title: ms28_prophase_I_male_germ_cell_deg_rep1

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

data_processing:
For assessing whether 21PHAS are targeted by miR2118, the sequence of miR2118 was mapped to both ends of 21PHAS (±50 bp). All of identified 21-nt phasiRNAs were mapped to maize cDNA sequences downloaded from maize genetics and genomics database (AGPv4) using psRobot_tar (-ts 3.5 –fp 2 –tp 17) (Wu et al., 2012). Mispair score was calculated by psRobot using the following rules: (1) mismatches, gaps or bulges incur a penalty of +1; (2) G:U pairs incur a penalty of +0.5; (3) penalty scores outside the core base-paired region (2–17) are reduced by half. 21PHAS that pair with miR2118 with mispair scores ≤ 3.5 were selected as potential miR2118 targets. cDNA sequences that pair with 21-nt phasiRNAs with mispair scores ≤ 3.5 were selected as potential 21-nt phasiRNA targets. The 5′-ends of degradome tags derived from 21-nt phasiRNA- or miR2118-directed cleavage products should precisely match the 10th nucleotide of 21-nt phasiRNA/miR2118 complementary sites. Such tags were searched in the degradome libraries using psRobot_deg (Wu et al., 2012). All hit transcripts were categorized based on the abundance of the diagnostic cleavage tag relative to the overall profile of degradome tags matching the target essentially as previously described (Addo-Quaye et al., 2009). Category 4, 1 degradome tag at the cleavage site; Category 3, degradome tags at the cleavage site >1, but ≤ the average number of degradome tags on the transcript; Category 2, degradome tags at the cleavage site >1, above the average but not the maximum on the transcript; Category 1, degradome tags at the cleavage site >1, equal to the maximum on the transcript, but there are >1 sites at the maximum value; Category 0, >1 degradome tags, equal to the maximum on the transcript, and there is only 1 site at the maximum value. Category 0, Category 1 or Category 2 transcripts in each sample that have ≥4 degradome tags at predicted miR2118 cleavage site, which account for ≥10% of the total degradome tags along the transcript, were annotated as miR2118 targets. Category 0 or Category 1 transcripts in each sample that have ≥4 degradome tags at predicted 21-nt phasiRNA cleavage site, which account for ≥10% of the total degradome tags along the transcript, were annotated as 21-nt phasiRNA targets. It was subsequently determined whether the 21-nt phasiRNA targets identified in an anther or male germ cell sample had cleavage signals at other developmental stages. For example, if a transcript was annotated as a 21-nt phasiRNA target in premeiotic anthers, we would check whether it had cleavage signals in prophase I anthers and tetrad/microspore-stage anthers. Even if it is not a Category 0 or Category 1 transcript but has ≥4 degradome tags at predicted 21-nt phasiRNA cleavage site, which account for ≥10% of the total degradome tags along the transcript, and fell into Category 2 in prophase I anthers or tetrad/microspore-stage anthers, the transcript was also considered as a 21-nt phasiRNA target in prophase I anthers or tetrad/microspore-stage anthers. The principle was applied to each anther sample or male germ cell sample. Counts of cleavage at 21-nt phasiRNA-directed cleavage sites in each library were calculated as RP10M (reads per 10 million) based on the total count of genome-matched reads in that library.
Assembly: Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary files format and content: our provided files contain clean small RNA sequences and their counts.
Library strategy: degradome-seq

organism: Zea mays

source_name: Germ cells

growth_protocol: Maize seeds of B73 and ms28 were sterilized with 2% NaClO containing 0.05% Tween-20 for 3h. The seeds were germinated and grown in either a paddy field in Shangzhuang District, Beijing, China (116.20°, 40.15°) from May to October or in a greenhouse with 40% humidity and daily cycles of 14 h of light at 32 °C and 10 h of dark at 26 °C.

extract_protocol:
Total RNA was isolated from embryos, anthers and male germ cells using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content (Kim et al., 2012). NaAc (pH 5.2) and glycogen were added to promote RNA precipitation. The extracted RNA was stored at −80°C in LoBind tubes (Eppendorf, 022431021).
Degradome sequencing was performed as previously described (Jiang et al., 2020). In brief, total RNA was ligated to 5’ RNA adapter with a MmeI recognition site at its 3′-end. After ligation, first-strand cDNA was reversely transcribed, purified with 2× AMPure XP beads (v/v) (Beckman, A63880), and amplified by PCR with 5’-biotin labeled forward primer and regular reverse primer. The amplified products were digested with ExoI and purified with 2× AMPure XP beads (v/v) (Beckman, A63880). The purified products were digested with Mmel (NEB, R0637L) and purified with Dynabeads MyOne Streptavidin C1 beads (Invitrogen, 65001). The DNA products bound to beads were used as templates for PCR with index-containing primers. The ~140-bp products were gel-purified and sequenced on an Illumina HiSeqX-Ten platform with specific sequencing primer (5’-CTACACGTTCAGAGTTCTACAGTCCGAC-3’) by Annoroad Gene Technology (Beijing).

value: Germ cells

tag: developmental stage

value: Prophase I


title: nanopore_ribo_minus_HS_rep1

status: Public on May 26 2025

type: SRA

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
First, we used Pychopper (v2.5.0, obtained from GitHub repository at https://github.com/epi2me-labs/pychopper) with parameters -Q 7 -z 50 to identify, orient and trim full-length nanopore cDNA reads. After the Pychopper step, the trimmed full-length reads from each sample were aligned to the CHM13 T2T human reference genome (V2.0, downloaded from GitHub repository at https://github.com/marbl/CHM13 in 2022.08) by using Minimap2 (v2.11). Next, we chose the FLAIR pipeline (v1.7.0) to identify specific transcripts from uniquely-mapped reads. Finally, the quantify module of FLAIR was applied to quantitate SatIII RNA expression in each sample.
Assembly: CHM13 T2T v2.0
Supplementary files format and content: text files include raw counts  in each sample for poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include raw counts  in each sample for ribo- nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from  poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from ribo- nanopore  RNA-seq.
Library strategy: Ribo-Seq

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

extract_protocol:
For polyadenylated nanopore RNA-seq, HeLa cells were plated onto 6-well plates. The next day, cells were performed SA, HS or control treatment Cells were washed in DPBS and prepared for RNA extraction according to the RNeasy protocol (Qiagen). For rRNA-depleted (ribo-) nanopore RNA-seq, HeLa cells were plated onto 6-well plates. The next day, cells were performed SA, HS or control treatment. Total RNAs were subjected to rRNA removal using the Ribo-off rRNA Depletion Kit.
For polyadenylated nanopore RNA-seq, the preparation of long-read cDNA library was followed the strand-switching protocol from Oxford Nanopore Technologies. Briefly, the cDNA-PCR Sequencing kit by Oxford Nanopore (SQK-PCS109) was used to prepare full-length cDNA libraries from the polyadenylated RNAs. Then the cDNA was amplified by PCR for 13–14 cycles with specific barcoded adapters from the Oxford Nanopore PCR Barcoding kit (SQKPBK004). Finally, the 1D sequencing adapter was ligated to the cDNA prior to loading onto a R9.4.1 FLO PRO002 flow cell for sequencing on a PromethION platform. Base calling of 1D PromethION reads was done with guppy v5.0.16 with the default options. For rRNA-depleted (ribo-) nanopore RNA-seq, adapters were ligated to the 3' ends of the rRNA-depleted RNAs using a ligase enzyme, then the ligation products were purified with RNA Clean beads (Vazyme). Subsequently, reverse transcription primers were annealed to the 3' end adapters of the RNAs, and TSO (Template Switching Oligo) sequences and reverse transcriptase were added to the annealed products to generate full-length cDNA. Following this, barcoded adapters from the Oxford Nanopore PCR Barcoding kit (SQKPBK004) were used for PCR amplification and labeling of different cDNA products, with 13-14 amplification cycles. The amplified products were processed for library construction according to the Oxford Nanopore Ligation Sequencing kit (SQK-LSK110). Finally, the final library was loaded onto an R9.4.1 FLO PRO002 flow cell and sequenced on a PromethION platform.

tag: cell line

value: HeLa

tag: treatment

value: HS stressed


title: E15.5 Wild Type scRNA-Seq Replicate 1

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

country: USA

institute: Johns Hopkins University

description:
Library name: TK67
10x Genomics scRNA-Seq

library_source: transcriptomic single cell

data_processing:
For sc/snRNA-Seq:Libraries for scRNA-Seq and snRNA-Seq were prepared using the 10x Genomics Chromium. Single Cell 3’ v3.0 and v3.1 platforms (Table S1), following the manufacturer’s protocols. Sequencing was conducted on an Illumina NovaSeq 6000, targeting a depth of 500 million reads per sample. Raw data were processed with the 10x Genomics Cell Ranger Software (v5) and aligned to the mm10 mouse genome reference (refdata-gex-mm10-2020-A).
For scATAC-Seq: scATAC-Seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC v1.1 platform (Table S1), with one-hour tagmentation and 9-10 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000, at a target depth of 600 million reads per sample. Raw data were processed with Cell Ranger ATAC (v2) and aligned to the mm10 mouse genome reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).
Assembly: mm10
Supplementary files format and content: sc/snRNA-Seq: matrix file in H5 format
Supplementary files format and content: scATAC-Seq: inside zip file contains matrix file (H5 format), fragments.tsv, singlecell.csv

