title: inf_24h_rep4

description:
Library name: Sample 23
column name in data_matrix_wx_vivo_inf.txt: typhi_24h_4

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples. Normalized data was log2-transformed, and a minimal expression threshold of 3 was set.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

source_name: PBMCs

extract_protocol:
The cells were then incubated for 4, 8, and 24h in a 37°c incubator with 5% CO2 before being used for RNA preparation.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

treatment_protocol: Salmonella Typhi Quailes strain was inoculated into LB media and grown for 14 hours at 37°c  to stationary phase with tightly closed tubes on a roller. After 14 hours, the bacteria were centrifuged (1min 11,000 RPM), the media was discarded, and the bacteria were resuspended with DPBS, with calcium and magnesium (Sartorius, 02-020-1A, from now on DPBS).  OD 600 was measured, and the bacteria were diluted to OD 600 0.1. PBMCs to be infected were defrosted. 5ul of the diluted bacteria stock (equal to MOI of 1, note that MOI refers to the number of total PBMCs in the well and not only to monocytes) or DPBS for controls were added to the PBMCs, the PBMCs were gently mixed by pipetting and incubated for 30 minutes for internalization in a 37°c incubator with 5% CO2. After 30 minutes, the PBMCs were centrifuged (500g for 5 min in RT), the medium was discarded, and the cells were washed with RPMI+ media supplemented with gentamycin (50 ug/ml) to eliminate Salmonella that were not internalized.  The cells were centrifuged again (500g for 5 min in RT), the media was discarded, and the cells were again resuspended with RPMI+ supplemented with gentamycin (50 ug/ml).

value: PBMCs

value: Mixture of immune cells

value: S. Typhi ex vivo infected


title: inf_24h_rep2

status: Public on Jul 02 2025

type: SRA

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

description:
Library name: Sample 21
column name in data_matrix_wx_vivo_inf.txt: typhi_24h_2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: replicate

tag: treatment

tag: time post_infection_(hours)


title: PP_inf_72h_5

description:
Library name: Sample 30
column name in data_matrix_bulk_mouse_tissues.txt:  PP_inf_72h_5

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Normalized data was log2-transformed, and a minimal expression threshold of 2 was set
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

organism: Mus musculus

source_name: Peyer's patches (PP)

extract_protocol:
0,24, and 72 hours post infection mice were sacrificed by cervical dislocation, and the desired tissues (ileum, caecum, Payer's patches and spleen) were removed for analysis.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

treatment_protocol: Female C57BL/6 mice, 7-9 weeks old, were orally infected with 1*10^9 CFU of Salmonella Typhimurium strain SL1344 (in 100μl suspension in DPBS) or treated with sterile DPBS (control).

value: Peyer's patches (PP)

value: enriched for immune cells

value: infected


title: inf_24h_rep3

description:
Library name: Sample 22
column name in data_matrix_wx_vivo_inf.txt: typhi_24h_3


title: MII oocyte from WT mice_rep2

city: Shanghai

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

country: China

institute: Tongji University

data_processing:
All of the RNA-Seq sequencing reads were processed using BBDuk (version 38.34) to remove adapters and low-quality reads
The filted reads were mapped to the mouse reference genome using STAR (version 0.6.0) with the default parameters excepting using the ‘‘–quantMode GeneCounts’’ parameter
Gene expression for each sample was quantified to FPKM using Stringtie (version 1.3.3b)
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include FPKM values for each transcript.
Supplementary files format and content: Bigwiggle files are generated through MASC14 with parameters(macs14 -t Sample.bam -c input.bam -g mm -n name -B -S).

molecule: polyA RNA

source_name: MII oocyte

extract_protocol:
Total oocyte RNA was isolated using the Arcturus PicoPure RNA isolation kit (applied biosystems Cat.no. KIT0204).
The RNA sequencing libraries were generated using a KAPA Stranded RNA-Seq Kit Illumina platform (Cat.no.KK8440).

treatment_protocol: Wild type, Obox1+/− or Obox1−/− female mice at 6-8 weeks of age were treated with 5 IU PMSG which was followed 46-48 hours later by treatment with 5 IU hCG.MII oocytes were collected from the oviducts of the mice after superovulation, and the adherent cumulus cells were removed by hyaluronidase treatment.

value: MII oocyte

tag: genotype

value: wild type

tag: strain background


title: Plasma-control_Freeze-thaw3_repb_PBArep3

type: protein

city: Guangzhou

first: Xueqi

last: Li

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

hyb_protocol: Oligonucleotide tags specific to each exosome were incorporated during the extension reaction using exosome tag templates. Indexing and sequencing adapters were integrated using specially designed primers during PCR.

scan_protocol: Sequencing was executed DNBSEQ-T7 platform (MGI, Shenzhen, China) using a PE150 sequencing kit.

data_processing: The output was generated as a bcl file for each sample transferred into fastq files with aid of bioinformatic tools MegaBolt, ultimately forming single EV protein count expression matrices within each sample.

label: biotin

molecule: protein

source_name: Plasma EVs

label_protocol: A panel of 262 antibodies, each labeled with oligonucleotides comprising distinct protein identifiers, molecular tags, and a universal primer-binding sequence, was employed. This setup facilitated the detection of biomarkers at an individual exosome level using PBA.

extract_protocol: Isolated EVs were centrifuged at 3000g for 10 minutes at 4°C, and the supernatant was collected for further analysis. To capture the exosomes, a 96-well plate was prepared with cholera toxin subunit B at 2 µg/mL in coating buffer which was incubated overnight at 4°C, then washed thrice with PBS containing 0.05% Tween 20 (PBST). One µL of each sample was diluted with 19 µL of PBA buffer and added to each well with CTB coating to enable exosome affinity capture via CTB-GM1 lipid membrane interactions.

tag: isolation methods

value: Plasma-control

tag: freezi-thaw condition

value: Freeze-thaw


title: PP_inf_72h_2

description:
Library name: Sample 28
column name in data_matrix_bulk_mouse_tissues.txt:  PP_inf_72h_2


title: MII oocyte from WT mice_rep1


title: Plasma-control_Freeze-thaw2_repb_PBArep3


title: PP_inf_72h_4

description:
Library name: Sample 29
column name in data_matrix_bulk_mouse_tissues.txt:  PP_inf_72h_4


title: Plasma-control_Freeze-thaw2_repa_PBArep3


title: MII oocyte from Obox1 KO mice_rep2

value: Obox1 KO


title: PP_inf_72h_1

description:
Library name: Sample 27
column name in data_matrix_bulk_mouse_tissues.txt:  PP_inf_72h_1


title: Spleen_naive_2

description:
Library name: Sample 32
column name in data_matrix_bulk_mouse_tissues.txt:  Spleen_naive_2

source_name: Spleen

value: Spleen

value: naive


title: MII oocyte from Obox1 KO mice_rep1


title: Plasma-control_Non-freeze-thaw1_repa_PBArep3

value: Non-freeze-thaw


title: Plasma-control_Non-freeze-thaw1_repb_PBArep3


title: inf_8h_rep3

description:
Library name: Sample 19
column name in data_matrix_wx_vivo_inf.txt: typhi_8h_3


title: inf_8h_rep2

description:
Library name: Sample 18
column name in data_matrix_wx_vivo_inf.txt: typhi_8h_2


title: Exo-CMDS_Freeze-thaw3_repb_PBArep3

value: Exo-CMDS


title: PP_naive_5

description:
Library name: Sample 26
column name in data_matrix_bulk_mouse_tissues.txt:  PP_naive_5


title: CTRL_B25

city: Suzhou

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

description:
Library name: B25
10xGenomics

data_processing:
After generating the single-cell RNA-seq library, the sequencing data is processed using the latest version of Cell Ranger.
Assembly: h38
Supplementary files format and content: Tab-separated valued files

extract_protocol:
For RNA extraction from human peripheral blood and kidney tissue samples  intended for 10x Genomics single-cell RNA sequencing, the process typically begins with the dissociation of cells to obtain a single-cell suspension. This is followed by cell lysis, where cells are lysed to release RNA while preserving the integrity of the RNA molecules. The lysate is then treated with a phenol-chloroform extraction or processed using a commercial RNA isolation kit to purify the RNA. Care is taken to minimize RNase contamination throughout the process, ensuring high-quality RNA suitable for downstream 10x Genomics library preparation and sequencing.
To prepare a 10x Genomics single-cell RNA-seq library, start by suspending the single-cell sample in a buffer solution. The cell suspension is loaded onto the 10x Genomics Chromium Controller, where individual cells are encapsulated into nanoliter-sized droplets along with barcoded gel beads and reagents. Inside each droplet, cells are lysed, and the mRNA is captured by barcoded oligonucleotides on the gel beads. The barcoded mRNA is then reverse transcribed into cDNA. After breaking the emulsion, the cDNA is purified and amplified using PCR. The resulting cDNA is then fragmented, and sequencing adapters are added to create the final library, which is ready for sequencing on a compatible high-throughput platform.

tag: cell line

value: Primary

value: Ctrl


title: PP_naive_4

description:
Library name: Sample 25
column name in data_matrix_bulk_mouse_tissues.txt:  PP_naive_4


title: PP_naive_3

description:
Library name: Sample 24
column name in data_matrix_bulk_mouse_tissues.txt:  PP_naive_3


title: inf_8h_rep1

description:
Library name: Sample 17
column name in data_matrix_wx_vivo_inf.txt: typhi_8h_1

value: PBMCs


title: Plasma-control_Freeze-thaw3_repa_PBArep3


title: Cr_B17

description:
Library name: B17
10xGenomics

value: PTRI


title: Exo-CMDS_Non-freeze-thaw1_repb_PBArep3


title: ind6_TD

description:
Library name: Sample 18
10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform alignment to the genome (GRCh38), barcode assignment for each cell, and gene counting by unique molecular identifier (UMI) counts for each sample. Each sample was run on a different lane (total of 18 lanes), and samples from all individuals and time points were merged together using cell ranger aggr.
Assembly: GRCh38
Supplementary files format and content: Tab seperated values files for barcodes and features and matrix files for UMI count

extract_protocol:
PBMCs were defrosted, counted ,  plated on 96- well-untreated plates (5* 10^5 cells/well, one well per individual) and incubated at 37°c and  5% CO2 over-night. After overnight incubation, samples were centrifuged, the media was discarded, and the samples were washed with DPBS -/-.  Detaching the cells from the dish was done by resuspension with 5 mM EDTA in DPBS -/-  followed by 5 min incubation in RT.  The samples were then centrifuged and resuspended in DPBS. Each sample was counted with viability staining  and resuspended with  0.04% BSA in DPBS.
Libraries were performed according to the Chromium Single Cell 3’ Reagent version 3 kit and Chromium Controller (10X Genomics, CA, USA)

value: Mixture of immune cells

tag: time post_salmonella_typhi_challenge

value: time of disease diagnosis

tag: outcome

value: developed typhois disease (TD)


title: inf_8h_rep4

description:
Library name: Sample 20
column name in data_matrix_wx_vivo_inf.txt: typhi_8h_4

value: S. Typhi ex vivo infected


title: inf_4h_rep4

description:
Library name: Sample 16
column name in data_matrix_wx_vivo_inf.txt: typhi_4h_4


title: PP_naive_2

description:
Library name: Sample 23
column name in data_matrix_bulk_mouse_tissues.txt:  PP_naive_2

