replicate 1 Cut&Run


title: CISD2 replicate 2 Cut&Run


title: BPS-2A


title: CISD1 replicate 2 Cut&Run


title: pre-treatment, LPS, Placebo NT026


title: pre-treatment, unstimulated control, Placebo NT025


title: pre-treatment, unstimulated control, Placebo NT041


title: BPS-1A


title: post-treatment, polyI:C, OM85 NT024


title: CISD1 replicate 1 Cut&Run


title: post-treatment, LPS, OM85 NT022


title: post-treatment,  unstimulated control, OM85 NT021


title: BRCA1 replicate 2 Cut&Run


title: Veh-6A

value: Veh


title: BRCA1 replicate 1 Cut&Run


title: pre-treatment, polyI:C, OM85 NT020


title: pre-treatment, LPS, OM85 NT018


title: Xenopus embryo, stage 35, 0.75X MMR, sample 1

city: Medford

first: Vaibhav

middle: P

last: Pai

address: 200 Boston Ave suite 4600

department: Biology

institute: Tufts University

data_processing:
Trim adapter and polyX tails: The RNAseq raw reads are single-end reads. The reads were trimmed for adapter “CTGTCTCTTATACACATCTCCGAGCCCACGAGAC” and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp (Chen et al., 2018).
Generating genome indexes: Xenopus laevis genome sequences and gene annotation were downloaded from the NCBI genome database, version 10.1. GenomeGenerate module of the STAR aligner (Dobin et al., 2013) was used to generate the genome indexes. STAR aligner option was set to sjdbOverhang = 75 for 76-bp reads, as was ideal.
Aligning reads to the genome: Adapter-trimmed reads were aligned to the genome using STAR aligner with the two-pass option. Reads were mapped across the genome to identify novel splice junctions in the first-pass. These new annotations were then incorporated into the reference indexes and reads were re-aligned with this new reference in the second pass. While more time-intensive, this step could aid in aligning across these junctions, especially in organisms where the transcriptome was not as well annotated. The resulting gene count table is at rsem_gene_count.tsv
Estimate expression: Gene expression was estimated from the gene alignments using RSEM tool for accurate quantification of gene and isoform expression from RNA-Seq data (Li and Dewey, 2011).The resulting gene count table is at rsem_gene_count.tsv
Filtering, normalization, and transformation: To filter out low expressing genes, we kept genes that had counts per million (CPM) more than 1.7 in at least 3 samples. There were 24661 genes after filtering. We then normalized counts by weighted trimmed mean of M-values (TMM) (Robinson and Oshlack 2010). If no normalization is needed, all the normalization factors would be 1. Here the normalization factors were between 0.99 and 1.02. To use linear models in the following analysis, we performed Voom transformation (Law et al. 2014) to transform counts into logCPM.
Differential expression analysis: To discover the differential genes, we use limma, an R package that powers differential expression analyses (Ritchie et al. 2015). We performed moderated t-tests to detect genes that were differentially expressed between 0.1X MMR and 0.75X MMR
Assembly: Xenopus laevis (NCBI genome database, version 10.1)
Supplementary files format and content: tab-delimited file includes a gene count table
Supplementary files format and content: tab-delimited file includes logCPM normalized values

organism: Xenopus laevis

source_name: whole embryo

growth_protocol: Xenopus laevis embryos were fertilized in vitro according to standard protocols in 0.1X Marc's Modified Ringer's (MMR) solution and kept at 14oC. At stage 9 a subset of embryos were transferred to 0.75X MMR solution. Both, embryos in 0.1X MMR and 0.75X MMR were kept in 14oC for 7 days (reaching stage 35) follwed by RNA extraction

extract_protocol:
Each sample (0.1X MMR and 0.75X MMR) of Xenopus embryos consisted of 10 pooled stage 35 Xenopus embryos and each was repeated 3 times. RNA was extracted using TRI Reagent (Molecular Research Center, Inc - MRC) as per the manufacturer’s protocol, and total RNA quality and quantity was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
RNA library preparation was done with the Illumina Stranded Total RNA with Ribo-Zero Plus. Libraries were then multiplexed, and an rRNA depletion run using single-end, 75-nucleotide sequencing was performed on Illumina HiSeq 2500.