organism: Mus musculus

source_name: Hypothalamus and Prethalamus

extract_protocol:
Animal model  Time-mated wild-type (WT) CD1 mice were obtained from Charles River Laboratories. Transgenic mouse lines were maintained on a mixed C67BL6/CD1 background. The following transgenic mouse lines were used in the study:  1) Foxd1-Cre (B6;129S4-Foxd1tm1(GFP/cre)Amc/J, JAX#012463), 2) Isl1-flox (gift from Dr. Lin Gan, (Pan et al. 2008)), 3) Lhx1-flox gift from Dr. Richard R Behringer (Kwan and Behringer 2002), 4) Nkx2.2-Cre (B6.129S6(Cg)-Nkx2-2tm4.1(cre/EGFP)Suss/J, JAX#026880), 5) Dlx1/2-flox (gift from Dr. Jay Lee, (B. Lee et al. 2018)).  Animals were housed in a temperature-controlled facility with a 14-hour dark/10-hour light cycle and had ad libitum access to food and water. All animal procedures followed the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the Johns Hopkins University Animal Care and Use Committee.
Tissue Collection and Dissections  Dissection of WT Mice  Tissues were collected from WT mice representing a random but equal mix of males and females across postnatal ages. For embryonic stages, 10-30 embryos were harvested from 3-4 pregnant dams, depending on the gestational age. Brain dissections followed previously established protocols(D. W. Kim et al. 2020). Meninges were removed, and dissections were completed in cold HBSS (#14170112, ThermoFisher Scientific) within 30 minutes for each age group.  Dissection of Mutant Mice  Embryos from mutant mice were collected from a minimum of five pregnant dams. Hypothalamic and prethalamic regions were dissected, and the remaining tissues of embryos were used for rapid genotyping (#4359187, Thermo Fischer Scientific), and grouped by genotype for further analysis. Dissected hypothalamic and prethalamic tissues were stored in HABG buffer (Hibernate-E (#A1247601, Thermo Fisher Scientific) for embryos or Hibernate-A (#A1247501, Thermo Fisher Scientific) for postnatal stages, both supplemented with 2% B-27 Supplement (#17504044, Thermo Fischer Scientific), and 0.5 mM GlutaMAX Supplement (#35050061, Thermo Fisher Scientific) until cell dissociation.   Preparations of cells and nuclei  Cell Dissociation for scRNA-Seq  To prepare samples for scRNA-Seq, tissues were dissociated in Hibernate medium (Hibernate-E Minus Calcium (#HECA500, BrainBits) for embryos or Hibernate-A Minus Calcium (#HACA500, BrainBits) for postnatal stages), supplemented with 2 mg/ml papain (#LS003119, Worthington Biochemical) and 0.5 mM Glutamax. The enzyme mixture was pre-incubated for 15 minutes, then added to tissues for 5 - 30 minutes with 0.1 U/μl RNase inhibitor (N2615, Promega). Toward the end of digestion, 100 μg/ml final DNase I (#4716728001, Sigma-Aldrich) was added. Cells were subsequently centrifuged, resuspended in HABG buffer, filtered through a 40 μm cell strainer (BAH136800040-50EA, Sigma-Aldrich), and resuspended in HABG buffer containing RNase inhibitor (0.5 U/μl). Cell viability and counts were assessed with Trypan Blue staining (#15250061, Thermo Fisher Scientific) and a hemocytometer.  Nuclei Preparation for scATAC-Seq  Nuclei for scATAC-Seq were extracted following post-cell dissociation and purified following a 10x Genomics protocol. Nuclei count and yield were verified with Trypan Blue staining and a hemocytometer.  Nuclei Preparation for snRNA-Seq  For snRNA-Seq, adult mouse brains were rapidly dissected, and 100 um coronal sections were prepared using a mouse brain matrice. Regions spanning the ZI, TRN, and thalamus were microdissected under a dissection microscope. Nuclei were extracted following a 10x Genomics protocol.
Sequencing Library Preparation and Data Processing  sc/snRNA-Seq  Libraries for scRNA-Seq and snRNA-Seq were prepared using the 10x Genomics Chromium. Single Cell 3’ v3.0 and v3.1 platforms (Table S1), following the manufacturer’s protocols. Sequencing was conducted on an Illumina NovaSeq 6000, targeting a depth of 500 million reads per sample. Raw data were processed with the 10x Genomics Cell Ranger Software (v5) and aligned to the mm10 mouse genome reference (refdata-gex-mm10-2020-A).  scATAC-Seq  scATAC-Seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC v1.1 platform (Table S1), with one-hour tagmentation and 9-10 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000, at a target depth of 600 million reads per sample. Raw data were processed with Cell Ranger ATAC (v2) and aligned to the mm10 mouse genome reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).

tag: tissue

value: Hypothalamus and Prethalamus

tag: library type

value: scRNA-Seq

tag: age

tag: strain

tag: genotype

value: Wild Type

tag: Sex

value: pooled male and female


title: E18.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK70
10x Genomics scRNA-Seq


title: B73_tetrad_male_germ_cell_deg_rep2

institute: Tsinghua University

value: Tetrad


title: E14.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK66
10x Genomics scRNA-Seq


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 24h, replicate 2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
Library name: Sample 77
C28

data_processing:
Raw RNA-Seq reads were trimmed for low-quality bases (Phred quality score < 20) and Illumina sequencing adapters using Cutadapt (v4.4). Reads shorter than 60 bases post-trimming were discarded.
Alignment of the trimmed sequencing reads to the Genome Reference Consortium Human Build (GRCh38) Ensembl version 110 was performed using HISAT2 (v2.2.1) with default settings.
Bam files were filtered for uniquely mapped reads (as flagged by "NH:i:1") and sorted by coordinates using Samtools (v1.18).
Read summarisation was conducted with the featureCounts function from the Rsubread package (v2.16.1) against the Ensembl GTF file version 110
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the bleomycin experiment
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the TGF-beta experiment

molecule: polyA RNA

source_name: HUVEC

growth_protocol: Human umbilical cord blood vein cells (HUVEC) were cultured in Endothelial Cell Growth Medium- 2 (EGM-2, Promocell #C-22011) at +37°C, and 5% CO2. Prior to the experiment, cells were expanded in T-75 flasks for 1-2 passages. For the experiments, passages 6-8 were used and cells were plated on 12-well plates with a density of 40 000 cells/cm2. Cells were settled for 24h prior to experimentation.

extract_protocol:
RNA was extracted from cells after 24h, 48h, and 72h of exposure using the RNeasy Mini kit (Qiagen). DNase 1 (Thermo Scientific, EN0521) treatment was used prior to downstream analyses.
RNA-Seq libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042) including polyA-tailed mRNA enrichment. RNA-Seq was performed in two batches i.e., the two exposure experiments of bleomycin and TGF-beta, respectively.

treatment_protocol: Cells were exposed to concentrations of 7, 14, and 21 µg/ml bleomycin or to concentrations of  5, 10, 20 ng/ml TGF-beta. Samples were taken 24h, 48h, and 72h after the start of exposure and from unexposed cells. The two different exposures, bleomycin and TGF-beta, were performed in two different experiments with each having their own controls (unexposed cells).

value: HUVEC

tag: cell type

value: umbilical vein endothelial cells

value: wildtype

value: 0 ng/ml TGF-beta

tag: time


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 24h, replicate 4

description:
Library name: Sample 78
C29

value: 20 ng/ml TGF-beta


title: nanopore_ribo_minus_UN_rep2

value: untreated


title: nanopore_ribo_minus_UN_rep1


title: E14.5 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK65
10x Genomics scRNA-Seq


title: B73_tetrad_male_germ_cell_deg_rep1


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 24h, replicate 3

description:
Library name: Sample 76
C25

value: 5 ng/ml TGF-beta


title: B73_microspore_male_germ_cell_deg_rep2

value: Microspore


title: E13.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK100
10x Genomics scRNA-Seq


title: nanopore_polya_plus_SA_rep2

data_processing:
First, we used Pychopper (v2.5.0, obtained from GitHub repository at https://github.com/epi2me-labs/pychopper) with parameters -Q 7 -z 50 to identify, orient and trim full-length nanopore cDNA reads. After the Pychopper step, the trimmed full-length reads from each sample were aligned to the CHM13 T2T human reference genome (V2.0, downloaded from GitHub repository at https://github.com/marbl/CHM13 in 2022.08) by using Minimap2 (v2.11). Next, we chose the FLAIR pipeline (v1.7.0) to identify specific transcripts from uniquely-mapped reads. Finally, the quantify module of FLAIR was applied to quantitate SatIII RNA expression in each sample.
Assembly: CHM13 T2T v2.0
Supplementary files format and content: text files include raw counts  in each sample for poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include raw counts  in each sample for ribo- nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from  poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from ribo- nanopore  RNA-seq.

