title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_P_scATAC

description: Library name: Naive_PATIENT_P_scATAC

data_processing:
Raw fastq files were run through 10x Genomics Cell ranger software to obtain filtered cell-level count data for ATAC and nuclear RNA. This information is provided and was utilized in R to perform downstream analyses.
Assembly: hg38
Supplementary files format and content: The following data files for these single cell Multiomic samples contain either the Cellranger output for ATAC seq libraries in fragments.tsv.gz files or they contain the associated nuclear RNA data from the same cells and 10X pipeline in an H5 file Deident_Naive_CONTROL_BC_scATAC_atac_fragments.tsv.gz Naive_CONTROL_BC_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_CONTROL_BE_scATAC_atac_fragments.tsv.gz Naive_CONTROL_BE_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_AD_scATAC_atac_fragments.tsv.gz Naive_PATIENT_AD_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_AH_scATAC_atac_fragments.tsv.gz Naive_PATIENT_AH_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_B_scATAC_atac_fragments.tsv.gz Naive_PATIENT_B_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_H_scATAC_atac_fragments.tsv.gz Naive_PATIENT_H_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_L_scATAC_atac_fragments.tsv.gz Naive_PATIENT_L_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_M_scATAC_atac_fragments.tsv.gz Naive_PATIENT_M_scGEX_filtered_feature_bc_matrix.h5 Deident_Naive_PATIENT_P_scATAC_atac_fragments.tsv.gz Naive_PATIENT_P_scGEX_filtered_feature_bc_matrix.h5

extract_protocol:
Cryopreserved PBMCs were thawed and enriched using negative selection (Stem Cell technologies human CD4 Isolation kit #100-0696) ) for CD4 T cells. They were then stained with flourescent antibodies and cells were sorted using flourescent activated cell sorter (Aria C). CD45RA+CD27+ naive TH cells were sorted. Immediately following sorting, cells were washed and nuclei were isolated by lysing cell membranes.  Nuclei were then used for  10X multi-ome for sc ATAC and sc nuclear RNA following manufacturer protocols.
Libaries construction for both scATAC and snRNA followed manufacturer protocols (10X genomics) for single cell Multi-omic protocols.

tag: tissue

value: Blood

tag: Sex

tag: cell type

value: A

value: Lupus

value: No

tag: ethnicity

value: Black/AfricanAmerican


title: P060_LUT

status: Public on Jan 17 2025

type: SRA

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program and subsequently trimmed using fastp 0.21.0 to remove Illumina adapter sequences. STAR 2.7.9a was used to index the human reference genome (hg38/GRCh38) and align the resultant fastq files. Mapped reads were then counted in annotated exons using featureCounts v1.5.1. The gene annotations (Homo_sapiens.GRCh38.101.gtf) and reference genome were obtained from Ensembl.
Assembly: hg38/GRCh38
Supplementary files format and content: Comma seperated file with raw gene counts for all luteal samples
Supplementary files format and content: Comma seperated file with normalized values of relevant luteal sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and placed in RLT Plus Lysis buffer (QIAGEN, Hilden, Germany), and homogenized using a TissueLyzer II machine (QIAGEN). An AllPrep DNA/RNA Mini Kit (QIAGEN) was used for RNA isolation and purification, and RNA quality was assessed by determining the RNA integrity number (RIN). A TruSeq mRNA SEq Library Prep kit (Illumina, San Diego, USA) was used to convert mRNA to cDNA libraries. Libraries (barcoded) were pooled and sequenced using Novaseq 6000 PE 150-bp (Illumina).
To construct libraries suitable for sequencing the Illumina stranded mRNA prep ligation protocol was used with starting concentration of 200 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined and the pools were sequenced on the Illumina NovaSeq S6000 on one lane of an S4-300 flowcell (PE 2X150).

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

value: Female

tag: time point

value: Luteal


title: NSCLC_BM24

city: New York

first: Somnath

last: Tagore

state: NY

address: 650W, 168th Street

country: USA

institute: Columbia University

description:
Single-nuclei RNA sequencing
STK_5dot1

library_source: transcriptomic single cell

data_processing:
library strategy: single nuclei RNAseq
Raw snRNA-seq data were analyzed using Cell Ranger (v5.0.1). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.2.0). Gene expression matrices were processed individually in R (v4.1.2) using Seurat (v4.0.5).
Filters were applied to keep cells with 500–10,000 genes, 1,000–60,000 UMIs, and <10% of mitochondrial reads in each individual sample.
Scrublet v0.2.1 (Wolock et al., 2019) was applied to identify and remove doublets with an expected doublet rate ranging from 2.8–6.4% based on the loading rate.
Assembly: GRCh38
Supplementary files format and content: mtx file (MatrixMarket format) of combined gene expression count matrix
Supplementary files format and content: csv file of gene names corresponding to the combined gene expression count matrix
Supplementary files format and content: csv file of integrated gene expression matrix

molecule: total RNA

source_name: NSCLC brain metastasis

extract_protocol:
Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST)  followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics  5' v1.1 or 5' v2.0 reagents and a Chromium controller.
Single-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 5' (V1.1 and V2) reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

value: STK11 c.836delG, p.G279fs

tag: kras mutation status

value: KRAS G12C

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq

value: yes


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_M_scGEX

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description: Library name: Naive_PATIENT_M_scGEX