value: whole embryo

value: WT

value: 0.75X MMR


title: Xenopus embryo, stage 35, 0.75X MMR, sample 2


title: Xenopus embryo, stage 35, 0.75X MMR, sample 3


title: Veh-4A


title: Veh-5A


title: pre-treatment, unstimulated control, OM85 NT017


title: APEX2 replicate 2 Cut&Run


title: Xenopus embryo, stage 35, 0.1X MMR, sample 3

value: 0.1X MMR


title: APEX2 replicate 1 Cut&Run


title: post-treatment, polyI:C, Placebo NT016


title: MVIR1-HS556-D1ETA1-MNGS1

city: San Francisco

first: Charles

last: Langelier

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

data_processing:
Alignment against human genome- kallisto
Differential expression with R package Limma
Assembly: HG-38, ENSEMBL v. 99
Supplementary files format and content: .csv file with genecounts

source_name: tracheal aspirate

growth_protocol: Clinical tracheal aspirate specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

value: Male

tag: age

tag: race

value: Caucasian

tag: ethnicity

value: Not Hispanic

value: No-BP


title: Xenopus embryo, stage 35, 0.1X MMR, sample 2


title: Veh-8A


title: Veh-3A


title: MVIR1-HS548-D1ETA1-MNGS1

value: Female


title: post-treatment,  unstimulated control, Placebo NT013


title: Veh-1A


title: Veh-2A


title: post-treatment, LPS, Placebo NT014


title: MVIR1-HS546-D1ETA1-MNGS1

value: Other/Multiple

value: Hispanic


title: pre-treatment, polyI:C, Placebo NT012


title: Veh-7A


title: MVIR1-HS545-D7ETA1-MNGS1


title: MVIR1-HS523-D11ETA1-MNGS1


title: Combination-2

city: Xiamen, China.

first: Jie

last: Zha

state: -- None selected --

address: Department of Hematology, The First Afﬁliated Hospital of Xiamen University, Xiamen, China.

institute: Xiamen University, Xiamen, China.

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. clean data were mapped to the reference genome of Homo sapiens from Homo_sapiens.GRCh38 using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Geneid: gene id number;
Supplementary files format and content: Chr: chromosome where the gene is located;
Supplementary files format and content: Start: starting position of the gene on the chromosome;
Supplementary files format and content: End: termination position of the gene on the chromosome;
Supplementary files format and content: Strand: orientation of the chromosome strand encoding the gene;
Supplementary files format and content: Length: length of the gene;
Supplementary files format and content: Name of each sample: the RPKM value of the gene in that sample.

growth_protocol: KG-1α cells were cultured in RPMI-1640 (HyClone; Thermo Fisher Scientiﬁc, Eugene, OR, USA),the culture media contained 10% FBS (PAN Seratech, Aidan Bach, Germany), 100 U/mL penicillin, and 100 μg/mL streptomycin. These cells were maintained in an incubator at 37°C and 5% CO2 environment.

extract_protocol:
All cells were collected and total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

treatment_protocol: 1 × 106 KG-1α cells were cultured in a 10-cm dish and treated with DMSO, (16 μM) chiglitazar and (4 μM) CS055 for 24 hours

value: Acute Myeloid Leukemia

value: DSM ACC 14

value: treated with (16 μM) chiglitazar and (4 μM) CS055 for 24 hours


title: Combination-3


title: Combination-1


title: BPS-4A

value: brown adipose tissue

value: BPS


title: KPC1199_Sin3Bsg1_HDAC1,Cut&tag

first: Zhengyan

last: Zhang

address: State Key Laboratory of Systems Medicine for Cancer, Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University,

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Pancreatic tumor

growth_protocol: KPC1199 cells were maintained in a humidified incubator at 37 °C with 5% CO2 and grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 100 IU m-1 of penicillin/streptomycin (P/S). All cell lines used were tested negative for Mycoplasma.

extract_protocol:
Briefly, tumor cell were generated and collected .CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

treatment_protocol: sgCtrL or Sin3Bsg1 KPC1199 cells + or – IFNγ indicates that PDAC cells were treated with or without 10 ng/ml IFNγ for 24 hours.

