title: Ef MV RNA 10h Z4

description:
Library name: V350158887_L03_2
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_2


title: Lc MV RNA 10h Z2

status: Public on Feb 20 2026

type: SRA

city: Saarbrücken

first: Shusruto

last: Rishik

state: Saarland

address: Informatik Campus E2.1

department: Zentrum für Bioinformatics

country: Germany

institute: Universität des Saarlandes

description:
Library name: V350158887_L01_100
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_100

library_source: transcriptomic

data_processing:
Snakepipes v2.7.3
Sequence reads were processed using Snakepipes where STAR was used to map to GRCh38 using default options.
FeatureCount from subreads was used to quantify mRNA counts with the parameters (-C -Q 10 --primary)
Assembly: GRCh38
Supplementary files format and content: tsv file contains raw read counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human colon adenocarcinoma cells, Caco-2 (ATCC HTB-37), were maintained in DMEM (Thermo Fisher Scientific) supplemented with 10 % (v/v) FCS (Thermo Fisher Scientific) and 1 % (v/v) non-essential amino acids (Thermo Fisher Scientific) at 37 °C and 5 % CO2. Medium was exchanged every 2-3 days, and the cells were split once a week. All experiments were performed during passage 19 ± 5.

extract_protocol:
Total RNA was isolated from the Caco-2 cells using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
DNA libraries were prepared with the high-throughput MGISP-960 sample preparation system using the MGIEasy rRNA Depletion Kit (MGI Technologies) and MGIEasy RNA Library Prep Set (MGI Technologies) according to the manufacturer’s recommendations. After PCR, different barcoded samples were pooled in equal amount and circularized to generate single stranded DNA libraries (ssDNA). DNA nanoball (DNB) were generated by rolling circle amplification. Paired-end sequencing (PE100) was performed using DNBSEQ-G400RS High-throughput Sequencing Reagent Set (MGI Technologies) on the DNBSEQ-G400 instrument.

treatment_protocol: See description for samples

tag: incubation time

tag: cell line

tag: bacterial strain

value: L. casei DSM 20011

tag: treatment

value: transfection with 100 ng BEV-RNA


title: Breast cancer serum sample 40

type: RNA

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

country: Spain

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

data_processing: Cq values were determined using the second derivative method in Roche LightCycler software. Quality control included melting curve analysis, exclusion of reactions with more than one melting temperature, deviation from reference melting temperatures, and low amplification efficiency. Endogenous miRNAs let-7d-5p and let-7i-5p were used as internal reference controls. Expression data were normalized and subsequently log2-transformed for statistical analysis. Batch information is provided in the sample annotations.

label: SYBR Green

source_name: Serum

label_protocol: Not applicable. Quantification was performed using SYBR Green chemistry.

growth_protocol: Not applicable. Human serum samples collected from participants in the MCC-Spain study.

extract_protocol: Total RNA was extracted from 200 µL of serum using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN). Serum samples were thawed on ice and centrifuged at 3,000×g for 5 minutes at 4 °C. Buffer RPL containing carrier RNA and spike-in template mix was added, followed by Buffer RPP. RNA was eluted in 50 µL according to the manufacturer’s protocol.

treatment_protocol: Blood samples were collected prior to any oncological treatment (surgery, chemotherapy, or radiotherapy).

tag: tissue

value: Serum

value: case

value: Luminal A

tag: age


title: SW620_INVIVO_CDK19_CL2_CON_6H_B

city: Sutton

first: Konstantinos

last: Mitsopoulos

state: London

address: 15 Cotswold Road

department: Cancer Therapeutics Unit

country: United Kingdom

institute: The Institute of Cancer Research

description: Replicate 2 of 3

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
# 1. Initialisation
library(limma)
# 2. Read in tab-delimited targets file
sw620_in_vivo_targets <- readTargets(sw620_in_vivo_sample_annotation.txt)
# 3. Use LIMMA's read.maimages function to load data into an RGList object
sw620_in_vivo_RG <- read.maimages(sw620_in_vivo_targets, source=agilent)
# 4. Subtract the background (optional, but recommended)
sw620_in_vivo_RG.b <- backgroundCorrect(sw620_in_vivo_RG, method=normexp, offset=50)
# 5. Normalize within and between the arrays - remove controls
sw620_in_vivo_MA.p <- normalizeWithinArrays(sw620_in_vivo_RG.b, method=loess)
sw620_in_vivo_MA.pAq <- normalizeBetweenArrays(sw620_in_vivo_MA.p, method=Aquantile)
sw620_in_vivo_MA2.pAq <- sw620_in_vivo_MA.pAq[sw620_in_vivo_MA.pAq$genes$ControlType==0,]
# 6. Use the avereps function to average replicate spots
sw620_in_vivo_MA2.ave <- avereps(sw620_in_vivo_MA2.pAq, ID=sw620_in_vivo_MA2.pAq$genes$ProbeName)
# 7. Whole spot contrasts (to use for deriving average expression):
write.table(sw620_in_vivo_MA2.ave$A, file = sw620_in_vivo_MA2_ave_A_expression_matrix.txt, sep=\t)
# 8. Within spot contrasts (to use for log2FC calculations)
write.table(sw620_in_vivo_MA2.ave$M, file = sw620_in_vivo_MA2_ave_M_expression_matrix.txt, sep=\t)

label_protocol: Cy5 (red): human reference standard (Stratagene), Cy3 (green): experimental samples

extract_protocol: standard protocol

tag: condition

value: in vitro

tag: cell line background

tag: cell type

value: colorectal cell line

tag: clone

value: CDK19 KO, clone2

tag: compound

value: Control

source_name: human reference standard

value: reference


title: human.PDAC.CAF.DMSO.1

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: Library name: SAM24526226

data_processing:
Quality check and trimming of raw reads were performed using fastp 0.23.4 with the parameters: --disable_quality_filtering -l 12 --disable_adapter_trimming --trim_poly_x.
Single-end (SE) trimmed reads were aligned to the human genome GRCh38 and a feature count matrix was generated using HTSeqGenie 4.4.6.
The expression profiles were filtered to drop low-expressed genes using edgeR::filterByExpr and then normalized using limma-voom.
Differential expression analysis was performed by fitting a linear model to the data using lmFit from limma. To identify DE calls, we used a logFC threshold of |0.58| to test the significance of fold change (limma::treat()). To report significant DE genes, we used logFC and FDR thresholds of |0.58| and 0.05, respectively.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing the gene-level feature count matrix (raw counts) generated by HTSeqGenie for all samples.
Supplementary files format and content: Tab-delimited text file containing the CPM (Counts Per Million) normalized expression matrix for all samples.

molecule: polyA RNA

source_name: PDAC CAF CAF08

growth_protocol: Commercially available human lung adenocarcinoma cancer-associated fibroblasts (CAF07-AD, Vitro Biopharma) and pancreatic adenocarcinoma cancer-associated fibroblasts (CAF08, Vitro Biopharma) were obtained from Vitro Biopharma. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose supplemented with 10% tetracycline-negative heat-inactivated fetal bovine serum and 1X GlutaMAX. Low-passage CAFs were seeded in 6-well tissue culture plates at 300,000 cells per well and grown to approximately 70% confluence.

extract_protocol:
After 48 hours of treatment, cells were harvested using 1X Gibco TrypLE (Thermo Fisher Scientific) and centrifuged at 5000 rpm for 5 minutes to collect cell pellets. Total RNA was isolated using the QIAGEN RNeasy Plus Mini Kit (QIAGEN) following the manufacturer’s instructions. RNA quality was assessed using High Sensitivity RNA ScreenTape on TapeStation 4200 (Agilent Technologies) and quantified using the Quant-iT RiboGreen RNA Kit (Thermo Fisher Scientific) on a Victor X2 Multilabel Microplate Reader.
Sequencing libraries were generated using the Illumina Stranded mRNA kit (Illumina) with an input of 100-1000 nanograms of total RNA. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific). The average library size was determined using D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq X Plus (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: Cells were treated with the TEAD inhibitor GNE-7883 at final concentrations of 1 µM or 3 µM. Control conditions were treated with DMSO to match the DMSO content of the drug-treated samples. Treatments were conducted for 48 hours.