molecule: nuclear RNA

source_name: Blood

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

value: Not Hispanic or Latino/a

tag: race

value: White


title: SFH-d84

city: Beijing

first: Bing

last: Peng

state: Beijing

address: Yiheyuan Road

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Assembly: mm10

organism: Mus musculus

extract_protocol:
DNA and RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

tag: cell line

tag: cell type

value: mESC

tag: genotype

value: WT

tag: treatment

value: cultured in SFH medium

tag: time


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_P_scGEX

description: Library name: Naive_PATIENT_P_scGEX

tag: tissue

value: Blood

tag: Sex

value: A

value: Lupus

value: Yes

value: Losartan

tag: ethnicity


title: P059_LUT

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

value: Female

tag: time point


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_M_scATAC

description: Library name: Naive_PATIENT_M_scATAC

library_source: genomic single cell

molecule: genomic DNA

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active

value: No


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_L_scGEX

description: Library name: Naive_PATIENT_L_scGEX

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

value: Black/AfricanAmerican


title: NSCLC_BM23

description:
Single-nuclei RNA sequencing
STK_3

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

value: STK11 splice site 863-1G>T

tag: kras mutation status

value: KRAS G13C

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: SFH-d80

tag: cell line

tag: cell type

value: mESC

tag: genotype

tag: treatment

tag: time


title: P058_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point

value: Luteal


title: SFH-d76

value: WT

value: cultured in SFH medium


title: NSCLC_BM22

description:
Single-nuclei RNA sequencing
STK_1

value: STK11 deletion exons 2-5

value: yes


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_L_scATAC

description: Library name: Naive_PATIENT_L_scATAC

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race


title: P057_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female


title: NSCLC_PT02

description:
Single-nuclei RNA sequencing
N586

source_name: NSCLC primary tumor

tag: metastatic site

value: PT

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq


title: NSCLC_PT01

description:
Single-nuclei RNA sequencing
N254


title: P056_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_H_scGEX

description: Library name: Naive_PATIENT_H_scGEX

tag: cell type

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active

value: No

tag: treatment acei_active

value: White


title: SFH-d68

tag: cell line

tag: genotype

tag: treatment

tag: time


title: SFH-d64


title: P054_LUT


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_H_scATAC

description: Library name: Naive_PATIENT_H_scATAC

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: NSCLC_BM21

description:
Single-nuclei RNA sequencing
PA141

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: NSCLC_BM20

description:
Single-nuclei RNA sequencing
PA125


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_B_scATAC

description: Library name: Naive_PATIENT_B_scATAC

tag: tissue

tag: Sex

tag: cell type

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active

tag: treatment acei_active

value: Black/AfricanAmerican


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_B_scGEX

description: Library name: Naive_PATIENT_B_scGEX

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: disease _severity_sledai


title: SFH-d52

tag: cell line

value: mESC

tag: genotype

value: WT

tag: treatment

tag: time


title: SFH-d56

value: cultured in SFH medium


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_AH_scGEX

description: Library name: Naive_PATIENT_AH_scGEX

tag: ethnicity

tag: race


title: NSCLC_BM18

description:
Single-nuclei RNA sequencing
PA080

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq

value: yes


title: NSCLC_BM19

description:
Single-nuclei RNA sequencing
PA104


title: P052_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point

value: Luteal


title: P053_LUT


title: SFH-d60

tag: cell type


title: SFH-d48

tag: cell line


title: P051_LUT


title: NSCLC_BM17

description:
Single-nuclei RNA sequencing
PA076


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_AD_scGEX

description: Library name: Naive_PATIENT_AD_scGEX

value: Blood

tag: timpoint

value: A

tag: disease

value: Healthy

tag: batch

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

value: UKN


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_AH_scATAC

description: Library name: Naive_PATIENT_AH_scATAC

value: Lupus

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race


title: SFH-d72

tag: genotype

tag: treatment

tag: time


title: P050_LUT

tag: tissue

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

value: Female

tag: time point


title: SFH-d44

tag: cell line

tag: cell type


title: SFH-d36


title: P049_LUT


title: human pbmc-derived sorted CD4 T cells Naive_PATIENT_AD_scATAC

description: Library name: Naive_PATIENT_AD_scATAC

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active


title: NSCLC_BM15

description:
Single-nuclei RNA sequencing
PA070

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq


title: P055_LUT


title: P047_LUT


title: SFH-d20

tag: genotype

tag: treatment

tag: time


title: NSCLC_BM13

description:
Single-nuclei RNA sequencing
PA067

value: snRNA-seq


title: human pbmc-derived sorted CD4 T cells Naive_CONTROL_BE_scGEX

description: Library name: Naive_CONTROL_BE_scGEX

tag: tissue

tag: Sex

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: SFH-d28

tag: cell line

tag: cell type


title: SFH-d32


title: human pbmc-derived sorted CD4 T cells Naive_CONTROL_BC_scGEX

description: Library name: Naive_CONTROL_BC_scGEX

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active


title: NSCLC_BM14

description:
Single-nuclei RNA sequencing
PA068

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq


title: P045_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point


title: SFH-d16

tag: genotype

tag: treatment

tag: time


title: P044_LUT


title: NSCLC_BM12

description:
Single-nuclei RNA sequencing
PA060


title: NSCLC_BM10

description:
Single-nuclei RNA sequencing
PA054


title: human pbmc-derived sorted CD4 T cells Naive_CONTROL_BC_scATAC

description: Library name: Naive_CONTROL_BC_scATAC

tag: cell type

tag: timpoint

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_Y_ATAC

description: Library name: NaiveCD4_PATIENT_Y_ATAC

library_source: genomic

data_processing:
Raw fastq Files were put through the ENCODE ATAC-seq pipeline in batches (up to seven samples of like cell type). ENCODE output of IDR (reproducible stringently called peaks) were then merged across different samples to create a consensus peak list. Bedtools Coverage function was then used to generate count level data for each peak in the consensus data set for each sample. This information was input into R for further analysis.
Assembly: hg38
Supplementary files format and content: Raw_unfiltered_ATAC_Fig1_Fig2.txt contains data from multiple CD4 T cell populations from the first cohort of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported.
Supplementary files format and content: Raw_unfiltered_ATAC_Fig5.txt  contains data from Naive CD4 T cells from the first and second cohorts of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported. Consensus peaks reflect the addition of new data in a second cohort which may change peaks.
Supplementary files format and content: Raw_unfiltered_ATAC_fig6.txt contains data from Naive CD4 T cells from the first, second, and third cohorts of lupus patients and healthy controls. The bulk isolated ATAC data is presented in the form of count data for stringently called consensus peaks. Consensus peaks were generated from merging individual peak sets reported. Consensus peaks reflect the addition of new data in a third cohort which may change peaks.

extract_protocol:
Cryopreserved PBMCs were thawed and enriched using negative selection (Stem Cell technologies human CD4 Isolation kit #100-0696) ) for CD4 T cells. They were then stained with flourescent antibodies and cells were sorted using flourescent activated cell sorter (Aria C). CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells were sorted. In most cases, 5000 cells were sorted. Immediately following sorting, cells were processed for ATAC-seq. OMNI ATAC protocol was followed (PMID: 28846090). Cells were transposed for 40 minutes in 37 degree still water bath before DNA was isoalted with Zymogen Clean and Concentrate Kit.
Libaries were prepared following standard protocols and utilizing Illumina indexes. Fractionation and size selection were performed. Size selection was done using bead-based enrichment.

value: CD45RA positive CD27 positive CD4 positive T cells

tag: disease

tag: batch

tag: treatment arb_active

value: Yes

value: Losartan

value: No

value: Black/AfricanAmerican


title: SFH-d12

tag: cell line

value: mESC

value: WT

value: cultured in SFH medium


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_Z_ATAC

description: Library name: NaiveCD4_PATIENT_Z_ATAC

tag: tissue

value: Blood

tag: Sex

value: A

value: White


title: SFH-d8

tag: genotype

tag: treatment


title: P043_LUT

tag: subject group

tag: time point

value: Luteal


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_X_ATAC

description: Library name: NaiveCD4_PATIENT_X_ATAC

tag: cell type

tag: timpoint

value: Healthy

tag: treatment arb_type

value: UKN


title: SFH-d4

tag: time


title: NSCLC_BM08

description:
Single-nuclei RNA sequencing
PA043

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq

value: yes


title: P042_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female


title: NSCLC_BM16

description:
Single-nuclei RNA sequencing
PA072

value: BM

value: snRNA-seq


title: NSCLC_BM09

description:
Single-nuclei RNA sequencing
PA048


title: P048_LUT


title: human pbmc-derived sorted CD4 T cells Naive_CONTROL_BE_scATAC

description: Library name: Naive_CONTROL_BE_scATAC

tag: disease

tag: batch

tag: treatment arb_active

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: P046_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_V_ATAC

description: Library name: NaiveCD4_PATIENT_V_ATAC

tag: cell type

value: CD45RA positive CD27 positive CD4 positive T cells

tag: timpoint

value: Lupus

value: Yes

tag: treatment arb_type

value: Valasartan

value: No

value: Not Hispanic or Latino/a


title: NSCLC_BM11

description:
Single-nuclei RNA sequencing
PA056

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq


title: SFH-d0

tag: cell line

value: mESC

tag: genotype

value: WT

tag: treatment

value: cultured in SFH medium

tag: time


title: P039_LUT

tag: tissue

value: Luteal


title: SL-d92

value: cultured in S/L medium


title: P038_LUT

tag: subject group


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_U_ATAC

description: Library name: NaiveCD4_PATIENT_U_ATAC

value: Blood

tag: Sex

value: A

tag: disease

tag: batch

tag: treatment arb_active

value: Losartan

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

tag: race

value: Asian


title: NSCLC_BM06

description:
Single-nuclei RNA sequencing
PA034

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq

value: yes


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_T_ATAC

description: Library name: NaiveCD4_PATIENT_T_ATAC

tag: tissue

value: Female

tag: cell type

value: CD45RA positive CD27 positive CD4 positive T cells

tag: timpoint

tag: treatment arb_type

value: Black/AfricanAmerican


title: NSCLC_BM05

description:
Single-nuclei RNA sequencing
PA025

value: snRNA-seq


title: P037_LUT

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

tag: time point


title: P036_LUT


title: NSCLC_BM04

description:
Single-nuclei RNA sequencing
PA019


title: SL-d80

tag: cell line

value: mESC

tag: genotype

tag: treatment

tag: time


title: SL-d76

value: WT


title: P035_LUT


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_R_ATAC

description: Library name: NaiveCD4_PATIENT_R_ATAC

tag: disease

value: Healthy

tag: batch

tag: treatment arb_active

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

value: UKN

tag: race


title: NSCLC_BM03

description:
Single-nuclei RNA sequencing
PA005

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq


title: P034_LUT

tag: tissue

tag: subject group

tag: Sex

tag: time point

value: Luteal


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_Q_ATAC_2

description: Library name: NaiveCD4_PATIENT_Q_ATAC_2

value: Blood

tag: cell type

tag: timpoint

value: B

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: Yes

tag: treatment arb_type

value: No

value: Not Hispanic or Latino/a

value: White


title: SL-d72

tag: cell line

tag: genotype

tag: treatment

value: cultured in S/L medium

tag: time


title: NSCLC_BM02

description:
Single-nuclei RNA sequencing
PA004

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

tag: kras mutation status

value: yes


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AC_ATAC

description: Library name: NaiveCD4_PATIENT_AC_ATAC

tag: tissue

value: Female

value: CD45RA positive CD27 positive CD4 positive T cells

value: A

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: SL-d88

tag: cell type

value: mESC

value: WT


title: NSCLC_BM01

description:
Single-nuclei RNA sequencing
PA001

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: P033_LUT

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

tag: time point

value: Luteal


title: SL-d68

tag: cell line

tag: genotype

tag: treatment

tag: time


title: NSCLC_BM07

description:
Single-nuclei RNA sequencing
PA042

tag: metastatic site

tag: patient id

tag: stk11 mutation

tag: kras mutation status


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AB_ATAC

description: Library name: NaiveCD4_PATIENT_AB_ATAC

tag: tissue

value: Blood

tag: timpoint

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

tag: treatment arb_type

value: Losartan

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

value: Black/AfricanAmerican


title: P032_LUT

tag: subject group

tag: Sex

tag: time point


title: SL-d60

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time


title: P031_LUT

tag: tissue


title: SL-d52


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_S_ATAC

description: Library name: NaiveCD4_PATIENT_S_ATAC

tag: timpoint

tag: disease

value: Yes

value: No

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race

value: White


title: RT4 Rep2

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

description:
Library name: SAM24434386
Luminal cell line

data_processing:
Adapters were trimmed using Cutadapt.
Reads were aligned to the reference genome GRCh38 with Bowtie2.
PCR duplicates were flagged by MarkDuplicates from Picard, and SAMTools was used to filter out duplicated, unpaired, and mitochondrial reads.
Bam files were converted to paired bed files with Bedtools bamtobed-bedpe, after which reads were shifted by 4 or 5 bp to account for the cutting bias introduced by Tn5.
MACS2 callpeak was used for peak calling with a p value threshold of 0.01. Peaks were filtered for GRCh38 blacklist regions. Diffbind was used for summarizing open chromatin regions across all samples and performing differential analysis. Motif enrichment within differentially accessible regions was done with AME.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: All cell lines were cultured in Roswell Park Memorial Institute (RPMI) medium 1640 containing 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin, 100 mg/mL streptomycin sulfate, and 1% L glutamine

extract_protocol:
Transposed DNA was purified using the MiniElute Reaction Cleanup kit (Qiagen) and eluted in 21 μL elution buffer.
Partially amplified libraries were generated by amplifying the purified transposed DNA for 5 cycles using NEBNext High-Fidelity 2X polymerase chain reaction (PCR) Master Mix (New England Biolabs). Partially amplified libraries were quantified by quantitative PCR  to determine the cycle number at which each sample produced 25% of maximum fluorescent intensity. The fluorescent intensity was used to estimate the number of additional PCR cycles required for each sample. Fully amplified libraries were purified using the SPRIselect beads (Beckman Coulter).

value: Urinary Bladder


title: RT4 Rep1

description:
Library name: SAM24434385
Luminal cell line


title: Human blood-derived CD4 T cell NaiveCD4_PATIENT_AA_ATAC

description: Library name: NaiveCD4_PATIENT_AA_ATAC

value: Female

value: CD45RA positive CD27 positive CD4 positive T cells

tag: batch

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

value: yes


title: SL-d48

value: mESC

value: WT

value: cultured in S/L medium


title: SW 780 Rep2

description:
Library name: SAM24434374
Luminal cell line


title: P030_LUT

value: Ectocervix

tag: subject group

value: Kenyan female sex workers


title: LN229 cells, 10Gy X-ray irradiated, bio_rep3

city: San Antonio

first: Luis Fernnado

last: Macedo Di Cristofaro

state: Texas

address: 7703 Floyd Curl Drive,

department: Neurosurgery

institute: UTHSCSA

data_processing:
cDNA was then A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated on the Agilent Tapestation 4200. After normalization and pooling, sequencing was performed on a NextSeq2000 (Illumina®).
Data quality was assessed by FastQC (v.0.11.5), removal of low-quality sequences (Trimmomatic v0.39) retaining high-quality single-end reads for further alignment and reads quantification (Kallisto v0.50.0)
Differential Expression assessed by EdgeR.
Assembly: hg19
Supplementary files format and content: .txt file with compilated data in matrix format.