value: SA stressed


title: nanopore_polya_plus_SA_rep1


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 24h, replicate 1

description:
Library name: Sample 74
C21

value: 10 ng/ml TGF-beta


title: E13.5 Wild Type scRNA-Seq Replicate 1

description:
Library name: TKX
10x Genomics scRNA-Seq


title: ms28_prophase_I_male_germ_cell_deg_rep2

value: Germ cells

value: Prophase I


title: E12.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK60
10x Genomics scRNA-Seq

value: Hypothalamus and Prethalamus


title: B73_microspore_male_germ_cell_deg_rep1


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 24h, replicate 2

description:
Library name: Sample 73
C1


title: B73_prophase_I_male_germ_cell_deg_rep2


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 24h, replicate 3

description:
Library name: Sample 75
C24


title: E12.5 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK59
10x Genomics scRNA-Seq

value: scRNA-Seq


title: B73_prophase_I_male_germ_cell_deg_rep1


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 24h, replicate 1

description:
Library name: Sample 72
C19


title: nanopore_polya_plus_HS_rep1

value: HeLa

value: HS stressed


title: nanopore_polya_plus_UN_rep2


title: E11.5 Wild Type scRNA-Seq

description:
Library name: TK64
10x Genomics scRNA-Seq

value: Wild Type

value: pooled male and female


title: B73_tetrad_microspore_deg_rep2

source_name: Anthers

value: Anthers

value: Tetrad/Microspore


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 72h, replicate 4

description:
Library name: Sample 71
C180

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype


title: B73_tetrad_microspore_deg_rep1


title: nanopore_polya_plus_HS_rep2


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 72h, replicate 4

description:
Library name: Sample 70
C178

value: 20 ng/ml TGF-beta


title: wat, Sham, rep3

city: Jena

first: Zhengyuan

last: Zhou

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz-HKI

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: wat

extract_protocol:
Nucleus isolation of tissue samples was done as previously described. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel.
We prepared single-nucleus RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).We prepared single nucleus suspensions from cultured cell lines and nuclei were suspended in PBS containing 0.04% BSA.The nuclei suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation. Captured nuclei were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per nucleus and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: wat

value: male

value: 20-24 weeks

value: Sham


title: wat, Sham, rep2


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 72h, replicate 4

description:
Library name: Sample 69
C177

value: 0 ng/ml TGF-beta


title: ms28_prophase_I_anther_deg_rep1

value: Prophase I


title: wat, Sham, rep1


title: WT zebrafish neurons

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

description: Library name: CEL221031AN_WT_18h

data_processing:
using Cell Ranger (version 3.1.0; 10X Genomics, Pleasanton, CA. USA)
Assembly: ZebraFishGRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: neuron

extract_protocol:
Twenty-two old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: neuron

value: mixed


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 72h, replicate 4

description:
Library name: Sample 68
C174

value: 5 ng/ml TGF-beta


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 72h, replicate 3

description:
Library name: Sample 67
C173


title: wat, CLP, rep3

value: CLP


title: B73_prophase_I_anther_deg_rep2


title: B73_prophase_I_anther_deg_rep1


title: wat, CLP, rep2


title: B73_premeiotic_anther_deg_rep4

value: Premeiotic


title: wat, CLP, rep1


title: B73_premeiotic_anther_deg_rep3

value: Anthers


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 24h, replicate 1

description:
Library name: Sample 65
C16


title: B73_premeiotic_anther_deg_rep2


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 72h, replicate 3

description:
Library name: Sample 64
C168


title: nanopore_polya_plus_UN_rep1

value: HeLa

value: untreated


title: ms28_prophase_I_anther_deg_rep2


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 72h, replicate 3

description:
Library name: Sample 63
C165

value: HUVEC

value: umbilical vein endothelial cells


title: liver, Sham, rep3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0.
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: liver

extract_protocol:
Nucleus isolation of tissue samples was done as previously described. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel.
We prepared single-nucleus RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller (10× Genomics). We prepared single nucleus suspensions from cultured cell lines and nuclei were suspended in PBS containing 0.04% BSA. The nuclei suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s recommendation. Captured nuclei were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol. The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per nucleus and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: liver

value: sham


title: liver, Sham, rep2

value: male


title: B73_premeiotic_anther_deg_rep1


title: liver, Sham, rep1


title: PC9-SORA-OSIM-2d-3

type: RNA

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

description: Sorafenib and Osimertinib co-treated (2 days) PC9 cell line - Replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 072363_D_F_20150612).
Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded.
Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies).

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 5.7±0.6 μg cRNA and specific activity was 9.9±1.0 pmol Cy3 per μg cRNA.

growth_protocol: PC9 cells (NSCLC) were obtained from ECACC (distributed by Sigma-Aldrich). PC9 cells were grown in RPMI1640 (2Mm L-Glutamine + 25 mM HEPES) supplemented with 10% FBS.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: PC9 cells were treated in triplicate with or without osimertinib (1 µM) and/or sorafenib (5 µM) for 1, 2 or 4 days (for the longest time point, the media was renewed after 2 days).

value: Sorafenib and Osimertinib - 2 days


title: PC9-OSIM-4d-3

description: Osimertinib-treated (4 days) PC9 cell line - Replicate 3

value: Osimertinib - 4 days


title: PC9-SORA-OSIM-2d-1

description: Sorafenib and Osimertinib co-treated (2 days) PC9 cell line - Replicate 1


title: PC9-OSIM-4d-2

description: Osimertinib-treated (4 days) PC9 cell line - Replicate 2


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 72h, replicate 2

description:
Library name: Sample 62
C162

value: wildtype

value: 20 ng/ml TGF-beta


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 72h, replicate 1

description:
Library name: Sample 61
C161


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 72h, replicate 3

description:
Library name: Sample 66
C170

value: 10 ng/ml TGF-beta


title: ms28_prophase_I_male_germ_cell_sRNA_rep1

data_processing:
For data analysis, adaptors and low-quality reads were removed using cutadapt3.5. Clean 18–30-nt reads were mapped to the maize B73 reference genome AGPv4 using bowtie v1.3.1, allowing no mismatches. Genome-matched reads from different samples were merged. 21PHAS were identified and characterized by PhaseTank as previously described (Guo et al., 2015). RPM (reads per million) values of 21-nt phasiRNAs were calculated based on the total count of genome-matched reads in that library.
Assembly: Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary files format and content: our provided files contain clean small RNA sequences and their counts.

extract_protocol:
Total RNA was isolated from embryos, anthers and male germ cells using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content (Kim et al., 2012). NaAc (pH 5.2) and glycogen were added to promote RNA precipitation. The extracted RNA was stored at −80°C in LoBind tubes (Eppendorf, 022431021).
Libraries for small RNA sequencing were constructed as previously described (Yang et al., 2016). In brief, total RNA was ligated to 3′ adaptor with adenylation using T4 RNA ligase 2, truncated KQ (NEB, M0373L). Following annealing with reverse transcription primer, RNA was ligated to 5′ RNA adaptor using T4 RNA ligase 1 (NEB, M0204L). After reverse transcription and PCR amplification, 135–160-bp products were gel-purified and sent for sequencing. Libraries were pair-end sequenced with Illumina Nova platform by Annoroad Gene Technology (Beijing).
sRNA-seq

value: Germ cells

value: Prophase I


title: PC9-OSIM-4d-1

description: Osimertinib-treated (4 days) PC9 cell line - Replicate 1


title: PC9-SORA-OSIM-2d-2

description: Sorafenib and Osimertinib co-treated (2 days) PC9 cell line - Replicate 2


title: PC9-OSIM-2d-3

description: Osimertinib-treated (2 days) PC9 cell line - Replicate 3

value: Osimertinib - 2 days


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 72h, replicate 2

description:
Library name: Sample 60
C160


title: liver, CLP, rep2

value: CLP


title: B73_tetrad_male_germ_cell_sRNA_rep2

value: Tetrad


title: liver, CLP, rep1


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 72h, replicate 2

description:
Library name: Sample 59
C157

value: 0 ng/ml TGF-beta


title: B73_tetrad_male_germ_cell_sRNA_rep1


title: PC9-OSIM-2d-2

description: Osimertinib-treated (2 days) PC9 cell line - Replicate 2


title: B73_microspore_male_germ_cell_sRNA_rep2

value: Microspore


title: kidney, Sham, rep2

source_name: kidney

extract_protocol:
Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel. Nucleus isolation of tissue samples was done as previously described109. Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with a 5 ml nuclei suspension buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted. A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel.
We prepared single-nucleus RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).We prepared single nucleus suspensions from cultured cell lines and nuclei were suspended in PBS containing 0.04% BSA.The nuclei suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation. Captured nuclei were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per nucleus and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: kidney

value: Sham


title: ms28_prophase_I_male_germ_cell_sRNA_rep2


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 72h, replicate 1

description:
Library name: Sample 58
C156

value: HUVEC

value: umbilical vein endothelial cells


title: PC9-OSIM-1d-2

description: Osimertinib-treated (1 day) PC9 cell line - Replicate 2

value: Osimertinib - 1 day


title: B73_microspore_male_germ_cell_sRNA_rep1


title: PC9-OSIM-2d-1

description: Osimertinib-treated (2 days) PC9 cell line - Replicate 1


title: kidney, CLP, rep3

value: male


title: PC9-OSIM-1d-3

description: Osimertinib-treated (1 day) PC9 cell line - Replicate 3


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 24h, replicate 2

description:
Library name: Sample 54
C13


title: liver, CLP, rep3

value: liver


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 72h, replicate 2

description:
Library name: Sample 57
C154

value: wildtype

value: 5 ng/ml TGF-beta


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 72h, replicate 1

description:
Library name: Sample 55
C150


title: kidney, CLP, rep2


title: B73_tetrad_microspore_anther_sRNA_rep2

value: Anthers

value: Tetrad/Microspore


title: B73_prophase_I_male_germ_cell_sRNA_rep2

value: Germ cells

value: Prophase I


title: PC9-OSIM-1d-1

description: Osimertinib-treated (1 day) PC9 cell line - Replicate 1


title: kidney, CLP, rep1

value: CLP


title: kidney, Sham, rep3


title: B73_tetrad_microspore_anther_sRNA_rep1


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 24h, replicate 1

description:
Library name: Sample 53
C12

value: 20 ng/ml TGF-beta


title: PC9-SORA-4d-1

description: Sorafenib-treated (4 day) PC9 cell line - Replicate 1

source_name: Sorafenib-treated (4 day) PC9 cell line

value: Sorafenib - 4 days


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 24h, replicate 4

description:
Library name: Sample 52
C11

value: 10 ng/ml TGF-beta


title: brain, Sham, rep3

source_name: brain

value: brain

value: sham


title: B73_premeiotic_anther_sRNA_rep2

value: Premeiotic


title: brain, Sham, rep2


title: kidney, Sham, rep1

value: kidney

value: Sham


title: PC9-SORA-4d-3

description: Sorafenib-treated (4 day) PC9 cell line - Replicate 3


title: PC9-SORA-4d-2

description: Sorafenib-treated (4 day) PC9 cell line - Replicate 2


title: B73_prophase_I_male_germ_cell_sRNA_rep1


title: PC9-SORA-2d-3

description: Sorafenib-treated (2 days) PC9 cell line - Replicate 3

value: Sorafenib - 2 days


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 48h, replicate 1

description:
Library name: Sample 51
C103

value: HUVEC

value: umbilical vein endothelial cells


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 48h, replicate 1

description:
Library name: Sample 50
C101

value: wildtype


title: brain, Sham, rep1

value: male


title: ms28_prophase_I_anther_sRNA_rep2

value: Anthers


title: PC9-SORA-2d-2

description: Sorafenib-treated (2 days) PC9 cell line - Replicate 2


title: ms28_prophase_I_anther_sRNA_rep1


title: brain, CLP, rep3

value: cecal ligation and puncture (CLP)