value: PDAC CAF CAF08

value: Cancer associated fibroblasts

value: DMSO


title: Ef MV RNA 10h Z3

description:
Library name: V350159056_L01_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_99

value: E. faecalis DSM 20478

value: transfection with 5 ng BEV-RNA


title: SW620_INVIVO_CDK19_CL2_CON_6H_A

description: Replicate 1 of 3


title: human.lung.CAF.3.uM.TEADi.3

description: Library name: SAM24526225

source_name: NSCLC CAF CAF07-AD

value: NSCLC CAF CAF07-AD

value: TEADi 3uM


title: Breast cancer serum sample 38

value: Basal-like


title: Lc MV 48h Z5

description:
Library name: V350158887_L03_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_44

value: L. casei DSM 20011

value: incubation with 1.5x10^11 BEVs


title: Breast cancer serum sample 39

value: Serum

value: case


title: Ef MV RNA 10h Z2

description:
Library name: V350158887_L01_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_98


title: human.lung.CAF.3.uM.TEADi.2

description: Library name: SAM24526224


title: Breast cancer serum sample 37

value: Luminal B


title: SW620_INVIVO_CDK19_CL2_CCT2431726_6H_B

description: Replicate 2 of 2

value: in vitro

value: colorectal cell line


title: Lc MV 48h Z4

description:
Library name: V350158887_L04_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_48


title: Breast cancer serum sample 36


title: human.lung.CAF.3.uM.TEADi.1

description: Library name: SAM24526223


title: SW620_INVIVO_CDK19_CL2_CCT2431726_6H_A

description: Replicate 1 of 2

value: CDK19 KO, clone2


title: Lc MV 48h Z3

description:
Library name: V350159056_L04_45
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_45


title: human.lung.CAF.1.uM.TEADi.3

description: Library name: SAM24526222

value: TEADi 1uM


title: SW620_INVIVO_CDK19_CL1_CON_6H_C

description: Replicate 3 of 3

value: CDK19 KO, clone1

value: Control

value: reference


title: human.lung.CAF.1.uM.TEADi.2

description: Library name: SAM24526221

value: Cancer associated fibroblasts


title: SW620_INVIVO_CDK19_CL1_CON_6H_B

description: Replicate 2 of 3


title: Lc MV 48h Z2

description:
Library name: V350159056_L02_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_46


title: Lc MV 24h Z5

description:
Library name: V350158887_L02_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_102


title: Lc MV 24h Z3

description:
Library name: V350159056_L01_101
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_101


title: Breast cancer serum sample 34


title: SW620_INVIVO_CDK19_CL1_CON_6H_A

description: Replicate 1 of 3


title: Breast cancer serum sample 33

value: Luminal A


title: Breast cancer serum sample 35


title: human.lung.CAF.1.uM.TEADi.1

description: Library name: SAM24526220

value: NSCLC CAF CAF07-AD


title: Lc MV 24h Z2

description:
Library name: V350158887_L01_2
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_2


title: human.lung.CAF.DMSO.3

description: Library name: SAM24526219

value: DMSO


title: human.lung.CAF.DMSO.1

description: Library name: SAM24526217


title: Breast cancer serum sample 32


title: SW620_INVIVO_CDK19_CL1_CCT2431726_6H_B

description: Replicate 2 of 3


title: human.lung.CAF.DMSO.2

description: Library name: SAM24526218


title: Ef MV 24h Z4

description:
Library name: V350158887_L04_42
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_42

value: E. faecalis DSM 20478

value: incubation with 7.5x10^9 BEVs


title: Ef MV 24h Z3

description:
Library name: V350158887_L01_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_43


title: Breast cancer serum sample 30


title: Breast cancer serum sample 31

value: Basal-like


title: SW620_INVIVO_CDK19_CL1_CCT2431726_6H_A

description: Replicate 1 of 3


title: Breast cancer serum sample 29

value: Serum


title: Ef MV 24h Z2

description:
Library name: V350159056_L02_48
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_48


title: Beads_T

city: Hefei

first: Mingqi

last: Hou

country: China

institute: USTC

description:
Library name: Sample6
Beads_T

library_source: transcriptomic single cell

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: peripheral blood

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v2 chemistry and barcoded with a 10× Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed and constructed sequencing libraries.
Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions.

value: peripheral blood

value: T cell

tag: genotype

value: NECA+TAIII


title: Breast cancer serum sample 28

value: case


title: SW620_INVIVO_CDK8_CL2_CON_6H_B

description: Replicate 2 of 3

value: in vitro

value: colorectal cell line

value: CDK8 KO, clone2


title: Beads_N

description:
Library name: Sample5
Beads_N

value: NECA


title: SW620_INVIVO_CDK8_CL2_CON_6H_C

description: Replicate 3 of 3

value: Control

value: reference


title: Breast cancer serum sample 27

value: Luminal B


title: Lc MV 10h Z5

description:
Library name: V350158887_L04_101
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_101

value: L. casei DSM 20011

value: incubation with 1.5x10^11 BEVs


title: Nalm6_T_2

description:
Library name: Sample4
Nalm6_T_2


title: SW620_INVIVO_CDK8_CL2_CON_6H_A

description: Replicate 1 of 3


title: Lc MV 10h Z4

description:
Library name: V350159056_L04_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_98


title: Breast cancer serum sample 26


title: Lc MV 10h Z3

description:
Library name: V350159056_L01_4
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_4


title: Nalm6_T_1

description:
Library name: Sample3
Nalm6_T_1


title: Nalm6_N_2

description:
Library name: Sample2
Nalm6_N_2


title: SW620_INVIVO_CDK8_CL2_CCT2431726_6H_A

description: Replicate 1 of 3


title: Nalm6_N_1

description:
Library name: Sample1
Nalm6_N_1


title: SW620_INVIVO_CDK8_CL2_CCT2431726_6H_C

description: Replicate 3 of 3


title: Breast cancer serum sample 25


title: Breast cancer serum sample 24

value: Luminal A


title: SW620_INVIVO_CDK8_CL2_CCT2431726_6H_B

description: Replicate 2 of 3


title: Lc MV 10h Z2

description:
Library name: V350158887_L01_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_99


title: Breast cancer serum sample 23


title: Ef MV 10h Z4

description:
Library name: V350158887_L03_4
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_4

value: E. faecalis DSM 20478

value: incubation with 7.5x10^9 BEVs


title: SW620_INVIVO_CDK8_CL1_CON_6H_B

description: Replicate 2 of 3

value: CDK8 KO, clone1


title: Ixodes scapularis adult female dissociated salivary glands group 5 replicate 3

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description:
Library name: SC_SG5_3
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.

data_processing:
Raw sequencing data were trimmed and aligned to the Ixodes scapularis reference genome (ASM1692078v2). We used the RNA-seek workflow (https://github.com/skchronicles/RNA-seek), which performs multiple steps including quality assessment with FastQC, FQScreen, Kraken, and BBTools; adaptor removal and quality trimming with Cutadapt; read alignments using STAR in 2-pass mode; and read quantification with RSEM.
Assembly: Ixodes scapularis reference genome (ASM1692078v2)
Supplementary files format and content: RSEM.genes.expected_count.all_samples.txt
Supplementary files format and content: RSEM.genes.FPKM.all_samples.txt
Supplementary files format and content: RSEM.genes.TPM.all_samples.txt

organism: Ixodes scapularis

source_name: salivary glands

extract_protocol:
Total RNA was isolated using the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies).
Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection.
RNA-seq was performed on an Illumina NovaSeq 6000 DNA sequencer (PE150).

value: salivary glands


title: Ef MV 10h Z5

description:
Library name: V350158887_L04_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_97


title: SW620_INVIVO_CDK19_CL1_CCT2431726_6H_C

description: Replicate 3 of 3

value: CDK19 KO, clone1


title: SW620_INVIVO_CDK8_CL1_CCT2431726_6H_C

description: Replicate 3 of 3


title: Ixodes scapularis adult female dissociated salivary glands group 5 replicate 2

description:
Library name: SC_SG5_2
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Breast cancer serum sample 22

value: Serum

value: Basal-like


title: Breast cancer serum sample 21

value: case


title: Ef MV 10h Z3

description:
Library name: V350159056_L01_98
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_98


title: Ef MV 10h Z2

description:
Library name: V350159056_L02_1
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_1


title: SW620_INVIVO_CDK8_CL1_CON_6H_C

description: Replicate 3 of 3

value: in vitro

value: colorectal cell line


title: SW620_INVIVO_CDK8_CL1_CON_6H_A

description: Replicate 1 of 3


title: Breast cancer serum sample 20


title: Ixodes scapularis adult female dissociated salivary glands group 2 replicate 3

description:
Library name: SC_SG2_3
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Ixodes scapularis adult female dissociated salivary glands group 2 replicate 2

description:
Library name: SC_SG2_2
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Ixodes scapularis adult female dissociated salivary glands group 2 replicate 1

description:
Library name: SC_SG2_1
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: ANC 100ng 48h Z4

description:
Library name: V350158887_L02_104
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_104

value: not applicable

value: transfection with 100 ng ANC


title: SW620_INVIVO_CDK8_CL1_CCT2431726_6H_B

description: Replicate 2 of 3

value: reference


title: Breast cancer serum sample 17

value: Control


title: ANC 100ng 48h Z3

description:
Library name: V350159056_L04_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_97


title: ANC 100ng 48h Z5

description:
Library name: V350158887_L04_99
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_99


title: Breast cancer serum sample 19


title: ANC 100ng 48h Z2

description:
Library name: V350159056_L02_4
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_4


title: SW620_INVIVO_CDK8CDK19_CL2_CON_6H_B

description: Replicate 2 of 3

value: CDK8 and CDK19 KO, clone2


title: Ixodes scapularis adult female dissociated salivary glands group unfed replicate 3

description:
Library name: SC_UF_3
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and cells were dissociated following a mechanical and enzymatic protocol. The average weight of the group unfed 1 is 1.6 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Ixodes scapularis adult female dissociated salivary glands group unfed replicate 2

description:
Library name: SC_UF_2
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and cells were dissociated following a mechanical and enzymatic protocol. The average weight of the group unfed 1 is 1.6 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: SW620_INVIVO_CDK8CDK19_CL2_CON_6H_A

description: Replicate 1 of 3


title: Ixodes scapularis adult female dissociated salivary glands group unfed replicate 1

description:
Library name: SC_UF_1
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and cells were dissociated following a mechanical and enzymatic protocol. The average weight of the group unfed 1 is 1.6 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: SW620_INVIVO_CDK8CDK19_CL2_CON_6H_C

description: Replicate 3 of 3


title: Breast cancer serum sample 16


title: SW620_INVIVO_CDK8CDK19_CL2_CCT2431727_6H_C

description: Replicate 3 of 3


title: ANC 2ng 24h Z4

description:
Library name: V350158887_L03_45
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_45

value: transfection with 2 ng ANC


title: Breast cancer serum sample 14

value: Luminal B


title: RNA-seq of Ixodes scapularis salivary glands SG-UN replicate 3

description:
Library name: SG-U-3_S8_L002_001
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and stored in RNAlater solution. The average weight of the group unfed is 1.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies).
Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection.
RNA-seq was performed on an Illumina NovaSeq 6000 DNA sequencer (PE150).