source_name: LN229 - Brain; Right frontal parieto-occipital cortex isolated from a white, 60-year-old, female patient with glioblastoma.

growth_protocol: Cells were growth in DMEM 10%FBS 1%P/S and kept on a 37 degrees incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen cat. No. 74104) and RNase-free DNase set (Qiagen, Cat. No: 79254), according to the manufacturer's instructions. RNA samples were run on an Agilent Tapestation 4200 to determine RNA quality, and all samples had a RIN score 8 or higher.
One microgram of total DNAse-treated RNA was then used for library preparation with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Polyadenylated RNA was purified and fragmented before strand specific cDNA synthesis.

value: glioblastoma

tag: Sex

tag: age


title: LN229 cells, 10Gy X-ray irradiated, bio_rep2

tag: cell line

value: Brain; Right frontal parieto-occipital cortex


title: SL-d40

tag: cell type


title: SW 780 Rep1

description:
Library name: SAM24434373
Luminal cell line


title: SL-d44

tag: genotype


title: P028_LUT

tag: time point

value: Luteal


title: LN229 cells, mock-irradiated, bio_rep3


title: RT-112 Rep2

description:
Library name: SAM24434368
Luminal cell line


title: P027_LUT


title: SL-d36

tag: treatment

tag: time


title: LN229 cells, mock-irradiated, bio_rep2

tag: tissue


title: RT-112 Rep1

description:
Library name: SAM24434367
Luminal cell line


title: P026_LUT


title: SL-d28


title: KU-19-19 Rep2

description:
Library name: SAM24434356
Basal cell line


title: LN229 cells, mock-irradiated, bio_rep1


title: SL-d24


title: LN229 cells, 10Gy X-ray irradiated, bio_rep1


title: P025_LUT


title: KU-19-19 Rep1

description:
Library name: SAM24434355
Basal cell line


title: P024_LUT


title: HT-1376 Rep2

description:
Library name: SAM24434350
Basal cell line


title: A172 cells, 10Gy X-ray irradiated, bio_rep2

source_name: A172 - glioblastoma cell line isolated from a 53yo male patient (purchased from ATCC)

value: Male


title: SL-d16


title: HT-1376 Rep1

description:
Library name: SAM24434349
Basal cell line


title: P029_LUT


title: P023_LUT


title: A172 cells, 10Gy X-ray irradiated, bio_rep1


title: 5637 Rep1

description:
Library name: SAM24434343
Basal cell line


title: SL-d12


title: SL-d8


title: 5637 Rep2

description:
Library name: SAM24434344
Basal cell line


title: A172 cells, mock-irradiated, bio_rep2


title: P021_LUT


title: A172 cells, mock-irradiated, bio_rep3


title: SL-d4


title: SL-d0


title: P020_LUT


title: A172 cells, mock-irradiated, bio_rep1


title: P019_LUT


title: NEC3

city: Shanghai

first: Ting

last: Guo

state: Shanghai

address: Shanghai Putuo District,Luding road No.355

department: Department of General surgery

institute: Shanghai Children's Hospital

description:
Library name: Sample 6
AG18101705

data_processing:
Illumina Hiseq 2500 platform used for basecalling
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: intestine

growth_protocol: Con group mice were fed with dam. NEC group mice were fed with  40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories) every 4 h for 96 h.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and chloroform, and RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.

treatment_protocol: NEC group mice was induced using formula gavage every 4 h for 96 h using 40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories). Meanwhile, pups were exposed to hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min) every 12 h. The control group were dam-fed without hypoxia and cold stress.

value: intestine

value: Fed with formula and PBS by gavage, hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min)


title: P018_LUT


title: SL-d20


title: mTBLC-ICG001

value: cultured in 2MYCP medium supplemented with ICG001


title: A172 cells, 10Gy X-ray irradiated, bio_rep3


title: P017_LUT


title: NEC2

description:
Library name: Sample 5
AG18101704


title: NEC1

description:
Library name: Sample 4
AG18102802


title: Ctnnb1-ko-p7

value: Ctnnb1-knock out

value: cultured in 2MYCP medium


title: P016_LUT

value: Female


title: P022_LUT


title: ZHBTC4-DOX-TBLC-P4

value: cultured in 2MYCP medium supplemented with dox


title: ZHBTC4-DOX-TBLC-P3


title: Control2

description:
Library name: Sample 2
AG18101703

value: PBS


title: Control3

description:
Library name: Sample 3
AG18102801


title: P013_LUT


title: P012_LUT


title: Control1

description:
Library name: Sample 1
AG18101701


title: P011_LUT


title: ZHBTC4-DOX-TBLC-P1

value: mESC


title: Control: NS_S_5

city: Nanjing

first: Yunshan

middle: of

last: Hu

state: Jiangsu

address: No. 264 Guangzhou Road, Nanjing

institute: Nanjing Brain Hospital

description:
Library name: Sample18
NS_S_5

data_processing:
Filter raw reads using the fastp (v0.19.5) to obtain clean reads for subsequent analysis. Remove sequencing primers; remove low-quality sequences (Q < 15) at the ends; remove sequences with fragment lengths < 40bp after the above steps.
Align the filtered reads to the reference database using STAR (v2.7.7a). The proportion of aligned bases can reflect the sequencing quality, the quality of the selected reference genome, and the reliability of subsequent analysis.
Use Picard (v2.18.29) to analyze the results of STAR alignment, and calculate the distribution of sequences in each sample across CODING (coding regions), UTR (untranslated regions), INTRONIC (introns), and INTERGENIC (intergenic regions) areas to assess any anomalies in the experimental library construction.
Use the Stringtie (v1.3.5) analysis pipeline to quantify the expression of known genes and transcripts, and normalize at the gene level.
Assembly: mm10
Supplementary files format and content: gene_count_matrix.csv files include raw counts for each Sample
Supplementary files format and content: fpkm_allSample.csv files include FPKM values for each Sample

source_name: left prelimbic cortex

growth_protocol: Four mice were kept in each group and subjected to a 12-hour light-dark cycle (lights on from 7:00 a.m. to 7:00 p.m.) at a room temperature of 23 - 25°C. The mice were allowed to feed and drink ad libitum.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA). Use no less than 2ug of total RNA to construct the sequencing library.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) following manufacturer's protocols.

treatment_protocol: 1.The SCZ group received intraperitoneal injections of MK-801 solution at a dose of 0.2 mg/kg daily for two weeks. The control group received an equivalent volume of saline (0.1 mL/10 g) via intraperitoneal injection once daily for 2 weeks, followed by behavioral tests. 2.The c-MSST comprised SPIO nanoparticles and a magnetic field (MF). The γ-Fe2O3 nanoparticles, known as Ferumoxytol, were manufactured by Jiangsu Zhengda Tianqing Pharmaceutical Co., Ltd. and have received approval from the Chinese Food and Drug Administration (CFDA) for clinical application. Administer SPIO into the left PrL of mice via stereotactic brain surgery. Upon regaining consciousness, place the mice within the influence of a pulsed magnetic field (MF) under an aluminum frame, permitting free movement within this area. The combined effect of the MF and SPIO nanoparticles stimulated and activated the left PrL. Each mouse received a single injection of SPIO nanoparticles during the experiment.

value: left prelimbic cortex


title: Control: NS_S_7

description:
Library name: Sample19
NS_S_7


title: ZHB-DOX-SL-P1

value: WT

value: cultured in S/L medium supplemented with dox


title: ZHBTC4

value: cultured inS/L medium


title: P009_LUT

value: Ectocervix

value: Kenyan female sex workers


title: CM2Y-P5

value: cultured in 2MYC medium


title: Control: NS_S_3

description:
Library name: Sample16
NS_S_3


title: P008_LUT

value: Luteal


title: CM2Y-P6


title: CM2Y-P4


title: Control: NS_S_2

description:
Library name: Sample15
NS_S_2


title: Control: NS_S_1

description:
Library name: Sample14
NS_S_1


title: P006_LUT


title: P014_LUT


title: CM2Y-P3


title: P007_LUT


title: Control+c-MSST: NS_M_7

description:
Library name: Sample13
NS_M_7


title: ZHBTC4-DOX-TBLC-P2


title: CM2Y-P2


title: CM2Y-P1


title: Kl-Input-repeat3

city: Taipei

first: Akshi

last: Gupta

state: Taiwan

address: IMB, 128, Academia Rd., Nangang, N411 lab

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Library name: IK123
paired with CK123 chip

data_processing:
All sequencing protocols were carried out as per the manufacture's instructions using the Illumina NextSeq500 and NextSeq software: base calling was performed using NextSeq Control Software NCS 2.2.0 and Real-time Analysis software RTA 2.4.11 to generate BCL files. The Illumina bcl2fastq2 Conversion Software v2.17 was used to demultiplex sequencing data and convert BCL files into FASTQ files.
The quality control and adaptor trimming of sequencing reads were processed by FastQC version 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and Trimmomatic version 0.36 with the parameters “2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:3 CROP:68”.
Trimmed reads were mapped to the S. cerevisiae S288C genome using Bowtie2 version 2.3.3.
Bowtie2 mapped BAM files were detected for the ChIP peaks using SPP version 1.13 with a false discovery rate (FDR) of 0.05.
The Tfc3 binding peaks were compared and merged among three biological replicates by SeqMonk version 1.0. Only peaks detected in all three biological repeats were used for the downstream analysis.
The text files were generated from seqmonk. The bigwig files are generated by deepTools.
Assembly: Saccharomyces cerevisiae S28C genome (R64-2-1)
Supplementary files format and content: Text files with binding positions and annotation, bigwig files

organism: Saccharomyces cerevisiae S288C

growth_protocol: Cells of S288C tfc7D::KanMX4 pRS413-tetO7-Sc-TFC7 TFC3-3Flag::HGB and S288C tfc7D::KanMX4 pRS413-tetO7-Kl-TFC7 TFC3-3Flag::HGB were grown in the YPD medium at 30°C overnight, subsequently diluted into each indicated medium in a cell density of 0.2 OD600/ml, and then incubated at 30°C to achieve 0.6-0.8 OD/ml.