title: brain, CLP, rep2


title: HUVEC cells exposed to 7 µg/ml bleomycin for 72h, replicate 4

description:
Library name: Sample 48
H_149

value: 7 µg/ml bleomycin


title: PC9-SORA-2d-1

description: Sorafenib-treated (2 days) PC9 cell line - Replicate 1


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 48h, replicate 1

description:
Library name: Sample 49
C100

value: 0 ng/ml TGF-beta


title: B73_prophase_I_anther_sRNA_rep2

value: Prophase I


title: PC9-SORA-1d-3

description: Sorafenib-treated (1 day) PC9 cell line - Replicate 3

source_name: Sorafenib-treated (1 day) PC9 cell line

value: Sorafenib - 1 day


title: HUVEC cells exposed to 0 µg/ml bleomycin for 72h, replicate 4

description:
Library name: Sample 47
H_146

value: 0 µg/ml bleomycin


title: brain, CLP, rep1

value: brain


title: PC9-SORA-1d-2

description: Sorafenib-treated (1 day) PC9 cell line - Replicate 2


title: gd T cells and ILCs, Salmonella typhimurium, GEX

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
The Cell Ranger Pipeline (version 6.0.1) to perform quality control, sample demultiplexing, barcode processing, alignment and gene counting.
Downstream analysis was performed in RStudio using Seurat Version 4.1 and Signac 1.5.
Assembly: mm10; Added ZsGreen (Zfp506) to mm10 genome
Supplementary files format and content: CellRanger mRNA output files: features.tsv.gz, matrix.mtx.gz, barcodes.tsv.gz
Supplementary files format and content: CellRanger ATAC output files: fragments.tsv.gz, fragments.tsv.gz.tbi, filtered_feature_bc_matrix.h5, per_barcode_metrics.csv

source_name: colon

extract_protocol:
The large intestine was fileted lengthwise, cut into 1 cm pieces, and transferred into PBS containing 1 mM DTT with shaking to remove mucus. Intestine pieces then underwent two rounds of incubation in PBS supplemented with 1 mM HEPES and 5 mM EDTA at 37°C with shaking to remove the epithelium, followed by washing with HBSS supplemented with 10% FBS. Digestion was performed by mincing tissue pieces in HBSS supplemented with 10% FBS, collagenase D (1 mg/mL), DNAseI (0.1 mg/mL), and dispase (0.1 U/mL) followed by incubation for 30 min at 37°C with shaking. The resulting cell suspension was filtered through a 100 μm cell strainer, followed by a discontinuous 40:80 Percoll gradient to remove large cells and debris. Cells were then collected from the interphase, washed, and resuspended in PBS for staining for the sort.
Total gd T cells (CD90+ CD3+ gdTCR+) were isolated and sorted from the coLP of 96 hour S. typhimurium-infected mice (sample pooled from 5 mice), and “naïve” Streptomycin-only treated mice (sample pooled from 4 mice). Total coLP ILCs (CD3- CD127+ CD90+) were also sorted from the same infected and naïve samples, and gd T cells and ILCs were combined for multiome assay.
Protocol for Single cell Multiome ATAC + Gene Expression v1 chemistry (https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevF.pdf)
Single cell Multiome ATAC + Gene Expression v1 chemistry was used. The naïve sample had 6,399 cells sequenced and the S. typhimurium sample had 6,510 cells sequenced.

treatment_protocol: Mice in both naïve and infection groups were fasted for four hours, followed by oral gavage with 20 mg of Streptomycin (Sigma-Aldrich) in 200ul of PBS. 20 hours later mice were fasted again for four hours. For infection, 5x107 colony forming units (CFU) of Salmonella typhimurium (Strain SL1344) in 200ul PBS were orally gavaged. 200ul of PBS was gavaged for naïve controls. Approximately 96 hours post infection, mice were euthanized and tissues were harvested.

value: colon

value: gd T cells and ILCs

value: RORcre Rosa26-lox-Stop-lox-ZsGreen

value: day 4 post Salmonella infection


title: HUVEC cells exposed to 21 µg/ml bleomycin for 72h, replicate 4

description:
Library name: Sample 46
H_144

value: 21 µg/ml bleomycin


title: B73_prophase_I_anther_sRNA_rep1


title: B73_embryo_sRNA_rep2

source_name: embryo

value: embryo


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 72h, replicate 1

description:
Library name: Sample 56
C152

value: HUVEC

value: umbilical vein endothelial cells

value: 10 ng/ml TGF-beta


title: PC9-SORA-1d-1

description: Sorafenib-treated (1 day) PC9 cell line - Replicate 1


title: B73_premeiotic_anther_sRNA_rep1

value: Anthers

value: Premeiotic


title: HUVEC cells exposed to 14 µg/ml bleomycin for 72h, replicate 4

description:
Library name: Sample 45
H_143

value: wildtype

value: 14 µg/ml bleomycin


title: gd T cells and ILCs, Salmonella typhimurium, ATAC

library_source: genomic

molecule: genomic DNA


title: PC9_Control_3

description: Untreated control PC9 cell line - Replicate 3

source_name: Untreated control PC9 cell line

value: Control


title: gd T cells and ILCs, naïve, GEX

value: Streptomycin treated, mock infected controls


title: PC9_Control_2

description: Untreated control PC9 cell line - Replicate 2


title: B73_embryo_sRNA_rep1


title: HUVEC cells exposed to 14 µg/ml bleomycin for 72h, replicate 3

description:
Library name: Sample 44
H_142


title: ms28_prophase_I_male_germ_cell_RNA_rep1

data_processing:
For data analysis, adapters and low-quality reads were removed using Trimmomatic v0.33 (Bolger et al., 2014). Clean RNA reads were mapped to the maize B73 reference genome AGPv4 by HISAT2 v2.2.1 (Kim et al., 2019). For differential gene expression analysis, the transcripts were assembled using the Cufflinks package (Trapnell et al., 2010) and gene expression levels were quantified using FeatureCounts v2.0.1 with raw counts (Liao et al., 2014). Differential gene expression analysis was performed using DEseq2 (Love et al., 2014). Genes with a ≥ 1.5-fold change and an FDR ≤ 0.05 were identified as differentially expressed genes. The expression level of each gene was then normalized to fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary files format and content: For RNA-Seq processed dataset，our provided file is the expression matrix of genes . The expression level of lncRNAs are estimated as FPKM

extract_protocol:
Total RNA was isolated from embryos, anthers and male germ cells using TRIzol (Takara, 9109). MgCl2 (final concentration: 0.2 M) was added to prevent loss of sRNAs with low GC content (Kim et al., 2012). NaAc (pH 5.2) and glycogen were added to promote RNA precipitation. The extracted RNA was stored at −80°C in LoBind tubes (Eppendorf, 022431021).
Libraries for RNA sequencing were prepared using the Smart-seq method with minor modifications, as previously described (Jiang et al., 2020; Picelli et al., 2014). In brief, total RNA was reverse transcribed and cDNA second strand was subsequently synthesized using SuperScript II reverse transcriptase (Invitrogen,18064-14) and template-switching oligos. After PCR preamplification and purification, the products were fragmented using TruePrepTM DNA Library Prep Kit (Vazyme, TD501). The fragments were amplified with index-containing primers and the 300–800-bp products were selected with AMPure XP beads. Libraries were pair-end sequenced on with Illumina Nova platform by Annoroad Gene Technology (Beijing).

value: Germ cells

value: Prophase I


title: ms28_prophase_I_male_germ_cell_RNA_rep2


title: HUVEC cells exposed to 7 µg/ml bleomycin for 72h, replicate 3

description:
Library name: Sample 42
H_140

value: 7 µg/ml bleomycin


title: B73_prophase_I_male_germ_cell_RNA_rep2


title: ATAC from P14 CD8 T cell day 7 KPC-GP

city: Chapel Hill

first: Justin

last: Milner

address: 450 West Drive, Lineberger Comprehensive Cancer Center Rm 11-117

institute: University of North Carolina at Chapel Hill

description: 10X Genomics GEX+ATAC

data_processing:
ATAC and Gene expression libraries were sequenced separately. Sequencing followed manufacturers protocols. Sequencing lanes were merged and demultiplexing was performed using cellranger-arc v2.0.0 (batch1) or v2.0.2 (batch2) with default settings.
ATAC (Read1: 50 cycles, i7 index: 8 cycles, i5 Index: 24 cycles, Read 2: 50 cycles)
GEX (Read1: 28 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2: 90 cycles)
Assembly: mm10
Supplementary files format and content: Filtered Cell Ranger Arc outs for demultiplexed files for each condition include: barcodes, features, matrix, and atac fragments.
Library strategy: Multiome

source_name: tumor

extract_protocol:
Nuclei were isolated from viable sorted cells using 10x Genomics Low Cell Input Nuceli isolation protocol per manufacturer's recommendation.
10x Genomics Chromium Controller and Chromium Next GEM Single Cell Multiome ATAC+Gene Expression Reagent Bundle per manufacturer's recommendation.