title: ANC 2ng 24h Z3

description:
Library name: V350158887_L01_104
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_104


title: Breast cancer serum sample 15


title: ANC 2ng 24h Z5

description:
Library name: V350158887_L04_47
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_47


title: Breast cancer serum sample 18


title: SW620_INVIVO_CDK8_CL1_CCT2431726_6H_A

description: Replicate 1 of 3


title: RNA-seq of Ixodes scapularis salivary glands SG-UN replicate 2

description:
Library name: SG-U-2_S7_L002_001
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and stored in RNAlater solution. The average weight of the group unfed is 1.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: RNA-seq of Ixodes scapularis salivary glands SG-UN replicate 1

description:
Library name: SG-U-1_S6_L002_001
Intact salivary glands (SG) from unfed Ixodes scapularis adult females were collected and stored in RNAlater solution. The average weight of the group unfed is 1.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Breast cancer serum sample 13

value: Luminal A


title: Breast cancer serum sample 12


title: ANC 2ng 24h Z2

description:
Library name: V350159056_L02_45
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_45


title: SW620_INVIVO_CDK8CDK19_CL2_CCT2431726_6H_A

description: Replicate 1 of 3


title: ANC 100ng 24h Z4

description:
Library name: V350158887_L02_44
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L02_44


title: ANC 100ng 24h Z5

description:
Library name: V350158887_L03_101
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_101


title: Ixodes scapularis adult female dissociated salivary glands group 5 replicate 1

description:
Library name: SC_SG5_1
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected and cells were dissociated following a mechanical and enzymatic protocol. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Breast cancer serum sample 11


title: SW620_INVIVO_CDK8CDK19_CL1_CON_6H_C

description: Replicate 3 of 3

value: CDK8 and CDK19 KO, clone1


title: RNA-seq of Ixodes scapularis salivary glands SG-G6 replicate 3

description:
Library name: SG-G6-3_S12_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 6 is 105 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: ANC 100ng 24h Z3

description:
Library name: V350158887_L01_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_46


title: Breast cancer serum sample 10


title: Breast cancer serum sample 8


title: Breast cancer serum sample 9


title: SW620_INVIVO_CDK8CDK19_CL1_CCT2431726_6H_C

description: Replicate 3 of 3


title: ANC 100ng 24h Z2

description:
Library name: V350159056_L01_104
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_104


title: RNA-seq of Ixodes scapularis salivary glands SG-G6 replicate 2

description:
Library name: SG-G6-2_S31_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 6 is 105 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: SW620_INVIVO_CDK8CDK19_CL1_CCT2431726_6H_B

description: Replicate 2 of 3


title: RNA-seq of Ixodes scapularis salivary glands SG-G5 replicate 3

description:
Library name: SG-G5-3_S29_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: SW620_INVIVO_CDK8CDK19_CL2_CCT2431726_6H_B

description: Replicate 2 of 3


title: SW620_INVIVO_CDK8CDK19_CL1_CON_6H_A

description: Replicate 1 of 3


title: RNA-seq of Ixodes scapularis salivary glands SG-G5 replicate 2

description:
Library name: SG-G5-2_S28_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: SW620_INVIVO_CDK8CDK19_CL1_CON_6H_B

description: Replicate 2 of 3


title: ANC 5ng 24h Z4

description:
Library name: V350158887_L04_46
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_46

value: transfection with 5 ng ANC


title: Breast cancer serum sample 7


title: SW620_INVIVO_CDK8CDK19_CL1_CCT2431726_6H_A

description: Replicate 1 of 3


title: dRBP-DDX24-FLAG_antiFLAG_RIPseq_rep1

city: Zhuhai

first: Simeng

last: He

address: 52 Meihuadong Road, Xiangzhou

institute: Sun Yat-sen University

description: Library name: dRBP-DDX24-FLAG_antiFLAG_RIPseq_rep1

data_processing:
Raw reads underwent initial processing, involving trimming for adaptor removal and elimination of low-quality reads, achieved through cutadapt (v2.0.dev0). Subsequently, alignment to the human genome (hg38) was executed using STAR (v2.4.2a), employing ENCODE standard options tailored for the long RNA-seq pipeline. The gencode transcriptome (gencode v39) served as the reference during this alignment. Read counts were quantified using featureCounts (v1.6.4) with default settings. Differential expression analysis for significantly differentially expressed (DE) genes was carried out using DESeq2 and gene selection was based on a p-value threshold of 5%.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes the TPM value for genes

source_name: cell line

extract_protocol:
For each immunoprecipitation, HUVECs stably expressing FLAG tagged DDX24-WT or DDX24-dRBD were pelleted; resuspended in an equal volume of ice-cold polysome lysis buffer (10mM HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor (Thermo Fisher Scientific), 1× protease inhibitor cocktail (Roche) and 0.4 mM RVC (NEB); incubated on ice for 15 minutes; snap frozen in liquid nitrogen. After the lysate was thawed on ice and centrifuged at 15,000 g for 15 minutes, the supernatant was pre-cleared with Dynabeads Protein G (Invitrogen) at 4 °C for 1 hour. 20 μL of the supernatant was saved as input and mixed with 1 mL of RNAzol. Subsequently, other 200 μL of the supernatant extract was diluted with 1 mL of NT2 buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor (Thermo Fisher Scientific), 1× protease inhibitor cocktail (Roche) and 20 mM EDTA. The extracts were mixed with 4 μg of an anti-FLAG antibody (Proteintech) or a normal IgG antibody (EMD Millipore) and incubated overnight at 4 °C with end-over-end rotation. The next day, the RNP/antibody complex was precipitated by incubation with Dynabeads Protein G at 4 °C for 4 hours. The beads were collected and washed five times in NT2 buffer. After the final wash, the beads were resuspended in 1 mL of RNAzol. RNAs of Input and FLAG were extracted for subsequent RIP-seq.
The immunoprecipitated RNA was then subjected to mRNA selection using Oligo dT-based Poly(A) mRNA Magnetic Isolation Module (NEB) and prepared for sequencing libraries using Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries were pooled and sequenced on an Illumina Hiseq 3000 PE150 platform.

value: cell line

value: HUVEC

value: Human umbilical vein endothelial cells

value: overexpression of RNA-bind domain deleted DDX24


title: RNA-seq of Ixodes scapularis salivary glands SG-G4 replicate 3

description:
Library name: SG-G4-3_S26_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 4 is 24.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.

value: salivary glands


title: RNA-seq of Ixodes scapularis salivary glands SG-G6 replicate 1

description:
Library name: SG-G6-1_S30_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 6 is 105 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: ANC 5ng 24h Z5

description:
Library name: V350158887_L04_103
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L04_103


title: dRBP-DDX24-FLAG_Input_RIPseq_rep2

description: Library name: dRBP-DDX24-FLAG_Input_RIPseq_rep2


title: RNA-seq of Ixodes scapularis salivary glands SG-G4 replicate 2

description:
Library name: SG-G4-2_S25_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 4 is 24.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Breast cancer serum sample 6

value: Serum

value: case


title: ANC 5ng 24h Z2

description:
Library name: V350159056_L01_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_43

value: not applicable


title: ANC 5ng 24h Z3

description:
Library name: V350159056_L02_97
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_97


title: Breast cancer serum sample 4


title: dRBP-DDX24-FLAG_Input_RIPseq_rep1

description: Library name: dRBP-DDX24-FLAG_Input_RIPseq_rep1


title: ANC 2ng 10h Z5

description:
Library name: V350158887_L03_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L03_41


title: RNA-seq of Ixodes scapularis salivary glands SG-G5 replicate 1

description:
Library name: SG-G5-1_S27_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 5 is 44.5 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Breast cancer serum sample 5


title: dRBP-DDX24-FLAG_antiFLAG_RIPseq_rep2

description: Library name: dRBP-DDX24-FLAG_antiFLAG_RIPseq_rep2


title: Breast cancer serum sample 3


title: ANC 2ng 10h Z3

description:
Library name: V350159056_L01_102
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_102


title: RNA-seq of Ixodes scapularis salivary glands SG-G4 replicate 1

description:
Library name: SG-G4-1_S24_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 4 is 24.6 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: DDX24-FLAG_antiFLAG_RIPseq_rep2

description: Library name: DDX24-FLAG_antiFLAG_RIPseq_rep2

value: overexpression of wild-type DDX24


title: DDX24-FLAG_antiFLAG_RIPseq_rep1

description: Library name: DDX24-FLAG_antiFLAG_RIPseq_rep1


title: ANC 2ng 10h Z2

description:
Library name: V350158887_L01_42
Column name in raw_counts_Caco2_RNASeq.tsv: V350158887_L01_42


title: Breast cancer serum sample 2


title: RNA-seq of Ixodes scapularis salivary glands SG-G3 replicate 2

description:
Library name: SG-G3-2_S22_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 3 is 15.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: DDX24-FLAG_Input_RIPseq_rep2

description: Library name: DDX24-FLAG_Input_RIPseq_rep2


title: ANC 100ng 10h Z5

description:
Library name: V350159056_L04_4
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_4

value: transfection with 100 ng ANC


title: Breast cancer serum sample 1

value: Control


title: RNA-seq of Ixodes scapularis salivary glands SG-G3 replicate 3

description:
Library name: SG-G3-3_S23_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 3 is 15.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Intrahepatic leukocytes, CCl4-4, scRNAseq