value: Peyer's patches (PP)

value: enriched for immune cells


title: inf_4h_rep2

description:
Library name: Sample 14
column name in data_matrix_wx_vivo_inf.txt: typhi_4h_2


title: PP_naive_1

description:
Library name: Sample 22
column name in data_matrix_bulk_mouse_tissues.txt:  PP_naive_1


title: Exo-CMDS_Non-freeze-thaw1_repa_PBArep3


title: ind6_T12

description:
Library name: Sample 17
10x Genomics

value: 12 hours


title: Exo-CMDS_Freeze-thaw3_repa_PBArep3

value: Freeze-thaw


title: inf_4h_rep3

description:
Library name: Sample 15
column name in data_matrix_wx_vivo_inf.txt: typhi_4h_3


title: ind5_TD

description:
Library name: Sample 15
10x Genomics


title: Exo-CMDS_Freeze-thaw2_repb_PBArep3


title: Cecum_inf_72h_3

description:
Library name: Sample 20
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_72h_3

source_name: Cecum

value: Cecum

value: infected


title: naïve_24h_rep4

description:
Library name: Sample 12
column name in data_matrix_wx_vivo_inf.txt: pbs_24h_4

value: naïve


title: inf_4h_rep1

description:
Library name: Sample 13
column name in data_matrix_wx_vivo_inf.txt: typhi_4h_1


title: ind5_T12

description:
Library name: Sample 14
10x Genomics


title: Cecum_inf_72h_2

description:
Library name: Sample 19
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_72h_2


title: naïve_24h_rep3

description:
Library name: Sample 11
column name in data_matrix_wx_vivo_inf.txt: pbs_24h_3


title: Exo-CMDS_Freeze-thaw2_repa_PBArep3


title: AF4_Non-freeze-thaw1_repa_PBArep3

value: Non-freeze-thaw


title: AF4_Freeze-thaw3_repa_PBArep3


title: ind5 T0

description:
Library name: Sample 13
10x Genomics

value: 0 hours


title: naïve_24h_rep2

description:
Library name: Sample 10
column name in data_matrix_wx_vivo_inf.txt: pbs_24h_2


title: Cecum_inf_72h_1

description:
Library name: Sample 18
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_72h_1


title: ind4_TD

description:
Library name: Sample 12
10x Genomics


title: Cecum_inf_24h_4

description:
Library name: Sample 17
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_24h_4


title: ind6 T0

description:
Library name: Sample 16
10x Genomics


title: ind4_T12

description:
Library name: Sample 11
10x Genomics


title: naïve_24h_rep1

description:
Library name: Sample 9
column name in data_matrix_wx_vivo_inf.txt: pbs_24h_1


title: Cecum_inf_24h_3

description:
Library name: Sample 16
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_24h_3


title: Cecum_inf_72h_4

description:
Library name: Sample 21
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_72h_4


title: AF4_Freeze-thaw3_repb_PBArep3


title: naïve_8h_rep4

description:
Library name: Sample 8
column name in data_matrix_wx_vivo_inf.txt: pbs_8h_4


title: Cecum_inf_24h_2

description:
Library name: Sample 15
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_24h_2


title: ind3_T7d

description:
Library name: Sample 9
10x Genomics

value: 7 days

value: did not developed disease (nTD)


title: AF4_Freeze-thaw2_repa_PBArep3


title: naïve_8h_rep3

description:
Library name: Sample 7
column name in data_matrix_wx_vivo_inf.txt: pbs_8h_3

value: PBMCs


title: Cecum_inf_24h_1

description:
Library name: Sample 14
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_inf_24h_1


title: naïve_8h_rep2

description:
Library name: Sample 6
column name in data_matrix_wx_vivo_inf.txt: pbs_8h_2


title: Cecum_naive_2

description:
Library name: Sample 13
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_naive_2

value: naive


title: Cecum_naive_1

description:
Library name: Sample 12
column name in data_matrix_bulk_mouse_tissues.txt:  Cecum_naive_1


title: Mel89_vem_2

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

country: USA

institute: Wayne State University

description: Library name: Mel89_vem_2

data_processing:
Aligned to mm10 with STAR
Tabulated to gene regions using htseq count
differential analyses in edgeR
Assembly: mm10
Supplementary files format and content: Excel file R results

growth_protocol: Parental M14 and A2058 cells were cultured in DMEM/F12 supplemented with 5% fetal bovine serum. VemR M14 and A2058 cells were maintained in same media supplemented with 100 nM or 4 mM vemurafenib, respectively. Mel-14-108 and Mel-14-089 cells were cultured in DMEM/F12 medium supplemented with 5% fetal bovine serum. All cells were grown in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total RNA was isolated from cell lines using RNA later followed by purification with RNeasy mini kit (Qiagen) using the manufacturer’s recommended in-solution DNase digestion.
Lexogen QuantSeq 3' mRNAseq

treatment_protocol: Parental M14 or A2058 cells, and their isogenic VemR counterparts were cultured in DMEM/F12 media containing 5% FBS. The VemR M14 and A2058 cells maintained in 100 nM or 4 mM vemurafenib, respectively, were rinsed three times to remove drug and incubated in drug free media prior to RNA isolation. Mel-14-108 and Mel-14-089 cells were treated overnight with 10 nM or 4 mM vemurafenib, respectively.

value: melanoma


title: naïve_8h_rep1

description:
Library name: Sample 5
column name in data_matrix_wx_vivo_inf.txt: pbs_8h_1

value: Mixture of immune cells


title: SEC_Freeze-thaw3_repb_PBArep3

value: SEC


title: ind2 T0

description:
Library name: Sample 4
10x Genomics


title: naïve_4h_rep4

description:
Library name: Sample 4
column name in data_matrix_wx_vivo_inf.txt: pbs_4h_4


title: Mel89_vem_1

description: Library name: Mel89_vem_1


title: ind2_T7d

description:
Library name: Sample 6
10x Genomics


title: SEC_Non-freeze-thaw1_repb_PBArep3


title: ind4 T0

description:
Library name: Sample 10
10x Genomics

value: developed typhois disease (TD)


title: naïve_4h_rep2

description:
Library name: Sample 2
column name in data_matrix_wx_vivo_inf.txt: pbs_4h_2


title: Mel89_vem_3

description: Library name: Mel89_vem_3


title: ind1_T7d

description:
Library name: Sample 3
10x Genomics


title: ind2_T12

description:
Library name: Sample 5
10x Genomics


title: naïve_4h_rep1

description:
Library name: Sample 1
column name in data_matrix_wx_vivo_inf.txt: pbs_4h_1


title: naïve_4h_rep3

description:
Library name: Sample 3
column name in data_matrix_wx_vivo_inf.txt: pbs_4h_3


title: SEC_Freeze-thaw2_repa_PBArep3


title: ind3 T0

description:
Library name: Sample 7
10x Genomics


title: SEC_Freeze-thaw2_repb_PBArep3


title: AF4_Freeze-thaw2_repb_PBArep3


title: SEC_Non-freeze-thaw1_repa_PBArep3


title: ind3_T12

description:
Library name: Sample 8
10x Genomics


title: Mel89_control_3

description: Library name: Mel89_control_3


title: AF4_Non-freeze-thaw1_repb_PBArep3


title: SEC_Freeze-thaw3_repa_PBArep3


title: ind1_T12

description:
Library name: Sample 2
10x Genomics


title: Plasma-control_Freeze-thaw3_repb_PBArep2

value: Plasma-control


title: Hypoxia_22h_rep3

description:
Library name: Sample 9
column name in data_matrix_hypoxia.txt: hypoxia22_3

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Normalized data was log2-transformed, and a minimal expression threshold of 3 was set
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

extract_protocol:
At the indicated time points after incubation, the samples were centrifuged (500g, 22°c, 5 min), the media was discarded, and the samples were washed with DPBS -/-. The samples were then resuspended with 5 mM EDTA in DPBS -/- and incubated for 5 min in RT, followed by gentle pipetting. This was done to detach cells that might attach to the dish. The samples were then centrifuged (500g, 22°c, 5 min) and resuspended in 350ul of RLT buffer (RNeasy Mini Kit, QIAGEN 74104) supplemented with 10ul beta-mercaptoethanol per 1ml RLT. Samples were kept at -80°c until RNA was extracted. RNA was extracted by RNeasy Mini Kit, QIAGEN 74104, including  Dnase digestion (QIAGEN  79254). RNA samples concentration was measured by iQuant™ RNA HS Assay Kit (ABP Biosciences, N017), and RNA quality was measured by tapestation (High Sensitivity RNA ScreenTape, Agilent 5067-5579 and High Sensitivity RNA ScreenTape Sample Buffer, Agilent 5067-5580). RNA samples were kept at -80°c until further use.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

treatment_protocol: Frozen PBMCs from healthy donor were defrosted and were either kept in normoxia (37°c  incubator with 5% CO2) for 22 hours or transferred to a hypoxia chamber (2% O2) for 15 or 22 hours, followed by RNA extraction.

value: hypoxia 2% O2

tag: time (hours)


title: Plasma-control_Freeze-thaw3_repa_PBArep2


title: Hypoxia_22h_rep2

description:
Library name: Sample 8
column name in data_matrix_hypoxia.txt: hypoxia22_2


title: Hypoxia_22h_rep1

description:
Library name: Sample 7
column name in data_matrix_hypoxia.txt: hypoxia22_1


title: ind1 T0

description:
Library name: Sample 1
10x Genomics


title: Mel89_control_1

description: Library name: Mel89_control_1


title: HCT116 TIM-mAID 5-Ph-IAA/ATRi, 40 h set3

city: Stony Brook

first: Hyungjin

last: Kim

state: New York

address: 101 Nicolls Rd. BST 8-120

institute: SUNY Stony Brook

description:
Library name: JAP12
5-Ph-IAA/ATRi

data_processing:
For bioinformatics analysis, read quantification was performed using the nf-core rnaseq pipeline v3.13.2.
sequencing QC was performed with FastQC v0.12.1 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Trim Galore v0.6.7 and Cutadapt v3.4.
Reads were mapped to the Gencode release 44 version of the human reference genome (GRCh38.p14) using STAR v2.7.9a.
Alignments were converted to BAM format and sorted using samtools v1.17. Transcript expression was then quantified with Salmon v1.10.1 and converted to gene-level counts with Tximport v1.12.0.
Assembly: GRCh38
Supplementary files format and content: tsv read count file

source_name: HCT116 TIM-mAID

growth_protocol: HCT116 TIM-mAID cells were maintained in McCoy’s 5A medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, following standard culture conditions and procedures.

extract_protocol:
RNA isolation was carried out using the miRNeasy Micro Kit (Qiagen) as per manufacturer’s protocol. An additional DNase digest step was carried out using RNase-Free DNase Set (Qiagen) as per manufacturer’s protocol. mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) as per manufacturer’s protocol.
RNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) as per manufacturer’s protocol.

treatment_protocol: 5-Phenyl-1H-indole-3-acetic acid (5-Ph-IAA) dissolved in DMSO to 10 and 1 mM stock, treated at 1 µM; Ceralasertib (ATRi) dissolved in DMSO to 10 and 1 mM stock, treated at 1 µM.

