title: 7.21 1 2.0mm 59s

description: UMI Matrix


title: 8.18.21 2 1.0mm 69s

status: Public on Jan 01 2023

type: SRA

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

country: USA

institute: Stanford University

description: UMI Matrix

library_source: transcriptomic single cell

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)

molecule: polyA RNA

organism: Zea mays

source_name: anther

growth_protocol: individuals were grown under greenhouse conditions in Stanford, CA, USA with 14-h day/10-h night lighting, approximating half of peak summer solar radiation including UV-A. Daily irrigation and fertilization maintained robust growth

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

tag: tissue

value: anther

tag: cell type

value: anther single cell

tag: genotype


title: 3.29.22 1 1.5mm 82s

description: UMI Matrix


title: 8.18.21 2 1.0mm 9s

description: UMI Matrix


title: 8.18.21 2 1.0mm 3s

description: UMI Matrix


title: 3.29.22 1 2.75mm 81s

description: UMI Matrix


title: 1.4.21 1 0.5mm 28s

description: UMI Matrix


title: 3.29.22 1 1.5mm 9s

description: UMI Matrix


title: 3.29.22 1 1.5mm 90s

description: UMI Matrix


title: 3.29.22 1 2.75mm 70s

description: UMI Matrix


title: 1.4.21 1.1 2.0mm 1s

description: UMI Matrix


title: 8.18.21 2 1.5mm 45s

description: UMI Matrix


title: 8.18.21 5 1.0mm 6s

description: UMI Matrix


title: 7.21 1 2.0mm 61s

description: UMI Matrix


title: 8.18.21 3 2.25mm 65s

description: UMI Matrix


title: 7.21 5 0.75mm 91s

description: UMI Matrix


title: 8.18.21 4 2.25mm 55s

description: UMI Matrix


title: 7.21 5 0.75mm 44s

description: UMI Matrix


title: 3.29.22 2 3.0mm 62s

description: UMI Matrix


title: 7.21 2 2.0mm 30s

description: UMI Matrix


title: 8.18.21 5 1.0mm 20s

description: UMI Matrix


title: 1.4.21 1.4 2.0mm 79s

description: UMI Matrix


title: 3.29.22 1 3.0mm 56s

description: UMI Matrix


title: 8.18.21 5 1.0mm 19s

description: UMI Matrix


title: 8.18.21 2 1.75mm 34s

description: UMI Matrix


title: 8.18.21 4 2.25mm 9s

description: UMI Matrix


title: 7.21 1 2.0mm 65s

description: UMI Matrix


title: 1.4.21 3 0.75mm 5s

description: UMI Matrix


title: 8.18.21 5 1.0mm 46s

description: UMI Matrix


title: 3.29.22 2 3.0mm 39s

description: UMI Matrix


title: 1.4.21 6 1.5mm 9s

description: UMI Matrix


title: 8.18.21 2 1.0mm 71s

description: UMI Matrix


title: 7.21 2 2.0mm 21s

description: UMI Matrix


title: 7.21 1 2.0mm 15s

description: UMI Matrix


title: 8.18.21 2 1.0mm 93s

description: UMI Matrix


title: 7.21 2 2.0mm 83s

description: UMI Matrix


title: 7.21 1 2.0mm 7s

description: UMI Matrix


title: 1.4.21 2 1.5mm 78s

description: UMI Matrix


title: 7.21 2 2.0mm 50s

description: UMI Matrix


title: 1.4.21 4 3.0mm 11s

description: UMI Matrix


title: 8.18.21 10 3.0mm 75s

description: UMI Matrix


title: 7.21 2 2.0mm 20s

description: UMI Matrix


title: 3.29.22 1 2.75mm 69s

description: UMI Matrix


title: 8.18.21 5 1.0mm 91s

description: UMI Matrix


title: 8.18.21 2 1.0mm 38s

description: UMI Matrix


title: 3.29.22 1 1.5mm 31s

description: UMI Matrix


title: 7.21 2 2.0mm 12s

description: UMI Matrix


title: 8.18.21 2 1.5mm 14s

description: UMI Matrix


title: 8.18.21 2 1.25mm 43s

description: UMI Matrix


title: 8.18.21 2 1.0mm 16s

description: UMI Matrix


title: 3.29.22 2 3.0mm 64s

description: UMI Matrix


title: 3.29.22 1 1.5mm 70s

description: UMI Matrix


title: 7.21 2 2.0mm 55s

description: UMI Matrix


title: 8.18.21 2 1.75mm 71s

description: UMI Matrix


title: 7.21 1 2.0mm 72s

description: UMI Matrix


title: 7.21 2 0.75mm 86s

description: UMI Matrix


title: 1.4.21 2.3 2.0mm 86s

description: UMI Matrix


title: 8.18.21 1 1.5mm 47s

description: UMI Matrix


title: 8.18.21 1 2.5mm 26s

description: UMI Matrix


title: 8.18.21 2 1.0mm 31s

description: UMI Matrix


title: 8.18.21 2 1.5mm 23s

description: UMI Matrix


title: 1.4.21 4 3.0mm 33s

description: UMI Matrix


title: 7.21 2 2.0mm 91s

description: UMI Matrix


title: 3.29.22 1 1.5mm 30s

description: UMI Matrix


title: 8.18.21 6 2.75mm 39s

description: UMI Matrix


title: 8.18.21 10 3.0mm 67s

description: UMI Matrix


title: 8.18.21 5 1.0mm 10s

description: UMI Matrix


title: 8.18.21 2 1.0mm 74s

description: UMI Matrix


title: 8.18.21 2 1.0mm 19s

description: UMI Matrix


title: 7.21 2 2.0mm 84s

description: UMI Matrix


title: 8.18.21 5 1.0mm 27s

description: UMI Matrix


title: 3.29.22 1 1.25mm 29s

description: UMI Matrix


title: 8.18.21 6 2.75mm 23s

description: UMI Matrix


title: 1.4.21 4 3.0mm 1s

description: UMI Matrix


title: 8.18.21 5 1.25mm 75s

description: UMI Matrix


title: 7.21 1 2.0mm 83s

description: UMI Matrix


title: 8.18.21 1 1.5mm 8s

description: UMI Matrix


title: 1.4.21 4 2.5mm 37s

description: UMI Matrix


title: 8.18.21 2 1.0mm 27s

description: UMI Matrix


title: 3.29.22 1 3.0mm 50s

description: UMI Matrix


title: 8.18.21 2 1.0mm 44s

description: UMI Matrix


title: 3.29.22 1 2.75mm 11s

description: UMI Matrix


title: 8.18.21 5 1.0mm 79s

description: UMI Matrix


title: 7.21 2 2.0mm 73s

description: UMI Matrix


title: 3.29.22 1 1.5mm 65s

description: UMI Matrix


title: 7.21 1 2.0mm 60s

description: UMI Matrix


title: 3.29.22 1 2.75mm 43s

description: UMI Matrix


title: 8.18.21 3 2.5mm 68s

description: UMI Matrix


title: 8.18.21 1 2.5mm 11s

description: UMI Matrix


title: 8.18.21 2 1.0mm 14s

description: UMI Matrix


title: 1.4.21 2 1.75mm 20s

description: UMI Matrix


title: 8.18.21 1 1.5mm 45s

description: UMI Matrix


title: 1.4.21 3 1.0mm 2s

description: UMI Matrix


title: 8.18.21 2 1.0mm 12s

description: UMI Matrix


title: 3.29.22 1 3.0mm 9s

description: UMI Matrix


title: 8.18.21 9 3.0mm 20s

description: UMI Matrix


title: 8.18.21 1 2.5mm 92s

description: UMI Matrix


title: 3.29.22 1 3.0mm 26s

description: UMI Matrix


title: 7.21 2 2.0mm 19s

description: UMI Matrix


title: 8.18.21 2 1.5mm 6s

description: UMI Matrix


title: 8.18.21 2 1.0mm 73s

description: UMI Matrix


title: 8.18.21 5 1.0mm 31s

description: UMI Matrix


title: 1.4.21 6 2.0mm 86s

description: UMI Matrix


title: 1.4.21 4 3.0mm 10s

description: UMI Matrix


title: 8.18.21 3 2.25mm 77s

description: UMI Matrix


title: 1.4.21 4 3.0mm 66s

description: UMI Matrix


title: 8.18.21 10 3.0mm 45s

description: UMI Matrix


title: 3.29.22 1 3.0mm 69s

description: UMI Matrix


title: 3.29.22 1 2.75mm 12s

description: UMI Matrix


title: 7.21 2 2.0mm 80s

description: UMI Matrix


title: 1.4.21 4 3.0mm 34s

description: UMI Matrix


title: 8.18.21 3 2.25mm 80s

description: UMI Matrix


title: 7.21 2 2.0mm 52s

description: UMI Matrix


title: 7.21 2 2.0mm 47s

description: UMI Matrix


title: 3.29.22 1 1.5mm 62s

description: UMI Matrix


title: 7.21 2 2.0mm 68s

description: UMI Matrix


title: 8.18.21 2 1.0mm 23s

description: UMI Matrix


title: 8.18.21 1 1.5mm 27s

description: UMI Matrix


title: 3.29.22 1 3.0mm 91s

description: UMI Matrix


title: 3.29.22 2 3.0mm 9s

description: UMI Matrix


title: 8.18.21 2 1.0mm 65s

description: UMI Matrix


title: 3.29.22 1 2.25mm 31s

description: UMI Matrix


title: 3.29.22 1 3.0mm 66s

description: UMI Matrix


title: 3.29.22 1 3.0mm 77s

description: UMI Matrix


title: 8.18.21 2 1.0mm 5s

description: UMI Matrix


title: 8.18.21 3 2.75mm 80s

description: UMI Matrix


title: 1.4.21 4 2.75mm 92s

description: UMI Matrix


title: 1.4.21 4 3.0mm 16s

description: UMI Matrix


title: 7.21 5 0.75mm 42s

description: UMI Matrix


title: 1.4.21 3 0.75mm 26s

description: UMI Matrix


title: 3.29.22 1 3.0mm 30s

description: UMI Matrix


title: 3.29.22 1 2.75mm 44s

description: UMI Matrix


title: 8.18.21 5 1.25mm 28s

description: UMI Matrix


title: 1.4.21 3 0.75mm 89s

description: UMI Matrix


title: 1.4.21 3 0.75mm 59s

description: UMI Matrix


title: 8.18.21 2 1.0mm 86s

description: UMI Matrix


title: 7.21 2 2.0mm 92s

description: UMI Matrix


title: 8.18.21 5 1.0mm 58s

description: UMI Matrix


title: 1.4.21 2 2.5mm 27s

description: UMI Matrix


title: 8.18.21 3 2.75mm 53s

description: UMI Matrix


title: 1.4.21 4 2.5mm 61s

description: UMI Matrix


title: 8.18.21 2 1.25mm 92s

description: UMI Matrix


title: 8.18.21 4 2.25mm 73s

description: UMI Matrix


title: 7.21 1 2.0mm 6s

description: UMI Matrix


title: 1.4.21 1 0.5mm 76s

description: UMI Matrix


title: 1.4.21 4 3.0mm 5s

description: UMI Matrix


title: 1.4.21 1 1.25mm 78s

description: UMI Matrix


title: 8.18.21 2 1.25mm 73s

description: UMI Matrix


title: 7.21 5 0.75mm 32s

description: UMI Matrix


title: 8.18.21 2 1.5mm 28s

description: UMI Matrix


title: 7.21 5 0.75mm 65s

description: UMI Matrix


title: 7.21 5 0.75mm 21s

description: UMI Matrix


title: 8.18.21 10 3.0mm 12s

description: UMI Matrix


title: 7.21 1 2.0mm 28s

description: UMI Matrix


title: 8.18.21 3 2.75mm 43s

description: UMI Matrix


title: 1.4.21 2 1.5mm 4s

description: UMI Matrix


title: 3.29.22 1 2.25mm 26s

description: UMI Matrix


title: 3.29.22 2 3.0mm 77s

description: UMI Matrix


title: 8.18.21 1 1.5mm 73s

description: UMI Matrix


title: 1.4.21 2 2.5mm 78s

description: UMI Matrix


title: 1.4.21 3 0.75mm 6s

description: UMI Matrix


title: 1.4.21 1 0.75mm 6s

description: UMI Matrix


title: 3.29.22 1 3.0mm 67s

description: UMI Matrix


title: 8.18.21 2 1.25mm 4s

description: UMI Matrix


title: 3.29.22 1 3.0mm 53s

description: UMI Matrix


title: 7.21 5 0.75mm 55s

description: UMI Matrix


title: 3.29.22 1 2.25mm 93s

description: UMI Matrix


title: 8.18.21 5 1.0mm 61s

description: UMI Matrix


title: 7.21 5 0.75mm 2s

description: UMI Matrix


title: 8.18.21 2 1.5mm 5s

description: UMI Matrix


title: 7.21 5 0.75mm 11s

description: UMI Matrix


title: 7.21 2 2.0mm 89s

description: UMI Matrix


title: 1.4.21 3 0.75mm 23s

description: UMI Matrix


title: 3.29.22 2 3.0mm 59s

description: UMI Matrix


title: 3.29.22 1 2.25mm 40s

description: UMI Matrix


title: 8.18.21 2 1.0mm 32s

description: UMI Matrix


title: 7.21 2 2.0mm 6s

description: UMI Matrix


title: 8.18.21 5 1.25mm 7s

description: UMI Matrix


title: 7.21 5 0.75mm 69s

description: UMI Matrix


title: 8.18.21 1 1.5mm 10s

description: UMI Matrix


title: 1.4.21 1 0.75mm 67s

description: UMI Matrix


title: 8.18.21 3 2.75mm 47s

description: UMI Matrix


title: 1.4.21 3 0.75mm 17s

description: UMI Matrix


title: 7.21 1 2.0mm 78s

description: UMI Matrix


title: 7.21 5 0.75mm 60s

description: UMI Matrix


title: 7.21 2 2.0mm 10s

description: UMI Matrix


title: 1.4.21 3 0.75mm 96s

description: UMI Matrix


title: 3.29.22 1 3.0mm 12s

description: UMI Matrix


title: 3.29.22 1 3.0mm 41s

description: UMI Matrix


title: 3.29.22 2 3.0mm 93s

description: UMI Matrix


title: 8.18.21 2 1.5mm 34s

description: UMI Matrix


title: 1.4.21 1 1.25mm 37s

description: UMI Matrix


title: 8.18.21 4 2.25mm 46s

description: UMI Matrix


title: 3.29.22 1 1.5mm 76s

description: UMI Matrix


title: 8.18.21 2 1.75mm 80s

description: UMI Matrix


title: 7.21 5 0.75mm 29s

description: UMI Matrix


title: 3.29.22 1 3.0mm 81s

description: UMI Matrix


title: 8.18.21 2 1.25mm 6s

description: UMI Matrix


title: 7.21 5 0.75mm 48s