extract_protocol:
For breaking cells, 500 OD600 of S288C tfc7D::KanMX4 pRS413-tetO7-Sc-TFC7 TFC3-3Flag::HGB and S288C tfc7D::KanMX4 pRS413-tetO7-Kl-TFC7 TFC3-3Flag::HGB, were thawed and resuspended in FA buffer (50 mM HEPES, pH 7.5; 140 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) with 1/100 PIC (Protease inhibitor cocktail Set IV, in DMSO; 539136, Merck) and 1 mM phenylmethanesulfonyl fluoride (PMSF, P7626, Sigma) at a concentration of 500 OD600/4ml. Every 4-ml cell suspension was divided into four 2-ml breaking tubes (Biospec, 10832, Microtube 2 ml with cap) containing 1 ml volume of glass beads (11079105, BioSpec Products). The lysis was performed by three cycles of 5-min beating followed by 1-min chilling on ice (Biospec Mini-BeadBeater-16). Cell lysates and glass beads were separated by punching a hole on the bottom of the tube with a red-hot 18G needle and slow centrifugation (500 g, 3 min, 4°C; Eppendorf 5810R centrifuge, A-4-62 rotor). The collected lysates were combined into a 15-ml centrifuge tube and washed with two cycles of 5 ml FA buffer followed by centrifugation (12K rpm, 5 min, 4C; Eppendorf 5810R centrifuge, F-34-6-38 rotor). The washed lysates were completely resuspended in 2 ml FA buffer with 1/100 PIC and 1 mM PMSF in a new 15-ml centrifuge tube (CFT011150, BIOFIL). Chromatin was sheared by sonication in a Bioruptor water bath sonicator (Diagenode) with 15 ml tube-chip unit (High intensity; 30 sec on, 30 sec off, 15 min/cycle; total 3 cycles) at 4°C. The sheared lysate was centrifuged at 12000 g for 10 min at 4°C (Eppendorf 5810R centrifuge, F-34-6-38 rotor). About 25 ml of supernatant corresponding to 5 OD600 of cells was collected, mixed with 200 ml TES buffer (50 mM Tris-Cl, pH 8; 10 mM EDTA, pH 8; 1% SDS) plus 175 ml TE buffer (10 mM Tris-Cl; 1 mM EDTA, pH 8), and stored at -20°C as the input-DNA. Immunoprecipitation was performed by incubating all the rest sheared chromatins with 300 ml Dynabeads® Pan Mouse IgG (11041, human anti-mouse IgG, Invitrogen) in 6 ml of FA buffer with 1/100 PIC and 1 mM PMSF. The binding was performed in a 15-ml tube with mixing using an end-over-end rotator (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at 4°C for 16 h. The magnetic beads were anchored with DynaMagTM-2 Magnet and the bound complexes were washed 4 times with 1 ml of each wash buffer for 5 min [FA buffer × 1, high-salt FA buffer (50 mM HEPES, pH 7.5; 500 mM NaCl; 0.1% SDS; 1 mM EDTA; 1% Triton X-100; 0.1% Deoxycholate, Na salt) × 1, DOC buffer (10 mM Tris·Cl; 1 mM EDTA, pH 8; 25 0mM LiCl; 0.5% IGEPAL® CA-630; 0.5% Deoxycholate, Na salt) × 1, and TE buffer × 1] with mixing (Fntelli-Mixer, RM-2L, F1 mode, 30 rpm) at room temperature. The bound complexes were eluted twice by heating at 65°C in 200 ml TES buffer for 20 min and in 200 ml TE buffer for 10 min. Two eluates were pooled as the ChIP-DNA. To remove RNA, both the input-DNA and ChIP-DNA (~400 ml each) were treated with 5 ml of 10 mg/ml RNase A (R5503, Sigma; 100 mM Tris-Cl, pH 7.4) at 37°C for 30 min. For de-crosslinking, both the RNase-treated input-DNA and ChIP-DNA were treated with 40 ml of 20 mg/ml Proteinase K (1.24568.0500, Merck; in 50 mM Tris-Cl, pH 8) at 42°C for 1 h and then 65°C for 16 h. De-crosslinked DNA was purified using the QIAquick DNA Purification Kit (28106, Qiagen) according to the manufacturer's instruction, with a modification of a two-cycle wash step using the PE buffer. Final ChIP-DNA and input-DNA were eluted with 50 ml EB buffer. DNA concentrations were measured by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific).
ChIP-seq analysis was performed from three biological replicates of S288C tfc7D::KanMX4 pRS413-tetO7-Sc-TFC7 TFC3-3Flag::HGB and S288C tfc7D::KanMX4 pRS413-tetO7-Kl-TFC7 TFC3-3Flag::HGB cells. The average fragment length of sonicated fragments was 150–1000 bp. For each condition, libraries were prepared from >3 ng of ChIP-DNA and input-DNA using the KAPA Hypr Library Preparation Kit for Illumina® platforms (KK8232, KAPA Biosystems by Roche) according to the manufacturer’s instruction. Notably, after adapter ligation, double-sided size selection between 250–450bp for adapter-ligated fragments was performed using the KAPA Pure Beads (KK8000/07983271001, KAPA Biosystems by Roche). Size-selected fragments were then PCR-amplified for 12 cycles. The size of each library was assessed using a Bioanalyzer 2100 instrument (Agilent Technologies) with the High Sensitivity DNA Kit (Agilent Technologies). The concentration of each library was quantified by using the Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen by Thermo Fisher Scientific) and qPCR. Single-read sequencing (75 bp) or paired-end sequencing (75 bp × 2) of the libraries was performed using the NextSeq 500/550 high output reagent kit V2_75 cycle (FC-404-2005, Illumina) on an Illumina NextSeq500 sequencer.

treatment_protocol: After 0.6-0.8 OD600/ml in YPD at 30°C was detected, cultures of log phase cells were fixed with 1% formaldehyde at 25°C for 15 min with shaking at 180 rpm and then quenched with 125 mM glycine at 25°C for 10 min with shaking at 180 rpm. All the following steps were performed in an ice-cold or 4°C environment. Cells were harvested, washed twice with TBS (20 mM Tris-Cl, pH 7.5; 150 mM NaCl), and stored at −80°C until use.

tag: strain

tag: chip antibody

value: MATa met15D0 ura3::CMV-tTA-FOA his3D1 trp1D63 leu2D0 tfc7D::KanMX4 pRS413-tetO7-Kl-TFC7 TFC3-3Flag::HGB

value: YPD, 30°C


title: Control+c-MSST: NS_M_4

description:
Library name: Sample11
NS_M_4


title: P005_LUT


title: g-TBLC-P8

value: cultured in 2MYCP medium in gelatin


title: P010_LUT


title: Control: NS_S_4

description:
Library name: Sample17
NS_S_4


title: Kl-Input-repeat2

description:
Library name: IK122
paired with CK122 chip

source_name: S288C tfc7D::KanMX4 pRS413-tetO7-Kl-TFC7 TFC3-3Flag::HGB


title: g-TBLC-P7


title: Kl-Input-repeat1

description:
Library name: IK121
paired with CK121 chip


title: P002_LUT


title: Control+c-MSST: NS_M_2

description:
Library name: Sample10
NS_M_2


title: 2mycp-TBLC-P19


title: Kl-ChIP-repeat3

description:
Library name: CK123
paired with IK123 input

value: Anti-FLAG ®  M2 magnetic beads for FLAG


title: Donor 2, Undifferentiated organoid 3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Quality of the sequencing data was assessed using fastqc, and then reads were aligned to the Ensembl GRCh38 p12 genome using the HiSat2 aligner.
Counts/gene were generated using the Bioconductor Rsubread package.
Assembly: Ensembl GRCh38 p12
Supplementary files format and content: BAM files generated using HiSat2

source_name: duodenal biopsy

growth_protocol: Undifferentiated duodenal organoids were obtained via endoscopy for clinically indicated conditions, where upper GI tract was endoscopically normal, from three donors (27 year old, female; 81 year old, female; 25 year old, male). Undifferentiated organoids were suspended and grown in Matrigel droplets in the presence of Intesticult™ Intestinal Organoid Growth Medium (Human) containing 1% (v/v) penicillin-streptomycin. Undifferentiated organoids were passaged after 7-10 days in culture, or until they reached a large, cystic morphology, by the addition of 0.5 mL of cold Cell Recovery Solution followed by 30 minutes of shaking at 4?C. Cells were then triturated until roughly 80% of the organoids were broken into small fragments followed by centrifugation for 10 minutes at 1200g at 4?C. The resulting supernatant was discarded and the cell pellet was resuspended with Matrigel and plated onto a 24-well plate in 50 µL droplets. The plate was then placed into a 37?C incubator for 10-15 minutes to allow for the Matrigel to polymerize, followed by the addition of 0.5 mL of Intesticult™ Growth Medium containing 10 µM Y-27632. Undifferentiated organoids were fed every two days with Intesticult™ Growth Medium without Y-27632. Cells were split from 1:2 to 1:5, depending on cell density.