value: HCT116 TIM-mAID

value: Colorectal cancer cell line

value: WT CRSIPR KI mAID

value: 1 µM 5-Ph-IAA/1 µM ATRi


title: HCT116 TIM-mAID ATRi, 40 h set3

description:
Library name: JAP11
ATRi

value: 1 µM ATRi


title: Mel108_Plus_Vem_1

description: Library name: Mel108_Plus_Vem_1


title: Mel108_Plus_Vem_2

description: Library name: Mel108_Plus_Vem_2


title: Plasma-control_Freeze-thaw2_repb_PBArep2

value: Freeze-thaw


title: Hypoxia_15h_rep3

description:
Library name: Sample 6
column name in data_matrix_hypoxia.txt: hypoxia15_3


title: Hypoxia_15h_rep1

description:
Library name: Sample 4
column name in data_matrix_hypoxia.txt: hypoxia15_1


title: HCT116 TIM-mAID DMSO, 40 h set3

description:
Library name: JAP9
DMSO

value: 1 µM DMSO


title: Hypoxia_15h_rep2

description:
Library name: Sample 5
column name in data_matrix_hypoxia.txt: hypoxia15_2


title: HCT116 TIM-mAID 5-Ph-IAA/ATRi, 40 h set2

description:
Library name: JAP8
5-Ph-IAA/ATRi


title: HCT116 TIM-mAID 5-Ph-IAA, 40 h set3

description:
Library name: JAP10
5-Ph-IAA

value: 1 µM 5-Ph-IAA


title: Naïve_rep3

description:
Library name: Sample 3
column name in data_matrix_hypoxia.txt: naïve_3

value: naïve


title: Plasma-control_Freeze-thaw2_repa_PBArep2


title: Mel108_control_3

description: Library name: Mel108_control_3


title: Plasma-control_Non-freeze-thaw1_repa_PBArep2

value: Non-freeze-thaw


title: Exo-CMDS_Freeze-thaw3_repb_PBArep2

value: Exo-CMDS


title: Mel108_control_2

description: Library name: Mel108_control_2

value: melanoma


title: HCT116 TIM-mAID ATRi, 40 h set2

description:
Library name: JAP7
ATRi


title: Mel108_control_1

description: Library name: Mel108_control_1


title: Mel89_control_2

description: Library name: Mel89_control_2


title: Exo-CMDS_Non-freeze-thaw1_repb_PBArep2


title: Naïve_rep2

description:
Library name: Sample 2
column name in data_matrix_hypoxia.txt: naïve_2

value: PBMCs

value: Mixture of immune cells


title: Mel108_Plus_Vem_3

description: Library name: Mel108_Plus_Vem_3


title: HCT116 TIM-mAID DMSO, 40 h set2

description:
Library name: JAP5
DMSO


title: HCT116 TIM-mAID 5-Ph-IAA, 40 h set2

description:
Library name: JAP6
5-Ph-IAA


title: Naïve_rep1

description:
Library name: Sample 1
column name in data_matrix_hypoxia.txt: naïve_1


title: M14VR_control_3

description: Library name: M14VR_control_3


title: M14VR_control_2

description: Library name: M14VR_control_2


title: scRNAseq Serum+/KD shRNA2, replicate2

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
ChIP-seq: Adaptors for raw reads were trimmed using fastp with default parameters and aligned to the human reference genome hg38 with parameters “--end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 100 -X 800” using bowtie2. Samtools were used to remove duplicates from mapped reads using `samtools rmdup` and then sort and index .bam files. ChIP-seq signals (.bigwig and .bedGraph) were derived from the bam files using bamCoverage from the deepTools suite. MACS2 was used to identify peaks of each ChIP-seq sample using IgG as background with parameters `--nomodel -q 0.1`.
scRNA-seq: Raw sequencing data were processed using the Cell Ranger pipeline (version 6.0.1) which takes the raw FASTQ files and aligned them to the hg38 genome to generate gene expression count matrix based on the reference refdata-gex-GRCh38-2020-A. Single cell gene expression count matrix is imported and processed by Seurat package.
Assembly: hg38
Supplementary files format and content: The processed data of ChIP-seq experiment include bigwig. The processed data for 10x scRNA-seq is the output from CellRanger pipeline.

source_name: Human Brain Organoid

growth_protocol: Human brain organoids were generated from H1 human embryonic stem cells using a cerebral organoid establishment Kit (STEMCELL Technologies, 08570). At the 130th day, the organoids were subjected to either normal medium or normal medium with added 10% human serum. Organoids were harvested on the 142th day for characterization.

extract_protocol:
For ChIP-seq, brain organoids were fixed with 1% formaldehyde at room tempture for 10 minutes. Cells lysis and chromatin fragmentation were performed using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9005). For scRNA-seq, single nuclear were prepared following the standard protocol of Chromium Nuclei Isolation Kit with RNase Inhibitor (10X Genomics, PN-1000494).
For ChIP-seq, libraries were prepared using NEBNext UltraTM II DNA Library Prep Kit for Illumina (NEB, E7645S). For scRNA-seq, library preparation was preformed following the manufacter's protocol of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000268).

treatment_protocol: At the 130th day, the organoids were subjected to either normal medium or normal medium with added 10% human serum. On the 133th day, organoids were infected by GFAP-promoter dirven AAV expressing scramble shRNA or shRNA against PHGDH. Organoids were harvested on the 142th day for characterization.

value: Human Brain Organoid

value: treated with Serum, PHGDH shRNA2


title: HCT116 TIM-mAID ATRi, 40 h set1

description:
Library name: JAP3
ATRi


title: scRNAseq Serum+/KD shRNA1, replicate2

value: treated with Serum, PHGDH shRNA1


title: HCT116 TIM-mAID 5-Ph-IAA, 40 h set1

description:
Library name: JAP2
5-Ph-IAA

value: HCT116 TIM-mAID


title: HCT116 TIM-mAID 5-Ph-IAA/ATRi, 40 h set1

description:
Library name: JAP4
5-Ph-IAA/ATRi

value: Colorectal cancer cell line


title: M14VR_control_1

description: Library name: M14VR_control_1


title: Exo-CMDS_Freeze-thaw3_repa_PBArep2


title: Plasma-control_Non-freeze-thaw1_repb_PBArep2

value: Plasma-control


title: M14P_control_2

description: Library name: M14P_control_2


title: M14P_control_3

description: Library name: M14P_control_3


title: scRNAseq Serum-/Scr, replicate2

value: no treatment


title: AF4_Non-freeze-thaw1_repa_PBArep2


title: Exo-CMDS_Freeze-thaw2_repb_PBArep2


title: Exo-CMDS_Freeze-thaw2_repa_PBArep2


title: Exo-CMDS_Non-freeze-thaw1_repa_PBArep2


title: AF4_Freeze-thaw3_repa_PBArep2


title: scRNAseq Serum+/KD shRNA2, replicate1


title: scRNAseq Serum+/Scr, replicate2

value: treated with Serum


title: Pulmonary endarterectomy specimen, replicate 5, scRNAseq

city: Toronto

first: Hon-Sum

middle: Jeffrey

last: Man

state: ON

address: 209 Victoria Street

department: Medicine

country: Canada

institute: University of Toronto

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pulmonary endarterectomy specimen

extract_protocol:
Fresh PEA tissue was washed with HBSS to remove any non- resident cells. The tissue was then cut into 3x3mm pieces and 4.5ml HBSS buffer + 200μL Collagenase A (10mg/mL) + 80μL DNAse (10mg/mL) were added and digested in GentleMACS at 37°C for 7 min after which the stopping buffer was added. Following collagenase treatment, the stop solution 10% FBS in HBSS was added into the tube and 40μm filter was used to collect the dissociated single cells. The process was repeated by running GentleMACS with collagenase/DNAse buffer for another 7 min at 37°C and filtered through 40μm cell strainer. The mixed cells were then incubated with RBC lysis buffer for 5 min and washed in HBSS and purified by centrifugation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pulmonary endarterectomy specimen


title: SEC_Freeze-thaw2_repa_PBArep2

value: SEC

value: Freeze-thaw


title: scRNAseq Serum+/KD shRNA1, replicate1


title: Pulmonary endarterectomy specimen, replicate 3, scRNAseq

description: 10x Genomics


title: scRNAseq Serum+/Scr, replicate1


title: AF4_Freeze-thaw2_repb_PBArep2


title: Pulmonary endarterectomy specimen, replicate 4, scRNAseq

description: 10x Genomics


title: I_HBER [J12I]

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

institute: Université Laval

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw_counts.csv file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: Isthmus

extract_protocol:
miRNeasy Mini Kit (QIAGEN, Hilden, Germany)
TruSeq Stranded mRNA Kit (Illumina)

value: Isthmus

value: HBER


title: scRNAseq Serum-/Scr, replicate1


title: HCT116 TIM-mAID DMSO, 40 h set1

description:
Library name: JAP1
DMSO

value: WT CRSIPR KI mAID

value: 1 µM DMSO


title: AF4_Freeze-thaw3_repb_PBArep2


title: MII oocytes vivo vitro 88

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: Library name: 88_vv

data_processing:
We processed a total of 88 libraries (88 oocytes), adapting and quality-trimming them using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) for sequences with a Phred score of less than 20. Additionally, one negative control was sequenced to detect any technical issues. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using HiSat2 version 2.1.0 in single-end mode. For the cumulus cell samples, feature counting at the gene and transcript isoform level was done using rsem-calculate-expression (RSEM v1.3.3) (Li et al., 2011). Data processing was done in R (v4.2.2) using the edgeR (v3.38.4) package for differential gene expression analysis (Chen et al., 2016).
A total of 46 scBS-seq libraries were processed for analysis. The initial 6 base pairs, which included the N portion of the random primers, adapters, and low-quality bases (Phred score <20), were trimmed using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) in single-end mode. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using Bismark version 0.18.2 (Krueger & Andrews, 2011) in single-end and nondirectional mode, followed by deduplication and methylation calling through Bismark functions.
Assembly: Bos Taurus (UMD3.1_v91)
Supplementary files format and content: Normalized counts
Supplementary files format and content: 20CpG_windows_methylation