description: UMI Matrix


title: 3.29.22 1 3.0mm 1s

description: UMI Matrix


title: 7.21 5 0.75mm 73s

description: UMI Matrix


title: 7.21 5 0.75mm 18s

description: UMI Matrix


title: 8.18.21 3 2.75mm 32s

description: UMI Matrix


title: H3

city: Hohhot

first: Yuting

last: Fu

address: university west road

country: China

institute: Inner Mongolia University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Matrix table with clean gene counts for every gene and every sample

molecule: total RNA

organism: Equus caballus

source_name: hiPSCs

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

value: ear epithelial cells

value: horse iPSCs

tag: cross

value: female horse mated with male horse


title: 3.29.22 1 2.25mm 23s

description: UMI Matrix


title: 8.18.21 2 1.5mm 62s

description: UMI Matrix


title: H2


title: 7.21 5 0.75mm 5s

description: UMI Matrix


title: H1


title: 3.29.22 1 3.0mm 44s

description: UMI Matrix


title: 8.18.21 2 1.75mm 87s

description: UMI Matrix


title: G3

source_name: HAFs

value: horse adult fibroblasts


title: 7.21 2 2.0mm 59s

description: UMI Matrix


title: G1


title: G2


title: 7.21 5 0.75mm 57s

description: UMI Matrix


title: 3.29.22 1 3.0mm 61s

description: UMI Matrix


title: 1.4.21 2 2.25mm 96s

description: UMI Matrix


title: 7.21 5 0.75mm 43s

description: UMI Matrix


title: 8.18.21 5 1.25mm 87s

description: UMI Matrix


title: 1.4.21 1 0.75mm 13s

description: UMI Matrix


title: 7.21 5 0.75mm 15s

description: UMI Matrix


title: 1.4.21 1 1.25mm 3s

description: UMI Matrix


title: Y139_G1_3

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
22L007406
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

library_source: genomic

data_processing:
Paired-end sequencing reads were mapped to the reference genome (Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa) using bowtie2 (version 2.4.5) with the parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 1000.
Read pairs were counted in 500 bp consecutive genomic windows using R/Bioconductor packages (R version 4.1.2, GenomicAlignments version 1.30.0 and GenomicRanges version 1.46.1). Reads mapped to the mitochondrial genome were excluded from the analysis.
Read counts were normalized by the total number of mapped reads and were converted to bedgraph files upon smoothing by the rollmean function (zoo package, version 1.8-10).
Assembly: Saccharomyces_cerevisiae.R64-1-1
Supplementary files format and content: bedGraph files with normalized read counts in 500 bp bins.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Logarithmic yeast cells were grown in YPD medium and arrested with alpha-factor and then either released into S-phase in the presence of hydroxyurea for 60min or released without addition of hydroxyurea for 24min.

extract_protocol:
Phenol-chloroform extraction of genomic DNA from S. cerevisiae cells.
NEBNext® Ultra™ II for DNA Library Preparation.

tag: strain

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

tag: cell cycle

tag: treatment


title: Y71_60_3

description:
22L007402
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

value: 60 min

value: hydroxyurea treated


title: Y139_24_3

description:
22L007407
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

value: 24 min


title: Y138_24_3

description:
22L007404
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y71_G1_3

description:
22L007400
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y71_24_3

description:
22L007401
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y138_G1_3

description:
22L007403
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 7.21 2 2.0mm 65s

description: UMI Matrix


title: Y45_60_3

description:
22L007399
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: Y138_60_3

description:
22L007405
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y45_24_3

description:
22L007398
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: 7.21 5 0.75mm 45s

description: UMI Matrix


title: 8.18.21 5 1.25mm 26s

description: UMI Matrix


title: Y139_60_3

description:
22L007408
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 1.4.21 1 0.75mm 10s

description: UMI Matrix


title: Y45_G1_3

description:
22L007397
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: 8.18.21 4 2.25mm 18s

description: UMI Matrix


title: 8.18.21 1 1.75mm 14s

description: UMI Matrix


title: 7.21 5 0.75mm 70s

description: UMI Matrix


title: 8.18.21 2 1.75mm 72s

description: UMI Matrix


title: 7.21 5 0.75mm 49s

description: UMI Matrix


title: 8.18.21 1 1.75mm 11s

description: UMI Matrix


title: 7.21 5 0.75mm 1s

description: UMI Matrix


title: 8.18.21 1 1.75mm 65s

description: UMI Matrix


title: Y16_G1_3

description:
22L007391
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y19_G1_3

description:
22L007394
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: Y19_60_3

description:
22L007396
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: 7.21 5 0.75mm 81s

description: UMI Matrix


title: Y139_24_2

description:
22L007389
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 1.4.21 2 1.75mm 85s

description: UMI Matrix


title: Y139_G1_2

description:
22L007388
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 3 2.75mm 61s

description: UMI Matrix


title: Y19_24_3

description:
22L007395
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: Y71_60_2

description:
22L007384
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 7.21 2 2.0mm 27s

description: UMI Matrix


title: 8.18.21 3 2.75mm 45s

description: UMI Matrix


title: 8.18.21 2 1.0mm 26s

description: UMI Matrix


title: Y138_60_2

description:
22L007387
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y71_24_2

description:
22L007383
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y71_G1_2

description:
22L007382
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y138_G1_2

description:
22L007385
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 1.4.21 3 0.75mm 20s

description: UMI Matrix


title: 1.4.21 2 2.75mm 64s

description: UMI Matrix


title: 3.29.22 1 1.25mm 70s

description: UMI Matrix


title: 8.18.21 4 2.25mm 83s

description: UMI Matrix


title: Y45_60_2

description:
22L007381
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: Y45_24_2

description:
22L007380
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: Y16_60_3

description:
22L007393
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y16_24_3

description:
22L007392
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y139_60_2

description:
22L007390
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 1 2.5mm 46s

description: UMI Matrix


title: 8.18.21 1 1.75mm 88s

description: UMI Matrix


title: Y45_G1_2

description:
22L007379
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: 8.18.21 2 1.5mm 80s

description: UMI Matrix


title: Y19_60_2

description:
22L007378
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: Y138_24_2

description:
22L007386
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 2 1.75mm 52s

description: UMI Matrix


title: Y19_G1_2

description:
22L007376
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: 8.18.21 2 1.5mm 41s

description: UMI Matrix


title: Y16_60_2

description:
22L007375
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: 8.18.21 2 1.75mm 20s

description: UMI Matrix


title: Y19_24_2

description:
22L007377
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: 1.4.21 3 0.75mm 21s

description: UMI Matrix


title: Y16_G1_2

description:
22L007373
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y16_24_2

description:
22L007374
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y139_60_1

description:
22L007372
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 5 1.25mm 38s

description: UMI Matrix


title: 3.29.22 1 1.5mm 37s

description: UMI Matrix


title: Y139_G1_1

description:
22L007370
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y138_60_1

description:
22L007369
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 2 1.25mm 3s

description: UMI Matrix


title: 8.18.21 3 2.75mm 75s

description: UMI Matrix


title: 8.18.21 1 2.5mm 90s

description: UMI Matrix


title: Y71_60_1

description:
22L007366
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y138_G1_1

description:
22L007367
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: Y71_24_1

description:
22L007365
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 3 2.75mm 19s

description: UMI Matrix


title: Y138_24_1

description:
22L007368
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 1 1.75mm 38s

description: UMI Matrix


title: 1.4.21 1 0.5mm 33s

description: UMI Matrix


title: Y45_G1_1

description:
22L007361
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: Y19_60_1

description:
22L007360
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: Y45_60_1

description:
22L007363
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: Y45_24_1

description:
22L007362
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4;RS_LEXA_NS-1_ARS313_NS+1_RS


title: 7.21 5 0.75mm 7s

description: UMI Matrix


title: Y139_24_1

description:
22L007371
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS313_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 7.21 5 0.75mm 26s

description: UMI Matrix


title: 3.29.22 1 2.75mm 3s

description: UMI Matrix


title: 1.4.21 2 1.75mm 14s

description: UMI Matrix


title: 8.18.21 3 2.75mm 6s

description: UMI Matrix


title: Y19_24_1

description:
22L007359
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: 8.18.21 2 1.75mm 29s

description: UMI Matrix


title: 8.18.21 1 1.5mm 50s

description: UMI Matrix


title: Y16_60_1

description:
22L007357
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: 8.18.21 1 1.5mm 23s

description: UMI Matrix


title: Y16_24_1

description:
22L007356
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: 1.4.21 3 0.75mm 87s

description: UMI Matrix


title: 8.18.21 1 1.75mm 70s

description: UMI Matrix


title: Y16_G1_1

description:
22L007355
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS305_NS+1_RS


title: Y71_G1_1

description:
22L007364
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS; Ask1-GlySer-V5-GlySer-lexA::Ura3


title: 8.18.21 5 1.0mm 71s

description: UMI Matrix


title: 8.18.21 2 1.75mm 83s

description: UMI Matrix


title: Y123_24_minaux_3

description:
22L007353
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc

value: MATa; ura3<delta>0; leu2<delta>0; his3<delta>1; met15<delta>0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* - 9x myc

value: no auxin control


title: Y123_60_minaux_3

description:
22L007354
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc

value: no auxin control + hydroxyurea treated


title: 1.4.21 3 0.75mm 56s

description: UMI Matrix

value: anther

value: anther single cell


title: Y123_G1_minaux_3

description:
22L007352
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_60_plusaux_3

description:
22L007351
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc

value: auxin + hydroxyurea treated


title: Y19_G1_1

description:
22L007358
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; RS_LEXA_NS-1_ARS316_NS+1_RS