extract_protocol:
Matched undifferentiated spheroids and differentiated enteroid monolayers cultured for 21 days from the same donor at the same passage number were lysed with 0.5 mL of RLT lysis buffer and stored at -80?C until analysis.
Samples were sent to Novogene America (Sacramento, California) where the RNA was isolated and messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. mRNA was then fragmented and the first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dTTP for non-directional library and sequenced by a NovaSeq 6000 system (Illumina, San Diego, CA)

treatment_protocol: Enteroid monolayers were grown on polyester, 0.4 µm pore-size Transwell® filter inserts for 24-well plates (catalog no. 3470; Corning Inc., NY). The day before seeding, 50 µL of 34 µg/mL collagen IV was added to each Transwell® and allowed to polymerize overnight in a 37?C incubator. The following day, undifferentiated organoids were removed from their Matrigel droplets (two Matrigel droplets per Transwell® insert plated) by the addition of 0.5 mL of cold Cell Recovery Solution followed by 30 minutes of shaking at 4?C. Cells were then triturated on ice until roughly 95% of the organoids were broken into small fragments/single cells followed by centrifugation for 10 minutes at 1200g at 4?C. The resulting supernatant was discarded and the cell pellet was resuspended with Intesticult™ Intestinal Organoid Differentiation Medium (Human) containing 1% (v/v) penicillin-streptomycin and 10 µM Y-27632. Buffer in the collagen IV-treated Transwell® inserts was then aspirated and the inserts washed with Advanced DMEM/F-12 before plating 100 µL of the cell suspension to each Transwell® insert (apical chamber) and addition of 0.5 mL of the Intesticult™ Differentiation Medium to the basolateral  chamber of the 24-well plate. Enteroid monolayers were fed every two days with Intesticult™ Differentiation Medium containing Y-27632. For undifferentiated monolayers, the cell pellet was resuspended with Intesticult™ Growth Medium containing Y-27632, plated, and then fed every two days with growth medium containing Y-27632.

value: duodenal biopsy

value: undifferentiated spheroids

value: Cultured in Intesticult Growth Medium


title: 2mycp-TBLC-P14

value: cultured in 2MYCP medium


title: SCZ: MK_S_5

description:
Library name: Sample8
MK_S_5


title: Kl-ChIP-repeat2

description:
Library name: CK122
paired with IK122 input


title: Donor 2, Undifferentiated organoid 2


title: 2mycp-TBLC-P8

value: mESC


title: SCZ: MK_S_3

description:
Library name: Sample7
MK_S_3

value: left prelimbic cortex


title: Control+c-MSST: NS_M_6

description:
Library name: Sample12
NS_M_6


title: P004_LUT

value: Female


title: SCZ: MK_S_2

description:
Library name: Sample6
MK_S_2


title: Kl-ChIP-repeat1

description:
Library name: CK121
paired with IK121 input


title: Donor 2, Differentiated organoid 3

value: enteroid monolayer

value: Differentiated using Intesticult Intestinal Organoid Differentiation Medium


title: SCZ: MK_S_1

description:
Library name: Sample5
MK_S_1


title: Donor 2, Undifferentiated organoid 1


title: P003_LUT

value: Ectocervix


title: 2mycp-TBLC-P6

value: WT


title: Sc-Input-repeat3

description:
Library name: IS63
paired with CS63 chip

source_name: S288C tfc7D::KanMX4 pRS413-tetO7-Sc-TFC7 TFC3-3Flag::HGB

value: MATa met15D0 ura3::CMV-tTA-FOA his3D1 trp1D63 leu2D0 tfc7D::KanMX4 pRS413-tetO7-Sc-TFC7 TFC3-3Flag::HGB


title: Sc-Input-repeat2

description:
Library name: IS62
paired with CS62 chip


title: Donor 2, Differentiated organoid 2


title: 2mycp-TBLC-P2


title: SCZ+c-MSST:MK_M_5

description:
Library name: Sample4
MK_M_5


title: 2mycp-TBLC-P1


title: Sc-Input-repeat1

description:
Library name: IS61
paired with CS61 chip


title: Control+c-MSST: NS_M_1

description:
Library name: Sample9
NS_M_1


title: SCZ+c-MSST:MK_M_4

description:
Library name: Sample3
MK_M_4


title: Sc-ChIP-repeat3

description:
Library name: CS63
paired with IS63 input


title: SCZ+c-MSST:MK_M_3

description:
Library name: Sample2
MK_M_3


title: Donor 3, Undifferentiated organoid 3


title: PSC

value: cultured in S/L medium


title: Sc-ChIP-repeat2

description:
Library name: CS62
paired with IS62 input


title: NICD_Pax333

city: Tianjin

first: Huiwen

last: Ren

address: 22 Qixiangtai Road

institute: Tianjin Medicial University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: R26NICD2/+pax8cre rep3

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

value: kidney


title: Sc-ChIP-repeat1

description:
Library name: CS61
paired with IS61 input

value: YPD, 30°C


title: Donor 3, Undifferentiated organoid 2


title: Donor 3, Undifferentiated organoid 1


title: 2mycp-TBLC-P4


title: SCZ+c-MSST:MK_M_2

description:
Library name: Sample1
MK_M_2


title: Control Tgfbr1 floxed male mouse #17B

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Single-nuclei 3' gene expression data were processed using the Cell Ranger pipeline version 7.1.0 with introns included.
Assembly: mm10
Supplementary files format and content: Count matrices for cell-called barcodes in Hierarchical Data Format HDF5.

source_name: Pituitary gland

extract_protocol:
Pituitary glands were flash frozen in liquid nitrogen and stored at -80C until nuclei isolation
Nuclei were isolated from each individual pituitary using OptiPrep Density gradient (STEMCELL Technologies, #07820) and counted using Propidium Iodide staining on a K2 Cellometer (Nexcelome, Lawrence, MA, USA), as described in (27, 60).  Next, single nucleus RNA-seq assay was performed using the Chromium Next GEM Single Cell 3’ reagent kit V3.1 (10X Genomics) following manufacturer’s instructions. Based on concentrations, nuclei were loaded to target 2,000 to 10,000 nuclei and to generate the single-cell emulsion (Chromium Next GEM Chip G PN-2000177). Reverse-transcription was performed in the emulsion, cDNA amplified, and libraries constructed with v3.1 chemistry. Libraries were indexed for multiplexing (Dual Index Plate TT Set A PN-3000431). Following preparation, libraries were quantified by Qubit 4 fluorometer (Invitrogen) and quality was assessed by Tapestation 4150 (Agilent Technologies, Santa Clara, CA, USA). Equivalent molar concentrations of libraries were pooled. The libraries were then sequenced on a Novaseq X sequencer (Illumina) at Cedars-Sinai Genomics Core using 98+26 paired-end reads.

value: Pituitary gland

value: Gonadotropes

value: Tgfbr1flox/flox;Gnrhr+/+ (Alk5-control)

value: 8-9 weeks old

value: Male


title: NICD_Pax329

source_name: R26NICD2/+pax8cre rep2


title: NICD_Pax325

source_name: R26NICD2/+pax8cre rep1


title: Donor 3, Differentiated organoid 3

value: duodenal biopsy


title: Donor 3, Differentiated organoid 2


title: Control Tgfbr1 floxed male mouse #52

description: Chromium Next GEM Single Cell 3’ reagent kit V3.1 (10X Genomics)


title: B cells; healthy individual

city: Manchester

first: Ian

middle: Edward

last: Prise

state: Select state

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
PBMC cells were isolated from fresh whole human blood using Ficoll-paque. Dead cells were labelled in PBS with a cell viability dye. Cells were labelled for FACS using CD19 and CD3 in PBS. Single, live, CD3-CD19+ B cells were isolated by FACS using a FACSAria III.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: blood

value: CD19+CD3- B cells


title: FLN_SC1

city: Ottawa

first: Laurent

last: Renesme

state: Ontario

address: 501 Smyth Road

country: Canada

institute: OHRI

data_processing:
Raw sequencing reads were processed using CellRanger v3.1.0, aligning reads to the GRCh38 build of the human genome. MULTI-seq barcode libraries were trimmed prior to demultiplexing using Trimmomatic (v0.36). Demultiplexing was performed using the deMULTIplex R package (v1.0.2)2,3. Only cells positive for a single barcode were kept for further analysis. Sample annotations were added to all cells in the data set. Pre-processing steps and downstream analysis were performed with Seurat (Seurat v4.0.0)
Assembly: GRCh38
Supplementary files format and content: fastq.gz
Supplementary files format and content: .csv metadata and UMI count

source_name: fetal lung tissue

extract_protocol:
Single nuclei isolation was performed according to Martelotto et al / multiplexing using MULTI-seq protocol
10x Chromium gene expression libraries

value: fetal lung tissue


title: Donor 2, Differentiated organoid 1

value: enteroid monolayer


title: NICD328

source_name: WT rep3

value: wild type


title: NICD327

source_name: WT rep2


title: Gonadotrope-specific Tgfbr1 conditional knockout male mouse #48B

value: Tgfbr1flox/flox;GnrhrCre/+ (Alk5-cKO)


title: Gonadotrope-specific Tgfbr1 conditional knockout male mouse #54


title: NICD324

source_name: WT rep1


title: Donor 1, Unifferentiated organoid 2

value: undifferentiated spheroids

value: Cultured in Intesticult Growth Medium


title: SDPP diet_gut_Pool3

type: RNA

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression for fish fed with SDPP diet (pool 3)

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

source_name: SDPP diet_gut_pool

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: test animals: Gilthead seabream fry (average body size 9.5 g) were obtained from a commercial hatchery (Piscimar SL, Andromeda Group, Spain) and transported by road to IRTA-Sant Carles de la Rapita research facilities (Sant Carles de la Ràpita, Spain).

extract_protocol: Total RNA was extracted individually from fish skin using QIAGEN RNeasy® Mini Kit following the manufacturer's recommendations. The total RNA concentration was quantified using a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity and quality checked with the Experion (Automated Electrophoresis Station, Bio-Rad) using the Experion Standard Sens RNA chip (Bio-Rad). Only the samples with an RNA integrity number (RIN) > 8.0 were chosen for further analysis.