source_name: MII oocytes

growth_protocol: For the collection of in vivo matured (IVO), in vitro matured (IVM) and in vivo + in vitro mature (VV) cumulus-oocytes complexes (COCs), four non-lactating and non-pregnant Holstein heifers (15 - 18 months of age) were used. For the collection of IVO and VV COCs, animals were synchronized using an intravaginal progesterone-releasing device (CIDR, Zoetis Belgium). Eight days later, the device was removed, and heifers received 2 mL (0.5 mg) of prostaglandin (PG; Cyclix Virbac, France). Estrus (=day 0) was confirmed two days later by ultrasound. To induce ovulation, 2.5 mL (10 µg) of Gonadotropin-releasing hormone (GnRH, Receptal, Intervet, Germany) was injected on day 8 of the estrous cycle. From day 10, animals were superovulated with 180 mg of follicle-stimulating hormone (FSH, Folltropin, Vetoquinol, Canada) administered twice daily for four days in decreasing doses. On day 12, animals received 3 mL (0.75 mg) of PG, and the luteinizing hormone (LH) surge was induced with 2.5 mL GnRH administered 40 h after  PG injection. Follicles ≥ 8mm in diameter were aspirated 24h after GnRH injection, using an 18 gauge needle. A 15-20 mL/min aspiration vacuum pressure was used due to the presence of expanded and sticky cumulus cells characteristic of oocyte maturation. Before follicle aspiration, the OPU tubing system was rinsed with polyvinylpyrrolidone (PVP) medium (0.3% PVP (PVP-360; Sigma) in Ca- and Mg-free PBS + 10 IU/mL heparin (Sigma)). The follicular content was collected in a 50 mL conical tube, and COCs were recovered under a stereomicroscope and stored in EmXcell medium without BSA (IMV-technologies, France) until the end of the collection procedure. After aspiration, COCs were collected under a stereomicroscope. Oocytes with evident cumulus expansion (IVO) were immediately denuded, whereas oocytes with poor cumulus expansion were submitted to IVM for 22 h (VV group), in groups (based on the cow of origin) in 50 µL bicarbonate-buffered TCM199 medium supplemented with gentamicin (50 mg/L) and epidermal growth factor (20 µl/mL). To assess maturation status, IVO and VV COCs were denuded individually in 0.1% hyaluronidase (Sigma) in PVP medium for approximately 2 min and by pipetting with a STRIPPER pipet holder and a 135-μm capillary (Origio, Cooper Surgical, CT, US) until all cumulus cells were removed from the oocyte. Denuded oocytes were classified as mature or immature oocytes based on the presence or absence of the polar body (PB), respectively. Mature IVO oocytes (n=28) and VV oocytes (n=20) were washed individually three times in PVP medium, treated with pronase to dissolve the zona pellucida (0.1% protease from S. griseus, in TCM-199), and immediately stored in 5 µl of Buffer RLT (Qiagen) at -80 °C until further use. Cumulus cells from IVO COCs were collected and pooled based on the cow of origin, and immediately stored in a lysis buffer for further analysis. For the collection of IVM oocytes, animals received GnRH (Receptal, Intervet, Germany) injection eight days after estrus and aspiration of follicles ≤ 8 mm was performed through an OPU procedure four days later. After aspiration, immature COCs (IVM group) were collected and underwent IVM as described above. After 22h, COCs were denuded, and mature oocytes (n=32) with their respective cumulus cells were processed and stored as described in the previous paragraph.

extract_protocol:
DNA and RNA from oocyte were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery. Total RNA was extracted from seven cumulus cells samples (four from in vivo matured, three from in vitro matured COCs) using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction. The RNA samples underwent quality and concentration assessments using an RNA 6000 Pico Chip (Agilent Technologies, Carlsbad, CA, USA).
ScRNA-seq and scBSseq

value: MII oocytes

value: Wild-type


title: AF4_Freeze-thaw2_repa_PBArep2


title: Pulmonary endarterectomy specimen, replicate 2, scRNAseq

description: 10x Genomics


title: Pulmonary endarterectomy specimen, replicate 1, scRNAseq

description: 10x Genomics


title: I_HBER [J10I]


title: wild-type embryos at 3-ss

type: RNA

city: Saitama

first: Kyo

last: Yamasu

state: Saitama

address: 255 Shimo-Okubo, Sakura-ku

department: Division of Life Science

country: Japan

institute: Saitama University Graduate School of Science and Technology

description:
Wild-type embryos were heat shocked at 3-ss, and total RNA was extracted.
HEP-_3s

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array in Hybridization Oven 640 110V. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software ver1.4.

organism: Danio rerio

source_name: wild-type embryos at 3-ss

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit User Manual Rev. 1, Affymetrix).

growth_protocol: Tg(hsp:en-pou5f3) embryos or wild-type embryos were raised at 25°C till 90% epiboly or 3-ss and then heat shocked. Treated embryos were allowed to develop for additional 30 minutes, and immediatly total RNA was extracted from the embryos.

extract_protocol: Genomic DNA and RNA were extracted separately from each embryo using Isogen. RNA was pooled from multiple treated embryos based on genotypes and used for analyses.

treatment_protocol: Embryos were treated at 37°C for 60 min (heat shock), and subjected to analysis.

tag: strain

value: RW

value: wild-type

tag: developmental stage


title: AF4_Non-freeze-thaw1_repb_PBArep2

value: Non-freeze-thaw


title: MII oocytes vivo vitro 87

description: Library name: 87_vv


title: Marginal_Aymptomatic_Patient20

first: Sneha

last: Raju

address: 101 College Street, PMCRT 3-309

data_processing:
DeSeq2, median normalization
Assembly: hg38, miRBase mature microRNAs (version 22)
Supplementary files format and content: median normalized counts

source_name: Carotid plaque tissue

extract_protocol:
EV enrichment via size exclusion chromotography
HTG EdgeSeq is a multiplexed nuclease protection assay with next-generation sequencing readout
HTG whole transcriptome miRNA-sequencing

value: Carotid plaque tissue

value: Vascular cells


title: en-pou5f3 induction at 90% epiboly

description:
Tg(hsp-en-pou5f3) embryos harboring en-pou5f3 were heat shocked at 90% epiboly, and total RNA was extracted.
HEP+_90%

source_name: en-pou5f3 induction at 90% epiboly

value: Tg

value: 90% epiboly


title: Plaque_Aymptomatic_Patient20


title: SEC_Freeze-thaw2_repb_PBArep2


title: MII oocytes vivo vitro 86

description: Library name: 86_vv


title: I_MBER [J9I]

value: MBER


title: SEC_Freeze-thaw3_repb_PBArep2


title: I_MBER [J8I]


title: MII oocytes vivo vitro 85

description: Library name: 85_vv


title: Marginal_Aymptomatic_Patient19


title: Plaque_Aymptomatic_Patient19


title: I_MBER [J7I]


title: MII oocytes vivo vitro 83

description: Library name: 83_vv


title: I_HBER [J11I]


title: SEC_Non-freeze-thaw1_repb_PBArep2


title: wild-type embryos at 90%-epiboly

description:
Wild-type embryos were heat shocked at 90% epiboly, and total RNA was extracted.
HEP-_90%

source_name: wild-type embryos at 90%-epiboly


title: en-pou5f3 induction at 3-ss

description:
Tg(hsp-en-pou5f3) embryos harboring en-pou5f3 were heat shocked at 3-ss, and total RNA was extracted.
HEP+_3s

source_name: en-pou5f3 induction at 3-ss


title: SEC_Non-freeze-thaw1_repa_PBArep2


title: SEC_Freeze-thaw3_repa_PBArep2


title: Marginal_Aymptomatic_Patient18


title: MII oocytes vivo vitro 82

description: Library name: 82_vv


title: Plaque_Aymptomatic_Patient18


title: A_HBER [J5A]

source_name: Ampulla

value: Ampulla


title: Plasma-control_Freeze-thaw3_repb_PBArep1

value: Plasma-control


title: MII oocytes vivo vitro 81

description: Library name: 81_vv


title: A_HBER [J4A]


title: Marginal_Aymptomatic_Patient17


title: Plaque_Aymptomatic_Patient17


title: MII oocytes vivo vitro 84

description: Library name: 84_vv


title: A_MBER [J3A]


title: Plasma-control_Freeze-thaw3_repa_PBArep1

value: Freeze-thaw


title: MII oocytes vivo vitro 80

description: Library name: 80_vv


title: MII oocytes vivo vitro 79

description: Library name: 79_vv


title: A_MBER [J2A]


title: A_MBER [J1A]


title: Plaque_Aymptomatic_Patient16


title: Plasma-control_Freeze-thaw2_repb_PBArep1


title: A_HBER [J6A]


title: MII oocytes vivo vitro 78

description: Library name: 78_vv


title: Plasma-control_Freeze-thaw2_repa_PBArep1


title: Marginal_Aymptomatic_Patient15


title: MII oocytes vivo vitro 77

description: Library name: 77_vv


title: Plaque_Aymptomatic_Patient15


title: Jurkat IgG

city: Beer Sheva

first: Ran

middle: Taube Pathology Rm

last: Taube

state: ISRAEL

address: Biotechnology Building 3, room 324

department: Microbiology

institute: Ben Gurion University

description: Library name: IgG-NC

library_source: genomic

data_processing:
We used SEACR, we do not have p-values for the peaks, but we used only the 0.01 highest scoring peaks as determined by the software.
CUT&RUN processing steps:  The analysis was carried out using the NeatSeq-Flow platform (Menachem et al, 2018). Raw sequencing data in fastq format were trimmed by Trim Galore (version 0.4.5) (length = 25, q =  25), and reads that were too short were discarded. FastQC, version 0.12.0, was used for reads quality control. BWA Mapper (version 0.7.12, default parameters t = 20, B = 5) (Li and Durbin, 2009) was used to align paired-end reads to reference human genome assembly hg38 and to the spike-in control (E coli) reference genome assembly. SAMtools (Danecek et al, 2021) was used to remove PCR duplicates and create coordinate-sorted BAM files. Normalization between samples and IgG was performed with a custom script that calculates read scaling factor based on spike-in DNA reads of each sample. The scaling factor was then used in bamCoverage to normalize each sample according to its spike-in. Bigwig files were created by bamCoverage function from deepTools (version 1.5.91) (Ramı´rez et al, 2016), and reads mapped to blacklisted areas designated by ENCODE (Amemiya et al, 2019) were filtered. Reads that refer to off-chromosome locations were removed with BedClip (version 377) and sorted by Bedtools (version 2.30.0) (Quinlan and Hall, 2010). Bigwig files were then created with bedGraphToBigWig by deepTools (Ramı´rez et al, 2016). ATF1 peaks were called by SEACR (version 1.3), the top 1% of enriched regions in target data were selected, and peaks 100 bp and less apart were merged.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Jurkat T

growth_protocol: Cells were grown in RPMI media supplemented with 10% FCS.

extract_protocol: According to the Epicipher Cut and Run protocol.

value: Jurkat T

tag: cut&run antibody

value: IgG


title: Plasma-control_Non-freeze-thaw1_repb_PBArep1


title: Plasma-control_Non-freeze-thaw1_repa_PBArep1


title: Marginal_Aymptomatic_Patient14


title: Exo-CMDS_Freeze-thaw3_repb_PBArep1

value: Exo-CMDS


title: Exo-CMDS_Non-freeze-thaw1_repb_PBArep1


title: MII oocytes vivo vitro 75

description: Library name: 75_vv


title: Marginal_Aymptomatic_Patient16


title: Plaque_Aymptomatic_Patient14


title: HA ATF1_replica 1

description: Library name: ATF1_Rep1

value: HA


title: MII oocytes vivo vitro 73

description: Library name: 73_vv

value: MII oocytes


title: Replicate 20 Treated RNA seq rep 2

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

data_processing:
Barcodes were mapped to the barcode map processed file to construct a barcode count matrix
Assembly: hg19
Supplementary files format and content: AD_MPRA_countTable.txt; barcode counts across all samples and their respective variant to be used for downstream processing, AD_MPRA_Barcode_Map.txt; barcode to variant mapping
Library strategy: MPRA

growth_protocol: THP-1 monocytes were cultured in RPMI 1640 media with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from resting and treated macrophages and reverse transcribed into cDNA. cDNA was amplified with GFP primers to select for barcodes.
Modified MPRA library preparation

treatment_protocol: THP-1 monocytes were transduced with lenti-MPRA and grown for 5 days before being differentiated into macrophages by treatingw ith 25 µM PMA for 24h. After 72h rest, macrophages were treated with 10 ng/mL of LPS and  20 ng/mL INFγ for 24h to induce a proinflammatory state.