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: Run_2D-B1 Sample ID:sample 8

data_processing:
Secondary analysis was conducted with CellRanger 9.0.0 with probe set Chromium_Mouse_Transcriptome_Probe_Set_v1.1.1_GRCm39-2024-A and combined data from 4 sequencing lanes. All FASTQ files should be processed together for new secondary analysis.
Assembly: GRCm39-2024-A
Supplementary files format and content: filtered .h5

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Sample preparation. Mouse livers were harvested after 6 weeks of twice weekly carbon tetrachloride (CCl4) or Olive oil administration. In situ tissue digestion was performed by perfusing the liver with collagenase P (COLLP-RO, Millipore Sigma) at a concentration of 64 mg/mL in a balanced salt solution. Digested livers were then homogenized in a petri dish in a solution containing 0.15 mg/mL DNase I (11284932001, MilliporeSigma).  The intrahepatic leukocyte fraction was obtained by 25%-50% Percoll gradient(28). Cells were processed following the 10x Genomics protocol for cell/nuclei fixation (CG000782). Briefly, suspensions containing up to ten million cells were spun down at 350 rcf for 5 minutes at 4ºC, then resuspended in 1 mL of Fixation Buffer (4% Formaldehyde, 1X Fix and Perm Buffer – 10x Genomics PN-2001301). Cells were fixed for 24 hours at 4ºC. To halt fixation, cells were spun down at 850 rcf for 5 minutes at room temperature and quenched with 0.5 mL of Quenching Buffer (1X Quench Buffer – 10x Genomics PN-2001300). Cell concentration and viability were assessed via AO/PI staining using a Cellometer K2 Cell Counter (Nexcelom), then processed according to the 10x Genomics Flex protocol for hybridization.
Sample hybridization. All hybridizations followed 10x Genomics recommendations (CG000787 Rev B). Hybridizations were set up in 40 µL of hybridization mix with 10 µL of Mouse WTA probes (10x Genomics PN-2001275-2001278). Hybridizations were performed at 42ºC for 16-24 hours. Afterward, samples were diluted in Post-Hyb Wash Buffer and measured via AO/PI staining with a Cellometer K2 Cell Counter. Pooled hybridized cells were washed three times in Post-Hyb Wash Buffer for 10 minutes at 42ºC. After washing, cells were resuspended in Post-Hyb Resuspension Buffer, filtered through a Miltenyi Biotec 30 μm filter, and measured to determine the volume required for the GEM-X Flex Gene Expression run. Before probe hybridization, an equal number of cells from each fixation were pooled (pre-hybridization normalization) to ensure equal contribution per sample. Gene Expression Flex Run. For Gel Beads-in-emulsion (GEM) generation, we followed the 10x Genomics protocol and guidelines on cell and reagent volumes based on targeted cell recovery. We aimed for 20,000 cells per sample. For the probe mixing strategy experiment, we targeted 80,000 cells per pool with equal contribution from each sample, except for the differential pooling strategy, where contributions varied. After loading the GEM-X FX Chip on the Chromium X, GEMs were recovered and processed as per 10x Genomics instructions. The product was then pre-amplified and indexed for library construction. Libraries were quality-checked using the fragment analyzer.Sequencing. Libraries were sequenced on the Illumina Nova-Seq X 1.5B platform according to 10x Genomics recommended settings, with a minimum of 10,000 read pairs per cell. For experiments involving probe mixing strategies, sequencing was conducted at a depth of 10,000 read pairs per sample, yielding 80,000 cells per library.

value: Liver

value: intrahepatic leukocytes


title: RNA-seq of Ixodes scapularis salivary glands SG-G3 replicate 1

description:
Library name: SG-G3-1_S21_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 3 is 15.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: RNA-seq of Ixodes scapularis salivary glands SG-G2 replicate 3

description:
Library name: SG-G2-3_S20_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: DDX24-FLAG_Input_RIPseq_rep1

description: Library name: DDX24-FLAG_Input_RIPseq_rep1


title: Intrahepatic leukocytes, CCl4-3, scRNAseq

description: Library name: Run_2D-B1 Sample ID:sample 7


title: HUVEC,siNC,rep3

data_processing:
Raw reads underwent initial processing, involving trimming for adaptor removal and elimination of low-quality reads, achieved through cutadapt (v2.0.dev0). Subsequently, alignment to the human genome (hg38) was executed using STAR (v2.4.2a), employing ENCODE standard options tailored for the long RNA-seq pipeline. The gencode transcriptome (gencode v39) served as the reference during this alignment. Read counts were quantified using featureCounts (v1.6.4) with default settings. Differential expression analysis for significantly differentially expressed (DE) genes was carried out using DESeq2 and gene selection was based on a p-value threshold of 5%.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample and log2 FoldChange for each protein coding gene.

source_name: HUVEC

growth_protocol: HUVEC was maintained in ECM medium (Sciencell) supplemented with 5% FBS, 1% Endothelial growth factor and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Trizol. mRNA was further purified using Oligo dT-based Poly(A) mRNA Magnetic Isolation Module (NEB).
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: HUVECs were transfected with siNC or siDDX24-1 at 50nM.

value: vasuclar endothelial cell

value: WT

value: siNC


title: ANC 100ng 10h Z3

description:
Library name: V350159056_L01_3
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_3


title: RNA-seq of Ixodes scapularis salivary glands SG-G2 replicate 1

description:
Library name: SG-G2-1_S19_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Intrahepatic leukocytes, CCl4-1, scRNAseq

description: Library name: Run_1D-A12 Sample ID:sample3


title: ANC 100ng 10h Z2

description:
Library name: V350159056_L01_45
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L01_45


title: HUVEC,siDDX24,rep3


title: ANC 100ng 10h Z4

description:
Library name: V350159056_L04_43
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_43


title: RNA-seq of Ixodes scapularis salivary glands SG-G2 replicate 2

description:
Library name: SG-G2-2_S11_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 2 is 7.4 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: HUVEC,siDDX24,rep2


title: RNA-seq of Ixodes scapularis salivary glands SG-G1 replicate 3

description:
Library name: SG-G1-3_S10_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 1 is 2.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: HUVEC,siNC,rep2


title: Intrahepatic leukocytes, CCl4-2, scRNAseq

description: Library name: Run_1D-A12 Sample ID:sample4


title: Intrahepatic leukocytes, OO-3, scRNAseq

description: Library name: Run_2D-B1 Sample ID:sample5

value: control


title: Intrahepatic leukocytes, OO-4, scRNAseq

description: Library name: Run_2D-B1 Sample ID:sample6


title: HUVEC,siDDX24,rep1


title: Intrahepatic leukocytes, OO-2, scRNAseq

description: Library name: Run_1D-A12 Sample ID:sample2


title: ANC 5ng 10h Z5

description:
Library name: V350159056_L04_3
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L04_3

value: transfection with 5 ng ANC


title: RNA-seq of Ixodes scapularis salivary glands SG-G1 replicate 1

description:
Library name: SG-G1-1_S9_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 1 is 2.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: HUVEC,siNC,rep1

value: HUVEC


title: ANC 5ng 10h Z3

description:
Library name: V350159056_L02_41
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_41


title: RNA-seq of Ixodes scapularis salivary glands SG-G1 replicate 2

description:
Library name: SG-G1-2_S18_L002_001
Intact salivary glands (SG) from partially fed Ixodes scapularis adult females feeding on rabbits were collected at different stages during the blood feeding and stored in RNAlater solution. Ticks were grouped by weight, the average weight of the group 1 is 2.9 mg. RNA extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to manufacturer`s specifications and analyzed with an TapeStation system (Agilent, USA). The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Intrahepatic leukocytes, OO-1, scRNAseq

description: Library name: Run_1D-A12 Sample ID:sample1


title: Female_LKO_rep3

status: Public on Feb 19 2026

city: HUDDINGE

first: Lin

last: Chen

address: Blickagången 16, Flemingsberg,Neo

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: F_LKO_rep3

data_processing:
Preprocessed reads were aligned to the hg38/mm10 transcriptome using the HISAT2 program, and read counts were determined using featureCounts v1.5.0-p3. Raw tag counts were imported into R and Bioconductor, and differential gene expression was analyzed using the edgeR package.
Assembly: hg38 and mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues and human cell lines using the E.Z.N.A.® Total RNA Kit I (Omega Bio-tek, R6834-02).
mRNA library preparation, including poly-A enrichment, was carried out using the Novogene NGS RNA Library Prep Set (PT042) following the manufacturer’s protocol.