treatment_protocol: Fish were acclimated in two 2000-L tanks for two weeks. After their acclimation, all fish were anesthetized (tricaine methanesulfonate [MS-222], 150 mg/L) and individually weighed for initial body weight (BWi) and measured for standard length (SLi) to the nearest 0.1 g and 1 mm, respectively, and then distributed into eight 500-L cyclindroconical tanks at a density of 50 fish per tank (4 tanks/replicates per diet).   Fish (BWi = 10.6 ± 0.1 g, n = 400, mean ± standard deviation, SD) were fed for 95 days with both experimental diets by means of automatic feeders (ARVO-TEC T Drum 2000; Arvotec, Huutokosk, Finland) at the rate of 2.5% of the stocked biomass, which approached apparent satiation. Feed ration was evenly distributed in 7 meals per day from 08:00 to 18:00 h. Fish were regularly sampled at a monthly basis in order to evaluate their growth in BW and adjust the feeding ratio to stocked biomass. During the trial, water temperature and pH (pH meter 507; Crison Instruments, Barcelona, Spain), salinity (MASTER-20T; ATAGO Co., Ltd., Tokyo, Japan), and dissolved oxygen (OXI330; Crison Instruments) were 22.1 ± 0.4 °C, 7.0 ± 0.01, 36 mg/L, and 7.2 ± 0.3 mg/L (mean ± SD), respectively. Water flow rate in experimental tanks was maintained at approximately 9.0-10.1 L/min via a recirculation system (IRTAmar®; Spain) that maintained adequate water quality (total ammonia and nitrite were ≤0.15 and 0.6 mg/L, respectively) through UV, biological, and mechanical filtration. Photoperiod followed natural changes according to the season of the year (November to February; 40°37′41″ N).   At the end of the trial, fish were anesthetized as described above. All fish in experimental tanks were measured for final BW and SL as indicated. Then, 10 fish per tank were sacrificed with an overdose of MS-222 (200 mg/L) for tissue sampling purposes. The intestinal cavity was exposed, and the intestine was removed with a scalpel. A small piece of the anterior intestine (0.5 cm) was dissected and immediately transferred into RNAlater (Ambion) incubated at 4 C overnight and frozen at -80°C until further RNA extraction.

value: Skin

value: juveniles, 88.2 ± 1.6 g

value: fed with SDPP diet


title: SDPP diet_gut_Pool4

description: Gene expression for fish fed with SDPP diet (pool 4)


title: CKI_Over3

source_name: R26NICD2/+Kspcre rep3

value: kidney

value: post natal day 3


title: SDPP diet_gut_Pool2

description: Gene expression for fish fed with SDPP diet (pool 2)


title: FLN_SC2


title: Control Acvr1b floxed female mouse #16

value: Pituitary gland

value: Gonadotropes

value: mixed background (129/SvJ and C57BL/6J)

value: Acvr1bflox/flox;Gnrhr+/+ (Alk4-control)

value: 12-13 weeks old

value: Female


title: CKI_Over2

source_name: R26NICD2/+Kspcre rep2


title: Donor 1, Undifferentiated organoid 1

value: duodenal biopsy


title: Control Acvr1b floxed female mouse #14


title: Donor 1, Differentiated organoid 2

value: enteroid monolayer

value: Differentiated using Intesticult Intestinal Organoid Differentiation Medium


title: CKI_Over1

source_name: R26NICD2/+Kspcre rep1


title: Donor 3, Differentiated organoid 1


title: Control Acvr1b floxed female mouse #35


title: SDPP diet_gut_Pool1

description: Gene expression for fish fed with SDPP diet (pool 1)


title: Donor 1, Undifferentiated organoid 3


title: CKI_Control3

value: wild type


title: Gonadotrope-specific Acvr1b conditional knockout female mouse #313

value: Acvr1bflox/flox;GnrhrCre/+ (Alk4-cKO)


title: CKI_Control2


title: Control diet_gut_Pool4

description: Gene expression for fish fed with control diet (pool 4)

source_name: Control diet_gut_pool

value: juveniles, 82.7 ± 3.2 g

value: fed with control diet


title: CKI_Control1


title: Gonadotrope-specific Tgfbr1 conditional knockout male mouse #53

value: Tgfbr1flox/flox;GnrhrCre/+ (Alk5-cKO)

value: 8-9 weeks old

value: Male


title: Caco-2, Mastitis group (Inflammation)

city: Pecs

first: Hairui

last: Ou

address: Rokus

country: Hungary

institute: University of Pecs

description:
Mastitis
SAMPLE 3

data_processing:
The qPCR data analysis was conducted using ExpressionSuite v1.3 (Thermo Fisher Scientific, Waltham, USA). The relative quantification (RQ) was calculated via the 2−△△Ct method, ensuring a 95% confidence level for the data derived.
For the normalization it uses the average of 3 housekeeping genes: HPRT1-Hs99999909_m1  GAPDH-Hs99999905_m1  GUSB-Hs99999908_m1.
Target gene signals normalized to housekeeping genes; 2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol], where ΔCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control ratios.

label: Taqman probe(FAM)

source_name: colorectal adenocarcinoma patient

label_protocol: Gene expression was determined using TaqMan Array Human Inflammation 96-well Plate (REF. 4418851, Applied Biosystems, USA).

growth_protocol: Human colorectal adenocarcinoma Caco-2 cells were purchased from the American Type Culture Collection and were used from passages 52 to 58 following the supplier’s recommendations. Caco-2 cells were cultured in DMEM medium (Biosera, Cholet, France) with 10% exosome-depleted FBS (Thermo Fisher Scientific, Waltham, USA). Cells (30,000 per well) were seeded in 24 well plates one day before treatment.

extract_protocol: After 48 hours of treatment, RNA was isolated from cultured cells using Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, USA), according to the manufacturer’s specifications. Subsequent determination of RNA concentrations was performed utilizing a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, USA). The isolated RNA was reverse transcribed to cDNA employing the 2720 Thermal Cycler (Applied Biosystems, Foster City, USA) using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, USA) adhering to the manufacturer's protocol. The cDNA synthesis protocol involved incubating samples for 10 minutes at 25 °C and 120 minutes at 37 °C, followed by a final extension for 5 minutes at 85 °C.

treatment_protocol: The supernatant from macrophages accounted for 1/3 of the total volume of the Caco-2 culture medium. The experimental groups were divided into negative control, healthy group and mastitis group.

tag: activation reagent

value: with mastitis ev treated macrophages supernatant

value: 2 days


title: Gonadotrope-specific Acvr1b conditional knockout female mouse #45

value: Pituitary gland

value: Gonadotropes


title: Caco-2, Healthy group (Inflammation)

description:
Healthy
SAMPLE 2

value: with healthy ev treated macrophages supernatant


title: Control diet_gut_Pool2

description: Gene expression for fish fed with control diet (pool 2)

value: Skin


title: Control diet_gut_Pool1

description: Gene expression for fish fed with control diet (pool 1)


title: Gonadotrope-specific Acvr1b conditional knockout female mouse #44

value: mixed background (129/SvJ and C57BL/6J)

value: 12-13 weeks old

value: Female


title: Caco-2, Negative control (Inflammation)

description:
Control
SAMPLE 1

value: without macrophages supernatant


title: YNN1 replicate 2 0nM Cbf1

status: Public on Jan 16 2025

city: State College

first: Shane

middle: Douglas

last: Stoeber

address: 406 South Frear Building

department: BMMB

institute: Penn State

description: Library name: YNN1 replicate 2 0nM Cbf1 MNase-seq

library_source: other

data_processing:
Paired-end reads were aligned to the corresponding reference sequence (Widom 601 or YNN with or without factor binding site) with Bowtie2 on galaxy (https://usegalaxy.org/) in paired-end mode.
Unpaired and unmapped reads were removed using samtools view in galaxy (https://usegalaxy.org/).
Nucleosome coverage was calculated from the read counts normalized to total reads in BPM using bamCoverage. The minimum and maximum fragment length was set to 130 bp and 160 bp respectively unless otherwise stated to enrich reads for mono-nucleosome fragments. Files were outputted as a bedgraph and plotted to visualize nucleosome occupancy.
The dyad position for each sequence was calculated using bamCoverage –MNase in which only the three center bp of each fragment was used for analysis and were normalized to total reads in BPM. Files were outputted as a bedgraph and plotted to visualize dyad location.
Supplementary files format and content: All nucleosome coverage and dyad analysis are bedgraph

molecule: other

organism: synthetic construct

source_name: PCR generated DNA molecule

extract_protocol:
Nucleosome binding experiments were performed by incubating 60 nM nucleosome with 0 nM or 60 nM of TFs (Reb1, Cbf1, or Pho4) for 20 minutes at room temperature. Nucleosomes-TF binding was confirmed on a 5% acrylamide native gel. The incubated samples were then digested with 0.3 U, 1 U, 3 U, 10 U of MNase (New England Biolabs) for 8 minutes at 37 ⁰C and immediately quenched by adding quench buffer (0.1 % SDS, 20 mM EDTA pH8.0, 0.01 U proteinase K). Proteinase K digestion was carried out by incubating the quenched samples for 1 hour at 50 ⁰C. The final digested samples were analyzed by agarose gel electrophoresis with a 1.5% gel in 0.5x TAE buffer (20 mM Tris base, 10 mM acetic acid, 0.5 mM EDTA pH 8.0) (Figure S4). The digest DNA samples were then purified by agarose gel electrophoresis and then gel extraction with a Freeze 'N Squeeze DNA extraction kit (Bio-Rad).
After gel purification of the MNase digested samples, sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: 1 unit micrococcal nuclease

value: 0nM Cbf1


title: YNN1 replicate 1 60nM Cbf1

description: Library name: YNN1 replicate 1 60nM Cbf1 MNase-seq

value: 60nM Cbf1


title: YNN1 replicate 1 0nM Cbf1

description: Library name: YNN1 replicate 1 0nM Cbf1 MNase-seq


title: YNN1 replicate 3 60nM Reb1

description: Library name: YNN1 replicate 3 60nM Reb1 MNase-seq

value: 60nM Reb1


title: YNN1 replicate 2 60nM Reb1

description: Library name: YNN1 replicate 2 60nM Reb1 MNase-seq


title: YNN1 replicate 2 60nM Cbf1

description: Library name: YNN1 replicate 2 60nM Cbf1 MNase-seq


title: YNN1 replicate 1 60nM Reb1

description: Library name: YNN1 replicate 1 60nM Reb1 MNase-seq


title: 601 replicate2 60nM Reb1

description: Library name: 601 replicate2 60nM Reb1 MNase-seq


title: Donor 1, Differentiated organoid 1

source_name: duodenal biopsy

value: duodenal biopsy

value: enteroid monolayer

value: Differentiated using Intesticult Intestinal Organoid Differentiation Medium


title: YNN1 replicate 2 0nM Reb1

description: Library name: YNN1 replicate 2 0nM Reb1 MNase-seq

value: 0nM Reb1


title: 601 replicate1 60nM Reb1

description: Library name: 601 replicate1 60nM Reb1 MNase-seq


title: YNN5 Fraction 2

description: Library name: YNN5 Fraction 2 MNase-seq


title: Control diet_gut_Pool3

description: Gene expression for fish fed with control diet (pool 3)