title: 7.21 5 0.75mm 47s

description: UMI Matrix


title: Y123_24_plusaux_3

description:
22L007350
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc

value: auxin treated


title: 8.18.21 1 1.5mm 54s

description: UMI Matrix


title: Y123_G1_minaux_2

description:
22L007346
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_24_minaux_2

description:
22L007347
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 1.4.21 2 1.75mm 28s

description: UMI Matrix


title: 8.18.21 2 1.75mm 61s

description: UMI Matrix


title: Y123_G1_plusaux_3

description:
22L007349
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 1.4.21 1 0.75mm 68s

description: UMI Matrix


title: Y123_60_plusaux_2

description:
22L007345
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 7.21 2 2.0mm 23s

description: UMI Matrix


title: 3.29.22 1 2.75mm 75s

description: UMI Matrix


title: Y123_G1_plusaux_2

description:
22L007343
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_60_minaux_2

description:
22L007348
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 1.4.21 1 0.75mm 86s

description: UMI Matrix


title: Y123_60_minaux_1

description:
22L007342
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_24_plusaux_2

description:
22L007344
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_24_minaux_1

description:
22L007341
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 8.18.21 5 1.0mm 26s

description: UMI Matrix


title: 7.21 5 0.75mm 38s

description: UMI Matrix


title: Y123_G1_minaux_1

description:
22L007340
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 3.29.22 1 1.25mm 47s

description: UMI Matrix


title: Y123_60_plusaux_1

description:
22L007339
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 7.21 5 0.75mm 23s

description: UMI Matrix


title: 8.18.21 3 2.75mm 10s

description: UMI Matrix


title: Y123_24_plusaux_1

description:
22L007338
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: Y123_G1_plusaux_1

description:
22L007337
MATa; ura3Δ0; leu2Δ0; his3Δ1; met15Δ0; bar1::kanMX4; pGPD-TIR1-3myc; Ask1-3x aid* – 9x myc


title: 7.21 5 0.75mm 46s

description: UMI Matrix


title: 8.18.21 2 1.0mm 82s

description: UMI Matrix


title: 8.18.21 1 1.75mm 9s

description: UMI Matrix


title: 1.4.21 7 1.25mm 15s

description: UMI Matrix


title: 5xmyc-LFY_K249R + (ASK1-UFO-3xFLAG) complex

city: Grenoble

first: Christel

last: Carles

address: 17 avenue des Martyrs

country: France

institute: CNRS

description: 5xmyc-LFY_K249R was produced produced by TnT in vitro transcription translation system from Promega, ASK1-UFO-3xFLAG complex is recombinant.

data_processing:
Alignement to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
Replicates are treated by MSPC to create consensus peaks
Consensus peaks are reworked around maximum of peaks.
Assembly: TAIR10
Supplementary files format and content: bed files (_narrowpeak.bed) contain MSPC-called consensus peaks for each genotype; bedgraph files contain reads-in-peaks-normalized coverage for each genotype.

organism: Arabidopsis thaliana

source_name: 2-weeks old seedlings

growth_protocol: 2-weeks old seedlings of Arabidopsis thaliana

extract_protocol:
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits

value: 2-weeks old seedlings

tag: tagged protein

value: 5xmyc-LFY_K249R + (ASK1-UFO-3xFLAG)

value: WT


title: 8.18.21 3 2.25mm 75s

description: UMI Matrix


title: 5xmyc-LFY + (ASK1-UFO-3xFLAG) complex

description: 5xmyc-LFY was produced produced by TnT in vitro transcription translation system from Promega, ASK1-UFO-3xFLAG complex is recombinant.

value: 5xmyc-LFY + (ASK1-UFO-3xFLAG)


title: 7.21 5 0.75mm 75s

description: UMI Matrix


title: 5xmyc-LFY_K249R

description: 5xmyc-LFY_K249R was produced produced by TnT in vitro transcription translation system from Promega.


title: 7.21 5 0.75mm 6s

description: UMI Matrix


title: 8.18.21 3 2.25mm 20s

description: UMI Matrix


title: 1.4.21 1 0.75mm 12s

description: UMI Matrix


title: 1.4.21 1 0.75mm 39s

description: UMI Matrix


title: Input DNA


title: 7.21 2 2.0mm 71s

description: UMI Matrix


title: 1.4.21 1 0.75mm 9s

description: UMI Matrix


title: 8.18.21 2 1.75mm 2s

description: UMI Matrix


title: 7.21 5 0.75mm 50s

description: UMI Matrix


title: 8.18.21 4 2.25mm 8s

description: UMI Matrix


title: 1.4.21 4 2.5mm 16s

description: UMI Matrix


title: 8.18.21 2 1.5mm 31s

description: UMI Matrix


title: 8.18.21 2 1.75mm 15s

description: UMI Matrix


title: MCF10A-sh-ARID1A

type: RNA

city: Shanghai

first: Jie

last: Wang

address: 416 Rm., MingdaoBldg., 131 Dongan Rd., Shanghai 200032, P.R.China

institute: Fudan University

description: Gene expression data from MCF10A-sh-ARID1A

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

organism: Homo sapiens

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: MCF10A and HMEC cells were cultured in DMEM/F12 media (HyClone) supplemented with 5% FBS, EGF (20 ng/mL), insulin (10 µg/mL), hydrocortisone (0.5 µg/mL), cholera toxin (100 ng/mL), 50 U/mL penicillin and 50 µg/mL streptomycin. The cells were incubated at 37°C in a humidified chamber containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: There was no extra treatment.

tag: cell

value: MCF10A-sh-ARID1A cell line


title: 8.18.21 2 1.0mm 92s

description: UMI Matrix


title: HMEC-sh-ARID1A

description: Gene expression data from HMEC-sh-ARID1A

value: HMEC-sh-ARID1A cell line


title: 7.21 5 0.75mm 37s

description: UMI Matrix


title: HMEC-pLKO.1

description: Gene expression data from HMEC-pLKO.1

value: HMEC-pLKO.1 cell line


title: A, A4.3.4, scRNAseq [A6-4]

city: Valencia

first: Pedro

last: de Castro

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

country: Spain

institute: IVI Foundation

description: 300-nt read

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made by Dreamgenics using the Genome One software v4.x.  (https://www.dreamgenics.com/#)
Assembly: GRCh37
Supplementary files format and content: Tab-separated values files and salmon output files

source_name: Blastomers

extract_protocol:
All samples were incubated with 2 μL of 10× Reaction Buffer (SMART-Seq v4 Ultra-Low Input RNA kit for Sequencing, (Takara Bio, USA) and preserved at −80°C until preparation analysis. Total RNA was extracted using a SMART-Seq V4 Ultra-Low Input RNA Sequencing kit (Clontech, CA, USA) that uses oligo(dT) priming. cDNA was synthesized with 3′SMART-Seq CDS primer II (Clontech, CA, USA) and PCR amplified (17 cycles) from 10 pg of RNA following manufacturer’s instructions. Briefly, cDNA was purified using AMPure XP magnetic beads (Illumina, USA).
After confirming cDNA integrity on a 2100 Bioanalyzer (Agilent Technologies, USA), a total of 50 ng of genomic DNA were fragmented with the TruSight One Sequencing Panel Library (Illumina, USA) according to manufacturer’s instructions. RNA-seq libraries were constructed using the same kit. Then, a RNA pool was generated using equal amounts of RNA (5 nM) per individual sample. Barcodes and adapters were included in the library to sequence and identify all samples.

value: Blastomers

tag: cell line

value: Androgenote

tag: developmental stage

value: Pre-implantation

value: Haploid


title: A, A4.3.6, scRNAseq [A6-6]

description: 300-nt read


title: A, A4.3.5, scRNAseq [A6-5]

description: 300-nt read


title: A, A4.3.7, scRNAseq [A6-7]

description: 300-nt read


title: 7.21 5 0.75mm 63s

description: UMI Matrix


title: 8.18.21 6 2.75mm 6s

description: UMI Matrix


title: A, A4.3.2, scRNAseq [A6-2]

description: 300-nt read


title: 3.29.22 1 3.0mm 63s

description: UMI Matrix


title: A, A4.3.3, scRNAseq [A6-3]

description: 300-nt read


title: 7.21 2 2.0mm 36s

description: UMI Matrix


title: 8.18.21 6 2.75mm 47s

description: UMI Matrix


title: 8.18.21 1 2.5mm 72s

description: UMI Matrix


title: A, A4.3.8, scRNAseq [A6-8]

description: 300-nt read


title: A, A4.2.8, scRNAseq [A3-8]

description: 300-nt read


title: 8.18.21 3 2.75mm 49s

description: UMI Matrix


title: A, A4.3.1, scRNAseq [A6-1]

description: 300-nt read


title: A, A4.2.6, scRNAseq [A3-6]

description: 300-nt read


title: A, A4.2.5, scRNAseq [A3-5]

description: 300-nt read


title: 3.29.22 1 2.25mm 64s

description: UMI Matrix


title: 3.29.22 1 2.75mm 76s

description: UMI Matrix


title: A, A4.2.7, scRNAseq [A3-7]

description: 300-nt read


title: 8.18.21 1 1.75mm 55s

description: UMI Matrix


title: A, A4.2.3, scRNAseq [A3-3]

description: 300-nt read


title: 1.4.21 1 1.0mm 20s

description: UMI Matrix


title: 7.21 5 0.75mm 61s

description: UMI Matrix


title: 7.21 5 0.75mm 72s

description: UMI Matrix


title: 3.29.22 1 1.5mm 11s

description: UMI Matrix


title: 8.18.21 2 1.75mm 26s

description: UMI Matrix


title: A, A4.1.6, scRNAseq [A1-6]

description: 300-nt read


title: A, A4.1.5, scRNAseq [A1-5]

description: 300-nt read


title: A, A4.1.7, scRNAseq [A1-7]

description: 300-nt read


title: A, A4.1.4, scRNAseq [A1-4]

description: 300-nt read


title: A, A4.2.2, scRNAseq [A3-2]

description: 300-nt read


title: A, A4.1.3, scRNAseq [A1-3]

description: 300-nt read


title: 1.4.21 2 2.75mm 18s

description: UMI Matrix


title: 1.4.21 6 1.75mm 17s

description: UMI Matrix


title: 1.4.21 1 0.75mm 73s

description: UMI Matrix


title: A, A3.3.4, scRNAseq [A10-4]

description: 300-nt read


title: A, A4.1.1, scRNAseq [A1-1]

description: 300-nt read


title: A, A3.3.3, scRNAseq [A10-3]

description: 300-nt read


title: A, A3.3.2, scRNAseq [A10-2]

description: 300-nt read


title: 8.18.21 6 2.75mm 93s

description: UMI Matrix


title: 8.18.21 6 2.75mm 46s

description: UMI Matrix


title: A, A3.3.1, scRNAseq [A10-1]

description: 300-nt read


title: A, A3.2.4, scRNAseq [A5-4]

description: 300-nt read


title: A, A3.2.3, scRNAseq [A5-3]

description: 300-nt read


title: 7.21 1 2.0mm 31s

description: UMI Matrix


title: 1.4.21 1 0.75mm 66s

description: UMI Matrix


title: A, A3.1.5, scRNAseq [A2-5]

description: 300-nt read


title: A, A3.2.2, scRNAseq [A5-2]

description: 300-nt read


title: A, A3.1.4, scRNAseq [A2-4]

description: 300-nt read


title: A, A4.1.2, scRNAseq [A1-2]

description: 300-nt read


title: A, A3.1.3, scRNAseq [A2-3]

description: 300-nt read


title: A, A3.1.2, scRNAseq [A2-2]

description: 300-nt read


title: 8.18.21 1 1.75mm 53s

description: UMI Matrix


title: A, A3.2.1, scRNAseq [A5-1]

description: 300-nt read


title: 8.18.21 2 1.75mm 91s

description: UMI Matrix


title: 8.18.21 2 1.75mm 42s

description: UMI Matrix


title: 8.18.21 2 1.75mm 74s

description: UMI Matrix


title: A, A3.1.1, scRNAseq [A2-1]

description: 300-nt read


title: 3.29.22 2 3.0mm 29s

description: UMI Matrix


title: A, ZA4, scRNAseq [A21]