value: liver


title: Female_LKO_rep4

description: Library name: F_LKO_rep4


title: Female_LKO_rep2

description: Library name: F_LKO_rep2


title: Female_LKO_rep1

description: Library name: F_LKO_rep1


title: Female_WT_rep4

description: Library name: F_WT_rep4


title: Female_WT_rep3

description: Library name: F_WT_rep3


title: ANC 5ng 10h Z2

description:
Library name: V350159056_L02_100
Column name in raw_counts_Caco2_RNASeq.tsv: V350159056_L02_100


title: Female_WT_rep1

description: Library name: F_WT_rep1


title: Male_LKO_rep5

description: Library name: M_LKO_rep5


title: Female_WT_rep5

description: Library name: F_WT_rep5


title: Male_LKO_rep3

description: Library name: M_LKO_rep3


title: Male_LKO_rep2

description: Library name: M_LKO_rep2


title: Female_WT_rep2

description: Library name: F_WT_rep2


title: Female_LKO_rep5

description: Library name: F_LKO_rep5


title: Male_LKO_rep1

description: Library name: M_LKO_rep1


title: Male_WT_rep4

description: Library name: M_WT_rep4


title: Male_WT_rep5

description: Library name: M_WT_rep5


title: Male_LKO_rep4

description: Library name: M_LKO_rep4


title: Male_WT_rep1

description: Library name: M_WT_rep1


title: Male_WT_rep3

description: Library name: M_WT_rep3


title: EVdPC12

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

country: Japan

institute: Tokyo Medical University

description:
Library name: Sample2
EV-microRNA

library_source: other

data_processing:
GeneGlobe/Strand NGS v4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: UCSC Rat mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

molecule: other

organism: Rattus norvegicus

source_name: EVs

extract_protocol:
EV-associated miRNA were isolated from cultured cells and purified EVs by QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.
Small RNA libraries were prepared using QIAseq miRNA library Kit and QIAseq miRNA NGS 96 Index IL for Illumina, and yields were evaluated using Agilent 2100 BioAnalyzer.

value: EVs

value: catecholamine cell


title: Male_WT_rep2

description: Library name: M_WT_rep2


title: EVuPC12

description:
Library name: Sample1
EV-microRNA


title: uPC12EVs-1

description: Library name: Sample3

data_processing:
StrandNGS 4.0/Star 2.7.8a
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: UCSC Rat mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

source_name: breast cancer cell

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library prep for Illumina, NEBNext rRNA Depletion Kit and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs), and yields were evaluated using Agilent 2100 BioAnalyzer.

value: breast cancer cell

value: add uPC12EVs


title: dPC12EVs-2

description: Library name: Sample6

value: add dPC12EVs


title: PBS-2

description: Library name: Sample2

value: add PBS


title: dPC12EVs-1

description: Library name: Sample5


title: DEK2,Input,ChIP

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

library_source: genomic

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of TAIR10.fasta
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam -c Input.bam -g 119481543 -q 0.05  -B -n --outdir "
Bigwig generation: takes an alignment of reads or fragments as input (BAM file) and generates a track with RPGC normalization.
Assembly: TAIR10
Supplementary files format and content: BigWig,narrowPeak

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 14 days old seedlings

growth_protocol: For growing A.thaliana under sterile conditions seeds were surface sterilized in a solution of bleach: ethanol: H2O (V:V:V::1:4:3) for 10 min and washed four times with sterile water. The seeds were then stratified by placing them at 4 °C for 48 h. Seedlings were grown on half strength MS plates. Plates were sealed with Micropore tape and placed on grid-like shelves in a plant growth chamber for 14 days at 21 °C with 75% relative humidity under 16 h of daylight.

extract_protocol:
ChIP-seq assays were performed according to Ramirez-Prado et al. (Ramirez-Prado et al, 2021) with minor modifications. Plant materials were cross-linked with 1%(v/v) formaldehyde under vacuum. Chromatin was isolated and fragmented by sonication using Covaris S220 sonicator. Later, the sonicated protein/DNA was incubated with anti-GFP antibodies (Abcam, ab290) overnight at 4 °C with gentle shaking, and then incubated with 50 μL of Dynabeads Protein A (Invitrogen, Ref. 100-02D) for 1h at 4 °C. After beads washing, samples were reverse crosslinked, treated with RNase A+T1 and proteinase K. Immunoprecipitated DNA was then recovered by phenol:chloroform extraction and ethanol precipitation. DNA was quantified with Qubit High Sensitivity kit (Life technologies).
ChIP-seq libraries were performed using 10ng of immunoprecipitated DNA and NebNext DNA Ultra II library preparation kit according to manufacturer's instructions.

value: 14 days old seedlings

value: dek2-1, pDEK2::DEK2-YFP

tag: chip antibody

value: none (input)


title: uPC12EVs-2

description: Library name: Sample4


title: PLGG_sample_86

type: genomic

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Restored DNA was assayed on Infinium MethylationEPIC kit (Illumina, USA), according to the Infinium HD FFPE Methylation Assay protocol (Illumina, USA).

scan_protocol: Prepared BeadChips were scanned on the NextSeq-550 (Illumina, USA). On-Chip quality metrics of each sample were carefully monitored including minimal CpG detection limits (>95% at p<0.05). Output of raw signal intensities were obtained via iDAT files as output from the NextSeq-550.

data_processing: Raw methylation (.idat) files were imported, pre-processed, and normalized (ssNoob method) using minfi46 (v1.44.0). Probes that failed to hybridize (detection P value > 0.01) in one or more samples were removed, as well as cross-reactive probes, those that overlapped with known single nucleotide polymorphisms (SNPs), and those targeting the X and Y chromosomes.

label: Cy3 and Cy5

source_name: formalin-fixed paraffin embedded

label_protocol: Standard Illumina Protocol.

extract_protocol: FFPE tissue had a minimum of 200 ng of genomic DNA bisulfite-converted (EZ DNA Methylation Kit, Zymo Research D5001) under the manufacturer’s specifications. Bisulfite-converted DNA was then subjected to the Infinium FFPE DNA Restore kit (Illumina, USA).

value: formalin-fixed paraffin embedded

tag: anatomic location

value: Cerebellum

tag: genetic alteration

value: BRAF V600E

tag: pathology

value: High grade astrocytoma

tag: dkfz classifier

value: GBM, MID


title: PLGG_sample_85

value: Diencephalon

value: Glioblastoma

value: PXA


title: PLGG_sample_83

value: Hemisphere


title: PLGG_sample_84


title: PLGG_sample_81

value: Pleomorphic xanthoastrocytoma


title: PLGG_sample_87

value: CONTR, REACT


title: PLGG_sample_82


title: DEK2,IP,ChIP,rep1

value: anti-GFP antibodies (Abcam, ab290)


title: PLGG_sample_78

value: Pilomyxoid astrocytoma

value: CONTR, INFLAM


title: PLGG_sample_75


title: PBS-1

description: Library name: Sample1

value: breast cancer cell

value: add PBS


title: PLGG_sample_73

value: Pilocytic astrocytoma


title: DEK2,IP,ChIP,rep2

value: 14 days old seedlings

value: dek2-1, pDEK2::DEK2-YFP


title: PLGG_sample_77

value: formalin-fixed paraffin embedded

value: BRAF V600E


title: PLGG_sample_72

value: Anaplastic ganglioglioma


title: PLGG_sample_76

value: Diencephalon

value: LGG, DIG/DIA


title: PLGG_sample_79

value: Ganglioglioma

value: PXA


title: PLGG_sample_70

value: Ganglioglioma (vs Pilocytic astrocytoma)