value: monocyte

value: WT

value: LPS+INFγ


title: Exo-CMDS_Non-freeze-thaw1_repa_PBArep1

value: Non-freeze-thaw


title: Marginal_Aymptomatic_Patient13

value: Carotid plaque tissue


title: MII oocytes vivo 72

description: Library name: 72_vivo

value: Wild-type


title: Exo-CMDS_Freeze-thaw3_repa_PBArep1


title: Jurkt_H3K4me3

description: Library name: K4-PC


title: Plaque_Aymptomatic_Patient13

value: Vascular cells


title: MII oocytes vivo vitro 76

description: Library name: 76_vv


title: Marginal_Aymptomatic_Patient12


title: Replicate 20 Control RNA seq rep 2


title: Exo-CMDS_Freeze-thaw2_repb_PBArep1


title: Exo-CMDS_Freeze-thaw2_repa_PBArep1


title: MII oocytes vivo vitro 71

description: Library name: 71_vv


title: MII oocytes vivo vitro 70

description: Library name: 70_vv


title: AF4_Non-freeze-thaw1_repa_PBArep1


title: MII oocytes vivo vitro 69

description: Library name: 69_vv


title: HA-ATF1_replica 2

description: Library name: ATF1_Rep2


title: MII oocytes vivo vitro 74

description: Library name: 74_vv


title: AF4_Freeze-thaw3_repa_PBArep1


title: Replicate 19 Treated RNA seq rep 2


title: Replicate 20 Control RNA seq rep 1


title: MII oocytes vivo vitro 68

description: Library name: 68_vv


title: Replicate 19 Treated RNA seq rep 1


title: Plaque_Aymptomatic_Patient11


title: Marginal_Aymptomatic_Patient11


title: MII oocytes vivo vitro 67

description: Library name: 67_vv


title: Replicate 19 Control RNA seq rep 2


title: Replicate 20 Treated RNA seq rep 1


title: SEC_Freeze-thaw2_repa_PBArep1

value: SEC


title: Replicate 19 Control RNA seq rep 1


title: MII oocytes vivo vitro 65

description: Library name: 65_vv


title: Marginal_Symptomatic_Patient10


title: Marginal_Symptomatic_Patient9


title: AF4_Freeze-thaw2_repb_PBArep1


title: Plaque_Aymptomatic_Patient12


title: Replicate 18 Treated RNA seq rep 2


title: MII oocytes vivo 64

description: Library name: 64_vivo


title: Plaque_Symptomatic_Patient10


title: AF4_Freeze-thaw2_repa_PBArep1


title: Replicate 18 Treated RNA seq rep 1


title: Plaque_Symptomatic_Patient9


title: AF4_Non-freeze-thaw1_repb_PBArep1


title: MII oocytes vivo 63

description: Library name: 63_vivo


title: Replicate 18 Control RNA seq rep 2


title: Marginal_Symptomatic_Patient8


title: MII oocytes vivo 62

description: Library name: 62_vivo


title: SEC_Freeze-thaw3_repb_PBArep1


title: Replicate 18 Control RNA seq rep 1


title: Plaque_Symptomatic_Patient8


title: SEC_Freeze-thaw2_repb_PBArep1


title: MII oocytes vivo 61

description: Library name: 61_vivo


title: MII oocytes vivo vitro 66

description: Library name: 66_vv


title: Marginal_Symptomatic_Patient7


title: MII oocytes vivo 60

description: Library name: 60_vivo


title: SEC_Non-freeze-thaw1_repb_PBArep1


title: AF4_Freeze-thaw3_repb_PBArep1


title: Replicate 17 Treated RNA seq rep 2


title: Replicate 17 Treated RNA seq rep 1


title: Marginal_Symptomatic_Patient6


title: MII oocytes vivo 59

description: Library name: 59_vivo


title: Replicate 17 Control RNA seq rep 2


title: Plaque_Symptomatic_Patient7


title: SEC_Non-freeze-thaw1_repa_PBArep1


title: MII oocytes vivo 58

description: Library name: 58_vivo


title: Replicate 17 Control RNA seq rep 1


title: SEC_Freeze-thaw3_repa_PBArep1


title: MII oocytes vivo 57

description: Library name: 57_vivo


title: Marginal_Symptomatic_Patient5


title: RAW 264.7, 0h, RRP1,CLIP,replicate4

first: Zhou

last: Yumei

address: No.100,Chongwen Road

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences

description: Library name: CLIP_Ctr_4

library_source: other

data_processing:
Basecalls were performed using bcl2fastq v2.17 for DNBSEQ-T7 outpuUt.
CLIP-seq reads were trimmed from 3' end until the final base had aquality score > 30,using Fastp v0.20.0, discarding reads left with < 50 bp.
CLIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.1 Only uniquely mapping reads with at most two mismatches were retained.
To create CLIP-seq coverage plots, the locations of the mapped CLIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to rreads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS2 v2.2.6 with the significance cut-off cvalue <=0.01.
Assembly: bigWig files were generated using the genomicRanges R package. Scorerepresents the normalized coverage of DNA fragments at a given genomic coordinate. naarrowPeak files were generated using MACS2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: iCLIP

molecule: other

growth_protocol: DMEM，with 10% FBS

extract_protocol:
Ultraviolet-crosslinked (400 mJ cm−2 ) RAW 264.7 were lysed in lysis buffer (50 mM Tris-HCl (pH 7.4), 100mM NaCl, 1% NP-40, 0.1%SDS, 0.5% sodium deoxycholate and protease inhibitors) and sonicated. Lysates were treated with RNase I (Thermo Fisher Scientific) to fragment RNA and DNase I to remove DNA. Anti-FLAG® M2 Beads were washed three times using lysis buffer and incubated with proteins lyastes for 6h at 4°C. A 3’ RNA adaptor was ligated onto the RNA with T4 RNA ligase (NEB). Protein-RNA complexes were run on a 4-12% gradient Bis-Tris Gels (Invitrogen), transferred to NC membranes, and RNA was isolated off the membrane identically to standard seCLIP. A fraction of sample was used for western blot of CLIPed Flag-tagged RRP1, indicating regions excised for seCLIP library preparation. After purification, RNAs were reverse transcribed with Superscript III reverse transcriptase (Invitrogen) with nested specific primer and a protected reverse PCR primer as previously reported, free primer was removed (ExoSap-IT, Affymetrix) and a 3’ cDNA adaptor was ligated onto the cDNA product with T4 RNA ligase (NEB).
Libraries were then amplified with Premix Taq PCR mix (Takara). Adapters and primers were designed according to the commercial indexing and sequencing primers.

treatment_protocol: IL1β 100ng/ml for 4h or not

value: macrophages

value: wilde tye

tag: time point

tag: batch

value: bcl2fastq v2.17


title: Replicate 16 Treated RNA seq rep 2

tag: cell type


title: RAW 264.7, 4h, RRP1,CLIP,replicate5

description: Library name: CLIP_IL1β_5


title: Plaque_Symptomatic_Patient6

tag: tissue


title: RAW 264.7, 4h, RRP1,CLIP,replicate4

description: Library name: CLIP_IL1β_4

tag: treatment


title: Replicate 16 Treated RNA seq rep 1


title: MII oocytes vitro 55

description: Library name: 55_vitro


title: Plaque_Symptomatic_Patient5


title: MII oocytes vitro 56

description: Library name: 56_vitro


title: RAW 264.7, 0h, RRP1,CLIP,replicate2

description: Library name: CLIP_Ctr_2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for DNBSEQ-T7 outpuUt.
CLIP-seq reads were trimmed from 3' end until the final base had aquality score > 30,using Fastp v0.20.0, discarding reads left with < 50 bp.
CLIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.1 Only uniquely mapping reads with at most two mismatches were retained.
To create CLIP-seq coverage plots, the locations of the mapped CLIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to rreads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS2 v2.2.6 with the significance cut-off cvalue <=0.01.
Assembly: bigWig files were generated using the genomicRanges R package. Scorerepresents the normalized coverage of DNA fragments at a given genomic coordinate. naarrowPeak files were generated using MACS2 with default settings.
Supplementary files format and content: mm10
Library strategy: iCLIP

source_name: cell line

value: wild type


title: MII oocytes vitro 54

description: Library name: 54_vitro


title: Replicate 16 Control RNA seq rep 2


title: RAW 264.7, 0h, RRP1,CLIP,replicate3

description: Library name: CLIP_Ctr_3


title: Plaque_Symptomatic_Patient4


title: Marginal_Symptomatic_Patient4


title: Replicate 16 Control RNA seq rep 1


title: Replicate 15 Treated RNA seq rep 2


title: MII oocytes vitro 53

description: Library name: 53_vitro


title: RAW 264.7, 0h, RRP1,CLIP,replicate1

description: Library name: CLIP_Ctr_1


title: Marginal_Symptomatic_Patient3


title: Plaque_Symptomatic_Patient3


title: RAW 264.7, 4h, RRP1,CLIP,replicate3

description: Library name: CLIP_IL1β_3


title: RAW 264.7, 4h, RRP1,CLIP,replicate2

description: Library name: CLIP_IL1β_2


title: Marginal_Symptomatic_Patient2


title: Replicate 15 Treated RNA seq rep 1


title: Replicate 15 Control RNA seq rep 2


title: MII oocytes vitro 51

description: Library name: 51_vitro


title: MII oocytes vitro 50

description: Library name: 50_vitro


title: RAW 264.7, 4h, RRP1,CLIP,replicate1

description: Library name: CLIP_IL1β_1


title: Replicate 15 Control RNA seq rep 1


title: MII oocytes vitro 49

description: Library name: 49_vitro


title: Plaque_Symptomatic_Patient2


title: Replicate 14 Treated RNA seq rep 2


title: MII oocytes vitro 48

description: Library name: 48_vitro


title: Replicate 14 Treated RNA seq rep 1


title: Plaque_Symptomatic_Patient1


title: MII oocytes vitro 47

description: Library name: 47_vitro


title: Replicate 14 Control RNA seq rep 2


title: MII oocytes vitro 52

description: Library name: 52_vitro


title: Aged kidney treated with BPTES, sample 2

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

description:
Library name: Kid_BPTES_2
10x Genomics GEM-X

data_processing:
The demultiplexing, barcoded processing, and gene counting were performed by conducting CellRanger software v8.0.1.
Assembly: Mouse mm10
Supplementary files format and content: TSV files for barcodes, features, and count matrix

source_name: Kidney

extract_protocol:
Kidneys were minced by a sharp blade and digested with liberase solution (50 μg/ml liberase TH, 2 Kunitz units/ml DNase I, and 10 mM HEPES in RPMI) at 37oC for 1 hr. During the digestion, the tissue suspensions were passed through 18 G and 21 G needles sequentially to further homogenize residual tissues. After the digestion, all samples were passed through 70-μm cell strainer and pelleted by centrifugation at 400g for 5 mins. After RBC lysis and FcR blocking, cells were stained with anti-CD45 on ice for 30 mins.
20,000 CD45- and 9,000 CD45+ cells from the same tissue were mixed for preparing one cDNA sample. The library with dual index was performed according to the manufacturer’s instructions (Chromium GEM-X Single Cell 3' Reagent Kits v4, 10x Genomics).