description: 300-nt read


title: 7.21 5 0.75mm 31s

description: UMI Matrix


title: 1.4.21 1 0.75mm 30s

description: UMI Matrix


title: A, ZA2, scRNAseq [A12]

description: 300-nt read


title: 1.4.21 3 0.75mm 82s

description: UMI Matrix


title: 8.18.21 4 2.25mm 60s

description: UMI Matrix


title: 8.18.21 3 2.75mm 12s

description: UMI Matrix


title: 8.18.21 1 2.5mm 51s

description: UMI Matrix


title: 7.21 5 0.75mm 56s

description: UMI Matrix


title: P, P4.2, scRNAseq 7

description: 300-nt read

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made by Dreamgenics using the Genome One software v4.x.  (https://www.dreamgenics.com/#)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and salmon output files

value: Parthenogenote


title: 8.18.21 2 1.75mm 28s

description: UMI Matrix


title: P, P4.2, scRNAseq 6

description: 300-nt read


title: P, P4.2, scRNAseq 5

description: 300-nt read


title: 8.18.21 1 2.5mm 7s

description: UMI Matrix


title: 1.4.21 2 2.25mm 65s

description: UMI Matrix


title: A, ZA1, scRNAseq [A11]

description: 300-nt read


title: 1.4.21 2 2.25mm 56s

description: UMI Matrix


title: 8.18.21 1 1.75mm 50s

description: UMI Matrix


title: A, ZA3, scRNAseq [A20]

description: 300-nt read


title: P, P4.2, scRNAseq 1

description: 300-nt read


title: 8.18.21 10 3.0mm 2s

description: UMI Matrix


title: 8.18.21 6 2.75mm 31s

description: UMI Matrix


title: P, P4.2, scRNAseq 4

description: 300-nt read


title: 7.21 5 0.75mm 25s

description: UMI Matrix


title: P, P4.1, scRNAseq 3

description: 300-nt read


title: 8.18.21 1 2.5mm 62s

description: UMI Matrix


title: 1.4.21 6 1.75mm 7s

description: UMI Matrix


title: P, P4.1, scRNAseq 4

description: 300-nt read


title: 1.4.21 1 0.75mm 94s

description: UMI Matrix


title: P, P3.2, scRNAseq 3

description: 300-nt read


title: 1.4.21 2 1.75mm 41s

description: UMI Matrix


title: 8.18.21 5 1.0mm 87s

description: UMI Matrix


title: 1.4.21 2 1.75mm 38s

description: UMI Matrix


title: P, P3.2, scRNAseq 1

description: 300-nt read


title: P, P4.1, scRNAseq 1

description: 300-nt read


title: P, P3.1, scRNAseq 3

description: 300-nt read


title: P, P3.1, scRNAseq 2

description: 300-nt read


title: 8.18.21 1 1.75mm 1s

description: UMI Matrix


title: P, P4.2, scRNAseq 2

description: 300-nt read


title: P, P4.2, scRNAseq 3

description: 300-nt read


title: 8.18.21 2 1.25mm 63s

description: UMI Matrix


title: 8.18.21 2 1.5mm 33s

description: UMI Matrix


title: P, ZP2, scRNAseq

description: 300-nt read


title: 8.18.21 3 2.75mm 77s

description: UMI Matrix


title: MCF10A-pLKO.1

description: Gene expression data from MCF10A-pLKO.1

value: MCF10A-pLKO.1 cell line


title: P, P3.1, scRNAseq 1

description: 300-nt read


title: 8.18.21 2 1.75mm 36s

description: UMI Matrix

value: anther


title: P, P4.1, scRNAseq 2

description: 300-nt read


title: 8.18.21 3 2.75mm 46s

description: UMI Matrix

value: anther single cell


title: P, ZP1, scRNAseq

description: 300-nt read


title: lifeAct_high_replicate_2

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

description:
RNA with rRNA depletion
Hi2_277_300_S14

data_processing:
After quality control, the clean reads were mapped to human genome (hg38) or mouse genome (mm10) using STAT.
Genes expression level were quantitated with featureCounts.
Differentially expressed genes (DEGs) were identified with DESeq2. An absolute log2 fold change >1 and the adjusted p-value (FDR) significance score <0.05 were used as thresholds to identify DEGs.
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

growth_protocol: We performed bulk RNA-seq of control, MKL1 overexpressed (OE)  and caMKL1 OE in LM2 and 4T1 cell lines . We also performed bulk RNA-seq of control, low and high expression of LifeAct in LM2 cell line.

extract_protocol:
Total RNA with polyA+ selection or rRNA depletion was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.
RNA-seq was performed at Illumina Hiseq 2500 platform that included quality control, library preparation, fragmentation and PCR enrichment of target RNA according to standardized procedures.
150 bp paired-end raw reads were initially processed to obtain clean reads by removing adaptor sequences, low quality sequences, empty reads.

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), from three replicates of each group.

value: breast cancer

value: high expression of LifeAct


title: 7.21 2 2.0mm 58s

description: UMI Matrix


title: 7.21 5 0.75mm 90s

description: UMI Matrix


title: 7.21 5 0.75mm 51s

description: UMI Matrix


title: lifeAct_high_replicate_1

description:
RNA with rRNA depletion
Hi1_194_383_S13


title: lifeAct_low_replicate_3

description:
RNA with rRNA depletion
Lo3_206_371_S12

value: low expression of LifeAct


title: 7.21 2 0.75mm 94s

description: UMI Matrix


title: P, P3.2, scRNAseq 2

description: 300-nt read


title: lifeAct_low_replicate_2

description:
RNA with rRNA depletion
Lo2_218_359_S11


title: LifeAct_neg_replicate_3

description:
RNA with rRNA depletion
Neg3_242_335_S9

value: control


title: 3.29.22 1 2.75mm 36s

description: UMI Matrix


title: lifeAct_low_replicate_1

description:
RNA with rRNA depletion
Lo1_230_347_S10

value: WT


title: 1.4.21 2 2.25mm 46s

description: UMI Matrix


title: 1.4.21 2 1.75mm 39s

description: UMI Matrix


title: LM2_caMKL1_OE_replicate_3

description:
RNA with polyA+ selection
caMKL1-3_265_312_S16

value: caMKL1 OE


title: LifeAct_neg_replicate_1

description:
RNA with rRNA depletion
Neg1_266_311_S7


title: LifeAct_neg_replicate_2

description:
RNA with rRNA depletion
Neg2_254_323_S8


title: LM2_caMKL1_OE_replicate_2

description:
RNA with polyA+ selection
caMKL1-2_277_300_S15


title: 1.4.21 1 0.75mm 36s

description: UMI Matrix


title: 7.21 2 0.75mm 2s

description: UMI Matrix


title: LM2_caMKL1_OE_replicate_1

description:
RNA with polyA+ selection
caMKL1-1_194_383_S14


title: lifeAct_high_replicate_3

description:
RNA with rRNA depletion
Hi3_265_312_S15


title: 3.29.22 1 2.75mm 86s

description: UMI Matrix


title: 8.18.21 5 1.0mm 52s

description: UMI Matrix


title: LM2_MKL1_OE_replicate_2

description:
RNA with polyA+ selection
MKL1-2_218_359_S12

value: WT MKL1 OE


title: 1.4.21 2.5 2.0mm 15s

description: UMI Matrix


title: LM2_MKL1_OE_replicate_1

description:
RNA with polyA+ selection
MKL1-1_230_347_S11


title: 8.18.21 2 1.75mm 11s

description: UMI Matrix


title: 7.21 5 0.75mm 19s

description: UMI Matrix


title: LM2_control_replicate_3

description:
RNA with polyA+ selection
Ctrl-3_242_335_S10


title: 8.18.21 1 2.5mm 45s

description: UMI Matrix


title: 8.18.21 6 2.75mm 61s

description: UMI Matrix


title: 3.29.22 1 2.75mm 46s

description: UMI Matrix


title: 8.18.21 2 1.0mm 18s

description: UMI Matrix


title: 7.21 2 0.75mm 45s

description: UMI Matrix


title: hTSC, unstimulated, Input

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Reads were trimmed with TrimGalore v0.6.4 and then aligned to the corresponding reference genome (GRCh38 for human) using Bowtie v2.3.5 with default settings. PCR duplicates were removed using the rmdup function of samtools v1.13. After confirming the data reproducibility, reads from biological replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.6 with default settings. The peaks were further cleaned by removing those overlapped with ENCODE Blacklist V2 regions.
Assembly: GRCh38
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: Human TSC

growth_protocol: Human TSCs were cultured in trophoblast stem cell medium (TSM), as described previously (Sun et al. 2021, PMID: 34320657)

extract_protocol:
ChIP-Seq for human TSCs was performed following our previous study (Sun et al. 2021, , PMID: 34320657).
Chromatin fragmentation was performed using Diagenode Bioruptor Plus Sonicator. The antibody for H3K27ac (Abcam, ab4729) is used. The amount of chromatin is 20 μg per reaction. ChIP-Seq libraries were constructed using Takara SMARTer ThruPLEX DNA-Seq Kit (Takara, R400674), and sequenced as 50 bp paired-end reads with HiSeq2500 (Illumina) platform.

treatment_protocol: Interferon stimulation is performed by adding 1000U/mL of IFN-γ (PBL, 11500-2) into the culturing medium of human TSCs. After 24 hours, untreated and IFN-γ treated samples are both collected for subsequent experiments.

value: Human TSC

value: Wild-type

tag: antibody


title: 7.21 2 0.75mm 18s

description: UMI Matrix


title: hTSC, IFN-gamma stimulated, Input


title: hTSC, unstimulated, H3K27ac, rep1

value: Abcam, ab4729


title: hTSC, unstimulated, H3K27ac, rep2


title: hTSC, IFN-gamma stimulated, H3K27ac, rep2


title: 7.21 5 0.75mm 84s

description: UMI Matrix


title: 8.18.21 3 2.75mm 35s

description: UMI Matrix


title: LM2_MKL1_OE_replicate_3

description:
RNA with polyA+ selection
MKL1-3_206_371_S13


title: 8.18.21 1 1.75mm 17s

description: UMI Matrix


title: hTSC, unstimulated, RNA-Seq, rep2

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4. To perform differential expression analysis, we aligned trimmed reads to the reference genome (GRCh38 for human) using STAR v2.7.3, and then obtained gene-level read counts using the featureCount function from subread v2.0.0. At last, differentially expressed genes were identified using DESeq2 v1.30.1 with the cutoff: FDR<0.05 and |log2Foldchange|>1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each sample

extract_protocol:
Total RNA for human TSCs was extracted using RNeasy Micro kit (Qiagen, 74004) with on-column DNase digestion.
RNA-Seq library is construction by TruSeq stranded mRNA sample preparation kit (Illumina), and then sequenced as 75 bp paired-end reads with HiSeq2500 (Illumina) platform.