value: Pancreatic tumor

value: Pancreatic tumor cell

value: Sin3B Knockout


title: KPC1199_sgCtrL_HDAC1,Cut&tag

institute: Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University,

value: WT


title: MVIR1-HS542-D1ETA1-MNGS1

value: Asian


title: post-treatment, polyI:C, OM85 NT008


title: MVIR1-HS521-D3ETA1-MNGS1

value: Male


title: DMSO-3

value: treated with DMSO for 24 hours


title: liver, CCl4+IPA

first: Yuan-Yuan

last: Luo

address: Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China

institute: Tongji University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger, version 3.1.0)
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Liver tissues were dissociated into single cells using a solution of 0.35% collagenase IV, 2 mg/ml papain, and 120 U/ml DNase I at 37°C with shaking for 20 minutes. Digestion was halted with 1× PBS/10% FBS, followed by filtration through a 70-30 µm strainer and centrifugation at 300g for 5 minutes at 4°C. The cell pellet was resuspended in 100 µl 1× PBS (0.04% BSA) and treated with 1× RBC lysis buffer (MACS 130-094-183), then centrifuged. Dead cells were removed using the Miltenyi® Dead Cell Removal Kit. The final cell suspension was washed, centrifuged, and resuspended in 50 µl 1× PBS (0.04% BSA). Viability (>85%) was confirmed with trypan blue exclusion, and cell concentration was adjusted to 700-1200 cells/µl using a hemocytometer or automated counter
Following the manufacturer’s instructions for the 10X Genomics Chromium Single-Cell 3’ kit (V3), the dissociated cells were loaded into the 10X Chromium instrument for cell capture. Libraries were sequenced on an Illumina NovaSeq 6000 system (paired-end multiplexing run, 150 bp) at a minimum depth of 20,000 reads per cell (LC-Bio Technology Co., Ltd., Hangzhou, China).

value: liver


title: pre-treatment, unstimulated control, Placebo NT009


title: DMSO-2


title: MVIR1-HS507-D7ETA1-MNGS1


title: DMSO-1


title: post-treatment,  unstimulated control, OM85 NT005


title: MVIR1-HS499-D6ETA1-MNGS1

value: Not Hispanic


title: post-treatment, LPS, OM85 NT006


title: pre-treatment, polyI:C, OM85 NT004


title: S8_N, healthy kidney, scRNA-Seq

first: Kevin

last: Bi

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

description: 10X Genomics

data_processing:
Demultiplexing of sequencing results, barcode processing, read alignment, and UMI counting were performed using the 10x Genomics CellRanger pipeline (v6.1.2) with the include_introns parameter set to “false”. Reads were aligned to the mm10-2020-A reference genome. After exclusion of low RNA content droplets, confidently mapped, non-PCR duplicate reads were counted to generate a gene-barcode matrix for each sample.
To abrogate sample-to-sample technical differences arising from cell-free RNA profiles, an ambient RNA decontamination step was performed on each sample individually using CellBender (v0.2.0). Briefly, raw counts for each sample were provided as input to the remove-background module of CellBender (3). Remove-background was run on all samples using the “full” model, 150 training epochs, a target false positive rate of 0.01, an empty drop training fraction of 0.5, and 40,000 total droplets included. For each sample, the expected cells parameter was derived from the estimate outputted by CellRanger.
Assembly: mm10-2020-A
Supplementary files format and content: h5 files containing matrices with filtered barcodes after ambient-RNA removal with Cellbender

source_name: Kidney

extract_protocol:
Mouse tumor and normal kidney samples (~50 mg per unit dissociation mix) were dissociated into single cell suspensions using a cocktail of collagenase (VitaCyte 001-2030 Collagenase MA, 13units/μL) and protease (VitaCyte 003-1000 BP Protease, 0.88 units/μL) in RPMI media at 37 C for 5 min. with pipetting to break up tissue as needed. The digestion mix was passed through a 70 μM mesh followed by a 40 μM mesh and quenched with cold PBS/10% FBS. The flow-through was centrifuged to remove the enzymes and quenching solution. Red blood cells (RBCs) were lysed with cold ACK buffer for 3 min. at room temperature. The single cell suspension was washed and counted using a hemocytometer-Trypan Blue. Single-cell suspensions were prepared for library construction by diluting cells to a concentration of 1000 cells/μL in 1x PBS with 0.04% BSA.
Single-cell RNA-seq libraries were generated utilizing the Chromium Next GEM Single Cell v 3.1 platform (10X Genomics, US). Single-cell suspensions  were integrated into a real-time polymerase chain reaction (RT-PCR) master mix with the aim of targeting approximately 10,000 cells. Following the manufacturer's instructions, this mixture was loaded into a Next GEM Chip G, along with Single Cell v3.1 gel beads and partitioning oil. The cDNA molecules underwent amplification, dual indexing, and pooling, as per the manufacturer's guidelines (10X Genomics, US) and sequencing libraries were quantified using the Agilent High Sensitivity ScreenTape. To ensure comprehensive sequencing, all single-cell libraries were subjected to a customized paired-end format with dual indexing (28/10/90-bp for v3.1 libraries), following the recommendations of 10X Genomics.