value: tumor

tag: condition

value: KPC-GP

value: P14 CD8 T cells

tag: disease

value: cancer


title: HUVEC cells exposed to 21 µg/ml bleomycin for 72h, replicate 3

description:
Library name: Sample 43
H_141

value: 21 µg/ml bleomycin


title: PC9_Control_1

description: Untreated control PC9 cell line - Replicate 1


title: Cannabis sativa L. Leaf, Heat stress, R2

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

description: Library name: Sample5

data_processing:
Raw reads were trimmed using Trimmomatic (v0.39; LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, and MINLEN:50) to remove adapter sequences and low-quality reads.
Contaminants were then removed using BBDUK (v38.95; k=31, mcf=0.5) based on Kraken2 RefSeq indexes standard database (archaea, bacteria, viral, human), as well as SILVA’s Small Subunit rRNA (SSR) and Large Subunit rRNA (LSR) databases.
Filtered reads were then used to build and index the C. sativa reference genome (RefSeq: GCF_029168945.1), with HISAT2 (v2.2.1; --no-mixed), and mapped to produce BAM files.
Gene-level read counts were obtained using HTSeq (v2.0.5). The resulting count matrix was analyzed in DESeq2.
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes HTSeq counts for each sample (header = F)
Supplementary files format and content: tab-delimited text file includes DESeq normalized counts for each sample (header = F).

organism: Cannabis sativa

source_name: Leaf

growth_protocol: Seeds of C. sativa L. cv. Pink Pepper were used in this study. The seeds were soaked in a 1% hydrogen peroxide solution (DAEJUNG Chemicals & Metals Co., Siheung, Korea) for 10 hours, then sown in a 105-well seedling tray (42 mL per well) filled with potting soil (Anong Sangto, Asiaseed Co., Seoul, Korea). Germination was carried out for 15 days under controlled conditions of 25 ± 2°C and 43 ± 7% relative humidity. During this period, each plant was supplied with 30 mL of tap water daily. After 15 days, the seedlings were transplanted into 600 mL pots and cultivated for an additional three weeks under 23 ± 2°C and 43 ± 7% relative humidity, with irrigation of 300 mL tap water per plant every three days.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany).
Libraries were prepared using the TruSeq standard mRNA. (Illumina Inc., San Diego, CA, USA).

treatment_protocol: To induce heat stress, C. sativa plants were maintained at 45 ± 2°C for 7 days in a growth chamber (HanKuk Scientific Co., Ltd., Hwaseong, Korea). Relative humidity was maintained at 40 ± 4%. For the control group, plants were kept under the same conditions except at a temperature of 23 ± 1°C.

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper

value: Heat stress


title: Cannabis sativa L. Leaf, Heat stress, R1

description: Library name: Sample4


title: Cannabis sativa L. Leaf, Heat stress, R3

description: Library name: Sample6


title: HUVEC cells exposed to 7 µg/ml bleomycin for 72h, replicate 2

description:
Library name: Sample 41
H_139

value: HUVEC

value: umbilical vein endothelial cells


title: ATAC from P14 CD8 T cell day 6 LCMV CL13 spleen

description: 10X Genomics GEX+ATAC

source_name: spleen

value: spleen

value: LCMV Clone13

value: chronic infection


title: B73_prophase_I_male_germ_cell_RNA_rep1

source_name: Germ cells


title: ATAC from P14 CD8 T cell day 7 B16-GP

description: 10X Genomics GEX+ATAC


title: HUVEC cells exposed to 14 µg/ml bleomycin for 48h, replicate 4

description:
Library name: Sample 40
H_138

value: wildtype

value: 14 µg/ml bleomycin


title: Cannabis sativa L. Leaf, Control, R2

description: Library name: Sample2

value: Control


title: ms28_prophase_I_anther_RNA_rep2

value: Anthers

value: Prophase I


title: ATAC from P14 CD8 T cell day 6 LCMV Arm spleen

description: 10X Genomics GEX+ATAC

value: LCMV Armstrong

value: acute infection


title: HUVEC cells exposed to 21 µg/ml bleomycin for 48h, replicate 4

description:
Library name: Sample 39
H_137


title: Cannabis sativa L. Leaf, Control, R1

description: Library name: Sample1


title: ATAC from P14 CD8 T cell day 6 LCMV Arm IEL

description: 10X Genomics GEX+ATAC

source_name: small intestine intraepithelial lymphocytes

value: P14 CD8 T cells


title: ms28_prophase_I_anther_RNA_rep1


title: HUVEC cells exposed to 21 µg/ml bleomycin for 48h, replicate 3

description:
Library name: Sample 38
H_136

source_name: HUVEC

value: 21 µg/ml bleomycin


title: EcN, CDCA, 180 min, rep3

city: South San Francisco

first: Barath

last: Udayasuryan

state: CA

address: 1 DNA Way

department: Department of Infectious Diseases and Host-Microbe Interactions

institute: Genentech Inc.

description: Library name: EcN_CDCA_180min_rep3

data_processing:
Low-quality bases were removed from the RNA-seq data using Trimmomatic (LEADING:27 TRAILING:27 SLIDINGWINDOW:4:20 MINLEN:3)
Trimmed reads were aligned to the EcN reference genome (GenBank accession no. CP007799.1) using Bowtie 2.
Aligned reads were counted with featureCounts, using the options to count all multi-overlapping reads (because reads could span two co-transcribed genes in an operon) but not multi-mapping reads.
Assembly: CP007799.1
Supplementary files format and content: Tab-delimited text file contains raw counts for each Sample.

organism: Escherichia coli Nissle 1917

source_name: Plasmid cured wildtype

growth_protocol: E. coli Nissle was grown overnight anaerobically in YCFA media at 37C, then subcultured into twelve replicate 4 mL cultures under the same condition at OD600 = 0.04 and grown to mid-log phase (OD600 = 0.4-0.6). Then, the cultures were treated with either 1% DMSO (solvent control), 100 µM LCA, or 100 µM CDCA and transferred to anaerobic 12-well non-tissue-culture-treated polystyrene plates (1 mL/well). The treated cultures were incubated anaerobically at 37C in the 12-well-plates for the specified periods of time, then the cells were collected by centrifugation, the pellets were snap-frozen in liquid nitrogen, and stored at -70C until RNA extraction.

extract_protocol:
RNA was harvested using the Qiagen RNeasy Mini kit, following the manufacturer's protocol with the following modifications: The cells were treated with 215 µL of lysozyme (15 mg/mL) and proteinase K (Qiagen, 1.5 mg/mL) in TE buffer at 37C for 10 min prior to the addition of Buffer RLT. The manufacturer's recommended on-column DNase treatment step was performed. After extraction, the RNA was treated with the Turbo DNA-free kit (Invitrogen) following the manufacturer's "rigorous" protocol.
Sequencing libraries were generated from 400 ng of total RNA using the TruSeq Stranded Total RNA Kit (Illumina, catalog no. 20020596) in combination with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, catalog no. 20037135).

value: Plasmid cured wildtype

value: 100 uM CDCA

value: 180 min


title: gd T cells and ILCs, naïve, ATAC

value: colon

value: gd T cells and ILCs

value: RORcre Rosa26-lox-Stop-lox-ZsGreen

value: Streptomycin treated, mock infected controls


title: EcN, CDCA, 180 min, rep2

description: Library name: EcN_CDCA_180min_rep2


title: GEX from P14 CD8 T cell day 7 KPC-GP

description: 10X Genomics GEX+ATAC

value: tumor

value: KPC-GP

value: cancer


title: B73_prophase_I_anther_RNA_rep1

source_name: Anthers


title: Cannabis sativa L. Leaf, Control, R3

description: Library name: Sample3

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper

value: Control


title: GEX from P14 CD8 T cell day 6 LCMV CL13 spleen

description: 10X Genomics GEX+ATAC

value: spleen

value: LCMV Clone13

value: chronic infection


title: HUVEC cells exposed to 7 µg/ml bleomycin for 48h, replicate 4

description:
Library name: Sample 37
H_135

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype

value: 7 µg/ml bleomycin


title: HUVEC cells exposed to 21 µg/ml bleomycin for 24h, replicate 4

description:
Library name: Sample 36
H_134

value: 21 µg/ml bleomycin


title: EcN, LCA, 180 min, rep3

description: Library name: EcN_LCA_180min_rep3

value: Plasmid cured wildtype

value: 100 uM LCA

value: 180 min


title: HUVEC cells exposed to 7 µg/ml bleomycin for 24h, replicate 4

description:
Library name: Sample 35
H_133


title: b73_premeiotic_anther_RNA_rep2

value: Anthers

value: Premeiotic


title: EcN, CDCA, 180 min, rep1

description: Library name: EcN_CDCA_180min_rep1

value: 100 uM CDCA


title: GEX from P14 CD8 T cell day 6 LCMV Arm spleen

description: 10X Genomics GEX+ATAC

value: LCMV Armstrong

value: P14 CD8 T cells

value: acute infection


title: HUVEC cells exposed to 0 µg/ml bleomycin for 24h, replicate 4

description:
Library name: Sample 34
H_132

value: 0 µg/ml bleomycin


title: GEX from P14 CD8 T cell day 7 B16-GP

description: 10X Genomics GEX+ATAC

value: tumor

value: cancer


title: Placenta, Deep placenta, preeclampsia preterm parturitions, 8

city: Daejeon

first: Tae Lyun

last: Ko

address: 245, Daehak-ro, Yuseong-gu

institute: Korea Institute of Science and Technology Information

description:
Library name: PePT_P8
10x Genomics

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (10xGenomics) against the Homo Sapience genome (GRCh38) provided by Cell Ranger
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Placenta (Deep placenta)

extract_protocol:
Placental tissues were obtained during Cesarean section, and the maternal-fetal (MF) and deep-placenta (PL) layers were freshly isolated. Samples underwent general cell processing steps, including viability and concentration assessment using a Countess II FL Automated Cell Counter (Thermo).
RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library Kit (10X Genomics) according to the manufacturer’s instructions. Samples containing more than 10,000 cells per condition were loaded onto the Chromium Controller for single-cell partitioning and barcoding. The resulting cDNA libraries were amplified and sequenced on an Illumina HiSeq-X sequencer, generating an average of 11,117.7 ± 3,057.9 single-cell transcriptomes per sample.