title: hTSC, unstimulated, RNA-Seq, rep1


title: hTSC, IFN-gamma stimulated, H3K27ac, rep1


title: 8.18.21 2 1.75mm 76s

description: UMI Matrix


title: hTSC, IFN-gamma stimulated, RNA-Seq, rep2


title: LM2_control_replicate_2

description:
RNA with polyA+ selection
Ctrl-2_254_323_S9


title: 7.21 5 0.75mm 71s

description: UMI Matrix


title: hTSC, IFN-gamma stimulated, RNA-Seq, rep1


title: 8.18.21 2 1.75mm 3s

description: UMI Matrix


title: 8.18.21 4 2.25mm 30s

description: UMI Matrix


title: LM2_control_replicate_1

description:
RNA with polyA+ selection
Ctrl-1_266_311_S8


title: 7.21 2 0.75mm 46s

description: UMI Matrix


title: 7.21 2 2.0mm 64s

description: UMI Matrix


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  1h -3

city: Beijing

first: Guan

last: Guiwen

state: Beijing

address: 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Day 0
siTP53BP2-1h-3
L1EGA271178--Sitp53hP21h_3

data_processing:
Row reads were maping to human genome (hg38) by using of hisat2. The count value of genes were calculated by using of featureCounts.
Count values were normalized by using of edgeR packages.
Supplementary files format and content: hg38
Supplementary files format and content: The file is tsv format with normalized expression level

source_name: HCC

extract_protocol:
RNA was extract by using trizol reagent.
RNA libraries for RNA-seq were prepared using illumina mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HCC

value: TP53BP2 knockdown

value: 1000 IU/ml interferon-alpha-2b 1h


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  2h -2

description:
Day 0
siTP53BP2-2h-2
L1EGA271180--Sitp53hP22h_2

value: 1000 IU/ml interferon-alpha-2b 2h


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  2h -3

description:
Day 0
siTP53BP2-2h-3
L1EGA271181--Sitp53hP22h_3


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  2h -1

description:
Day 0
siTP53BP2-2h-1
L1EGA271179--Sitp53hP22h_1


title: 8.18.21 3 2.75mm 48s

description: UMI Matrix


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  1h -2

description:
Day 0
siTP53BP2-1h-2
L1EGA271177--Sitp53hP21h_2


title: 3.29.22 1 1.5mm 4s

description: UMI Matrix


title: 8.18.21 1 1.75mm 27s

description: UMI Matrix


title: TP53BP2 knockdown in HepG2-3

description:
Day 0
siTP53BP2-3
L1EGA271175--Sitp53hP2oh_3

value: PBS


title: 8.18.21 5 1.25mm 61s

description: UMI Matrix

value: anther


title: TP53BP2 knockdown in HepG2-2

description:
Day 0
siTP53BP2-2
L1EGA271174--Sitp53hP2oh_2


title: 1.4.21 2 1.75mm 90s

description: UMI Matrix

value: anther single cell


title: 8.18.21 2 1.75mm 56s

description: UMI Matrix


title: HepG2-interferon-α-2b-2h-3

description:
Day 0
siControl-2h-3
L1EGA271172--Sinc2h_3


title: TP53BP2 knockdown in HepG2-1

description:
Day 0
siTP53BP2-1
L1EGA271173--Sitp53hP2oh_1


title: 7.21 2 0.75mm 5s

description: UMI Matrix


title: HepG2-interferon-α-2b-2h-2

description:
Day 0
siControl-2h-2
L1EGA271171--Sinc2h_2


title: HepG2-interferon-α-2b-2h-1

description:
Day 0
siControl-2h-1
L1EGA271170--Sinc2h_1


title: 7.21 2 0.75mm 61s

description: UMI Matrix


title: 8.18.21 5 1.0mm 60s

description: UMI Matrix


title: 8.18.21 2 1.75mm 60s

description: UMI Matrix


title: HepG2-interferon-α-2b-1h-1

description:
Day 0
siControl-1h-1
L1EGA271167--Sinc1h_1


title: HepG2-interferon-α-2b-1h-2

description:
Day 0
siControl-1h-2
L1EGA271168--Sinc1h_2


title: HepG2-interferon-α-2b-1h-3

description:
Day 0
siControl-1h-3
L1EGA271169--Sinc1h_3


title: 8.18.21 3 2.75mm 86s

description: UMI Matrix


title: 8.18.21 2 1.5mm 15s

description: UMI Matrix


title: HepG2-1

description:
Day 0
siControl-1
L1EGA271164--Sincoh_1


title: 1.4.21 2 1.75mm 55s

description: UMI Matrix


title: HepG2-2

description:
Day 0
siControl-2
L1EGA271165--Sincoh_2


title: TP53BP2 knockdown in HepG2-1 wihh interferon treated  1h -1

description:
Day 0
siTP53BP2-1h-1
L1EGA271176--Sitp53hP21h_1


title: 7.21 2 0.75mm 47s

description: UMI Matrix


title: HepG2-3

description:
Day 0
siControl-3
L1EGA271166--Sincoh_3


title: TP53BP2 knockdown HepAD38 treated with 1000 IU/mL interferon-α-2b -1

description:
Day 0
siTP53BP2-interferon-12h-1
ggw_10_S118_L004_R1_001_val_1

value: 1000 IU/ml interferon-alpha-2b


title: TP53BP2 knockdown HepAD38 treated with 1000 IU/mL interferon-α-2b -2

description:
Day 0
siTP53BP2-interferon-12h-2
ggw_11_S119_L004_R1_001_val_1


title: 8.18.21 1 1.75mm 44s

description: UMI Matrix


title: HepAD38 treated with 1000 IU/mL interferon-α-2b -3

description:
Day 0
siControl-1-interferon-12h-3
ggw_9_S113_L003_R1_001_val_1


title: 8.18.21 5 1.0mm 67s

description: UMI Matrix


title: 3.29.22 1 2.75mm 29s

description: UMI Matrix


title: TP53BP2 knockdown HepAD38 treated with 1000 IU/mL interferon-α-2b -3

description:
Day 0
siTP53BP2-interferon-12h-3
ggw_12_S120_L004_R1_001_val_1


title: HepAD38 treated with 1000 IU/mL interferon-α-2b -1

description:
Day 0
siControl-1-interferon-12h-1
ggw_7_S111_L003_R1_001_val_1


title: TP53BP2 knockdown in HepAD38-3

description:
Day 0
siTP53BP2-3
ggw_6_S110_L003_R1_001_val_1


title: 8.18.21 2 1.0mm 58s

description: UMI Matrix


title: 7.21 2 0.75mm 10s

description: UMI Matrix


title: HepAD38 treated with 1000 IU/mL interferon-α-2b -2

description:
Day 0
siControl-1-interferon-12h-2
ggw_8_S112_L003_R1_001_val_1


title: TP53BP2 knockdown in HepAD38-2

description:
Day 0
siTP53BP2-2
ggw_5_S109_L003_R1_001_val_1


title: 8.18.21 2 1.0mm 8s

description: UMI Matrix


title: 8.18.21 1 1.75mm 25s

description: UMI Matrix


title: 7.21 2 0.75mm 69s

description: UMI Matrix


title: TP53BP2 knockdown in HepAD38-1

description:
Day 0
siTP53BP2-1
ggw_4_S108_L003_R1_001_val_1


title: HepAD38-3

description:
Day 0
siControl-3
ggw_3_S107_L003_R1_001_val_1


title: 8.18.21 2 1.75mm 93s

description: UMI Matrix


title: 8.18.21 6 2.75mm 85s

description: UMI Matrix


title: 1.4.21 1 1.25mm 76s

description: UMI Matrix


title: 1.4.21 2 1.75mm 62s

description: UMI Matrix


title: 8.18.21 2 1.75mm 65s

description: UMI Matrix


title: 7.21 2 0.75mm 43s

description: UMI Matrix


title: HepAD38-2

description:
Day 0
siControl-2
ggw_2_S106_L003_R1_001_val_1


title: 8.18.21 5 1.25mm 9s

description: UMI Matrix


title: Nuli_8h_801829_R3

city: Barcelona

first: Marc

last: Torrent Burgas

address: Carrer de la Vall Moronta

department: Biochemistry and Molecular Biology

institute: Universitat Autònoma de Barcelona

description: Dual RNA-seq of pathogen and host

data_processing:
Illumina’s bcl2fastq2 Software v2.20.0 was used for basecalling
Quality control of RNA-Seq reads was performed with FastQC. Sequenced reads were trimmed for adaptor content with Trimmomatic. Reads were mapped to Homo sapiens reference genome (GRCh38) using STAR aligner (version 2.6.1b) with default settings.
Mapped data was transformed to gene level counts using human Gencode annotations and FeatureCounts software.
Time-series differential expression analysis was carried out for each time point, by comparing the data obtained at 2, 5 and 8 hours-post-infection to the data in the sample at  0 hours (control conditions) and using the DESeq2 Bioconductor package. Differential expressed genes (DEGs) were defined using the following criteria: |log2-fold change| >= 1 and adjusted p-val <= 0.05.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: NuLi-1 infected

growth_protocol: NuLi-1 and CuFi-1 cell cultures were grown in BEGM Bronchial Epithelial Cell Growth  Medium BulletKit (Lonza, Basel, Switzerland) an incubated in a humidified incubator with 5%  CO2 at 37ºC. Before each passage, the culture flasks were pre-coated with 60 μg/mL solution of  Human Placental Collagen Type IV (Sigma, Darmstadt, Germany) at least 18 hours in advance,  air-dried and rinsed 2-3 times with Phosphate Buffer Saline (PBS, Gibco, Waltham, MA). For  seeding purposes, the cells were routinely passaged and subcultured when the culture is about  70-80% confluence with a 1:3 sub-cultivation ratio.

extract_protocol:
RNA extraction protocol as described in the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Infected by Pseudomonas aeruginosa. At each point post infection time cells are rinsed and RNA extracted with TRIZOL

value: NuLi-1  Cell Line

tag: biomaterial provider

value: NuLi-1 (CRL-4011™, ATCC, Manassas, VA)

value: epithelial


title: HepAD38-1

description:
Day 0
siControl-1
ggw_1_S105_L003_R1_001_val_1

value: WT


title: 1.4.21 2 1.75mm 91s

description: UMI Matrix


title: 8.18.21 1 2.5mm 38s

description: UMI Matrix


title: Control_Nuli_3873_R1

description: Dual RNA-seq of pathogen and host

source_name: NuLi-1 Control


title: Control_Nuli_3873_R2

description: Dual RNA-seq of pathogen and host


title: 8.18.21 3 2.75mm 58s

description: UMI Matrix


title: 8.18.21 3 2.75mm 84s

description: UMI Matrix


title: Control_Cufi_801829_R2

description: Dual RNA-seq of pathogen and host

source_name: CuFi-1 Control

value: CuFi-1 Cell Line

value: CuFi-1 (CRL-4013™, ATCC, Manassas, VA)