value: LGG, PA MID


title: PLGG_sample_74


title: PLGG_sample_71

value: Hemisphere

value: Glioblastoma

value: GBM, MID


title: PLGG_sample_69

value: Cerebellum

value: Diffuse astrocytoma

value: LGG, PA PF


title: PLGG_sample_65

value: Pilocytic astrocytoma

value: CONTR, REACT


title: PLGG_sample_66

value: formalin-fixed paraffin embedded

value: LGG, GG


title: PLGG_sample_80

value: BRAF V600E

value: Pleomorphic xanthoastrocytoma


title: PLGG_sample_67

value: Brainstem


title: PLGG_sample_63

value: Ganglioglioma


title: PLGG_sample_64

value: Diencephalon


title: PLGG_sample_61


title: PLGG_sample_62

value: PXA


title: PLGG_sample_59


title: PLGG_sample_58

value: CONTR, CEBM


title: PLGG_sample_68

value: Hemisphere

value: Glioneural tumor

value: LGG, PA/GG ST


title: PLGG_sample_57


title: PLGG_sample_46


title: PLGG_sample_51

value: Oligodendroglioma

value: IHG


title: PLGG_sample_54

value: Dysembryonic neuroectodermal tumor

value: LGG, DNT


title: PLGG_sample_49

value: CONTR, REACT


title: PLGG_sample_45

value: formalin-fixed paraffin embedded


title: PLGG_sample_41

value: Diffuse astrocytoma

value: LGG, GG


title: PLGG_sample_44

value: BRAF V600E


title: PLGG_sample_38


title: PLGG_sample_47

value: Brainstem

value: Low grade astrocytoma

value: LGG, PA PF


title: PLGG_sample_42

value: Cerebellum

value: Pilocytic astrocytoma


title: PLGG_sample_53

value: Hemisphere


title: PLGG_sample_39


title: PLGG_sample_40


title: PLGG_sample_60

value: Ganglioglioma


title: PLGG_sample_43


title: PLGG_sample_36

value: Diencephalon


title: PLGG_sample_34

value: LGG, PA MID


title: PLGG_sample_48


title: PLGG_sample_55


title: PLGG_sample_35

value: MNG


title: PLGG_sample_56

value: Pleomorphic xanthoastrocytoma

value: PXA


title: PLGG_sample_31


title: PLGG_sample_37

value: CONTR, REACT


title: PLGG_sample_32

value: formalin-fixed paraffin embedded


title: PLGG_sample_33


title: PLGG_sample_52

value: Diffuse astrocytoma


title: PLGG_sample_30

value: CONTR, INFLAM


title: PLGG_sample_50

value: BRAF V600E

value: CPH, PAP


title: PLGG_sample_29

value: BRAF fusion

value: CONTR, CEBM


title: PLGG_sample_28

value: LGG, PA PF


title: PLGG_sample_24

value: Pilocytic astrocytoma


title: PLGG_sample_27


title: PLGG_sample_25

value: Brainstem


title: PLGG_sample_23

value: Ganglioglioma


title: PLGG_sample_20

value: Cerebellum


title: PLGG_sample_22

value: Hemisphere

value: Low grade astrocytoma

value: LGG, PA/GG ST


title: PLGG_sample_21

value: Diencephalon

value: LGG, PA MID


title: PLGG_sample_16

value: formalin-fixed paraffin embedded

value: Pilomyxoid astrocytoma


title: PLGG_sample_17


title: PLGG_sample_14

value: Olgoastrocytoma

value: LGG, DNT


title: PLGG_sample_15


title: PLGG_sample_13


title: PLGG_sample_11


title: PLGG_sample_10


title: PLGG_sample_7


title: PLGG_sample_6


title: PLGG_sample_9


title: PLGG_sample_3


title: PLGG_sample_5


title: PLGG_sample_18

value: Diffuse astrocytoma


title: PLGG_sample_26

value: BRAF fusion


title: PLGG_sample_8


title: PLGG_sample_4


title: PLGG_sample_2


title: PLGG_sample_19


title: PLGG_sample_12


title: PLGG_sample_1


title: Colorectal cancer, patient-derived organoid, monoculture, replicate 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Library name: BB250_p30

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCh38.p13
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

growth_protocol: For the PDO/monocyte co-cultures, freshly isolated monocytes and 5-7 days old PDOs were resuspended in co-culture medium containing 20 ng/ml M-CSF and liquid 5% BME at a ratio of 2:1 (immune cell: PDO cell). The co-culture medium was freshly prepared by mixing equal parts of monocyte medium (RPMI supplemented with 10% heat-inactivated FCS, 100 U/ml Pen/Strep, 1 mM Sodium Pyruvate, 1X NEAA, 55 µM β mercaptoethanol), and PDO medium (Betge et al., Nature Communications 2022 13:1. 2022;13:1–15. doi: 10.1038/s41467-022-30722-9) excluding the apoptosis inhibitor Y-27632 and Nicotinamide. Monocyte/PDO co-culture were culture as suspension culture in UpCell cell culture plates for 4 days at 37°C. After culture, PDO30 from 4 days of mono- or co-culture were dissociated to single cells using TrypLE and prepared for FACS sorting. Live EpCAM+ cells were sorted into chilled RLT lysis buffer

extract_protocol:
QIAGEN RNeasy Mini Kit including gDNA digest
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: PDO30 was either cultured in monoculture or in co-culture with primary human monocytes

value: Monoculture

tag: batch


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 2, replicate 3

description: Library name: BB250_p30_D2

value: Co-culture with Monocytes


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 2, replicate 2

description: Library name: BB246_p30_D2


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 1, replicate 3

description: Library name: BB250_p30_D1


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 1, replicate 2

description: Library name: BB246_p30_D1


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 1, replicate 1

description: Library name: BB221_p30_D1


title: Colorectal cancer, patient-derived organoid, monoculture, replicate 2

description: Library name: BB246_p30


title: Colorectal cancer, patient-derived organoid, monoculture, replicate 1

description: Library name: BB221_p30


title: control mammary tissue, sample 8

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

hyb_protocol: Hybridization to the CanGene 1.1 Array strips was carried out at 48ºC for 20 hours

scan_protocol: GeneAtlas® System (Affymetrix)

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Transcriptome Analysis Console (TAC) 4.0.1 (Thermo Fisher Scientific Co.) using the Robust Multi-array Average (RMA) algorithm

label: biotin

organism: Canis lupus familiaris

source_name: control mammary tissue

label_protocol: Total RNA (400 ng/sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Co.), according to the manufacturer’s instructions

growth_protocol: Samples were kept in RNAlater (Thermo Fisher Scientific®) before RNA extraction

extract_protocol: Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.

treatment_protocol: Four female dogs, aged between 2 and 4 years, were presented at Luiz Quintiliano de Almeida Veterinary Hospital at the School of Veterinary Medicine, São Paulo State University (Unesp) for mastectomy. Immediately after resection, samples (n = 12, 3 per animal) were collected under ethical approval #2008-007478. Subsequently, part of each tissue sample underwent histopathological analysis and immunophenotyping, while the remainder was preserved in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. Control samples (n = 4) were harvested from the mammary tissue of female dogs that were ethically euthanized from non-infectious unrelated conditions. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions.

tag: Sex

value: female

value: mammary


title: 1920B013 day 14, FACS sorted non-naïve CD8, TCR

city: Saint Louis

first: Philip

last: Mudd

state: Missouri

address: 660 S. Euclid Ave.

department: Emergency Medicine

institute: Washington University in Saint Louis School of Medicine

description: Library name: 1920B013-Mem_CD8_d14_TCR

data_processing:
Single cell data were parsed with Cell Ranger v6.0.1 using the GRCh38 reference.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz.
Supplementary files format and content: airr_rearrangement.tsv contains annotated contigs and consensus sequences of V(D)J rearrangements in the AIRR format
Supplementary files format and content: clonotypes.csv provides high-level descriptions of each V(D)J clonotype
Supplementary files format and content: filtered_contig_annotations.csv provides high-level annotations of each high-confidence contig from cell-associated barcodes and productive contigs
Library strategy: TCR-Seq

source_name: blood

extract_protocol:
Non-naïve CD8+ T cells were FACS sorted from cryopreserved PBMC using a FACSAriaII (BD Biosciences) cell sorter. The following antibodies were employed: CD3 FITC (clone HIT3a, BioLegend), CD8 PE (clone RPA-T8, BioLegend), CD45RO Pacific Blue (clone UCHL1, BioLegend), CCR7 APC-R700 (clone 3D12, BD Biosciences), and live-dead discrimination with Zombie Aqua Fixable Viability Kit (BioLegend). We sorted all live CD3+CD8+ PBMC that were not CD45RO-CCR7+ for inclusion in the single cell RNAseq. Total cryopreserved BALF immune cells were thawed and further purified using the EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies) prior to single cell RNAseq. Following purification, non-naïve CD8+ T cells or BALF cells were re-suspended in PBS supplemented with 0.05% bovine serum albumin.
10x Genomics Chromium Single Cell 5’ v2 Gene Expression Dual Index libraries and Chromium Single Cell V(D)J Dual Index libraries were prepared according to the manufacturer’s instructions without modifications.

value: blood

value: FACS sorted CD8 T cells

tag: time

value: day 14


title: 1920B013 day 14, FACS sorted non-naïve CD8, GEX

description: Library name: 1920B013-Mem_CD8_d14_GEX

data_processing:
Single cell data were parsed with Cell Ranger v6.0.1 using the GRCh38 reference.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz.
Supplementary files format and content: airr_rearrangement.tsv contains annotated contigs and consensus sequences of V(D)J rearrangements in the AIRR format
Supplementary files format and content: clonotypes.csv provides high-level descriptions of each V(D)J clonotype
Supplementary files format and content: filtered_contig_annotations.csv provides high-level annotations of each high-confidence contig from cell-associated barcodes and productive contigs


title: Colorectal cancer, patient-derived organoid, co-culture with monocytes, Donor 2, replicate 1