value: Placenta (Deep placenta)

tag: sample description

value: preterm birth

tag: gestational week

tag: offspring sex

value: male


title: GEX from P14 CD8 T cell day 6 LCMV Arm IEL

description: 10X Genomics GEX+ATAC

value: small intestine intraepithelial lymphocytes


title: EcN, LCA, 180 min, rep1

description: Library name: EcN_LCA_180min_rep1


title: HUVEC cells exposed to 7 µg/ml bleomycin for 24h, replicate 3

description:
Library name: Sample 33
H_131

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype

value: 7 µg/ml bleomycin


title: Placenta, Maternal-Fetal interface, preeclampsia preterm parturitions, 8

description:
Library name: PePT_MF8
10x Genomics

source_name: Placenta (Maternal - Fetal interface)

value: Placenta (Maternal - Fetal interface)


title: B73_prophase_I_anther_RNA_rep2

value: Anthers

value: Prophase I


title: HUVEC cells exposed to 0 µg/ml bleomycin for 24h, replicate 3

description:
Library name: Sample 32
H_130


title: G-BMSC-3W-2

city: Xi'an

first: Yazhen

last: Wang

address: 169 West Changle Road

institute: The Fourth Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophage were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 20ng/ml M-CSF and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were subjected to hypergravity by centrifugation at 15 G, or kept at 0 G for controls, for 15 min. The total duration of the intervention was about one or three weeks.

value: bone marrow

value: bone mesenchymal stem cells

value: Hypergravity stimulation for 3 week (mice)


title: G-BMSC-3W-1


title: Placenta, Deep placenta, normal, 7

description:
Library name: Norm_P7
10x Genomics

value: full term birh

value: female


title: Normal-BMSC-3W-2

value: Normal fed(mice)


title: HUVEC cells exposed to 14 µg/ml bleomycin for 24h, replicate 4

description:
Library name: Sample 31
H_129

value: 14 µg/ml bleomycin


title: EcN, DMSO, 180 min, rep1

description: Library name: EcN_DMSO_180min_rep1

value: Plasmid cured wildtype

value: 1% DMSO

value: 180 min


title: HUVEC cells exposed to 21 µg/ml bleomycin for 24h, replicate 3

description:
Library name: Sample 30
H_128

value: HUVEC

value: 21 µg/ml bleomycin


title: HUVEC cells exposed to 14 µg/ml bleomycin for 24h, replicate 3

description:
Library name: Sample 29
H_127

value: umbilical vein endothelial cells

value: wildtype


title: Placenta, Deep placenta, normal, 6

description:
Library name: Norm_P6
10x Genomics

value: Placenta (Deep placenta)

value: male


title: Placenta, Maternal-Fetal interface, normal, 7

description:
Library name: Norm_MF7
10x Genomics

value: Placenta (Maternal - Fetal interface)


title: EcN, LCA, 180 min, rep2

description: Library name: EcN_LCA_180min_rep2

value: 100 uM LCA


title: b73_premeiotic_anther_RNA_rep1

value: Anthers

value: Premeiotic


title: G-BMSC-3

value: bone marrow

value: bone mesenchymal stem cells

value: Hypergravity stimulation for 1 week (mice)


title: EcN, CDCA, 90 min, rep2

description: Library name: EcN_CDCA_90min_rep2

value: 100 uM CDCA

value: 90 min


title: HUVEC cells exposed to 14 µg/ml bleomycin for 24h, replicate 2

description:
Library name: Sample 28
H_126

value: 14 µg/ml bleomycin


title: Normal-BMSC-3W-1

value: Normal fed(mice)


title: EcN, CDCA, 90 min, rep1

description: Library name: EcN_CDCA_90min_rep1

value: Plasmid cured wildtype


title: Placenta, Deep placenta, preeclampsia preterm parturitions, 5

description:
Library name: PePt_P5
10x Genomics

value: preterm birth


title: EcN, CDCA, 90 min, rep3

description: Library name: EcN_CDCA_90min_rep3


title: HUVEC cells exposed to 21 µg/ml bleomycin for 24h, replicate 2

description:
Library name: Sample 27
H_125

value: HUVEC

value: umbilical vein endothelial cells

value: 21 µg/ml bleomycin


title: EcN, DMSO, 180 min, rep3

description: Library name: EcN_DMSO_180min_rep3

value: 1% DMSO

value: 180 min


title: EcN, LCA, 90 min, rep3

description: Library name: EcN_LCA_90min_rep3

value: 100 uM LCA


title: HUVEC cells exposed to 7 µg/ml bleomycin for 24h, replicate 2

description:
Library name: Sample 26
H_124

value: wildtype

value: 7 µg/ml bleomycin


title: EcN, DMSO, 180 min, rep2

description: Library name: EcN_DMSO_180min_rep2


title: EcN, LCA, 90 min, rep2

description: Library name: EcN_LCA_90min_rep2


title: Placenta, Deep placenta, normal, 4

description:
Library name: Norm_P4
10x Genomics

value: Placenta (Deep placenta)

value: full term birh

value: male


title: Normal-BMSC-3

value: bone marrow

value: bone mesenchymal stem cells


title: HUVEC cells exposed to 7 µg/ml bleomycin for 24h, replicate 1

description:
Library name: Sample 25
H_123


title: Placenta, Maternal-Fetal interface, normal, 4

description:
Library name: Norm_MF4
10x Genomics

value: Placenta (Maternal - Fetal interface)


title: Normal-BMSC-2

value: Normal fed(mice)


title: EcN, LCA, 90 min, rep1

description: Library name: EcN_LCA_90min_rep1

value: Plasmid cured wildtype

value: 90 min


title: Placenta, Deep placenta, preeclampsia preterm parturitions, 3

description:
Library name: PePT_P3
10x Genomics

value: preterm birth


title: HUVEC cells exposed to 0 µg/ml bleomycin for 24h, replicate 2

description:
Library name: Sample 24
H_122

value: HUVEC

value: umbilical vein endothelial cells

value: 0 µg/ml bleomycin


title: EcN, DMSO, 90 min, rep3

description: Library name: EcN_DMSO_90min_rep3

value: 1% DMSO


title: HUVEC cells exposed to 0 µg/ml bleomycin for 24h, replicate 1

description:
Library name: Sample 23
H_121


title: Placenta, Maternal-Fetal interface, normal, 6

description:
Library name: Norm_MF6
10x Genomics


title: Normal-BMSC-1


title: G-BMDM-3W-2

value: bone marrow-derived macrophage

value: Hypergravity stimulation for 3 week (mice)


title: Placenta, Maternal-Fetal interface, preeclampsia preterm parturitions, 3

description:
Library name: PePT_MF3
10x Genomics


title: Placenta, Deep placenta, preeclampsia preterm parturitions, 2

description:
Library name: PePT_P2
10x Genomics

value: female


title: Placenta, Maternal-Fetal interface, preeclampsia preterm parturitions, 5

description:
Library name: PePT_MF5
10x Genomics


title: G-BMSC-1

value: Hypergravity stimulation for 1 week (mice)


title: G-BMSC-2


title: HUVEC cells exposed to 21 µg/ml bleomycin for 24h, replicate 1

description:
Library name: Sample 21
H_116

value: wildtype

value: 21 µg/ml bleomycin


title: G-BMDM-3W-1

value: bone marrow


title: Placenta, Maternal-Fetal interface, preeclampsia preterm parturitions, 2

description:
Library name: PePT_MF2
10x Genomics


title: EcN, CDCA, 30 min, rep3

description: Library name: EcN_CDCA_30min_rep3

value: 100 uM CDCA

value: 30 min


title: HUVEC cells exposed to 0 µg/ml bleomycin for 72h, replicate 3

description:
Library name: Sample 20
H_114


title: Placenta, Deep placenta, normal, 1

description:
Library name: Norm_P1
10x Genomics

value: Placenta (Deep placenta)

value: full term birh


title: Normal-BMDM-3W-1

value: Normal fed(mice)


title: Normal-BMDM-3W-2


title: EcN, CDCA, 30 min, rep2

description: Library name: EcN_CDCA_30min_rep2

value: Plasmid cured wildtype


title: HUVEC cells exposed to 0 µg/ml bleomycin for 72h, replicate 2

description:
Library name: Sample 19
H_113

value: HUVEC


title: Placenta, Maternal-Fetal interface, normal, 1

description:
Library name: Norm_MF1
10x Genomics

value: Placenta (Maternal - Fetal interface)


title: EcN, CDCA, 30 min, rep1

description: Library name: EcN_CDCA_30min_rep1


title: G-BMDM-2


title: HUVEC cells exposed to 0 µg/ml bleomycin for 72h, replicate 1

description:
Library name: Sample 18
H_112

value: umbilical vein endothelial cells

value: 0 µg/ml bleomycin


title: Tumor tissue_3

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include Normalized count values for each Sample.