value: Kidney

tag: Sex

value: Male

value: BPTES


title: Aged kidney treated with DMSO, sample 1

description:
Library name: Kid_DMSO_1
10x Genomics GEM-X

tag: genotype

value: DMSO


title: YBX1_KO_10Gy_IR_r3

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
small-RNASeq adapters were trimmed using Cutadapt (version 4.4)  in single end mode and the quality of the resulting fastq files were assessed using FastQC
The trimmed reads were then aligned to human hg38 reference genome using STAR aligner
Bigwig files from bamfiles were created using deepTools bamCoverage with binsize set at 1 with RPKM normalization
ComputeMatrix operation of deepTools was then used to calculate RPKM coverage across annotated YRNA genes.
Coverage across various smallRNA species were calculated using bedtools multicov in stranded mode. For tRNA derived fragments (tsRNA), MINTmap was used to generate unique read counts for various tsRNAs.
Assembly: hg38
Supplementary files format and content: Counts_Supplementary.xlsx contains raw read counts across various small RNA species based on hg38 annotation
Supplementary files format and content: Bigwig files contain RPKM normalized read counts across each  nucleotide position across the genome for a specific sample

growth_protocol: Wild Type HEK293T or YBX1-/- HEK293T cells were maintained in DMEM supplemented with 10% FBS, 1% L-glutamine and 1% pen-strep at 37°C and 5% CO2

extract_protocol:
Exosomes were isolated via size exclusion chromatography. RNA was extracted from exosome samples using miRVana miRNA isolation kit, following manufacturer's protocol for enrichment of small RNA.
Libraries were constructed using NEBNext® Multiplex Small RNA Library Prep Set (New England BioLabs)

treatment_protocol: Cell culture medium was replaced with exosome-depleted medium then cells immediately treated with 10Gy ionising radiation if applicable.

value: embryonic kidney

value: YBX1 KO 10Gy IR


title: Aged kidney treated with BPTES, sample 1

description:
Library name: Kid_BPTES_1
10x Genomics GEM-X


title: MII oocytes vitro 46

description: Library name: 46_vitro

value: MII oocytes


title: YBX1_KO_10Gy_IR_r2

value: WT


title: MII oocytes vitro 45

description: Library name: 45_vitro


title: YBX1_KO_10Gy_IR_r1


title: Replicate 14 Control RNA seq rep 1

value: monocyte

value: LPS+INFγ


title: MII oocytes vitro 44

description: Library name: 44_vitro

value: Wild-type


title: WT_10Gy_IR_r3

value: 10Gy IR


title: Replicate 13 Treated RNA seq rep 1


title: Replicate 13 Treated RNA seq rep 2


title: Aged kidney treated with DMSO, sample 2

description:
Library name: Kid_DMSO_2
10x Genomics GEM-X


title: Replicate 13 Control RNA seq rep 2


title: MII oocytes vitro 43

description: Library name: 43_vitro


title: Marginal_Symptomatic_Patient1

value: Carotid plaque tissue

value: Vascular cells


title: WT_10Gy_IR_r2


title: MII oocytes vitro 42

description: Library name: 42_vitro


title: Aged lung treated with BPTES, sample 1

description:
Library name: Lung_BPTES_1
10x Genomics GEM-X

source_name: Lung

extract_protocol:
Lungs were minced by a sharp blade and digested with liberase solution (50 μg/ml liberase TM, 2 Kunitz units/ml DNase I, and 10 mM HEPES in RPMI) at 37oC for 1 hr. During the digestion, the tissue suspensions were passed through 18 G and 21 G needles sequentially to further homogenize residual tissues. After the digestion, all samples were passed through 70-μm cell strainer and pelleted by centrifugation at 400g for 5 mins. After RBC lysis and FcR blocking, cells were stained with anti-CD45 on ice for 30 mins.
20,000 CD45- and 9,000 CD45+ cells from the same tissue were mixed for preparing one cDNA sample. The library with dual index was performed according to the manufacturer’s instructions (Chromium GEM-X Single Cell 3' Reagent Kits v4, 10x Genomics).

value: Lung


title: Aged lung treated with DMSO, sample 1

description:
Library name: Lung_DMSO_1
10x Genomics GEM-X


title: Aged lung treated with DMSO, sample 2

description:
Library name: Lung_DMSO_2
10x Genomics GEM-X


title: Aged lung treated with BPTES, sample 2

description:
Library name: Lung_BPTES_2
10x Genomics GEM-X


title: WT_10Gy_IR_r1


title: Replicate 13 Control RNA seq rep 1


title: Aged lung from p16 mouse treated with TAM+DT, sample 3

description:
Library name: Lung_p16_3
10x Genomics GEM-X

value: C57BL/6, p16-CreERT2

value: TAM+DT


title: WT_No_IR_r3


title: MII oocytes vitro 41

description: Library name: 41_vitro


title: MII oocytes vitro 40

description: Library name: 40_vitro


title: Replicate 12 Control RNA seq rep 2


title: Replicate 12 Control RNA seq rep 1


title: WT_No_IR_r2


title: MII oocytes vitro 39

description: Library name: 39_vitro


title: WT_No_IR_r1


title: Replicate 11 Treated RNA seq rep 2


title: Aged lung from p16-DTR mouse treated with TAM+DT, sample 3

description:
Library name: Lung_p16DTR_3
10x Genomics GEM-X

value: C57BL/6, p16-CreERT2/R26-LSL-DTR


title: BT935 patient-derived GBM cells, TMZRT treated cells with UK-5099 replicate 3

city: Winnipeg

first: Tanveer

last: Sharif

state: MB

address: 727 McDermot Avenue

institute: University of Manitoba

data_processing:
Raw data were processed using bcl2fastq v2.20.0.422 to generate demultiplexed fastq files.
Adaptors were trimmed from the raw FASTQ files using Cutadapt (v2.3) and the resulting reads were aligned to the human reference genome (GRCh38.p14) using STAR (v2.6.1a).
Gene counts were obtained using FeatureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: comma separated values file includes raw unnormalized counts for all samples

source_name: Glioblastoma brain tumor

growth_protocol: Patient-derived GBM cells were maintained in serum-free DMEM/F12 medium supplemented with 1X N2 supplement, 1X SM1 supplement, 20 ng/mL EGF, 10 ng/mL bFGF, 2 µg/mL of Heparin, and 1X antibiotic-antimycotic and propagated as non-adherent neurospheres.

extract_protocol:
RNA was extracted from cells using the BioRad Aurum™ Total RNA Mini Kit per manufacturer’s protocol.
Libraries were prepared using the Illumina Stranded mRNA kit and sequenced on the Illumina NextSeq, generating 74bp paired-end reads.

treatment_protocol: GBM cells received 25 µM of temozolomide and controls received equal volumes of DMSO vehicle. Immediately following TMZ treatment, cells were exposed to 1 Gy of X-ray irradiation using the Rad Source 2000 and incubated at 37°C in a 5% CO2 incubator for 1 hour. To mimic the exposure time of chemotherapy received by patients, where the half-life of TMZ is approximately 1-2 hours in circulation, the drug treatment was washed out of the patient-derived GBM cells after 1 hour and replaced with fresh media. The concurrent chemoradiotherapy treatment regimen was repeated daily for 5 consecutive days. After the 5th treatment day, patient-derived GBM cells received a 2-day treatment holiday prior to collection and subsequent analysis. Chemoradiotherapy naive or TMZRT-resistant GBM cells received 100 µM of UK-5099 or equal volumes of DMSO vehicle.

value: Glioblastoma brain tumor

value: Tumor cell

value: TMZRT + UK5099


title: BT935 patient-derived GBM cells, TMZRT treated cells with UK-5099 replicate 2


title: MII oocytes vivo 19

description: Library name: 36_vivo


title: Aged lung from p16-DTR mouse treated with TAM+DT, sample 2

description:
Library name: Lung_p16DTR_2
10x Genomics GEM-X

value: Male


title: Replicate 11 Treated RNA seq rep 1


title: Replicate 10 Treated RNA seq rep 2


title: Aged lung from p16 mouse treated with TAM+DT, sample 2

description:
Library name: Lung_p16_2
10x Genomics GEM-X


title: BT935 patient-derived GBM cells, TMZRT treated cells with UK-5099 replicate 1


title: Aged lung from p16-DTR mouse treated with TAM+DT, sample 1

description:
Library name: Lung_p16DTR_1
10x Genomics GEM-X


title: Replicate 9 Treated RNA seq rep 2


title: MII oocytes vivo 18

description: Library name: 35_vivo


title: BT935 patient-derived GBM cells, Naïve cells treated with UK-5099 replicate 3

value: Naive + UK5099


title: MII oocytes vivo 17

description: Library name: 34_vivo

value: MII oocytes


title: BT935 patient-derived GBM cells, Naïve cells treated with UK-5099 replicate 2


title: Aged lung from p16 mouse treated with TAM+DT, sample 1

description:
Library name: Lung_p16_1
10x Genomics GEM-X


title: Replicate 10 Treated RNA seq rep 1

value: WT


title: granulosa cell from hierarchical follicles

city: Leshan

first: Shigang

last: Yu

address: No. 778, Binhe Road, shizhong distinct

institute: Leshan normal university

description:
Library name: G
10X Genomics

data_processing:
The raw base call ﬁles were demultiplexed and converted to FASTQ ﬁles. The FASTQ files were processed and aligned to chicken reference genome (GRCg7b) using Cell Ranger software (version 7.0.1) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: GRCg7b
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Gallus gallus

source_name: follicle

extract_protocol:
The GC layers of hierarchical follicles (group HF-GCs) and prehierarchical follicles (group PHF-GCs) were collected.GC layers were cut into pieces and then digested with 1 mg/ml of collagenase type IV (Sigma) in PBS for 10 min at 37 °C until cells were completely separated. Dissociated cells were ﬁltered through a 40-µm cell strainer, and were washed twice by resuspension in DMEM. Cell viability of GCs exceeded 90% after their isolation. The cell density was adjusted to the concentration of 700–1200 cells/μL. High quality single cell suspensions were subjected to 10x scRNA-seq library preparation using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, Pleasanton, California, USA) according to the manufacturer’s protocol.
The GC suspensions were loaded on the Chromium Single Cell Controller Instrument (10× Genomics, Pleasanton, California, USA) to generate single-cell GEMs (gel beads in emulsions). After that, the RNA from the barcoded cells was subsequently reverse-transcribed to obtain the full-length cDNA. The cDNA libraries were quantiﬁed by Agilent 2100 Bioanalyzer, and subsequently sequenced by OE Biotech Co., Ltd (Shanghai, China) using an BGI-T7 sequencing system (BGI, Shenzhen, China).

value: follicle

value: granulosa cells

value: hierarchical follicles


title: Replicate 9 Control RNA seq rep 2

value: monocyte

value: LPS+INFγ


title: MII oocytes vivo 16

description: Library name: 33_vivo

value: Wild-type


title: BT935 patient-derived GBM cells, Naïve cells treated with UK-5099 replicate 1


title: MII oocytes vivo 21

description: Library name: 38_vivo


title: Replicate 9 Treated RNA seq rep 1


title: Naive and infected cells, mixed sample (non-demultiplexed)