title: Control_Cufi_801829_R3

description: Dual RNA-seq of pathogen and host


title: 7.21 2 0.75mm 23s

description: UMI Matrix


title: 8.18.21 2 1.0mm 42s

description: UMI Matrix


title: Control_Cufi_801829_R1

description: Dual RNA-seq of pathogen and host


title: Cufi_5h_3873_R1

description: Dual RNA-seq of pathogen and host

source_name: CuFi-1 infected


title: Cufi_5h_3873_R2

description: Dual RNA-seq of pathogen and host


title: 8.18.21 6 2.75mm 37s

description: UMI Matrix


title: 1.4.21 2 1.75mm 93s

description: UMI Matrix


title: 1.4.21 1 0.5mm 64s

description: UMI Matrix


title: 8.18.21 2 1.75mm 84s

description: UMI Matrix


title: 8.18.21 2 1.75mm 17s

description: UMI Matrix


title: 7.21 2 0.75mm 19s

description: UMI Matrix


title: Nuli_2h_3873_R3

description: Dual RNA-seq of pathogen and host


title: Nuli_2h_801829_R3

description: Dual RNA-seq of pathogen and host


title: 8.18.21 4 2.25mm 10s

description: UMI Matrix


title: Nuli_2h_3873_R2

description: Dual RNA-seq of pathogen and host


title: Nuli_2h_3873_R1

description: Dual RNA-seq of pathogen and host


title: Nuli_8h_801829_R2

description: Dual RNA-seq of pathogen and host


title: 7.21 2 0.75mm 6s

description: UMI Matrix


title: 1.4.21 2 1.5mm 26s

description: UMI Matrix


title: Cufi_2h_801829_R3

description: Dual RNA-seq of pathogen and host


title: 7.21 2 0.75mm 15s

description: UMI Matrix


title: Cufi_2h_801829_R2

description: Dual RNA-seq of pathogen and host


title: 7.21 2 0.75mm 48s

description: UMI Matrix


title: Cufi_2h_3873_R2

description: Dual RNA-seq of pathogen and host


title: 8.18.21 6 2.75mm 96s

description: UMI Matrix


title: Cufi_2h_3872_R1

description: Dual RNA-seq of pathogen and host


title: 8.18.21 2 1.0mm 24s

description: UMI Matrix


title: Cufi_2h_3873_R3

description: Dual RNA-seq of pathogen and host


title: Nuli_2h_801829_R2

description: Dual RNA-seq of pathogen and host


title: 7.21 2 0.75mm 3s

description: UMI Matrix


title: Nuli_2h_801829_R1

description: Dual RNA-seq of pathogen and host


title: 8.18.21 7 0.5mm 25s

description: UMI Matrix


title: 3.29.22 1 2.75mm 87s

description: UMI Matrix


title: Nuli_5h_801829_R3

description: Dual RNA-seq of pathogen and host


title: Control_Nuli_3873_R3

description: Dual RNA-seq of pathogen and host


title: 1.4.21 6 1.5mm 21s

description: UMI Matrix


title: 3.29.22 1 1.5mm 91s

description: UMI Matrix


title: 7.21 2 0.75mm 64s

description: UMI Matrix


title: Nuli_5h_801829_R2

description: Dual RNA-seq of pathogen and host


title: Nuli_5h_801829_R1

description: Dual RNA-seq of pathogen and host


title: Nuli_5h_3873_R2

description: Dual RNA-seq of pathogen and host


title: Nuli_5h_3873_R3

description: Dual RNA-seq of pathogen and host


title: 1.4.21 2 1.5mm 85s

description: UMI Matrix


title: 8.18.21 8 0.5mm 4s

description: UMI Matrix


title: 3.29.22 1 2.25mm 61s

description: UMI Matrix


title: 1.4.21 2 1.75mm 5s

description: UMI Matrix


title: Nuli_5h_3873_R1

description: Dual RNA-seq of pathogen and host


title: Cufi_5h_801829_R3

description: Dual RNA-seq of pathogen and host


title: Cufi_2h_801829_R1

description: Dual RNA-seq of pathogen and host


title: 8.18.21 8 0.5mm 3s

description: UMI Matrix


title: 1.4.21 2 1.75mm 46s

description: UMI Matrix


title: 8.18.21 6 2.75mm 30s

description: UMI Matrix


title: 1.4.21 3 0.5mm 26s

description: UMI Matrix


title: Cufi_5h_801829_R1

description: Dual RNA-seq of pathogen and host


title: Cufi_5h_3873_R3

description: Dual RNA-seq of pathogen and host


title: Nuli_8h_3873_R3

description: Dual RNA-seq of pathogen and host


title: Nuli_8h_3873_R2

description: Dual RNA-seq of pathogen and host


title: 8.18.21 2 1.5mm 27s

description: UMI Matrix


title: 8.18.21 1 1.5mm 13s

description: UMI Matrix


title: 1.4.21 1 1.0mm 26s

description: UMI Matrix


title: Cufi_8h_801829_R2

description: Dual RNA-seq of pathogen and host


title: Cufi_8h_801829_R3

description: Dual RNA-seq of pathogen and host


title: Cufi_8h_801829_R1

description: Dual RNA-seq of pathogen and host


title: 8.18.21 8 0.5mm 43s

description: UMI Matrix


title: 8.18.21 8 0.5mm 59s

description: UMI Matrix


title: Cufi_8h_3873_R3

description: Dual RNA-seq of pathogen and host


title: 1.4.21 6 1.5mm 69s

description: UMI Matrix


title: Cufi_5h_801829_R2

description: Dual RNA-seq of pathogen and host


title: 8.18.21 6 2.75mm 41s

description: UMI Matrix


title: 8.18.21 6 2.75mm 33s

description: UMI Matrix


title: 3.29.22 1 1.5mm 20s

description: UMI Matrix


title: Cufi_8h_3873_R1

description: Dual RNA-seq of pathogen and host


title: 3.29.22 1 1.5mm 16s

description: UMI Matrix


title: AC16 cell line-R3_Input

city: Guangzhou

first: Haiqiong

last: Liu

state: Guangdong

address: Gongye Avenue 253

institute: Zhujiang Hospoital, Southern Medical University

data_processing:
Data quality control
Sequence Alignment
frag_ Size forecast
Peak Calling and motif analysis
GO and KEGG Enrichment analysis
Genome_build: Difference analysis
Supplementary_files_format_and_content: peak files

source_name: AC16 cardiomyocyte cell line

growth_protocol: The AC16 human cardiomyocyte cell line was purchased from Merck-Millipore (SCC109, USA)[13]. Cell line authentication is shown in the Supplementary File (Report of Human Cell Line Authentication). Cells were incubated with DMEM supplemented with 100 U/ml penicillin–streptomycin and 12.5% FBS at 37℃˚C with 5% CO2. Cells at 70-80% confluence were used for subsequent experiments.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
After the DNA sample passes the test, it is randomly interrupted by covaris ultrasonic crusher, and then repaired at the end, added with a tail and added with a tail，The whole library was prepared by sequencing, purification and PCR amplification. After the library is built, qubit2.0 is used first perform preliminary quantification, dilute the library to 1.5ng/ul, and then use Agilent 2100 to detect the insert size of the library. After the size meets the expectation, the effective concentration of the library is accurately quantified by Q-PCR (the effective concentration of the library is > 2nm), to ensure the quality of the library.

treatment_protocol: Control group(C) with no ttreatment. For H/R group(R1,R2,R3),  PBS was used to replace the former medium, and cells were cultured in a triple gas incubator with 95% N2 and 5% CO2 at 37 ℃ for 3 h under hypoxia. Reoxygenation was then initiated by medium change to replace PBS, and cells were placed back into incubated in a normal incubator at 37℃.

value: human cardiomyocyte cell line

value: hypoxia 3h and reoxygenation 3h

tag: chip antibody


title: AC16 cell line-R3_IgG

value: Normal IgG(CST, #2729)


title: Nuli_8h_801829_R1

description: Dual RNA-seq of pathogen and host


title: AC16 cell line-R3_ATF3


title: 8.18.21 6 2.75mm 32s

description: UMI Matrix


title: 8.18.21 1 1.5mm 41s

description: UMI Matrix


title: Nuli_8h_3873_R1

description: Dual RNA-seq of pathogen and host


title: AC16 cell line-R2_Input


title: AC16 cell line-R2_ATF3


title: 8.18.21 8 0.5mm 92s

description: UMI Matrix


title: 8.18.21 6 2.75mm 79s

description: UMI Matrix


title: 8.18.21 8 0.5mm 56s

description: UMI Matrix


title: AC16 cell line-R1_Input


title: 8.18.21 3 2.75mm 88s

description: UMI Matrix


title: 8.18.21 8 0.5mm 42s

description: UMI Matrix


title: AC16 cell line-R1_IgG


title: Cufi_8h_3873_R2

description: Dual RNA-seq of pathogen and host


title: AC16 cell line-C3_IgG

value: untreated


title: AC16 cell line-R1_ATF3


title: AC16 cell line-C3_Input


title: AC16 cell line-C3_ATF3


title: 8.18.21 1 1.5mm 17s

description: UMI Matrix


title: AC16 cell line-R2_IgG


title: 8.18.21 6 2.75mm 14s

description: UMI Matrix


title: 8.18.21 3 2.25mm 17s

description: UMI Matrix


title: 7.21 5 0.75mm 36s

description: UMI Matrix


title: 8.18.21 6 2.75mm 54s

description: UMI Matrix


title: 8.18.21 1 2.5mm 47s

description: UMI Matrix


title: AC16 cell line-C2_Input


title: AC16 cell line-C2_ATF3


title: 1.4.21 2 1.75mm 23s

description: UMI Matrix


title: 8.18.21 4 2.25mm 50s

description: UMI Matrix


title: AC16 cell line-C2_IgG


title: AC16 cell line-C1_IgG


title: 1.4.21 1 1.0mm 3s

description: UMI Matrix


title: AC16 cell line-C1_ATF3


title: AC16 cell line-C1_Input


title: 8.18.21 1 1.5mm 34s

description: UMI Matrix


title: 8.18.21 2 1.5mm 29s

description: UMI Matrix


title: PLC PSPH A-2

first: ZHIPENG

last: PENG

address: Xin Gang Xi Lu 135#

institute: Sun Yet-sen university

description: PLC PSPH A-2

data_processing:
Illumina Casava1.7 software used for basecalling.
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp  paired-end reads, according to the manufacturer’s instructi
Raw data (raw reads) of fastq format were firstly processed through primary quality control. In this step, clean data (clean reads) were obtained by removing read pairs that contain N more than 3 or the proportion of base with quality value below 5 is more than 20%, in any end,or adapter sequence was founded. All the downstream analyses were based on the clean data with high quali
Paired-end clean reads were aligned to the reference genome using TopHat. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tool
HTSeq was used to count the reads numbers mapped to each
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: raw counts

source_name: Hepatocellular Carcinoma

growth_protocol: PLC/PRF/5 and SNU449 were grown in RPMI1640, with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin antibiotics

extract_protocol:
RNA of the cells was extracted by TRIzol method
A total amount of 2 µg RNA per sample was used as input material for the RNA sample  preparations. Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep  Kit for Illumina following manufacturer’s recommendations and index codes were added to  attribute sequences to each sample. Briefly, mRNA was purified from total RNA using  poly-T oligo-attached magnetic beads. Fragmentation was carried out using fragmentation  buffer. First strand cDNA was synthesized and second strand cDNA synthesis was  subsequently performed. Remaining overhangs were converted into blunt ends. After  adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated. Then the PCR was performed. At last, Qubit HS quantification, Agilent 2100  Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of

treatment_protocol: TNF-a treated for 24h

value: Hepatocellular Carcinoma Cell Line

value: TNF-a treated for 24h

value: shPSPH


title: 3.29.22 1 1.5mm 59s

description: UMI Matrix


title: 8.18.21 2 1.75mm 59s

description: UMI Matrix


title: PLC PLKO A-2

description: PLC PLKO A-2

value: shPLKO


title: PLC PSPH A-1

description: PLC PSPH A-1


title: PLC PLKO A-1

description: PLC PLKO A-1


title: 1.4.21 2 1.5mm 60s

description: UMI Matrix

value: anther


title: SNU449 PSPH A-2

description: SNU449 PSPH A-2


title: SNU449 PLKO A-1

description: SNU449 PLKO A-1


title: SNU449 PSPH A-1

description: SNU449 PSPH A-1


title: SNU449 PLKO A-2

description: SNU449 PLKO A-2


title: 8.18.21 2 1.75mm 82s

description: UMI Matrix

value: anther single cell


title: 8.18.21 4 2.25mm 47s

description: UMI Matrix


title: 8.18.21 8 0.5mm 74s

description: UMI Matrix


title: 8.18.21 1 1.75mm 81s

description: UMI Matrix


title: 8.18.21 4 2.25mm 6s

description: UMI Matrix


title: SF_control_rep3_ChIPseq_H3K27me3

city: Schlieren

first: Caroline

last: Ospelt

address: Wagistrasse 14

department: Department of Rheumatology

country: Switzerland

institute: University Hospital Zurich

data_processing:
Sequencing data reads were quality-checked with FastQC. Reads were trimmed with Trimmomatic and aligned to the reference genome and transcriptome (FASTA and GTF files, respectively, Ensembl GRCh37) with STAR. Gene expression was quantified using the R/Bioconductor package Rsubread version 1.22. Differentially expressed genes between conditions were identified using the R/Bioconductor package DESeq2.
Reads were aligned to the reference genome (hg19) using using BWA v. 0.7.5a. Samples were filtered for regions blacklisted by the ENCODE project. Subsequently samples were deduplicated using SAMtools version 1.3.1. Alignment coordinates were converted to BED format using BEDTools v.2.17. Peaks were annotated on gene and transcript level using the "ChIPpeakAnno", "ChIPQC", and "ChIPseeker" packages of R. "DiffBind" package was used for differential binding.
ScRNAseq data from cultured SF transfected with either control or HOTAIR targeting GapmeR (n = 3) were integrated with SF of publicly available datasets and two in-house datasets. R with Seurat package (version 4.0) was used. The standard Seurat protocol was followed and for the final integration we applied harmony within the Seurat workflow. First 30 PC’s were the defined dimensionality of the dataset and a resolution of 0.1 was set for the downstream clustering. Annotation of the different clusters were performed based on the expression or absence of known SF marker genes: CD55, THY1, CXCL12, POSTN, CD34 and MKI67.
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: xlsx file including normalized count and FPKM values for each sample
Supplementary_files_format_and_content: bed files including peak score
Supplementary_files_format_and_content: xlsx file with metadata

source_name: cultured synovial fibroblasts, transfected with CONTROL

extract_protocol:
Total RNA was isolated with the miRNeasy Mini kit (Qiagen) including on-column DNaseI digestion from SF silenced for HOTAIR and control (n = 3 each) 48h after. For measurements of H3K27me3 marks after HOTAIR silencing, SF pellets from OA knees transfected with GapmeR HOTAIR and GapmeR Control (n = 3 each) were prepared using the iDeal ChIP seq kit for Histones (Diagenode) with a shearing of 12 cycles (30′′ON 30′′OFF, Bioruptor Pico). 15’000 unsorted synovial cells (viability 60-88%) per patient were prepared for single cell analysis using the Chromium Single Cell 3’ Reagent kit (v3.1 chemistry; 10x Genomics).
Bulk RNAseq libraries were prepared using the Illumina TruSeq Stranded total RNA protocol; ChIPseq libraries were prepared using the MicroPLEX v2 protocol; scRNAseq libraries were prepared using the Chromium Single Cell 3’ Reagent kit (v3.1 chemistry; 10x Genomics)

treatment_protocol: Synovial fibroblasts were transfected with 50 nM antisense LNA HOTAIR GapmeR (Exiqon, Sequence: 5′-AGGCTTCTAAATCCGT-3′) using Lipofectamine 2000 (Invitrogen). Antisense LNA GapmeR Negative Control A (Cat No 300610) was used as transfection control.