value: juveniles, 82.7 ± 3.2 g

value: fed with control diet


title: YNN4

description: Library name: YNN4 MNase-seq


title: YNN5 Fraction 1

description: Library name: YNN5 Fraction 1 MNase-seq


title: 601 replicate1 0nM Reb1

description: Library name: 601 replicate1 0nM Reb1 MNase-seq


title: 601 replicate2 0nM Reb1

description: Library name: 601 replicate2 0nM Reb1 MNase-seq


title: YNN3 Fraction 2

description: Library name: YNN3 Fraction 2 MNase-seq


title: YNN2

description: Library name: YNN2 MNase-seq


title: TeloHAEC oePLVAP rep4

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

description: Library name: TeloHAEC_oePLVAP_rep4

data_processing:
Fastq files were processed using the nf-core RNA-Seq pipeline (version 3.12; https://nf-co.re/rnaseq/) using the default settings and the GRCh38 human genome with Ensembl release 98 transcript definitions.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes raw gene counts for each sample

source_name: TeloHAEC

growth_protocol: Human aortic endothelial cells (primary HAECs, ATCC-PCS-100-011, and TeloHAECs, ATCC CRL-4052) were maintained in Vascular Cell Basal Medium (ATCC PCS-100-030) supplemented with the VEGF growth kit (ATCC PCS-100-041) and antibiotics.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB, cat T2010).
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen). The libraries were quantified with the Qubit dsDNA HS Assay (Fisher Scientific) and their length was assessed using a Fragment Analyzer with the HS NGS Fragment Kit (Agilent).

treatment_protocol: Cells were transduced with lentiviral vectors to overexpress (oe) PLVAP, FAM110D or control vector (CTL). Transduced cells were selected with 6 µg/mL blasticidin (Fisher Scientific) for 6-7 days.

value: TeloHAEC

value: endothelial

value: female

tag: overexpression

value: PLVAP

tag: replicate


title: YNN1

description: Library name: YNN1 MNase-seq


title: YNN3 Fraction 1

description: Library name: YNN3 Fraction 1 MNase-seq


title: TeloHAEC oePLVAP rep3

description: Library name: TeloHAEC_oePLVAP_rep3


title: TeloHAEC oePLVAP rep1

description: Library name: TeloHAEC_oePLVAP_rep1


title: TeloHAEC oeFAM110D rep4

description: Library name: TeloHAEC_oeFAM110D_rep4


title: TeloHAEC oeFAM110D rep2

description: Library name: TeloHAEC_oeFAM110D_rep2


title: TeloHAEC oeFAM110D rep3

description: Library name: TeloHAEC_oeFAM110D_rep3


title: TeloHAEC oeFAM110D rep1

description: Library name: TeloHAEC_oeFAM110D_rep1


title: TeloHAEC oeCTL rep3

description: Library name: TeloHAEC_oeCTL_rep3

value: Control


title: TeloHAEC oeCTL rep4

description: Library name: TeloHAEC_oeCTL_rep4


title: YNN1 replicate 1 0nM Reb1

description: Library name: YNN1 replicate 1 0nM Reb1 MNase-seq


title: TeloHAEC oeCTL rep2

description: Library name: TeloHAEC_oeCTL_rep2


title: TeloHAEC oeCTL rep1

description: Library name: TeloHAEC_oeCTL_rep1


title: HAEC oePLVAP rep3

description: Library name: HAEC_oePLVAP_rep3

source_name: HAEC

value: HAEC

value: male


title: HAEC oeFAM110D rep4

description: Library name: HAEC_oeFAM110D_rep4


title: HAEC oePLVAP rep1

description: Library name: HAEC_oePLVAP_rep1


title: HAEC oeFAM110D rep2

description: Library name: HAEC_oeFAM110D_rep2


title: HAEC oePLVAP rep4

description: Library name: HAEC_oePLVAP_rep4


title: HAEC oeCTL rep4

description: Library name: HAEC_oeCTL_rep4


title: HAEC oeCTL rep3

description: Library name: HAEC_oeCTL_rep3


title: HAEC oePLVAP rep2

description: Library name: HAEC_oePLVAP_rep2


title: HAEC oeCTL rep1

description: Library name: HAEC_oeCTL_rep1


title: HAEC oeFAM110D rep1

description: Library name: HAEC_oeFAM110D_rep1


title: HAEC oeCTL rep2

description: Library name: HAEC_oeCTL_rep2


title: P2S5_meningioma_tumor_G1_(240409_DX_Hs_P2S5_MG1_AB_0401)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_G1

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw).
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: Brain

extract_protocol:
https://www.protocols.io/edit/cutac-for-ffpes-c5huy36w
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: Brain

tag: group

value: Tumor

value: Human meningioma tumor; U Washington; PMID 38788713

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: TeloHAEC oePLVAP rep2

description: Library name: TeloHAEC_oePLVAP_rep2


title: P2S5_meningioma_tumor_Z1_(240409_DX_Hs_P2S5_MZ1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_Z1


title: P2S5_meningioma_tumor_X1_(240409_DX_Hs_P2S5_MX1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_X1


title: P2S5_meningioma_tumor_Y1_(240409_DX_Hs_P2S5_MY1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_Y1


title: P2S5_meningioma_tumor_V1_(240409_DX_Hs_P2S5_MV1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_V1


title: P2S5_meningioma_normal_U1_(240409_DX_Hs_P2S5_MU1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_U1


title: P2S5_meningioma_tumor_T1_(240409_DX_Hs_P2S5_MT1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_T1


title: P2S5_meningioma_tumor_W1_(240409_DX_Hs_P2S5_MW1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_W1


title: P2S5_meningioma_tumor_R1_(240409_DX_Hs_P2S5_MR1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_R1


title: P2S5_meningioma_tumor_P1_(240409_DX_Hs_P2S5_MP1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_P1


title: P2S5_meningioma_tumor_Q1_(240409_DX_Hs_P2S5_MQ1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_Q1


title: P2S5_meningioma_tumor_N1_(240409_DX_Hs_P2S5_MN1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_N1


title: P2S5_meningioma_tumor_O1_(240409_DX_Hs_P2S5_MO1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_O1


title: HAEC oeFAM110D rep3

description: Library name: HAEC_oeFAM110D_rep3


title: P2S5_meningioma_tumor_I1_(240409_DX_Hs_P2S5_MI1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_I1


title: P2S5_meningioma_tumor_L1_(240409_DX_Hs_P2S5_ML1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_L1


title: P2S5_meningioma_normal_K1_(240409_DX_Hs_P2S5_MK1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_K1


title: P2S5_meningioma_tumor_M1_(240409_DX_Hs_P2S5_MM1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_M1


title: P2S5_meningioma_tumor_J1_(240409_DX_Hs_P2S5_MJ1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_J1


title: P2S5_meningioma_tumor_G2_(240409_DX_Hs_P2S5_MG2_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_G2


title: P2S5_meningioma_tumor_H1_(240409_DX_Hs_P2S5_MH1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_H1


title: P2S5_meningioma_tumor_C2_(240409_DX_Hs_P2S5_MC2_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_C2


title: P2S5_meningioma_tumor_E1_(240409_DX_Hs_P2S5_ME1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_E1


title: P2S5_meningioma_tumor_B1_(240409_DX_Hs_P2S5_MB1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_B1


title: P2S5_meningioma_tumor_F1_(240409_DX_Hs_P2S5_MF1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_F1


title: P2S5_meningioma_tumor_C1_(240409_DX_Hs_P2S5_MC1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_C1


title: P2S5_meningioma_tumor_D2_(240409_DX_Hs_P2S5_MD2_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_D2


title: P2S5_meningioma_tumor_AE1_(240409_DX_Hs_P2S5_MAE1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_AE1


title: P2S5_meningioma_tumor_AD1_(240409_DX_Hs_P2S5_MAD1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_AD1


title: P2S5_meningioma_tumor_B2_(240409_DX_Hs_P2S5_MB2_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_B2


title: P2S5_meningioma_tumor_D1_(240409_DX_Hs_P2S5_MD1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_D1


title: P2S5_meningioma_tumor_AB1_(240409_DX_Hs_P2S5_MAB1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_AB1


title: P2S5_meningioma_tumor_AA1_(240409_DX_Hs_P2S5_MAA1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_AA1


title: P2S5_meningioma_tumor_A3_(240409_DX_Hs_P2S5_MA3_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_A3


title: P2S5_meningioma_tumor_A1_(240409_DX_Hs_P2S5_MA1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_A1


title: P2S5_meningioma_tumor_A2_(240409_DX_Hs_P2S5_MA2_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_A2


title: P2S5_stomach_tumor_3_(20240125_SH_Hs_P2S5_StT1_0120)

description: Human Stomach Tumor RNAPIIS5p

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: Stomach

value: Stomach

value: Normal

tag: tumor biochain

value: Tumor Biochain T8235248PT


title: P2S5_stomach_tumor_4_(20240125_SH_Hs_P2S5_StT2_0120)

description: Human Stomach Tumor RNAPIIS5p


title: P2S5_stomach_tumor_2_(20240108_SH_Hs_P2S5_StT2_1225)

description: Human Stomach Tumor RNAPIIS5p


title: P2S5_stomach_tumor_1_(20240108_SH_Hs_P2S5_StT1_1225)

description: Human Stomach Tumor RNAPIIS5p


title: P2S5_stomach_normal_4_(20240201_SH_Hs_P2S5_StN1_0128)

description: Human Stomach Normal RNAPIIS5p

value: Tumor Biochain T8235248PP


title: P2S5_stomach_normal_3_(20240125_SH_Hs_P2S5_StN2_0120)

description: Human Stomach Normal RNAPIIS5p


title: P2S5_stomach_normal_1_(20240108_SH_Hs_P2S5_StN1_1225)

description: Human Stomach Normal RNAPIIS5p


title: P2S5_rectum_tumor_6_(20240201_SH_Hs_P2S5_ReT1_0128)

description: Human Rectum Tumor RNAPIIS5p

source_name: Rectum

value: Rectum

value: Tumor Biochain T8235206PT


title: P2S5_stomach_normal_2_(20240125_SH_Hs_P2S5_StN1_0120)