value: Kidney

value: LSL-Cas9/+; Pax8-Cre


title: liver, CCl4

description: 10X Genomics


title: pre-treatment, LPS, Placebo NT010


title: DKOwBF_3

city: Potsdam

first: Salim

last: Seyfried

address: Karl-Liebknecht-Str. 24-25

institute: University of Potsdam

data_processing:
base-calling, alignment, filtering, peak-calling, generation of normalized counts has been done by staff of sequecing facility using usegalaxy.eu platform
Assembly: GRCz10
Supplementary files format and content: bigwig file includes raw count for each sample

organism: Danio rerio

source_name: heart

growth_protocol: 2 day-old zebrafish embryo

extract_protocol:
RNA extraction, DNase treatment was done using Zymo Quick-RNA Microprep Kit. RNA later was checked integrity and concentration by D1000 Agilent ScreenTape. Samples with RIN values ranged from 7.2-9.3 were further librarized with 30ng of RNA as starting point.
RNA library was prepared using NebNext Ultra II kit following manufacturer's protocol

value: heart

value: enriched endothelial cells


title: DKOwBF_4


title: S6_T, Cre-less model tumor, scRNA-Seq

description: 10X Genomics

source_name: Tumor

value: Tumor


title: pre-treatment, LPS, OM85 NT002


title: MVIR1-HS474-D7ETA1-MNGS1

value: Female


title: Xenopus embryo, stage 35, 0.1X MMR, sample 1

value: whole embryo

value: 0.1X MMR


title: pre-treatment, unstimulated control, OM85 NT001


title: S5_N, healthy kidney, scRNA-Seq

description: 10X Genomics


title: DKOwBF_2


title: S3_T, Cre-less model tumor, scRNA-Seq

description: 10X Genomics


title: DKOwBF_1


title: UMC026 PRAME1 7months2

city: Miami

first: Stefan

last: Kurtenbach

address: 1501 NW 10th Avenue

institute: University of Miami

data_processing:
Treads were trimmed with Trim Galore!
Reads were aligned with STAR
Gene expression and statisticss was computed with edgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include edgeR outputs with statistics

source_name: uveal melanoma

extract_protocol:
RNA was extracted with the Quick-RNA Miniprep Kit (Zymo)
Illumina truseq stranded ribo-depleted, according to manufacturer

value: uveal melanoma

value: Melanocyte

value: PRAME OE


title: MVIR1-HS473-D4ETA1-MNGS1

value: Other/Multiple

value: Hispanic


title: S12_N, healthy kidney, scRNA-Seq

description: 10X Genomics


title: MVIR1-HS471-D2ETA1-MNGS1

value: Male


title: UMC026 PRAME1 7months1


title: ccm2_4


title: S9_T, Cre-less model tumor, scRNA-Seq

description: 10X Genomics


title: S11_T, Cre-less model tumor, scRNA-Seq

description: 10X Genomics


title: ccm2_3


title: MVIR1-HS498-D6ETA1-MNGS1

value: Native Hawaiian/Other Pacific Islander

value: No-BP


title: UMC026 PRAME2


title: S10_N, healthy kidney, scRNA-Seq

description: 10X Genomics


title: ccm2_2


title: UMC026 PRAME1


title: MVIR1-HS450-D0ETA1-MNGS1

value: Asian

value: Not Hispanic


title: B16F10 metastatic lung 6h (set3)