source_name: Tumor tissue_3

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: patient diagnosis

value: papillary thyroid carcinoma

tag: subject number

value: Tumor tissue


title: HUVEC cells exposed to 14 µg/ml bleomycin for 24h, replicate 1

description:
Library name: Sample 22
H_119

tag: cell line

value: 14 µg/ml bleomycin


title: EcN, DMSO, 90 min, rep2

description: Library name: EcN_DMSO_90min_rep2

tag: treatment

value: 1% DMSO

value: 90 min


title: EcN, LCA, 30 min, rep3

description: Library name: EcN_LCA_30min_rep3

value: 100 uM LCA


title: G-BMDM-1

tag: tissue

value: bone marrow

value: bone marrow-derived macrophage

value: Hypergravity stimulation for 1 week (mice)


title: Normal tissue_3

source_name: Normal tissue_3

value: Normal tissue


title: HUVEC cells exposed to 14 µg/ml bleomycin for 72h, replicate 2

description:
Library name: Sample 17
H_111

value: wildtype


title: EcN, DMSO, 90 min, rep1

description: Library name: EcN_DMSO_90min_rep1


title: HUVEC cells exposed to 14 µg/ml bleomycin for 72h, replicate 1

description:
Library name: Sample 16
H_110


title: Normal-BMDM-2

value: Normal fed(mice)


title: EcN, LCA, 30 min, rep2

description: Library name: EcN_LCA_30min_rep2

value: Plasmid cured wildtype

value: 30 min


title: Tumor tissue_2

source_name: Tumor tissue_2


title: Normal-BMDM-3


title: Normal tissue_2

source_name: Normal tissue_2


title: Normal-BMDM-1


title: HUVEC cells exposed to 21 µg/ml bleomycin for 72h, replicate 2

description:
Library name: Sample 15
H_109

value: HUVEC

value: 21 µg/ml bleomycin


title: EcN, DMSO, 30 min, rep3

description: Library name: EcN_DMSO_30min_rep3


title: EcN, LCA, 30 min, rep1

description: Library name: EcN_LCA_30min_rep1


title: EcN, DMSO, 30 min, rep2

description: Library name: EcN_DMSO_30min_rep2


title: Tumor tissue_1

source_name: Tumor tissue_1


title: Normal tissue_1

source_name: Normal tissue_1


title: WTNT3

city: Ithaca

first: John

last: Schimenti

state: NY

address: T9 014A Veterinary Research Tower, Box 17

department: Biomedical Sciences

institute: Cornell University

description: Library name: WTNT3

data_processing:
The raw fastq reads were first processed with trim-galore (Barbraham Institute) package to: Trim for low quality reads; 2 color chemistry bias (next-seq); Trim for noisy short fragments; Trim for adapter sequence
The filtered reads were then aligned to GRCm38 reference genome with ENSEMBL annotations via STAR
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files contain raw read counts for each sample

growth_protocol: V6.5 embryonic stem cells were grown in 2i+LIF medium on laminin-coated 6-well plates.

extract_protocol:
RNA extracted with Zymo Research Quick RNA Miniprep Kit, per manufacturer's instructions. 1 ug of RNA was used for libray preparation
NEBNext Ultra II [Directional] RNA kit with rRNA depletion

treatment_protocol: 150 nM MMC or an equivalent volume of DMSO were added to media for a 24 hour treatment

value: Embryonic Stem Cell

value: WT

value: NT

tag: batch


title: EcN, CDCA, 15 min, rep3

description: Library name: EcN_CDCA_15min_rep3

value: 100 uM CDCA

value: 15 min


title: EcN, DMSO, 30 min, rep1

description: Library name: EcN_DMSO_30min_rep1

value: 1% DMSO


title: HUVEC cells exposed to 7 µg/ml bleomycin for 72h, replicate 1

description:
Library name: Sample 13
H_107

value: umbilical vein endothelial cells

value: 7 µg/ml bleomycin


title: mtTF1_0d

city: Bern

first: Torsten

last: Ochsenreiter

state: Bern

address: Blatzerstrasse 4

department: Biology

country: Switzerland

institute: Institute of Cell Biology

description:
Library name: AEKC-3
Med mode

data_processing:
Unique Molecular Identifiers (UMI)s-tools were used to detect UMI sequences and remove bases corresponding to illumina adapters.
Assembly: MK584625 (https://www.ncbi.nlm.nih.gov/nuccore/MK584625 [ncbi.nlm.nih.gov]) and annotated_mOs_T.brucei_EATRO1125_AnTat1.1.gbk (https://figshare.com/articles/dataset/Trypanosoma_brucei_EATRO1125_AnTat1_1_assembled_and_annotated_minicircle_genome/7756808/1?file=15352502)
Supplementary files format and content: Excel files containing the counts and normalized counts. The normalization factor was determined based on mapping to the nuclear genome of TbruceiLister427 (Trypanosoma_brucei_Lister_strain_427_2018; https://tritrypdb.org/tritrypdb/app/search/genomic- sequence/SequencesByTaxon)

organism: Trypanosoma brucei

growth_protocol: Transgenic T. brucei cell lines were generated using the procyclic form (PCF) strain 29-13 and the bloodstream form (BSF) strain NYsm and yL262P (Dean et al., 2013; Motyka & Englund, 2004; Wirtz et al., 1999). The PCF were grown in exponential phase (up to 1×107 cells/ml) in semi-defined medium 79 (SDM-79, Bioconcept, #9-04V01-M) supplemented with 10% fetal calf serum (FCS) at 27 °C. BSF were grown in exponential phase (up to 1×106 cells/ml) in Hirumi’s modified Iscove’s medium 9 (HMI-9) at 37° C (with 5% CO2 and water) (Hirumi & Hirumi, 1989).

extract_protocol:
A total of 1x108 cells were harvested by centrifugation at 2500 rpm for 8 min at room temperature. The pellet was washed with 1 ml PBS, transferred to a 1.5 ml tube and centrifuged again at 2500 rpm for 8 min at room temperature. After removing the supernatant, the cell pellet was resuspended in 1 ml TRIzol (Tri-Reagent, Merck, #9424). Subsequently, 200 µl of chloroform was added and the samples were vortexed vigorously. The mixture was then centrifuged at 12000 rpm for 15 min at 4°C. The upper aqueous phase (400 µl) was carefully transferred to a new tube containing 500 µl of ice-cold isopropanol, ensuring that the interphase was not disturbed. The tube was inverted several times to mix the solution. RNA was precipitated by centrifugation at 12000 rmp for 15 min at 4°C. Subsequently, the supernatant was removed and discarded. The RNA pellet was washed twice with 1 ml 70% ethanol followed by centrifugation at 7500 rpm for 5 min at 4°C. The ethanol was removed, and the tube was inverted and left open at room temperature to air-dry for at least 5 min. Finally, the RNA pellet was resuspended in 50 µl RNase-free water and incubated at 55°C for 5 min on a heating block. RNA concentration was determined using a Nanodrop spectrophotometer and RNA integrity was assessed by running 1 µg of RNA on a 1% agarose gel for 40 min at 100 V. RNA was stored at -80°C or used directly for DNase treatment and cDNA synthesis.
Total RNA are processd into short fragments (150-200 bp) and treatet with kinase. Libraries are prepared using the QIAseq-miRNA kit

treatment_protocol: RNAi targets the open reading frame of mtRNAP (position: 575-1045) or mtTF1 (position: 98- 567) , respectively and was induced with tetracycline

value: mtTF1 RNAi -Tet


title: HUVEC cells exposed to 7 µg/ml bleomycin for 48h, replicate 3

description:
Library name: Sample 12
H_103

data_processing:
Raw RNA-Seq reads were trimmed for low-quality bases (Phred quality score < 20) and Illumina sequencing adapters using Cutadapt (v4.4). Reads shorter than 60 bases post-trimming were discarded.
Alignment of the trimmed sequencing reads to the Genome Reference Consortium Human Build (GRCh38) Ensembl version 110 was performed using HISAT2 (v2.2.1) with default settings.
Bam files were filtered for uniquely mapped reads (as flagged by "NH:i:1") and sorted by coordinates using Samtools (v1.18).
Read summarisation was conducted with the featureCounts function from the Rsubread package (v2.16.1) against the Ensembl GTF file version 110
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the bleomycin experiment
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the TGF-beta experiment

extract_protocol:
RNA was extracted from cells after 24h, 48h, and 72h of exposure using the RNeasy Mini kit (Qiagen). DNase 1 (Thermo Scientific, EN0521) treatment was used prior to downstream analyses.
RNA-Seq libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042) including polyA-tailed mRNA enrichment. RNA-Seq was performed in two batches i.e., the two exposure experiments of bleomycin and TGF-beta, respectively.


title: HUVEC cells exposed to 0 µg/ml bleomycin for 48h, replicate 4

description:
Library name: Sample 11
H_102

value: 0 µg/ml bleomycin


title: PehC_6h_R3

city: Wuhan

first: ying

last: yuan

address: No.1 Lion Mountain Street, Hongshan District

department: Molecular Building

institute: Huazhong Agricultural University

data_processing:
Cutadapt was used to remove sequences with adapters at the 3' end and reads with an average quality score lower than Q20.
Use trimmomatic(v0.39) to remove the first fifteen bases of each read.
Trimmed sequence reads were mapped to Slycopersicum_691_SL4.0 using Hisat2(v2.2.1).
Read count extraction and normalization were performed using featureCounts in subread package(v2.0.3).
Obtaining differentially expressed genes with DESeq2(v1.30.1).
Assembly: SL4.0
Supplementary files format and content: tab-delimited text files include genes counts for each Sample.