description: Human Stomach Normal RNAPIIS5p


title: P2S5_rectum_tumor_7_(20240201_SH_Hs_P2S5_ReT2_0128)

description: Human Rectum Tumor RNAPIIS5p


title: P2S5_rectum_tumor_5_(20240125_SH_Hs_P2S5_ReT2_0120)

description: Human Rectum Tumor RNAPIIS5p


title: P2S5_rectum_tumor_4_(20240125_SH_Hs_P2S5_ReT1_0120)

description: Human Rectum Tumor RNAPIIS5p


title: P2S5_rectum_tumor_1_(20240108_SH_Hs_P2S5_RT1_1223)

description: Human Rectum Tumor RNAPIIS5p

value: Tumor Biochain T8235206PP


title: P2S5_rectum_normal_6_(20240201_SH_Hs_P2S5_ReN1_0128)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_meningioma_tumor_AC1_(240409_DX_Hs_P2S5_MAC1_0401)

description:
Human meningioma tumor RNAPiiS5p
P2S5_meningioma_tumor_AC1


title: P2S5_rectum_normal_3_(20240118_SH_Hs_P2S5_Re1_0113)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_rectum_normal_4_(20240125_SH_Hs_P2S5_ReN1_0120)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_lung_tumor_7_(20240201_SH_Hs_P2S5_LuT2_0128)

description: Human Lung Tumor RNAPIIS5p

source_name: Lung

value: Lung

value: Tumor Biochain T8235152PT


title: P2S5_rectum_normal_1_(20240108_SH_Hs_P2S5_RN1_1223)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_rectum_normal_5_(20240125_SH_Hs_P2S5_ReN2_0120)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_rectum_tumor_2_(20240108_SH_Hs_P2S5_RT2_1223)

description: Human Rectum Tumor RNAPIIS5p


title: P2S5_rectum_normal_2_(20240108_SH_Hs_P2S5_RN2_1223)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_stomach_tumor_5_(20240201_SH_Hs_P2S5_StT1_0128)

description: Human Stomach Tumor RNAPIIS5p


title: P2S5_rectum_normal_7_(20240201_SH_Hs_P2S5_ReN2_0128)

description: Human Rectum Normal RNAPIIS5p


title: P2S5_stomach_normal_5_(20240201_SH_Hs_P2S5_StN2_0128)

description: Human Stomach Normal RNAPIIS5p


title: P2S5_lung_tumor_5_(20240125_SH_Hs_P2S5_LuT2_0120)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_lung_tumor_4_(20240125_SH_Hs_P2S5_LuT1_0120)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_lung_tumor_3_(20240108_SH_Hs_P2S5_LuT2_1225)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_lung_normal_4_(20240125_SH_Hs_P2S5_LuN2_0120)

description: Human Lung Normal RNAPIIS5p

value: Tumor Biochain T8235152PP


title: P2S5_lung_normal_3_(20240125_SH_Hs_P2S5_LuN1_0120)

description: Human Lung Normal RNAPIIS5p


title: P2S5_lung_tumor_1_(20240118_SH_Hs_P2S5_Lu2_0113)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_rectum_tumor_3_(20240118_SH_Hs_P2S5_Re2_0113)

description: Human Rectum Tumor RNAPIIS5p


title: P2S5_liver_tumor_5_(20240125_SH_Hs_P2S5_LiT2_0120)

description: Human Liver Tumor RNAPIIS5p

source_name: Liver

value: Liver

value: Tumor Biochain T8235149PT


title: P2S5_lung_normal_6_(20240201_SH_Hs_P2S5_LuN2_0128)

description: Human Lung Normal RNAPIIS5p


title: P2S5_lung_normal_5_(20240201_SH_Hs_P2S5_LuN1_0128)

description: Human Lung Normal RNAPIIS5p


title: P2S5_liver_tumor_7_(20240201_SH_Hs_P2S5_LiT2_0128)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_liver_normal_7_(20240201_SH_Hs_P2S5_LiN2_0128)

description: Human Liver Normal RNAPIIS5p

value: Tumor Biochain T8235149PP


title: P2S5_lung_normal_1_(20240118_SH_Hs_P2S5_Lu1_0113)

description: Human Lung Normal RNAPIIS5p


title: P2S5_liver_normal_3_(20240118_SH_Hs_P2S5_Li1_0113)

description: Human Liver Normal RNAPIIS5p


title: P2S5_liver_normal_5_(20240125_SH_Hs_P2S5_LiN2_0120)

description: Human Liver Normal RNAPIIS5p


title: P2S5_liver_normal_2_(20240108_SH_Hs_P2S5_LN2_1223)

description: Human Liver Normal RNAPIIS5p


title: P2S5_liver_tumor_6_(20240201_SH_Hs_P2S5_LiT1_0128)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_liver_tumor_4_(20240125_SH_Hs_P2S5_LiT1_0120)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_liver_normal_1_(20240108_SH_Hs_P2S5_LN1_1223)

description: Human Liver Normal RNAPIIS5p


title: P2S5_liver_tumor_2_(20240108_SH_Hs_P2S5_LT2_1223)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_liver_tumor_1_(20240108_SH_Hs_P2S5_LT1_1223)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_lung_tumor_6_(20240201_SH_Hs_P2S5_LuT1_0128)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_liver_normal_4_(20240125_SH_Hs_P2S5_LiN1_0120)

description: Human Liver Normal RNAPIIS5p


title: P2S5_lung_tumor_2_(20240108_SH_Hs_P2S5_LuT1_1225)

description: Human Lung Tumor RNAPIIS5p


title: P2S5_lung_normal_2_(20240108_SH_Hs_P2S5_LuN1_1225)

description: Human Lung Normal RNAPIIS5p


title: P2S5_liver_tumor_3_(20240118_SH_Hs_P2S5_Li2_0113)

description: Human Liver Tumor RNAPIIS5p


title: P2S5_kidney_tumor_6_(20240201_SH_Hs_P2S5_KiT3_0128)

description: Human Kidney Tumor RNAPIIS5p

source_name: Kidney

value: Kidney

value: Tumor Biochain T823514PT


title: P2S5_kidney_normal_6_(20240201_SH_Hs_P2S5_KiN3_0128)

description: Human Kidney Normal RNAPIIS5p

value: Tumor Biochain T823514PP


title: P2S5_kidney_tumor_3_(20240118_SH_Hs_P2S5_KT1_0113)

description: Human Kidney Tumor RNAPIIS5p

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: P2S5_kidney_tumor_4_(20240201_SH_Hs_P2S5_KiT1_0128)

description: Human Kidney Tumor RNAPIIS5p


title: P2S5_kidney_tumor_5_(20240201_SH_Hs_P2S5_KiT2_0128)

description: Human Kidney Tumor RNAPIIS5p


title: P2S5_kidney_tumor_2_(20240108_SH_Hs_P2S5_KT3_1223)

description: Human Kidney Tumor RNAPIIS5p


title: P2S5_kidney_tumor_1_(20240108_SH_Hs_P2S5_KT1_1223)

description: Human Kidney Tumor RNAPIIS5p


title: P2S5_colon_tumor_3_(20240118_SH_Hs_P2S5_CoT_0113)

description: Human Colon Tumor RNAPIIS5p

source_name: Colon

value: Colon

value: Tumor Biochain T8235090PT


title: P2S5_colon_tumor_5_(20240201_SH_Hs_P2S5_CoT2_0128)

description: Human Colon Tumor RNAPIIS5p

value: Normal


title: P2S5_colon_tumor_4_(20240201_SH_Hs_P2S5_CoT1_0128)

description: Human Colon Tumor RNAPIIS5p


title: P2S5_colon_tumor_1_(20240108_SH_Hs_P2S5_CoT1_1225)

description: Human Colon Tumor RNAPIIS5p


title: P2S5_kidney_normal_4_(20240201_SH_Hs_P2S5_KiN1_0128)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_kidney_normal_5_(20240201_SH_Hs_P2S5_KiN2_0128)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_kidney_normal_3_(20240118_SH_Hs_P2S5_KN2_0113)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_liver_normal_6_(20240201_SH_Hs_P2S5_LiN1_0128)

description: Human Liver Normal RNAPIIS5p


title: P2S5_kidney_normal_2_(20240108_SH_Hs_P2S5_KN4_1223)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_kidney_normal_1_(20240108_SH_Hs_P2S5_KN2_1223)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_colon_normal_4_(20240125_SH_Hs_P2S5_CoN1_0120)

description: Human Colon Normal RNAPIIS5p

value: Tumor Biochain T8235090PP


title: P2S5_colon_tumor_2_(20240108_SH_Hs_P2S5_CoT2_1225)

description: Human Colon Tumor RNAPIIS5p


title: P2S5_breast_tumor_4_(20240201_SH_Hs_P2S5_BrT1_0128)

description: Human Breast Tumor RNAPiiS5p

source_name: Breast

value: Breast

value: Tumor Biochain T8235086PT


title: P2S5_breast_tumor_1_(20240108_SH_Hs_P2S5_BrT1_1225)

description: Human Breast Tumor RNAPiiS5p


title: P2S5_kidney_normal_7_(20240201_SH_Hs_P2S5_KiN4_0128)

description: Human Kidney Normal RNAPIIS5p


title: P2S5_colon_normal_6_(20240201_SH_Hs_P2S5_CoN1_0128)

description: Human Colon Normal RNAPIIS5p


title: P2S5_breast_normal_1_(20240108_SH_Hs_P2S5_BrN1_1225)

description: Human Breast Normal RNAPiiS5p

value: Tumor Biochain T8235086PP


title: P2S5_breast_normal_2_(20240201_SH_Hs_P2S5_BrN1_0128)

description: Human Breast Normal RNAPiiS5p


title: P2S5_colon_normal_7_(20240201_SH_Hs_P2S5_CoN2_0128)

description: Human Colon Normal RNAPIIS5p


title: P2S5_colon_normal_5_(20240125_SH_Hs_P2S5_CoN2_0120)

description: Human Colon Normal RNAPIIS5p


title: P2S5_colon_normal_2_(20240108_SH_Hs_P2S5_CoN1_1225)

description: Human Colon Normal RNAPIIS5p