city: Helsinki

first: Niina

middle: M

last: Santio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: 10x Genomics

data_processing:
The CellRanger software (10xGenomics) was used for generation of expression matrices; multiplexing and mapping to the mouse genome was done using CellRanger 7.2.0.
Data were aggregated using Cell Ranger software, features.tsv.gz processed file is similar for both sets, other files are unique. Processing of the raw data was continued in R versions ranging from 3.6.2. to 4.3.1 (www.r-project.org) by utilizing Rstudio 2021.09.2+382 (rstudio.com) and the package Seurat Version 4.4.0 (functions: Read10x, CreateSeuratObject) according to instructions by the Satija laboratory (https://satijalab.org/seurat/).
Quality control was performed by selecting genes expressed in more than 5 cells (min.cells = 5) and cells expressing 1000-5000 genes (nFeature_RNA).
Additional quality control was performed by selecting cells in which less than 5 % of unique molecular identifiers (UMIs) were derived from the mitochondrial genome and in which ribosomal marker content was less than 20%.
For data processing the following functions were utilized: NormalizeData (default settings), FindVariableFeatures (nfeatures = 4500), FindIntegrationAnchors and IntegrateData (4500 anchor features), ScaleData (default settings), RunPCA, FindNeighbors and FindClusters and RunUMAP (Uniform Manifold Approximation and Projection for Dimension Reduction). Reclustering of the data or integration with other data sets was also performed by utilizing 4500 anchor features.
Assembly: mm10
Supplementary files format and content: Tab separated value fles
Supplementary files format and content: Matrix files

source_name: Lung

growth_protocol: Mice were housed in  ventilated cages in a pathogen free facility. The Mus musculus skin melanoma cell line B16-F10 (American Type Culture Collection, ATCC®CRL-6475) was cultured in Dulbecco’s modified Eagle medium (Lonza) supplemented with 10% fetal bovine serum, 50 U/ml of penicillin, 50 μg/ml of streptomycin and 2 mM L-glutamin. CellTracker™ Green CMFDA Dye (ThermoFisher Scientific) was used according to manufacturer´s protocol to label B16-F10.

extract_protocol:
For sorting, tissues were minced on ice and digested for 1 h at 37°C using 1 mg ml-1 collagenase Type I (Gibco/Thermo Fisher Scientific), 0.1% BSA and 7.5 µl ml-1 of DNAseI (Roche, Basel, Switzerland) in DPBS (Gibco/Thermo Fisher Scientific). Thereafter, samples were vortexed and passed through a 40 µm Nylon cell strainer (Corning Life Sciences or Thermo Fisher Scientific), centrifuged at 1200 rpm for 7 min, resuspended in red blood cell (RBC) lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA) for 2 min and washed using 0.1% BSA, 2 mm EDTA in PBS (FACS buffer).  Cells were stained using fluorochrome conjugated antibodies anti-Pecam1-PE and anti-Cd45-APC  in FACS buffer for 30 minn, washed twice with FACS buffer and sorted using BD InfluxTM (BD Biosciences, Franklin Lakes, NJ, USA). Pecam1 positive and Ptprc negative cells from each sample type along with melanoma cells from the 6h samples were used for 10x library preparation using the Chromium Single Cell 3´ Reagent Kits v2 (10x Genomics; Pleasantom; CA, USA). The cell recovery aim for each library was 7000 cells.
Libraries were sequenced using NovaSeq 6000 system (Illumina, San Diego, CA, USA) using S4 flow cell with read length of 28+10+10+91. Sequencing was performed by the Sequencing laboratory of Institute for Molecular Medicine Finland FIMM Technology Centre, University of Helsinki.

treatment_protocol: PBS or B16-F10 melanoma cell suspension (400 000 cells per 100 µl /mouse) in PBS were injected via the tail vein intravenously, two mice/ treatment. After 6h mice were sacrifed for lung isolation, lung tissue was minced and endothelial cells were sorted among Pecam1-PE positive and Ptprc-APC negative cells after staining. Also melanoma cells were collected based on GFP-tracker treatment from the metastatic lung samples.