value: cultured synovial fibroblast

value: transfected with Gapmer control

tag: localisation

value: Knee


title: SF_KD_HOTAIR_rep3_ChIPseq_H3K27me3

source_name: cultured synovial fibroblasts, transfected with HOTAIR

value: transfected with Gapmer Hotair


title: SF_control_rep2_ChIPseq_H3K27me3


title: SF_KD_HOTAIR_rep2_ChIPseq_H3K27me3


title: 8.18.21 4 2.25mm 45s

description: UMI Matrix


title: SF_control_rep1_ChIPseq_H3K27me3


title: 8.18.21 6 2.75mm 42s

description: UMI Matrix


title: 3.29.22 1 1.5mm 71s

description: UMI Matrix


title: 8.18.21 8 0.5mm 1s

description: UMI Matrix


title: HDF161_SIPS_rep_2

city: Heidelberg

first: Martin

last: Kos

address: Im Neuenheimer Feld 328

department: Biochemistry Center (BZH)

institute: University of Heidelberg

data_processing:
Illumina base calling
Reads were trimmed for adaptors using BBDuk and aligned to the human genome (GRCh38) using Geneious software
the coverage of 5' and 3' ends of the reads was counted using bedtools genomcov and bam alignment files
the RMS (methylation) scores were calculated in Excel, using the algorithm of Krogh et al., 2017, Nucleic Acids Research 44, 7884–7895.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel (xlsx) files with 5' and 3' end read coverage and calculated RMS scores for each donor. Summarized RMS scores for all experiments are in the file RiboMethSeq_Summary.xlsx

source_name: Primary dermal fibroblasts

growth_protocol: HDF cells were cultured in DMEM/Ham’s F-12 (1:1 mixture)

extract_protocol:
total RNA was isolated using TRI Reagent (Sigma Aldrich, Cat# T9424) following the manufacturer’s protocol.
5 μg total RNA was hydrolyzed in 50 mM Carbonate-Bicarbonate buffer pH 9.2 and 10 mM MgCl2 at 95°C for 5 min, then put on ice. RNA cleavage was stopped by addition of 2 μl of 0.5 M EDTA pH 8.0. The RNA was precipitated by addition of 1/10 volume of 3 M sodium acetate and 2 volumes of 100% ice-cold EtOH, washed with 70% ice-cold EtOH and resuspended in nuclease-free water. RNA fragments were separated on a denaturing 6% acryl.:bis (19:1), 8 M urea gel. The fragments in the size range of 20 to 40 nt were extracted from the gel. The 5´ ends of the RNA fragments were dephosphorylated with Shrimp Alkaline Phosphatase (rSAP, New England Biolabs Cat# M0371S) as described in the manufacturer’s protocol. The sequencing library was prepared using NEB SmallRNA for Illumina Kit (New England Biolabs) and sequenced as single-end reads in two technical replicas
small RNA RNA-Seq NEB for Illumina)

treatment_protocol: Cells were seeded at a density of 3,500 cells/cm² and left to attach to the surface overnight. The following day, stress treatment was started. 30% H2O2 stock solution (Sigma Aldrich Cat# H1009) was freshly diluted and added to the medium to a final concentration of 60-80 μM. After incubation at 37°C for one hour, the medium was replaced to remove residual H2O2. This hydrogen peroxide treatment was performed on four consecutive days, followed by two days break, another five consecutive days of treatment, and finally 5-6 days recovery.

value: Primary dermal fibroblasts

value: senescence induced by H2O2


title: 8.18.21 4 2.25mm 31s

description: UMI Matrix


title: 8.18.21 2 1.5mm 78s

description: UMI Matrix


title: 8.18.21 6 2.75mm 20s

description: UMI Matrix


title: HDF161_Quiescent_rep_2

treatment_protocol: grown until reaching confluence and becoming contact inhibited. The medium was exchanged once per week

value: confluent, contact inhibited


title: HDF161_Quiescent_rep_1


title: 8.18.21 4 2.25mm 2s

description: UMI Matrix


title: HDF161_Proliferating_rep_2

treatment_protocol: passaged two to three times a week

value: sub-confluent


title: 8.18.21 8 0.5mm 2s

description: UMI Matrix


title: 3.29.22 1 2.25mm 17s

description: UMI Matrix


title: 8.18.21 2 1.5mm 37s

description: UMI Matrix


title: 1.4.21 2 1.5mm 8s

description: UMI Matrix


title: 1.4.21 1 1.25mm 93s

description: UMI Matrix


title: HDF85_SIPS_rep_1


title: HDF85_Quiescent_rep_2


title: HDF85_SIPS_rep_2


title: HDF85_Quiescent_rep_1


title: 8.18.21 2 1.5mm 73s

description: UMI Matrix


title: HDF161_Proliferating_rep_1


title: HDF85_Proliferating_rep_2


title: 3.29.22 1 1.5mm 36s

description: UMI Matrix


title: HDF85_Proliferating_rep_1


title: 3.29.22 1 1.5mm 66s

description: UMI Matrix


title: SF_KD_HOTAIR_rep1_ChIPseq_H3K27me3


title: HDF161_SIPS_rep_1


title: HDF76_SIPS_rep_1


title: 8.18.21 8 0.5mm 90s

description: UMI Matrix


title: HDF76_SIPS_rep_2


title: HDF76_Quiescent_rep_2


title: 8.18.21 1 1.75mm 41s

description: UMI Matrix


title: HDF76_Quiescent_rep_1


title: 8.18.21 8 0.5mm 34s

description: UMI Matrix


title: HDF76_Proliferating_rep_2


title: 1.4.21 2 1.5mm 58s

description: UMI Matrix


title: 1.4.21 2.2 2.0mm 24s

description: UMI Matrix


title: 8.18.21 2 1.5mm 66s

description: UMI Matrix


title: HDF76_Proliferating_rep_1


title: FUUR1_7 48 hr

first: Jinxiu

last: Li

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

description:
13914X7
13914R_48hr_vs_0hr_results.xlsx

data_processing:
RTA v1.18.61 used for basecalling.
Trim adapters with cutadapt, Align to hg38 with STAR -2.7.5a
Generate count matrices with featureCounts and RSEM
Perform differential expression with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts, DeSeq2 results and normalized value for every gene and every sample

source_name: human cell line

extract_protocol:
Cells were lysed in Trizol Reagent (Ambion) and total RNA was purified with Direct-zol RNA Miniprep Plus Kit (Zymo Research) including DNase I treatment
Libarary was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: CB5083 treated

tag: time

value: 48 hours


title: 8.18.21 5 1.25mm 32s

description: UMI Matrix

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)

source_name: anther


title: FUUR1_6 24 hr

description:
13914X6
13914R_24hr_vs_0hr_results.xlsx

value: 24 hours


title: 8.18.21 8 0.5mm 12s

description: UMI Matrix


title: 8.18.21 1 1.75mm 5s

description: UMI Matrix


title: FUUR1_4 2 hr

description:
13914X4
Samples 13914X3 and 13914X4 were designed for a 2-hour treated group, which is too short for CB5083 treatment and no change was observed consequently. This group was not included in our study.

value: 2 hours


title: FUUR1_3 2 hr

description:
13914X3
Samples 13914X3 and 13914X4 were designed for a 2-hour treated group, which is too short for CB5083 treatment and no change was observed consequently. This group was not included in our study.


title: 8.18.21 2 1.25mm 54s

description: UMI Matrix


title: 7.21 5 0.75mm 66s

description: UMI Matrix


title: 8.18.21 8 0.5mm 70s

description: UMI Matrix


title: 3.29.22 1 1.5mm 41s

description: UMI Matrix


title: FUUR1_2 0 hr

value: Control

value: 0 hours


title: 8.18.21 5 1.25mm 56s

description: UMI Matrix


title: 8.18.21 2 1.0mm 22s

description: UMI Matrix


title: FUUR1_1 0 hr


title: ASPS_Human_soft_thigh_H3K4me1

data_processing:
Paired-end 75bp sequencing on an Illumina HiSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a combined normalized pileup signal

source_name: human ASPS tumor

extract_protocol:
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

value: human ASPS tumor


title: ASPS_Human_soft_thigh_input

value: input


title: 8.18.21 1 1.5mm 40s

description: UMI Matrix

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

value: anther

value: anther single cell


title: 7.21 5 0.75mm 92s

description: UMI Matrix


title: 1.4.21 2 1.5mm 66s

description: UMI Matrix


title: ASPS_Human_soft_thigh_H3K27me3


title: 10894_input


title: FUUR1_8 48 hr

description:
13914X8
13914R_48hr_vs_0hr_results.xlsx


title: 8.18.21 6 2.75mm 62s

description: UMI Matrix


title: 10894_H3K4me1


title: 8.18.21 2 1.75mm 50s

description: UMI Matrix


title: ASPS_Human_soft_thigh_H3K36me3


title: 8.18.21 8 0.5mm 57s

description: UMI Matrix


title: 8.18.21 1 1.5mm 35s

description: UMI Matrix


title: 10894_H3K36me3


title: 10894_H3K27ac


title: FUUR1_5 24 hr

description:
13914X5
13914R_24hr_vs_0hr_results.xlsx


title: 8.18.21 2 1.0mm 2s

description: UMI Matrix


title: 7.21 2 2.0mm 31s

description: UMI Matrix


title: 1.4.21 4 2.5mm 31s

description: UMI Matrix


title: Sms_2_RNA

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

data_processing:
Reads were aligned to the hg38 assembly of human genome using bowtie2 and tophat2.
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ATAC-seq and RNA-seq.
Peaks were called using peakdeck.
Raw counts were obtained using Htseq in genes for RNAseq or peaks for ATAC-seq.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Normalized_30_RNAseq_samples.txt
Supplementary_files_format_and_content: *_ATAC.narrowPeak

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit. RNA libraries were prepared for sequencing using standard Illumina protocols.
For ATAC-seq, nuclei were prepared from 50,000 cells for each transposition reaction. ATAC-seq sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.