organism: Solanum lycopersicum

source_name: root

growth_protocol: Tomato seedlings were grown on half-strength (1/2) MS plates containing 1% (w/v) sucrose and 0.8 % (w/v) agar for about 2 weeks at 22°C

extract_protocol:
The collected plant samples were stored in liquid nitrogen and sent to Shanghai Personalbio Biotechnology for RNA extraction
RNA libraries for RNA-seq were prepared using following manufacturer's protocols.

treatment_protocol: Two-weeks old tomato seedling roots were treated with or without 10 μg/ml GST-PehC for 1 h and 6 h.

value: root

value: tomato root cells

tag: cultivar

value: MoneyMarker

value: GST-PehC


title: EcN, CDCA, 15 min, rep2

description: Library name: EcN_CDCA_15min_rep2

value: Plasmid cured wildtype


title: PehC_6h_R4


title: EcN, CDCA, 15 min, rep1

description: Library name: EcN_CDCA_15min_rep1


title: HUVEC cells exposed to 14 µg/ml bleomycin for 48h, replicate 3

description:
Library name: Sample 10
H_101

value: HUVEC

value: wildtype

value: 14 µg/ml bleomycin


title: WTMMC3

description: Library name: WTMMC3

value: Embryonic Stem Cell

value: WT

value: MMC


title: HUVEC cells exposed to 21 µg/ml bleomycin for 48h, replicate 2

description:
Library name: Sample 9
H_100

value: 21 µg/ml bleomycin


title: HUVEC cells exposed to 21 µg/ml bleomycin for 72h, replicate 1

description:
Library name: Sample 14
H_108


title: FANCMMMC3

description: Library name: FANCMMMC3

value: Fancm


title: mtTF1_2d

description:
Library name: AEKC-4
Med mode

tag: strain

value: mtTF1 RNAi +Tet


title: FANCMNT3

description: Library name: FANCMNT3

tag: genotype

value: NT


title: EcN, LCA, 15 min, rep2

description: Library name: EcN_LCA_15min_rep2

value: 100 uM LCA

value: 15 min


title: PehC_1h_R4

value: root


title: PehC_6h_R2

value: tomato root cells


title: WTMMC2

description: Library name: WTMMC2


title: PehC_6h_R1

value: MoneyMarker


title: EcN, LCA, 15 min, rep1

description: Library name: EcN_LCA_15min_rep1


title: HUVEC cells exposed to 14 µg/ml bleomycin for 48h, replicate 2

description:
Library name: Sample 8
H_099

value: umbilical vein endothelial cells


title: EcN, LCA, 15 min, rep3

description: Library name: EcN_LCA_15min_rep3

value: Plasmid cured wildtype


title: WTNT2

description: Library name: WTNT2


title: PehC_1h_R3

value: GST-PehC


title: HUVEC cells exposed to 21 µg/ml bleomycin for 48h, replicate 1

description:
Library name: Sample 6
H_097

value: HUVEC

value: wildtype


title: FANCMNT2

description: Library name: FANCMNT2

value: Embryonic Stem Cell


title: PehC_1h_R2


title: EcN, DMSO, 15 min, rep2

description: Library name: EcN_DMSO_15min_rep2

value: 1% DMSO


title: HUVEC cells exposed to 14 µg/ml bleomycin for 48h, replicate 1

description:
Library name: Sample 7
H_098

value: 14 µg/ml bleomycin


title: CK_0h_R2


title: HUVEC cells exposed to 0 µg/ml bleomycin for 48h, replicate 3

description:
Library name: Sample 3
H_094

value: 0 µg/ml bleomycin


title: HUVEC cells exposed to 7 µg/ml bleomycin for 48h, replicate 2

description:
Library name: Sample 5
H_096

value: 7 µg/ml bleomycin


title: EcN, DMSO, 15 min, rep3

description: Library name: EcN_DMSO_15min_rep3


title: CK_0h_R4


title: PehC_1h_R1


title: HUVEC cells exposed to 7 µg/ml bleomycin for 48h, replicate 1

description:
Library name: Sample 4
H_095


title: FANCMMMC2

description: Library name: FANCMMMC2

value: Fancm

value: MMC


title: WTMMC1

description: Library name: WTMMC1

value: WT


title: HUVEC cells exposed to 0 µg/ml bleomycin for 48h, replicate 2

description:
Library name: Sample 2
H_093


title: CK_0h_R3


title: FANCMMMC1

description: Library name: FANCMMMC1


title: EcN, DMSO, 15 min, rep1

description: Library name: EcN_DMSO_15min_rep1

value: 15 min


title: HUVEC cells exposed to 0 µg/ml bleomycin for 48h, replicate 1

description:
Library name: Sample 1
H_092


title: FANCMNT1

description: Library name: FANCMNT1

value: NT


title: SH-SY5Y, H1.2 Si

status: Public on May 25 2025

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

description: Library name: H1.2 Si

data_processing:
Sequenced reads were aligned to the UCSC Genome Sequencing Consortium reference genome (human hg38) using the vast-tools v2.5.1 67 align command with default options.
The quality of sequenced reads was evaluated using the FASTQC tool
Assembly: hg38
Supplementary files format and content: tab-delimited files including cRPKM values for each Sample , no quantile normalization

source_name: Bone; Marrow

extract_protocol:
Total RNA extraction was performed using TRI reagent (Sigma) according to the manufacturer’s instructions.
TruSeq Stranded Total RNA with Ribo-Zero H/M/R

value: Bone; Marrow

value: Neuroblastoma

value: H1.2 Si


title: CK_0h_R1

value: root

value: tomato root cells

value: MoneyMarker


title: SH-SY5Y, H1.2 Si + H1.5 Si

description: Library name: H1.2 Si + H1.5 Si


title: SH-SY5Y, H1.5 Si

description: Library name: H1.5 Si

value: H1.5 Si


title: SH-SY5Y, WT_Si

description: Library name: WT_Si


title: WTNT1

description: Library name: WTNT1

value: Embryonic Stem Cell


title: SH-SY5Y, H1.2 OE + H1.5 OE_rep2

description: Library name: H1.2 OE + H1.5 OE_rep2


title: SH-SY5Y, H1.2 OE + H1.5 OE

description: Library name: H1.2 OE + H1.5 OE


title: SH-SY5Y, H1.5 OE

description: Library name: H1.5 OE

value: H1.5 OE


title: SMJN

city: Minami-ku, Hiroshima-shi

first: Takuto

last: Uyama

state: Hiroshima

address: 1-2-3 Kasumi

country: Japan

institute: Hiroshima University

description: Gene expression data from umbilical metastasis

hyb_protocol: 2.3 μg of single-stranded DNA was hybridized to the Clariom™ S Array, human (Thermo Fisher Scientific, catalog number: 902926) using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific, catalog number: 900720) in the GeneChip® Hybridization Oven 645 (Affymetrix, catalog number: 00-0331).

scan_protocol: Arrays were stained and washed using the GeneChip® Fluidics Station 450 (Affymetrix, catalog number: 00-0079), and scanned with the GeneChip® Scanner 3000 7G (Affymetrix, catalog number: 00-0210).

data_processing:
Scanned data were automatically saved as CEL files, which were analyzed using Transcriptome Analysis Console (TAC) software version 4.0 to generate expression data and visualization. For Gene Ontology (GO) enrichment analysis, we selected differentially expressed genes with a fold change greater than 4. Enriched GO terms were extracted using a significance threshold of p < 0.05.
Transcriptome Analysis Console (TAC) software version 4.0

label: biotin

source_name: umbilical metastasis

label_protocol: A total of 250 ng of RNA was processed into cRNA and subsequently into biotin-labeled single-stranded DNA using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA, catalog number: 902280).

extract_protocol: Total RNA was extracted using the RNeasy® Plus Mini Kit (Qiagen, Hilden, Germany, catalog number: 74136).

value: navel, FIGO stage IVB fallopian tube carcinoma

tag: age

tag: Sex

value: female


title: SH-SY5Y, WT_rep3

description: Library name: WT_rep3

tag: cell type


title: SH-SY5Y, H1.2 OE

description: Library name: H1.2 OE

value: H1.2 OE


title: Lymph

description: Gene expression data from lymph node

source_name: inguinal lymph node metastasis

value: lymph node, FIGO stage IVB fallopian tube carcinoma


title: Primary

description: Gene expression data from fallopian tube carcinoma

source_name: the primary site (right fallopian tube)

value: fallopian tube, FIGO stage IVB fallopian tube carcinoma


title: SH-SY5Y, WT_rep2

description: Library name: WT_rep2

value: WT


title: SH-SY5Y, WT

description: Library name: WT


title: KO2 rep3

first: Hao

last: Wu

state: Tianjin

address: No. 22, Weidai Road, Heping District

department: Department of Immunology

institute: Tianjin Medical University

data_processing:
The image data are transformed into sequence data (reads) by CASAVA v1.6
The raw paired end reads were trimmed and quality controlled using a custom Perl script.
Trimmed sequencing reads were aligned to the reference genome using Hisat2 (v2.0.5).
The FeatureCounts software (version 1.5.0-p3) was employed to extract reads count mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RAW counts for each sample.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: Lung

extract_protocol:
Total RNA was extracted from the cells using TRIzol® Reagent according the manufacturer’s instructions.
Libraries were generated with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s instructions, and carried out with the Illumina NovaSeq 6000.

value: Lung

value: Lung adenocarcinoma cells

value: BCKDK Knockout


title: SH-SY5Y, WT_rep4

description: Library name: WT_rep4

value: Bone; Marrow

value: Neuroblastoma


title: KO1 rep2


title: KO2 rep1


title: KO1 rep3