value: Lung

tag: strain

value: endothelial cell, melanoma

value: WT

value: 6 hour B16F10 injection via tail vein


title: MVIR1-HS441-D6ETA1-MNGS1


title: ccm2_1

value: heart

value: enriched endothelial cells


title: MVIR1-HS477-D6ETA1-MNGS1


title: UMC026 Ctrl3

value: Ctrl


title: wt_4

value: wild-type


title: MVIR1-HS427-D7ETA1-MNGS1

value: Caucasian


title: wt_3


title: UMC026 Ctrl2

value: uveal melanoma

value: Melanocyte


title: UMC026 Ctrl1


title: MVIR1-HS410-D4ETA1-MNGS1

value: Female

value: Other/Multiple


title: wt_2


title: B16F10 metastatic lung 30h (set2)

description: 10x Genomics

data_processing:
The CellRanger software (10xGenomics) was used for generation of expression matrices; multiplexing and mapping to the mouse genome was done using CellRanger 7.2.0.
Data were aggregated using Cell Ranger software, features.tsv.gz processed file is similar for all sets, other files are unique. Processing of the raw data was continued in R versions ranging from 3.6.2. to 4.3.1 (www.r-project.org) by utilizing Rstudio 2021.09.2+382 (rstudio.com) and the package Seurat Version 4.4.0 (functions: Read10x, CreateSeuratObject) according to instructions by the Satija laboratory (https://satijalab.org/seurat/).
Quality control was performed by selecting genes expressed in more than 5 cells (min.cells = 5) and cells expressing 1000-5000 genes (nFeature_RNA).
Additional quality control was performed by selecting cells in which less than 5 % of unique molecular identifiers (UMIs) were derived from the mitochondrial genome and in which ribosomal marker content was less than 20%.
For data processing the following functions were utilized: NormalizeData (default settings), FindVariableFeatures (nfeatures = 4500), FindIntegrationAnchors and IntegrateData (4500 anchor features), ScaleData (default settings), RunPCA, FindNeighbors and FindClusters and RunUMAP (Uniform Manifold Approximation and Projection for Dimension Reduction). Reclustering of the data or integration with other data sets was also performed by utilizing 4500 anchor features.
Assembly: mm10
Supplementary files format and content: Tab separated value fles
Supplementary files format and content: Matrix files

growth_protocol: Mice were housed in ventilated cages in a pathogen free facility. The Mus musculus skin melanoma cell line B16-F10 (American Type Culture Collection, ATCC®CRL-6475) was cultured in Dulbecco’s modified Eagle medium (Lonza) supplemented with 10% fetal bovine serum, 50 U/ml of penicillin, 50 μg/ml of streptomycin and 2 mM L-glutamin. CellTracker™ Green CMFDA Dye (ThermoFisher Scientific) was used according to manufacturer´s protocol to label B16-F10.

extract_protocol:
For sorting, tissues were minced on ice and digested for 1 h at 37°C using 1 mg ml-1 collagenase Type I (Gibco/Thermo Fisher Scientific), 0.1% BSA and 7.5 µl ml-1 of DNAseI (Roche, Basel, Switzerland) in DPBS (Gibco/Thermo Fisher Scientific). Thereafter, samples were vortexed and passed through a 40 µm Nylon cell strainer (Corning Life Sciences or Thermo Fisher Scientific), centrifuged at 1200 rpm for 7 min, resuspended in red blood cell (RBC) lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA) for 2 min and washed using 0.1% BSA, 2 mm EDTA in PBS (FACS buffer).  Cells were stained using fluorochrome conjugated antibodies anti-Pecam1-PE and anti-Cd45-APC  in FACS buffer for 30 min, washed twice with FACS buffer and sorted using BD InfluxTM (BD Biosciences, Franklin Lakes, NJ, USA). Pecam1 positive and Ptprc negative cells from each sample type along with melanoma cells from the 6h samples were used for 10x library preparation using the Chromium Single Cell 3´ Reagent Kits v2 (10x Genomics; Pleasantom; CA, USA). The cell recovery aim for each library was 10 000 cells.
Libraries were sequenced using NovaSeq 6000 system (Illumina, San Diego, CA, USA) using S4 flow cell with read length of 28+10+10+91. Sequencing was performed by the Sequencing laboratory of Institute for Molecular Medicine Finland FIMM Technology Centre, University of Helsinki.