tag: cancer type

value: B-ALL

value: cell line

tag: genotype/variation

value: CRLF2 Low


title: Sms_1_RNA

tag: cell type


title: 8.18.21 5 1.0mm 29s

description: UMI Matrix

tag: tissue

tag: genotype


title: 10894_H3K27me3


title: Mutz_2_RNA


title: 8.18.21 1 1.75mm 21s

description: UMI Matrix


title: 3.29.22 1 1.5mm 44s

description: UMI Matrix


title: Mutz_1_RNA


title: ASPS_Human_soft_thigh_H3K27ac


title: 8.18.21 5 1.0mm 14s

description: UMI Matrix


title: 8.18.21 6 2.75mm 58s

description: UMI Matrix


title: Call_4_RNA


title: Call_3_RNA


title: 1.4.21 4 2.5mm 8s

description: UMI Matrix


title: 3.29.22 2 3.0mm 11s

description: UMI Matrix


title: Call_1_RNA


title: ATAC_BALL_6

value: B-cell leukemia peripheral blood


title: 8.18.21 1 1.5mm 2s

description: UMI Matrix


title: ATAC_BALL_5


title: Call_2_RNA


title: 8.18.21 2 1.75mm 30s

description: UMI Matrix


title: 8.18.21 2 1.5mm 2s

description: UMI Matrix


title: ATAC_BALL_3


title: 8.18.21 3 2.5mm 45s

description: UMI Matrix


title: ATAC_CRLF2-High_7


title: ATAC_CRLF2-High_6


title: ATAC_BALL_4


title: ATAC_CRLF2-High_5


title: 8.18.21 10 3.0mm 50s

description: UMI Matrix


title: ATAC_CRLF2-High_3


title: 8.18.21 5 1.0mm 39s

description: UMI Matrix


title: ATAC_CRLF2-High_4


title: ATAC_CRLF2-High_2


title: 8.18.21 2 1.0mm 63s

description: UMI Matrix


title: 8.18.21 1 1.75mm 43s

description: UMI Matrix


title: 1.4.21 4 2.5mm 39s

description: UMI Matrix


title: ATAC_CRLF2-High_1


title: ATAC_BALL_2


title: 1.4.21 4 2.5mm 46s

description: UMI Matrix


title: 8.18.21 2 1.0mm 85s

description: UMI Matrix


title: 8.18.21 8 0.5mm 86s

description: UMI Matrix


title: ATAC_BALL_1


title: RNA_BALL_14

description:
CRLF2-High_14
Normalized_30_RNAseq_samples.txt


title: 3.29.22 1 1.5mm 12s

description: UMI Matrix


title: 8.18.21 8 0.5mm 45s

description: UMI Matrix


title: 8.18.21 2 1.0mm 30s

description: UMI Matrix


title: RNA_BALL_15

description:
CRLF2-High_15
Normalized_30_RNAseq_samples.txt


title: 8.18.21 3 2.75mm 9s

description: UMI Matrix


title: RNA_BALL_13

description:
CRLF2-High_13
Normalized_30_RNAseq_samples.txt


title: 8.18.21 2 1.5mm 1s

description: UMI Matrix


title: RNA_BALL_12

description:
CRLF2-High_12
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_11

description:
CRLF2-High_11
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_10

description:
CRLF2-High_10
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_8

description:
CRLF2-High_8
Normalized_30_RNAseq_samples.txt


title: 1.4.21 4 2.5mm 73s

description: UMI Matrix


title: 1.4.21 4 2.5mm 94s

description: UMI Matrix


title: 7.21 5 0.75mm 33s

description: UMI Matrix


title: RNA_BALL_9

description:
CRLF2-High_9
Normalized_30_RNAseq_samples.txt


title: 8.18.21 2 1.0mm 91s

description: UMI Matrix


title: RNA_BALL_7

description:
CRLF2-High_7
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_6

description:
CRLF2-High_6
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_5

description:
CRLF2-High_5
Normalized_30_RNAseq_samples.txt


title: 1.4.21 4 2.5mm 36s

description: UMI Matrix


title: 7.21 2 2.0mm 72s

description: UMI Matrix


title: 8.18.21 2 1.25mm 19s

description: UMI Matrix


title: 8.18.21 10 3.0mm 19s

description: UMI Matrix


title: 8.18.21 5 1.25mm 20s

description: UMI Matrix


title: RNA_BALL_2

description:
CRLF2-High_2
Normalized_30_RNAseq_samples.txt


title: RNA_BALL_4

description:
CRLF2-High_4
Normalized_30_RNAseq_samples.txt


title: 8.18.21 8 0.5mm 94s

description: UMI Matrix


title: RNA_BALL_3

description:
CRLF2-High_3
Normalized_30_RNAseq_samples.txt


title: RNA_CRLF2-High_15

description:
BALL_15
Normalized_30_RNAseq_samples.txt

value: CRLF2 High


title: RNA_BALL_1

description:
CRLF2-High_1
Normalized_30_RNAseq_samples.txt


title: 3.29.22 1 1.5mm 68s

description: UMI Matrix


title: RNA_CRLF2-High_14

description:
BALL_14
Normalized_30_RNAseq_samples.txt


title: 8.18.21 1 1.5mm 7s

description: UMI Matrix


title: 8.18.21 2 1.5mm 81s

description: UMI Matrix


title: RNA_CRLF2-High_13

description:
BALL_13
Normalized_30_RNAseq_samples.txt


title: 8.18.21 8 0.5mm 61s

description: UMI Matrix


title: 8.18.21 1 1.75mm 36s

description: UMI Matrix


title: 1.4.21 4 2.5mm 11s

description: UMI Matrix


title: RNA_CRLF2-High_8

description:
BALL_8
Normalized_30_RNAseq_samples.txt


title: RNA_CRLF2-High_9

description:
BALL_9
Normalized_30_RNAseq_samples.txt


title: RNA_CRLF2-High_10

description:
BALL_10
Normalized_30_RNAseq_samples.txt


title: 3.29.22 2 3.0mm 1s

description: UMI Matrix


title: RNA_CRLF2-High_11

description:
BALL_11
Normalized_30_RNAseq_samples.txt


title: 7.21 2 2.0mm 13s

description: UMI Matrix


title: 8.18.21 5 1.0mm 42s

description: UMI Matrix


title: RNA_CRLF2-High_7

description:
BALL_7
Normalized_30_RNAseq_samples.txt


title: 8.18.21 8 0.5mm 17s

description: UMI Matrix


title: 1.4.21 2 1.75mm 84s

description: UMI Matrix


title: RNA_CRLF2-High_6

description:
BALL_6
Normalized_30_RNAseq_samples.txt


title: RNA_CRLF2-High_5

description:
BALL_5
Normalized_30_RNAseq_samples.txt


title: 8.18.21 2 1.5mm 76s

description: UMI Matrix


title: RNA_CRLF2-High_3

description:
BALL_3
Normalized_30_RNAseq_samples.txt


title: 8.18.21 3 2.5mm 6s

description: UMI Matrix


title: 8.18.21 2 1.5mm 82s

description: UMI Matrix


title: RNA_CRLF2-High_2

description:
BALL_2
Normalized_30_RNAseq_samples.txt


title: RNA_CRLF2-High_12

description:
BALL_12
Normalized_30_RNAseq_samples.txt


title: 7.21 2 0.75mm 70s

description: UMI Matrix


title: RNA_CRLF2-High_1

description:
BALL_1
Normalized_30_RNAseq_samples.txt


title: 1.4.21 1 0.5mm 14s

description: UMI Matrix


title: 8.18.21 1 1.5mm 68s

description: UMI Matrix


title: 8.18.21 2 1.5mm 94s

description: UMI Matrix


title: 8.18.21 1 1.75mm 4s

description: UMI Matrix


title: 8.18.21 2 1.0mm 79s

description: UMI Matrix


title: 3.29.22 1 1.5mm 50s

description: UMI Matrix


title: RNA_CRLF2-High_4

description:
BALL_4
Normalized_30_RNAseq_samples.txt


title: 8.18.21 1 1.75mm 86s

description: UMI Matrix


title: 8.18.21 8 0.5mm 48s

description: UMI Matrix


title: 8.18.21 2 1.5mm 92s

description: UMI Matrix


title: Fb_LL2_16_rep2

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological duplicate group (drought stage) were calculated.
Supplementary_files_format_and_content: Excel sheet (SDataset1.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts, rpm for each sample and mean rpm for biological duplicates

organism: Flaveria bidentis

source_name: Leaf

growth_protocol: Flaveria bidentis (C4) and Flaveria robusta (C3) plants were grown in the green house for 36 days and in a controlled growth chamber (10 hr light, 22 ˚C / 14 hr dark, 20 ˚C) for 6 days

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 100 bp read length) on an Illumina HiSeq 2000 platform.

treatment_protocol: After two days under entrained (10 hr light, 14 hr dark) conditions, plants were subjected to two days of free-running (constant light) conditions

tag: time of the day

tag: zeitgeber time

tag: light regime

value: Light

tag: day/night anticipation

value: Subjective night (free-running)


title: Fb_LL2_12_rep1


title: Fb_LL3_00_rep1

value: Subjective day (free-running)


title: 8.18.21 1 2.5mm 48s

first: D.

last: Marchant

address: Gilbert Biological Sciences Building, 371 Serra Mall

institute: Stanford University

description: UMI Matrix


title: Fb_LL3_00_rep2


title: Fb_LL2_12_rep2


title: Fb_LL2_20_rep1


title: Fb_LL2_16_rep1


title: Fb_LL2_08_rep1


title: 7.21 2 0.75mm 11s

description: UMI Matrix


title: Fb_LL2_04_rep2


title: Fb_LL2_04_rep1


title: 8.18.21 2 1.5mm 3s

description: UMI Matrix


title: 8.18.21 5 1.25mm 4s

description: UMI Matrix


title: 3.29.22 1 1.5mm 45s

description: UMI Matrix


title: 1.4.21 3 0.5mm 56s

description: UMI Matrix


title: Fb_LL2_00_rep2


title: Fb_LL2_20_rep2


title: Fb_LL1_20_rep2


title: 8.18.21 2 1.25mm 17s

description: UMI Matrix


title: Fb_LL1_20_rep1


title: 8.18.21 10 3.0mm 25s

description: UMI Matrix


title: 8.18.21 2 1.5mm 52s

description: UMI Matrix


title: Fb_LL2_08_rep2


title: Fb_LL1_16_rep2


title: 7.21 5 0.75mm 10s

description: UMI Matrix


title: Fb_LL1_12_rep2


title: 8.18.21 2 1.5mm 56s

description: UMI Matrix


title: 8.18.21 8 0.5mm 41s

description: UMI Matrix


title: Fb_LL1_12_rep1


title: Fb_LL1_04_rep2

value: Day (free-running)


title: Fb_LL1_08_rep1


title: 1.4.21 4 2.5mm 93s

description: UMI Matrix


title: Fb_LL1_16_rep1


title: Fb_LL1_04_rep1


title: Fb_LL1_08_rep2


title: 1.4.21 2 2.5mm 28s

description: UMI Matrix


title: 8.18.21 2 1.5mm 30s

description: UMI Matrix


title: Fb_LL1_00_rep1


title: 1.4.21 4 2.5mm 6s

description: UMI Matrix


title: 8.18.21 2 1.75mm 75s

description: UMI Matrix


title: 8.18.21 2 1.5mm 60s

description: UMI Matrix


title: Fb_LL1_00_rep2


title: Fb_LL2_00_rep1


title: Fb_LD2_20_rep1

value: Dark

value: Night (entrained)


title: 8.18.21 5 1.25mm 40s

description: UMI Matrix


title: Fb_LD2_16_rep1


title: 8.18.21 1 2.5mm 73s

description: UMI Matrix


title: Fb_LD2_12_rep2


title: 1.4.21 4 2.5mm 56s

description: UMI Matrix


title: 8.18.21 5 1.0mm 83s

description: UMI Matrix


title: 8.18.21 8 0.5mm 67s

description: UMI Matrix


title: Fb_LD2_20_rep2


title: Fb_LD2_12_rep1


title: Fb_LD2_08_rep2

value: Day (entrained)


title: 8.18.21 1 1.75mm 24s

description: UMI Matrix


title: 8.18.21 1 2.5mm 42s

description: UMI Matrix


title: Fb_LD2_08_rep1


title: Fb_LD2_04_rep2


title: 8.18.21 8 0.5mm 44s

description: UMI Matrix


title: 8.18.21 1 2.5mm 25s

description: UMI Matrix


title: 3.29.22 1 1.25mm 39s

description: UMI Matrix


title: Fb_LD2_00_rep2


title: Fb_LD2_00_rep1


title: Fb_LD2_16_rep2


title: 8.18.21 5 1.25mm 3s

description: UMI Matrix


title: Fb_LD2_04_rep1


title: Fb_LD1_20_rep2


title: Fb_LD1_16_rep2


title: 8.18.21 8 0.5mm 65s

description: UMI Matrix


title: Fb_LD1_20_rep1


title: 8.18.21 1 1.5mm 91s

description: UMI Matrix


title: 3.29.22 1 2.75mm 74s

description: UMI Matrix


title: 8.18.21 1 1.75mm 10s

description: UMI Matrix


title: Fb_LD1_12_rep2


title: Fb_LD1_16_rep1


title: Fb_LD1_12_rep1


title: 8.18.21 8 0.5mm 7s

description: UMI Matrix


title: Fb_LD1_08_rep1


title: 8.18.21 5 1.0mm 76s

description: UMI Matrix


title: 8.18.21 7 0.5mm 15s

description: UMI Matrix


title: Fb_LD1_04_rep2


title: Fb_LD1_00_rep2


title: Fb_LD1_04_rep1