description: Library name: BB221_p30_D2

tag: treatment


title: control mammary tissue, sample 7

tag: tissue


title: control mammary tissue, sample 6


title: 1920B011 day 7, FACS sorted non-naïve CD8, GEX

description: Library name: 1920B011-Mem_CD8_d7_GEX

value: day 7


title: tumor mammary tissue, sample 4

source_name: tumor mammary tissue


title: control mammary tissue, sample 5


title: 1920B007 day 20, FACS sorted non-naïve CD8, TCR

description: Library name: 1920B007-Mem_CD8_d20_TCR

value: day 20


title: tumor mammary tissue, sample 3


title: 1920B007 day 20, FACS sorted non-naïve CD8, GEX

description: Library name: 1920B007-Mem_CD8_d20_GEX


title: 1920B004 day 13, FACS sorted non-naïve CD8, TCR

description: Library name: 1920B004-Mem_CD8_d13_TCR

value: day 13


title: tumor mammary tissue, sample 2


title: 1920B013 day 14, BAL, TCR, biol rep 2

description: Library name: 1920B013-BAL_d14B_TCR

source_name: bronchoalveolar lavage cells

value: bronchoalveolar lavage cells


title: 1920B004 day 13, FACS sorted non-naïve CD8, GEX

description: Library name: 1920B004-Mem_CD8_d13_GEX


title: tumor mammary tissue, sample 1


title: 1920B011 day 7, BAL, TCR, biol rep 2

description: Library name: 1920B011-BAL_d7B_TCR


title: 1920B011 day 7, FACS sorted non-naïve CD8, TCR

description: Library name: 1920B011-Mem_CD8_d7_TCR


title: 1920B013 day 14, BAL, GEX, biol rep 2

description: Library name: 1920B013-BAL_d14B_GEX


title: 1920B011 day 7, BAL, TCR, biol rep 1

description: Library name: 1920B011-BAL_d7A_TCR


title: 1920B011 day 7, BAL, GEX, biol rep 2

description: Library name: 1920B011-BAL_d7B_GEX


title: ChIP-OHSC-H3K9me3-rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Library name: Sample 68

data_processing:
cutadapt
BWA-mem alignment
deepTools, normalized 10M reads
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Bone marrow

extract_protocol:
ChIP-seq was performed as described previously with Chromatin Immunoprecipitation (ChIP) Assay Kit (17-295, Millipore). 10,000 sorted cells were crosslinked with 1% formaldehyde (F8775, Sigma-Aldrich) at room temperature (RT) for 10 min
Libraries were prepared with TruSeq Nano DNA Low Throughput Library Prep Kit (20015964, Illumina) according to manufacturer's instructions.

value: Bone marrow

value: HSC

value: WT

tag: antibody


title: 1920B013 day 14, BAL, GEX, biol rep 1

description: Library name: 1920B013-BAL_d14A_GEX


title: 1920B013 day 14, BAL, TCR, biol rep 1

description: Library name: 1920B013-BAL_d14A_TCR


title: ChIP-OHSC-H3K9me3-rep1

description: Library name: Sample 67


title: 1920B011 day 7, BAL, GEX, biol rep 1

description: Library name: 1920B011-BAL_d7A_GEX


title: 1920B007 day 20, BAL, GEX, biol rep 2

description: Library name: 1920B007-BAL_d20B_GEX


title: ChIP-YHSC-H3K9me3-rep1

description: Library name: Sample 65


title: input, WNV 6dpi, isotype control 7

city: St Louis

first: Fang

middle: R

last: Zhao

state: MO

institute: Washington University in St Louis

description: Library name: sample.7I

data_processing:
Sequencing data was demultiplexed using Illumina’s DRAGEN and BCLconvert version 4.2.4 software. Reads were then aligned and mapped to the Ensembl release 101 primary assembly with STAR version 2.7.9a. A count matrix containing all expression data was then generated from the number of uniquely aligned unambiguous read using Subread:featureCount version 2.0.3  and isoform expression of known Ensembl transcripts quantified with Salmon version 1.5.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
Assembly: Ensembl release 101 primary assembly with STAR version 2.7.9a
Supplementary files format and content: Excel table read counts

source_name: distal part of small intestine

extract_protocol:
Samples were homogenized using homogenization buffer (50 mM Tris, pH 8.0; 100 mM KCl; 12 mM MgCl2; 1 % Igepal; 1 mg/mL sodium heparin; 100 µg/mL cycloheximide; 0.2 U/µL SUPERaseIn RNase Inhibitor, 2 mM DTT). After centrifugation (10,000 x g; 10 min; 4oC) 25 µg of primary antibody against GFP (rabbit; # AB290; Abcam) was added, and samples were rotated for 1 h at 4 oC. Subsequently, 200 µl of DynabeadsTM Protein G (# 10004D; Invitrogen) were added, and samples were incubated rotating overnight at 4 C. The beads were washed four times with high-salt buffer (50 mM Tris, pH 8.0; 300 mM KCl; 12 mM MgCl2; 1 % Igepal; 100 µg/mL cycloheximide). RNA was extracted and purified with Arcturus PicoPure RNA Isolation Kit (ThermoFisher: Kit0204 - Applied biosystems; 12204-01) according to the manufacturer’s instructions. To prevent contamination with DNA, RNase-Free DNase Set (Qiagen; # 29254) was used according to the manufacturer's instructions.
Library preparation was performed with 1-50 ng of total RNA.  cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer's protocol and then fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, an A base was added to the 3' ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: distal part of small intestine

value: Plp1CreERT2 - B6.Cg-Tg(Plp1-cre/ERT)3Pop/J; NuTRAP - B6;129S6-Gt(ROSA)26Sortm2(CAG-NuTRAP)Evdr/J

value: WNV


title: 1920B007 day 20, BAL, TCR, biol rep 1

description: Library name: 1920B007-BAL_d20A_TCR


title: ChIP-YHSC-H3K9me3-rep2

description: Library name: Sample 66


title: input, WNV 6dpi, isotype control 6

description: Library name: sample.6I


title: 1920B007 day 20, BAL, GEX, biol rep 1

description: Library name: 1920B007-BAL_d20A_GEX


title: input, WNV 6dpi, isotype control 5

description: Library name: sample.5I


title: input, WNV 6dpi, aCSF1R 1

description: Library name: sample.1I


title: 1920B004 day 13, BAL, GEX, biol rep 1

description: Library name: 1920B004-BAL_d13A_GEX


title: 1920B004 day 13, BAL, TCR, biol rep 2

description: Library name: 1920B004-BAL_d13B_TCR


title: input, WNV 6dpi, aCSF1R 4

description: Library name: sample.4I


title: 1920B004 day 13, BAL, TCR, biol rep 1

description: Library name: 1920B004-BAL_d13A_TCR


title: 1920B007 day 20, BAL, TCR, biol rep 2

description: Library name: 1920B007-BAL_d20B_TCR


title: input, WNV 6dpi, aCSF1R 2

description: Library name: sample.2I


title: LMO2 ReplicateB, shRNA2-2, 6 days

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

description:
Library name: SHL6B_day6
SHL6B_day6

data_processing:
Raw data (raw reads) of fastq format were processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Q20, Q30 and GC content were calculated. All the downstream analyses were based on clean data with high quality.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: MCF10A cells were maintained in Advanced DMEM 1X/F12 media (Fisher Scientific) with 5% of Horse serum (Life Technologies), 1% of PSA (Fisher Scientific), 100ug/ml of human EGF (Peproptech), 100 ng/ml of Cholera toxin (Sigma Aldrich), 9.5-11 mg/ml of Insulin (Neta Scientific), 5ug/ml of Hydrocortisone (Sigma-Aldrich Company).

extract_protocol:
RNA was isolated according to manufacturer’s instructions (Qiagen RNEasy Plus Micro Kit).
Bulk RNA sequencing was performed by Novogene on MCF10A cells transduced with either control (pSicoR) or shLMO2 knockdown vectors. RNA was isolated according to manufacturer’s instructions (Qiagen RNEasy Plus Micro Kit). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: The lentivirus plasmid pSicoR (Plasmid #11579, Addgene) was utilized as the backbone for generating lentivirus plasmids containing the human short hairpin RNA insertions targeting LMO2. The sequences for the LMO2 shRNA are 5′-GACGCATTTCGGTTGAGAA-3′ and 5′-GCATCCTGTGACAAGCGGATT-3′. MCF10As were transduced with control vector and LMO2 knockdown virus with at an MOI of 10, then media was changed after 6 hours. Cells were grown for either 6 or 21 days post-transduction before RNA extraction. Knockdown was confirmed through GFP expression and qPCR.