treatment_protocol: PBS or B16-F10 melanoma cell suspension (200 000 cells per 100 µl /mouse) in PBS were injected via the tail vein intravenously, two mice/ treatment. After 6h or 30h mice were sacrifed for lung isolation, lung tissue was minced and endothelial cells were sorted among Pecam1 positive and Ptprc negative cells after staining. Also melanoma cells were collected based on GFP-tracker treatment from the metastatic lung samples.

value: endothelial cell

value: 30 hour B16F10 injection via tail vein


title: Mel290 Ctrl 2

value: Cancer


title: Mel290 Ctrl 1


title: MVIR1-HS469-D7ETA1-MNGS1

value: Male

value: Hispanic

value: No-BP


title: B16F10 metastatic lung 6h (set2)

description: 10x Genomics

value: Lung

value: endothelial cell, melanoma

value: WT


title: Control  (set3)

description: 10x Genomics

value: 6 hour after PBS injection via tail vein


title: MVIR1-HS320-D10ETA1-MNGS1


title: MVIR1-HS292-D15ETA1-MNGS2


title: MVIR1-HS357-D10ETA1-MNGS2


title: cochear,differentiation,rep3 [day18_3]

city: Nanjing

first: Guoqiang

last: Wan

address: Xuefu Road

institute: Nanjing University

data_processing:
Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).
the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
clean reads were separately aligned to reference genome with orientation mode using TopHat (version2.1.1) software
R statistical package software EdgeR was utilized for differential expression analysis
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: cochlear

growth_protocol: culture in advanced DMEM/F12 medium including B27,N2,Pencillin and Glutamax

extract_protocol:
Collect 5-8 wells of cochlear organoid in RNA trizol(Takara), extract 1ug of total RNA
prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA

treatment_protocol: culture in advanced DMEM/F12 medium in EGF,FGF,IGF,616452,pvc,Vpa and CHIR99021 or CHIR99021 and LY411575

value: cochlear

value: cochlear progenitor cell

value: wild type

value: differentiation


title: cochear,differentiation,rep4 [day18_4]


title: Ctrl 2

value: uveal melanoma

value: Ctrl


title: cochear,differentiation,rep1 [day18_1]


title: cochear,differentiation,rep2 [day18_2]


title: ZNF277_REP2

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

institute: UCSD

description: RNA bind n seq experiment

library_source: other

data_processing:
Raw data provided is demultiplexed reads with adapters removed and only unique synthetic reads.
Assembly: N/A
Supplementary files format and content: Raw data provided is demultiplexed reads with adapters removed and only unique synthetic reads.
Library strategy: RBNS

molecule: other

organism: synthetic construct

source_name: synthetic RNA

growth_protocol: N/A synthetic RNA

extract_protocol:
N/A synthetic RNA
Protein-bound RNA was concentrated via phenol-chloroform extraction. RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified Individual libraries were analyzed via Qubit then normalized for concentration match prior to pooling and sequencing.

treatment_protocol: RNA bind-n-seq experiment to determine RNA specificity

value: synthetic RNA

value: Protein-bound RNA


title: Input_REP2

description: RNA bind n seq experiment

value: Input RNA


title: Input_REP1

description: RNA bind n seq experiment


title: MVIR1-HS419-D3ETA1-MNGS1

value: Other/Multiple


title: MEL290 PRAME 2

value: Cancer

value: PRAME OE


title: Ctrl 1


title: wt_1

value: heart

value: enriched endothelial cells

value: wild-type


title: MVIR1-HS271-D9ETA1-MNGS1

value: Female

value: Asian

value: Not Hispanic

value: No-BP


title: Control (set2)

description: 10x Genomics

value: Lung

value: endothelial cell

value: WT

value: 6 hour PBS injection via tail vein


title: cochlear,proliferation,rep3 [day10_3]

value: cochlear

value: cochlear progenitor cell

value: wild type

value: proliferation


title: cochlear,proliferation,rep4 [day10_4]


title: MVIR1-HS254-D14ETA1-MNGS1

value: Male

value: Other/Multiple

value: Hispanic


title: CRISPR PRAME 2

value: uveal melanoma

value: Cancer

value: PRAME KO


title: CRISPR PRAME 1


title: MEL290 PRAME 1

value: PRAME OE


title: MVIR1-HS253-D3ETA1-MNGS1


title: MVIR1-HS250-D23ETA1-MNGS1


title: cochlear,proliferation,rep2 [day10_2]


title: cochlear,proliferation,rep1 [day10_1]


title: 921_Input

data_processing:
FASTQ files were trimmed with Trim Galore!
Reads were aligned with Bowtie2
Peak files and coverage tracks were computed by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEB Next Ultra 2 library prep kit according to the manufacturers reccomendations.