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

institute: Weizmann

description:
Library name: Sample 1
Naïve and infected cells

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform alignment to the genome (mm10), barcode assignment for each cell, gene counting by unique molecular identifier (UMI) counts, and samples demultiplexing based on the TotalSeq B hashing indexes (hash index TGCCTATGAAACAAG for naïve PP and hash index CCGATTGTAACAGAC for infected PP at 72 hpi).
Assembly: mm10
Supplementary files format and content: Text files with UMI counts table for each gene in each cell in the naïve and infected samples

source_name: Peyer's patches

extract_protocol:
Naïve and 72 hours post infection mice were sacrificed, Peyer's patches were removed for single cell RNA-seq.
Cells extracted from mice PP (naïve and infected) were counted, resuspended with  0.04% BSA in DPBS, and barcoded with hashing antibodies (TotalSeq B hashing indexes (BioLegend, 199902), hash index TGCCTATGAAACAAG for naïve PP and hash index CCGATTGTAACAGAC for infected PP at 72 hpi) according to the manufacturer’s instructions. The samples were then directly used for single-cell sequencing by the Chromium Single Cell 3′ Reagent version 3 kit and Chromium Controller (10X Genomics, CA, USA), and run on one 10X lane.

value: Peyer's patches

value: mixture of immune cells

value: Naïve or infected cells


title: MII oocytes vivo 20

description: Library name: 37_vivo


title: BT935 patient-derived GBM cells, TMZRT treated replicate 3

value: TMZRT + DMSO vehicle


title: MII oocytes vivo 15

description: Library name: 32_vivo


title: granulosa cell from prehierarchical follicles

description:
Library name: PHF_GCs
10X Genomics

value: prehierarchical follicles


title: MII oocytes vivo 14

description: Library name: 31_vivo


title: Replicate 8 Treated RNA seq rep 2


title: BT935 patient-derived GBM cells, TMZRT treated replicate 2

value: Glioblastoma brain tumor

value: Tumor cell


title: Replicate 8 Treated RNA seq rep 1


title: Ileum_inf_72h_1

description:
Library name: Sample 9
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_72h_1

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Normalized data was log2-transformed, and a minimal expression threshold of 2 was set
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

source_name: Ileum

extract_protocol:
0,24, and 72 hours post infection mice were sacrificed by cervical dislocation, and the desired tissues (ileum, caecum, Payer's patches and spleen) were removed for analysis.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

value: Ileum

value: enriched for immune cells

value: infected

tag: time post_infection_(hours)

tag: replicate


title: MII oocytes vivo 12

description: Library name: 29_vivo

value: MII oocytes


title: Ileum_inf_24h_5

description:
Library name: Sample 8
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_24h_5


title: Replicate 8 Control RNA seq rep 2

value: WT


title: BT935 patient-derived GBM cells, Naïve control replicate 3

value: Naive + DMSO vehicle


title: MII oocytes vivo 11

description: Library name: 28_vivo


title: BT935 patient-derived GBM cells, Naïve control replicate 2


title: Replicate 8 Control RNA seq rep 1


title: MII oocytes vivo 10

description: Library name: 27_vivo


title: Ileum_inf_72h_4

description:
Library name: Sample 11
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_72h_4


title: Ileum_inf_24h_3

description:
Library name: Sample 6
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_24h_3


title: BT935 patient-derived GBM cells, Naïve control replicate 1


title: Replicate 7 Treated RNA seq rep 2


title: MII oocytes vivo 9

description: Library name: 26_vivo


title: Ileum_inf_24h_2

description:
Library name: Sample 5
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_24h_2


title: Ileum_inf_72h_3

description:
Library name: Sample 10
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_72h_3


title: BT935 patient-derived GBM cells, TMZRT treated replicate 1


title: Ileum_inf_24h_1

description:
Library name: Sample 4
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_24h_1


title: MII oocytes vivo 7

description: Library name: 24_vivo


title: MII oocytes vivo 13

description: Library name: 30_vivo


title: Ileum_naive_3

description:
Library name: Sample 3
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_naive_3

value: naive


title: Replicate 7 Control RNA seq rep 2

value: monocyte


title: MII oocytes vivo 8

description: Library name: 25_vivo


title: Input FADU

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

institute: IRCCS Regina Elena National Cancer Institute

data_processing:
The libraries were sequenced using the NextSeq 500 system from Illumina, CA. Reads were quality controlled with FastQC v0.11.9  and aligned to the human hg19 reference using bowtie v2.3.4.3
The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools v1.7
P63 and ZNF148 peaks were called with MACS2 v2.2.6 (command-line parameters: -callpeak -B --SPMR --call-summits -q 0.001 -g hs) using matched input DNA as a control.
QC statistics of the whole workflow were obtained with multiqc v1.12
Assembly: hg19
Supplementary files format and content: bigwig and narrow peaks (excluded input samples)

source_name: FADU

extract_protocol:
DNA fragments from three independent ChIP assays were purified with QIAquick PCR Purification Kit (QIAGEN #28106).
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)
Adapter ligation ChIP-seq

value: FADU

tag: chip antibody


title: Replicate 9 Control RNA seq rep 1

tag: cell line

value: LPS+INFγ


title: Input HEKn

source_name: KEHn

value: KEHn


title: Replicate 7 Treated RNA seq rep 1


title: Replicate 7 Control RNA seq rep 1


title: ChIP ZNF148 KEHn


title: MII oocytes vivo 6

description: Library name: 23_vivo

source_name: MII oocytes

value: Wild-type


title: Ileum_naive_2

description:
Library name: Sample 2
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_naive_2


title: Replicate 6 Treated RNA seq rep 2


title: Ileum_naive_1

description:
Library name: Sample 1
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_naive_1


title: ChIP p63 KEHn


title: Ileum_inf_24h_4

description:
Library name: Sample 7
column name in data_matrix_bulk_mouse_tissues.txt:  Ileum_inf_24h_4


title: MII oocytes vivo 5

description: Library name: 22_vivo


title: Replicate 6 Treated RNA seq rep 1


title: mut_inf_PP_3

description:
Library name: Sample 11
column name in data_matrix_bulk_mut_exp.txt:  mut_inf_PP_3

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (mm10), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Normalized data was log2-transformed, and a minimal expression threshold of 3 was set
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized number of reads (log2 scale) for each sample

extract_protocol:
0 and 72 hours post infection mice were sacrificed by cervical dislocation, and the Payer's patches were removed for analysis.
RNA-seq libraries were prepared according to Cel-seq libraries protocol81 with a minor modification: the starting material was purified bulk RNA (up to 1ng RNA per library).

treatment_protocol: Female C57BL/6 mice, 7-9 weeks old, were orally infected with wild-type or triple mutant (invA/fliC/fljB) Salmonella Typhimurium strain IR715

value: Peyer's patches

value: mutant infected


title: MII oocytes vivo 4

description: Library name: 21_vivo


title: ChIP ZNF148 FADU


title: ChIP p63 FADU


title: Replicate 6 Control RNA seq rep 2


title: MII oocytes vivo 3

description: Library name: 20_vivo


title: mut_inf_PP_2

description:
Library name: Sample 10
column name in data_matrix_bulk_mut_exp.txt:  mut_inf_PP_2


title: MII oocytes vivo 2

description: Library name: 19_vivo


title: Replicate 6 Control RNA seq rep 1


title: LSEC SW-CSCI rep 2

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
Library name: LSEC SW-CSCI rep 2
replicate 2

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the human reference genome hg38 using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts and annotation with Cufflinks.
Variance stabilization performed using log2 scaling.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include log2 counts values for each sample

source_name: Liver Sinusoidal Endothelial Cell (LSEC)

growth_protocol: LSECs were stimulated with conditioned media derived from differentiated colorectal cancer cells and cancer stem cells (CSCs), the latter generated by reprogramming SW620 and CT26 cell lines.

extract_protocol:
RNA was harversted using mini plus kit (Qiagen). Roughly 200ng of high quality total RNA was used for the transcriptomic assays.
Library construction was performed following Ilumina recommendation. Sequencing library was prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation. The fragmentation and ligation reactions were performed in a single step that increases the efficiency of the library preparation process.  Then, adapter-ligated fragments were amplified by PCR and purified in a gel. Subsequently, library was loaded into a flow cell where fragments were captured on a lawn of surface-bound oligos complementary to the library adapters.

treatment_protocol: After performing quality control, checking the RIN value of each sample was bigger than 6, and ensuring RNA quantity was higher than 200ng.

value: LSEC conditioned with Cancer Stem Cells (CSCs) derived in absence of PCSK9 from metastatic colorectal adenocarcinoma cell line SW620


title: Replicate 5 Treated RNA seq rep 2


title: mut_inf_PP_1

description:
Library name: Sample 9
column name in data_matrix_bulk_mut_exp.txt:  mut_inf_PP_1


title: MII oocytes vivo 1

description: Library name: 18_vitro


title: Replicate 5 Treated RNA seq rep 1


title: wt_inf_PP_4

description:
Library name: Sample 8
column name in data_matrix_bulk_mut_exp.txt:  wt_inf_PP_4

value: wild-type infected


title: LSEC SW-CSCI rep 3

description:
Library name: LSEC SW-CSCI rep 3
replicate 3

value: Liver Sinusoidal Endothelial Cell (LSEC)


title: wt_inf_PP_2

description:
Library name: Sample 6
column name in data_matrix_bulk_mut_exp.txt:  wt_inf_PP_2


title: wt_inf_PP_3

description:
Library name: Sample 7
column name in data_matrix_bulk_mut_exp.txt:  wt_inf_PP_3


title: Replicate 5 Control RNA seq rep 2


title: LSEC SW-CSCI rep 1

description:
Library name: LSEC SW-CSCI rep 1
replicate 1


title: MII oocytes vitro 15

description: Library name: 15_vitro


title: Replicate 4 Control RNA seq rep 2


title: LSEC SW-CSC rep 2

description:
Library name: LSEC SW-CSC rep 2
replicate 2

value: LSEC conditioned with Cancer Stem Cells (CSCs) derived from metastatic colorectal adenocarcinoma cell line SW620


title: LSEC SW-CSC rep 3

description:
Library name: LSEC SW-CSC rep 3
replicate 3


title: naïve_PP_4

description:
Library name: Sample 4
column name in data_matrix_bulk_mut_exp.txt:  naïve_PP_4

value: enriched for immune cells

value: naïve


title: MII oocytes vitro 16

description: Library name: 16_vitro

value: MII oocytes


title: naïve_PP_3

description:
Library name: Sample 3
column name in data_matrix_bulk_mut_exp.txt:  naïve_PP_3


title: Replicate 4 Control RNA seq rep 1

value: WT


title: MII oocytes vitro 14

description: Library name: 14_vitro


title: LSEC SW-CSC rep 1

description:
Library name: LSEC SW-CSC rep 1
replicate 1


title: Replicate 3 Treated RNA seq rep 2


title: naïve_PP_2

description:
Library name: Sample 2
column name in data_matrix_bulk_mut_exp.txt:  naïve_PP_2


title: MII oocytes vitro 12

description: Library name: 12_vitro


title: LSEC SW-620 rep 3

description:
Library name: LSEC SW-620 rep 3
replicate 3

value: LSEC conditioned with metastatic colorectal adenocarcinoma cell line SW620


title: LSEC SW-620 rep 1

description:
Library name: LSEC SW-620 rep 1
replicate 1


title: Replicate 3 Treated RNA seq rep 1


title: MII oocytes vitro 17

description: Library name: 17_vitro


title: Replicate 5 Control RNA seq rep 1


title: LSEC SW-620 rep 2

description:
Library name: LSEC SW-620 rep 2
replicate 2


title: c-JUN_Cal33_ChIP-seq

city: papagou, athens

first: THEODOROS

last: RAMPIAS

state: N/A = Not Appli

address: 4 SORANOU EPHESIOU STR, PAPAGOU, BRFAA

department: Systems Biology

country: Greece

institute: Biomedical research foundation Academy of Athens

data_processing:
The quality of sequencing reads was evaluated by the application of FastQC (Galaxy Version 0.73). Adaptors’ contaminants and low-quality sequencing reads were trimmed by the application of Trim Galore (Galaxy Version 0.6.7).
Trimmed sequencing reads were aligned to the human (hg19) reference genome assembly by utilizing Bowtie2 (Galaxy Version 2.4.2)32 and selecting the “-very-sensitive” parameter.
Duplicate reads were extracted from the analysis using the RmDup tool (Galaxy 2.0.1) from SAMtools package.
Peaks were captured through MACS2 callpeak (v2.1.2.2) (--bw 300, - -qvalue 0.05, --keep-dup 1).
Peaks mapped unambiguously in unplaced contigs (chrUn, chrM and Random assemblies) or overlapped with ENCODE hg19 blacklisted regions were excluded from the downstream steps of analyses.
Assembly: hg19
Supplementary files format and content: bigwig file (RPKM normalized signal), bed file of total peaks

growth_protocol: Cells were cultured in complete medium containing Dulbecco’s modified Eagle medium (DMEM, Sigma Aldrich, #D6429) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco, #1050064) and penicillin (100 units/ml)/streptomycin (100 μg/ml) (Gibco, #15140122) in a humidified atmosphere at 37°C with 5% CO2. The cells were passaged twice a week according to confluence.