tag: cell line

value: Mammary Epithelial

value: LMO2 Knockdown


title: LMO2 ReplicateC, shRNA2-2, 6 days

description:
Library name: SHL6C_day6
SHL6C_day6


title: enriched, WNV 6dpi, isotype control 6

description: Library name: sample.6


title: 1920B004 day 13, BAL, GEX, biol rep 2

description: Library name: 1920B004-BAL_d13B_GEX


title: enriched, WNV 6dpi, isotype control 7

description: Library name: sample.7


title: enriched, WNV 6dpi, isotype control 5

description: Library name: sample.5


title: input, WNV 6dpi, aCSF1R 3

description: Library name: sample.3I


title: LMO2 ReplicateA, shLMO2-2, 6 days

description:
Library name: SHL6A_day6
SHL6A_day6


title: LMO2 ReplicateC, shLMO2-1, 6 days

description:
Library name: SHL1C_day6
SHL1C_day6


title: LMO2 ReplicateB, shLMO2-1, 6 days

description:
Library name: SHL1B_day6
SHL1B_day6


title: enriched, WNV 6dpi, aCSF1R 4

description: Library name: sample.4


title: LMO2 ReplicateA, shLMO2-1, 6 days

description:
Library name: SHL1A_day6
SHL1A_day6


title: enriched, WNV 6dpi, aCSF1R 3

description: Library name: sample.3


title: enriched, WNV 6dpi, aCSF1R 2

description: Library name: sample.2


title: ControlC, 6 days

description:
Library name: PSICORC_day6
PSICORC_day6


title: ControlB, 6 days

description:
Library name: PSICORB_day6
PSICORB_day6


title: LMO2 Replicate3, shLMO2-1, 21 days

description:
Library name: SHL1_3_day21
SHL1_3_day21


title: input, WNV 6dpi, isotype control 15

description: Library name: sample.15_I


title: input, WNV 6dpi, isotype control 14

description: Library name: sample.14_I


title: LMO2 Replicate1, shLMO2-1, 21 days

description:
Library name: SHL1_1_day21
SHL1_1_day21


title: enriched, WNV 6dpi, aCSF1R 1

description: Library name: sample.1


title: input, WNV 6dpi, isotype control 13

description: Library name: sample.13_I


title: LMO2 Replicate2, shLMO2-1, 21 days

description:
Library name: SHL1_2_day21
SHL1_2_day21


title: input, WNV 6dpi, isotype control 16

description: Library name: sample.16_I


title: ControlA, 6 days

description:
Library name: PSICORA_day6
PSICORA_day6


title: input, WNV 6dpi, aCSF1R 12

description: Library name: sample.12_I


title: input, WNV 6dpi, aCSF1R 10

description: Library name: sample.10_I


title: Control2, 21 days

description:
Library name: PSICOR2_day21
PSICOR2_day21


title: input, WNV 6dpi, aCSF1R 11

description: Library name: sample.11_I


title: Control3, 21 days

description:
Library name: PSICOR3_day21
PSICOR3_day21


title: input, sham, isotype control 8

description: Library name: sample.8_I

value: sham


title: Control1, 21 days

description:
Library name: PSICOR1_day21
PSICOR1_day21


title: caSTAT5, day14 (caS5_day14)

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

description: Library name: caS5_day14

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed with low-quality bases using fastp. Read lengths less than 15 nucleotides or a PHRED Quality Score of less than 15 were removed.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.2.1).
Read counts for each gene were calculated using featureCounts of the Subread package (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Calculated raw read counts for individual genes are shown in a tab-delimited text file.

source_name: CD8+ T cells

growth_protocol: Human T cells were stimulated on day 0 with K562 cells engineered to express an anti-CD3 monoclonal antibody (clone OKT3)-derived scFv fused to the transmembrane and cytoplasmic domains of CD8α, along with CD80 (K562-OKT3/CD80). On day 2, the stimulated T cells were retrovirally transduced with an anti-mesothelin CAR construct (ss1-28z) alone, or in combination with either constitutively active STAT3 (caSTAT3) or STAT5 (caSTAT5). The CAR-T cells were then expanded in vitro in RPMI medium supplemented with 10% FBS and 100 IU/mL recombinant human IL-2.

extract_protocol:
CD8+ CAR-T cell populaiton was isolated by an MA900 Cell Sorter (Sony). Total RNA was isolated from the purified CD8+ T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the SMART-Seq mRNA HT LP RNA-seq Library Prep Kit for Illumina according to standard Illumina protocols.

treatment_protocol: Control, caSTAT3, or caSTAT5-expressing CAR-T cells were intravenously infused into NSG mice inoculated with AsPC-1 cells on day 5. Tumor-infiltrating CAR-T cells were harvested between days 17 and 20.

value: CD8+ T cells

value: CAR and caSTAT5


title: caSTAT5, day15 (caS5_day15)

description: Library name: caS5_day15


title: input, sham, isotype control 6

description: Library name: sample.6_I


title: input, WNV 6dpi, aCSF1R 9

description: Library name: sample.9_I


title: caSTAT5, day13 (caS5_day13)

description: Library name: caS5_day13


title: input, sham, aCSF1R 4

description: Library name: sample.4_I


title: input, sham, isotype control 5

description: Library name: sample.5_I


title: caSTAT3, day14 (caS3_day14)

description: Library name: caS3_day14

value: CAR and caSTAT3


title: input, sham, aCSF1R 3

description: Library name: sample.3_I


title: MEF_untreated_rep3

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
Library name: MEF_untreated_rep3
peaks called with macs2 on filtered bam files (see methods)

data_processing:
Raw reads were processed with bcl2fastq (v 2.19.1), adapters were trimmed with cutadapt (v 2.2.0), reads were mapped to mm10 using bowtie2 (v 2.2.5) (-X 1500 –no-mixed –no-discordant).
chrM and duplicate reads were removed, quality filtering was performed with samtools (v 1.4.1) (-b -f3 -F4 -F8 -q7) and reads in blacklisted regions from (Buenrostro et al, 2013) and (Encode Project Consortium, 2012) were removed.
Peaks were called using macs2 (v 2.2.0) (-f BAMPE, -q 0.001), consensus peaks per condition were defined as peaks present in all 3 biological replicates, these peaks were combined and reads within defined peaks were counted using bedtools, v 2.26.0, coverage  to generate a count table for downstream analysis in R.
References: Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Meth 10, 1213.; ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74.
Assembly: mm10
Supplementary files format and content: For nascent/ replicated repli-ATAC-seq and matched unreplicated ATAC-seq libraries, processed files contain the mm10 coordinates for loci called as peaks from each condition's merged replicates.

source_name: Fibroblasts

growth_protocol: Reprogramming MEFs Mouse embryonic fibroblasts (MEFs) were cultured in MEF media: DMEM (Gibco, 31966021) supplemented with 10% heat-inactivated FCS (GE Hyclone, SV30160.03), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acids (Gibco, 11140050), 55 µM beta-mercaptoethanol (Gibco, 21985023), and 1X penicillin-streptomycin (Gibco, 15140122) and incubated at 37 °C with 5% oxygen.  ESCs to EpiLCs ESC were cultured on 0.1% gelatin in serum free media containing N2B27 (Neurobasal medium and DMEM:F12 (Gibco) supplemented with N2 (made in house), B27 (Gibco),  L-glutamine and 100 μM 2-mercaptoethanol (Sigma)) supplemented with 3 μM Gsk3i (Chir99021: Axon Medchem) and 1μM MEKi (PD0325901: Sigma) and LIF. 24hrs prior to EpiLC induction, MEKi was exchanged with FGFR inhibitor (PD173074 from Sigma-Aldrich) at 250 nM.

extract_protocol:
After the appropriate treatment, cells were trypsinized and collected in media. Samples were then processed and tagmented using TD buffer and TDE1 enzyme (Illumina).
EdU-positive samples were biotinylated via Click-IT (Invitrogen) and purified with Ampure XP beads (Beckman Coulter). Biotinylated products were captured using MyOne Streptavidin T1 beads (Thermo Fisher Scientific), and the unbound fraction (unreplicated/ bulk) in the supernatant from streptavidin pulldown was purified using the MinElute Reaction Cleanup kit (Qiagen). Samples were amplified using NEBNext High-Fidelity 2x PCR Master Mix (NEB) and final libraries were purified using Ampure XP beads.

treatment_protocol: Reprogramming MEFs Reprogramming was induced by seeding 6 x 106 MEFs on 10 cm plates coated with 0.2% gelatin (Sigma, G9391) and culturing in reprogramming media: KnockOut DMEM (Gibco, 10829018) supplemented with 15% heat-inactivated FCS (GE Hyclone, SV30160.03), 1X Glutamax (Gibco, 35050061), 1X non-essential amino acids (Gibco, 11140050), 55 µM beta-mercaptoethanol (Gibco, 21985023), 1X penicillin-streptomycin (Gibco, 15140122), custom-made LIF, 2 µg/mL doxycycline (Sigma, D9891), and 50 µg/mL L-ascorbic acid (Sigma, A4544) incubated at 37 °C with atmospheric oxygen levels. To prevent DNA replication, MEFs were cultured and induced to reprogram as above. 4 hours after reprogramming induction,  aphidicolin (5 µg/mL, Sigma, A0781) was added and both treated and untreated controls were cultured for a further 10 hours before being harvested for ATAC-seq generation.  ESCs to EpiLCs For EpiLC induction 10.000cells/cm2 were plated on fibronectin in N2B27 supplemented with FGF2 (10ng/mL) and Activin A (20ng/mL) both from Peprotech.  EdU Labelling EdU-positive samples were incubated in media containing EdU (20 uM final concentration) for 10 minutes, then either collected for processing (nascent samples) or cultured for 1 hour 50 minutes (total time since label: 2 hours) in media containing 10 uM thymidine before processing.  CellViolet Staining For ATAC-seq in proliferative subpopulations, 5 x 106 MEFs cultured in hypoxic conditions as described above were washed once in 1X PBS, resuspended in 5 mL 1X PBS containing 1X CellTrace Violet dye (Thermo Fisher, C34557), and incubated at 37 °C with atmospheric oxygen levels for 20 minutes in the dark. Labelling was stopped by addition of 10 mL MEF media and further incubation at 37 °C with atmospheric oxygen levels for 5 minutes in the dark. Labelled cells were then divided evenly between two 10 cm plates, one coated as above containing reprogramming media and one uncoated and containing MEF media (uninduced control). Both dishes were incubated at 37 °C with atmospheric oxygen levels for 60 hours before harvesting.

value: Fibroblasts

value: OKSM reprogramming intermediates from MEFs

value: Col1a1::tetOP-OKSM het; R26-M2rtTA het; Oct4GFP het

tag: timepoint

tag: passages