value: cancer

tag: chip antibody


title: MVIR1-HS244-D5ETA1-MNGS1

value: Female

value: No-BP


title: ZNF277_REP1

description: RNA bind n seq experiment

value: synthetic RNA

value: Protein-bound RNA


title: MVIR1-HS290-D9ETA1-MNGS1


title: B16F10 metastatic lung

description: 10x Genomics

data_processing:
The CellRanger software (10xGenomics) was used for generation of expression matrices; multiplexing and mapping to the mouse genome was done using CellRanger, 10xGenomics, version 2.1.1..
Data were aggregated using Cell Ranger software, while processing of the raw data was continued in R versions ranging from 3.6.2. to 4.2.2 (www.r-project.org) by utilizing Rstudio 2021.09.2+382 (rstudio.com) and the package Seurat (functions: Read10x, CreateSeuratObject) according to instructions by the Satija laboratory (https://satijalab.org/seurat/).
Quality control was performed by selecting genes expressed in more than 5 cells (min.cells = 5) and cells expressing 1500-4500 genes (nFeature_RNA).
Additional quality control was performed by selecting cells in which less than 3 % of unique molecular identifiers (UMIs) were derived from the mitochondrial genome and in which ribosomal marker content was less than 15%.
For data processing the following functions were utilized: NormalizeData (default settings), FindVariableFeatures (nfeatures = 3000), FindIntegrationAnchors and IntegrateData (4500 anchor features), ScaleData (default settings), RunPCA, FindNeighbors (dims = 1:39) and FindClusters (resolution 0.4), RunTSNE (T-Distributed Stochastic Neighbor Embedding) and RunUMAP (Uniform Manifold Approximation and Projection for Dimension Reduction) (dims = 1:39).
Assembly: mm10
Supplementary files format and content: Tab separated value fles
Supplementary files format and content: Matrix files

extract_protocol:
For sorting, tissues were minced on ice and digested for 1 h at 37°C using 1 mg ml-1 collagenase Type I (Gibco/Thermo Fisher Scientific), 0.1% BSA and 7.5 µl ml-1 of DNAseI (Roche, Basel, Switzerland) in DPBS (Gibco/Thermo Fisher Scientific). Thereafter, samples were vortexed and passed through a 40 µm Nylon cell strainer (Corning Life Sciences or Thermo Fisher Scientific), centrifuged at 1200 rpm for 7 min, resuspended in red blood cell (RBC) lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA) for 2 min and washed using 0.1% BSA, 2 mm EDTA in PBS (FACS buffer).  Cells were stained using anti-Pecam1-PE-conjugated antibody in FACS buffer for 30 min, washed twice with FACS buffer and sorted using BD InfluxTM (BD Biosciences, Franklin Lakes, NJ, USA). Anti-Pecam1-PE positive cells were used for 10x library preparation using the Chromium Single Cell 3´ Reagent Kits v2 (10x Genomics; Pleasantom; CA, USA). The cell recovery aim for each library was 8000 cells.
Libraries were sequenced using NovaSeq 6000 system (Illumina, San Diego, CA, USA) using S4 flow cell with read length of 28+8+89. Sequencing was performed by the Sequencing laboratory of Institute for Molecular Medicine Finland FIMM Technology Centre, University of Helsinki.

treatment_protocol: PBS or B16-F10 melanoma cell suspension (200 000 cells per 100 µl /mouse) in PBS were injected via the tail vein intravenously, two mice/ treatment. After 6h mice were sacrifed for lung isolation, lung tissue was minced and endothelial cells were sorted among Pecam1-PE positive cells after staining.

value: Lung

value: endothelial cell

value: WT

value: 6 hour B16F10 injection via tail vein


title: MVIR1-HS243-D6ETA1-MNGS1


title: Control

description: 10x Genomics

value: 6 hour after PBS injection via tail vein