extract_protocol: Chromatin was prepared from Cal-33 cells with the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling, #9003) according to the manufacturer's instructions.

value: human head and neck squamous cell carcinoma cells

value: c-Jun (60A8) Rabbit mAb (#9165, Cell signaling)


title: naïve_PP_1

description:
Library name: Sample 1
column name in data_matrix_bulk_mut_exp.txt:  naïve_PP_1


title: MII oocytes vitro 11

description: Library name: 11_vitro

data_processing:
We processed a total of 88 libraries (88 oocytes), adapting and quality-trimming them using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) for sequences with a Phred score of less than 20. Additionally, one negative control was sequenced to detect any technical issues. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using HiSat2 version 2.1.0 in single-end mode. For the cumulus cell samples, feature counting at the gene and transcript isoform level was done using rsem-calculate-expression (RSEM v1.3.3) (Li et al., 2011). Data processing was done in R (v4.2.2) using the edgeR (v3.38.4) package for differential gene expression analysis (Chen et al., 2016).
A total of 46 scBS-seq libraries were processed for analysis. The initial 6 base pairs, which included the N portion of the random primers, adapters, and low-quality bases (Phred score <20), were trimmed using Trim Galore version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) in single-end mode. High-quality reads were aligned to the bovine reference genome (UMD3.1.1) using Bismark version 0.18.2 (Krueger & Andrews, 2011) in single-end and nondirectional mode, followed by deduplication and methylation calling through Bismark functions.
Assembly: Bos Taurus (UMD3.1_v91)
Supplementary files format and content: Normalized counts
Supplementary files format and content: 20CpG_windows_methylation

extract_protocol:
DNA and RNA from oocyte were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery. Total RNA was extracted from seven cumulus cells samples (four from in vivo matured, three from in vitro matured COCs) using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction. The RNA samples underwent quality and concentration assessments using an RNA 6000 Pico Chip (Agilent Technologies, Carlsbad, CA, USA).
ScRNA-seq and scBSseq


title: wt_inf_PP_1

description:
Library name: Sample 5
column name in data_matrix_bulk_mut_exp.txt:  wt_inf_PP_1


title: Replicate 3 Control RNA seq rep 2

value: monocyte


title: MII oocytes vitro 10

description: Library name: 10_vitro


title: DMM4

city: Quanzhou

first: wei

last: zhang

address: NO. 1028 Anji South Road, Fengze District

institute: quanzhou first hospital affiliated to fujian medical university

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Hisat2 v2.0.5
Supplementary files format and content: FPKM values for each sample

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher). 1.5 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Kidney

value: UUO

value: DMM


title: Replicate 3 Control RNA seq rep 1

value: LPS+INFγ


title: DMM5


title: RHH4133

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

description: Library name: LV 12.12. Wü (RHH4133)

data_processing:
Sequencing was performed on the Illumina Hiseq2000 high-output with 2 × 100 sequencing length. Fastq files were aligned to the genomes (hg19 and mm9) using Tophat2 (version 2.2.0.12) with default parameters. Circular RNAs were quantified with to circbase annotations. Counts were normalized using DESeq2
Assembly: Hg19
Supplementary files format and content: csv

source_name: heart tissue

extract_protocol:
Samples for RNA-seq were 1 μg in 10 μl, as assessed by the Agilent Bioanalyzer for RNA integrity, prior to library preparation.For RNaseR treatment, total RNA was first subjected to large ribosomal RNAs removal using RiboMinus™ Transcriptome Isolation Kit (ThermoScientific) before treatment with RNase R (epicentre) at 3 U of RNase R per µg of RNA. Digested RNA was purified with standard RNA Phenol/Chloroform/Isoamylic alcohol extraction.
Library preparation was performed using the Illumina Truseq kit according to manufacturer’s protocol.

value: heart tissue

tag: disease state

value: end stage heart failure


title: RHH4132

description: Library name: LV 13.11.99 Wü (RHH4132)


title: MII oocytes vitro 13

description: Library name: 13_vitro

value: Wild-type


title: DMM3


title: Replicate 2 Treated RNA seq rep 2


title: RHH4131

description: Library name: LV 4.7.99 Wü (RHH4131)


title: DMM2


title: Replicate 2 Treated RNA seq rep 1


title: RHH4130

description: Library name: LV 4.6.99 Wü (RHH4130)


title: MII oocytes vitro 6

description: Library name: 6_vitro


title: Replicate 2 Control RNA seq rep 2


title: DMM1


title: RHH4129

description: Library name: LV 25.3.99 Wü (RHH4129)


title: Replicate 2 Control RNA seq rep 1


title: RHH4123

description: Library name: H-113 (RHH4123)

value: healthy


title: MII oocytes vitro 5

description: Library name: 5_vitro


title: CTL5

value: control


title: CTL4


title: MII oocytes vitro 4

description: Library name: 4_vitro


title: MII oocytes vitro 3

description: Library name: 3_vitro


title: RHH4121

description: Library name: H-106 (RHH4121)


title: MII oocytes vitro 9

description: Library name: 9_vitro


title: Replicate 1 Treated RNA seq rep 2


title: CTL2


title: MII oocytes vitro 2

description: Library name: 2_vitro


title: MII oocytes vitro 8

description: Library name: 8_vitro


title: Replicate 1 Treated RNA seq rep 1


title: RHH4122

description: Library name: H-108 (RHH4122)


title: Replicate 1 Control RNA seq rep 2


title: Replicate 1 Control RNA seq rep 1


title: CTL1


title: RHH4120

description: Library name: H-105 (RHL4120)


title: MII oocytes vitro 7

description: Library name: 7_vitro


title: MII oocytes vitro 1

description: Library name: 1_vitro


title: PCR_14c

status: Public on Jul 01 2025

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: processed data file: Count_Table_PCR_Experiment.xlsx

data_processing:
library strategy: DNA-seq (PCR product sequencing)
The HiSeq Real Time Analysis software (RTA 1.12) was used for processing image files, the Illumina CASAVA_v1.8.2 was used for converting binary base calls and qualities to fastq format.
The fastq files for each lane were concatenated and aligned with Phix using Bowtie2
Data were filtered using the following procedure: PhiX mapped reads were filtered, the remaining sequence reads were adapter trimmed and de-barcoded based on barcode indices with 0-mismatch, 1-mismatch or 2-mismatch.
Duplicate reads were collapsed to obtain unique read counts in each instance. The read counts for each barcode oligos are calculated to get overall count and unique count.
Clustering analysis was performed using 1-Pearson correlations with average linking
Genome_build: None
Supplementary_files_format_and_content: Each Excel file contains the count table to measure the abundance of the oligonucleotides sequenced for each sample in  a specific experiment.

organism: synthetic construct

source_name: Oligos_PCR Experiment

extract_protocol:
Antibody conjugates bearing a cleavable covalently attached anchor oligonucleotides were generated by commercially available hydrazine-carbonyl conjugation chemistry.  Synthetic signature oligonucleotides comprised of all necessary Illumina adapter sequences and an extended barcode were hybridized to the universal anchor DNA sequence.
Following cleavage and isolation of the oligonucleotide complexes, libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.  Following preamplification, the final purified products are quantitated by qPCR before cluster generation and sequencing.

tag: sample group/info.

value: PCR cycle 14

tag: antibody binding

value: unique counts cycle 14

tag: molecule type

value: Oligos; PCR product


title: PCR_12c

value: PCR cycle 12

value: unique counts cycle 12


title: PCR_6c

value: PCR cycle 6

value: unique counts cycle 6


title: PCR_8c

value: PCR cycle 8

value: unique counts cycle 8


title: PCR_10c

value: PCR cycle 10

value: unique counts cycle 10


title: PCR_9c

value: PCR cycle 9

value: unique counts cycle 9


title: CTL3

value: Kidney

value: WT

value: UUO


title: PCR_4c

value: PCR cycle 4

value: unique counts cycle 4


title: PCR_1c

value: PCR cycle 1

value: unique counts cycle 1


title: PCR_2c

value: PCR cycle 2

value: unique counts cycle 2

value: Oligos; PCR product


title: ST

description: processed data file: Count_Table_Her2_Singleplex_Experiment.xlsx

source_name: Oligos_Her2 Experiment - Singleplex

value: standards

value: slide


title: RHH4119

description: Library name: H-103 (RHH4119)

value: heart tissue

value: healthy


title: UBQLN2(P506T)_3

city: baltimore

first: Yang

last: Liu

address: 615 N wolfe street

department: BMB

institute: Johns Hopkins

data_processing:
Raw reads were processed with TrimGalore v0.6.7 and controlled for quality with FastQC v.0.11.9. The processed reads were mapped to the human genome (hg38) and GENCODE v19 annotated transcripts using Hisat2 v2.2.1 and quantified with featureCounts v2.0.1. Raw gene counts were loaded into R to perform differential expression analysis with edgeR.
Assembly: human genome (hg38)
Supplementary files format and content: excel contain the normalized reads

source_name: motor neurons

extract_protocol:
Total RNAs were isolated using an RNeasy Plus mini kit (Qiagen, 74136)
RNA libraries for sequencing were constructed with a commercial kit (Invitrogen, A39005096)

value: motor neurons

value: glucose starvation for 33 hours


title: Mil_load

description: processed data file: Count_Table_Tissue_Experiment_Two.xlsx

source_name: Oligos_Tissue Experiment 2

value: additional 709 standards and loading control experiment

value: oligos on slide


title: Mil_C

description: processed data file: Count_Table_Tissue_Experiment_One.xlsx

source_name: Oligos_Tissue Experiment 1

value: 709 standards and  control experiments


title: UBQLN2(P506T)_2

value: glucose starvation for 32 hours


title: UBQLN2(P506T)_1

value: glucose starvation for 31 hours


title: UBQLN2(P497H)_1

value: glucose starvation for 27 hours