title: HiC_Setdb1KO_rep2

city: Hong Kong

first: Lut Fei

last: Tam

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon

department: LIFS

country: Hong Kong

institute: HKUST

data_processing:
The alignment was processed by Juicer v1.5.6 (Durand et al., 2016) mapped to mouse reference genome mm10 (GRCm38). All the other parameters of Juicer were set to default.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C files were genreated from Juicer; The contents are contact matrices.
Supplementary_files_format_and_content: BigWig files for directionality index were generated by Hi-C Domain Caller and UCSC utilities; Scores represent directionality index under 25 kb resolution for replicates merged samples

source_name: Embryonic stem cell

growth_protocol: ES cells were maintained in ES medium (DMEM with 15% certified FBS (Life Technologies), 20 mM HEPES, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.05 mM streptomycin, 1 U/ml Leukemia-inhibitory factor (LIF) and 2mM glutamine). Cells were passaged at 80% confluence. Setdb1 conditional KO ES cells were induced by the addition of 800 nM (Z)-4-Hydroxytamoxifen (4-OHT) (Abcam, 141943) for 4 days and harvested on day 6 post 4-OHT treatment.

extract_protocol:
Hi-C was performed using Arima-HiC Kit (Arima Genomics) according to manufacturer protocol.
HiC libraries were built using KAPA Hyper Prep kit according to manufacturer protocol.

treatment_protocol: Cell were crosslinked using 2% formaldehyde for 10 minutes at room temperature then quenched with glycine.

value: Embryonic stem cell

value: TT2 (C57BL/6/CBA F1)

value: Setdb1 KO


title: RB6891_35

status: Public on Nov 01 2023

type: SRA

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

country: USA

institute: University of Arizona

library_source: transcriptomic

data_processing:
fastq files were mapped to rat cDNA library(ensembl release 104) using Salmon to get counts for each transcript
Tximport was used to get counts for each gene
DESeq2 was used to get normalized counts for each gene
Assembly: Rat ensembl release 104
Supplementary files format and content: count

molecule: polyA RNA

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Enrichment of mRNA and library preparation of cDNA were done using a stranded mRNA (poly(A) - selected) sample preparation kit.
RNA-Seq was conducted on hippocampal RNA at Vanderbilt Technologies for Advanced Genomics (VANTAGE))
Only RNA samples with an acceptable RNA quality indicator score (RQI >7) were used for sequencing.  RNA-Seq was conducted on hippocampal RNA at Vanderbilt Technologies for Advanced Genomics (VANTAGE)). Only RNA samples with an acceptable RNA quality indicator score (RQI >7) were used for sequencing.  Sequencing was performed at 100bp paired-end on NovaSeq600, targeting 30 million reads per sample

tag: tissue

value: hippocampus

tag: strain

value: Sprague Dawley

tag: treatment

value: OVX+Vehicle


title: RB6891_34


title: HiC_WT_rep2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype

value: WT


title: Batch1_Patient11600-15149_AF01_2

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
AF01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

library_source: transcriptomic single cell

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2

organism: Homo sapiens

source_name: Fallopian tube

growth_protocol: Fallopian tube WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.

value: Fallopian tube


title: Batch1_Patient11600-15149_AF02_1

description:
AF02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HiC_Setdb1KO_rep1


title: RB6891_33


title: Batch1_Patient11600-15149_AF01_1

description:
AF01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HiC_WT_rep1


title: MUC26011

city: Munich

first: Gildas

last: Lepennetier

address: Ismaninger Straße 22

department: Neurology

country: Germany

institute: Klinikum Rechts der Isar

description:
HTO
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_C_CSP

data_processing:
Library strategy: HTO-seq
cellranger-5.0.1 multi, refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0, refdata-gex-mm10-2020-A, default options
Hashtag Oligo used described in file Feature_mouse_10x.csv
Genome_build: GRCm38

molecule: total RNA

source_name: J9 HTO Spleen+Blood

growth_protocol: Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 25±6 days after disease onset.

extract_protocol:
Blood was collected by cardiac puncture. After thorough perfusion with PBS the spleen, inguinal lymph nodes, lumbar lymph nodes and spinal cord were dissected, and meninges were detached from the spinal cord using fine forceps.  Organs were passed through cell strainers. Erythrocyte lysis was performed for spleen and blood. Samples were enriched for CD45+ cells using a MACS (Miltenyi Biotech) with anti‐CD45 mouse MAb‐conjugated microbeads (Miltenyi Biotech, #130-052-301). Fc receptors were blocked and samples were incubatedwith DNA barcoded TotalSeq antibodies against CD4 (TotalSeq-C0001 anti-mouse CD4, clone RM4-5, Biolegend), CD8a (TotalSeq-C0002 anti-mouse CD8a , clone 53-6.7, Biolegend), CD19 (TotalSeq-C0093 anti-mouse CD19, clone 6D5, Biolegend), Ly6G (TotalSeq-C0015 anti-mouse Ly6G , clone 1A8, Biolegend), and NK1.1 (TotalSeq-C0118 anti-mouse NK-1.1, clone PK136, Biolegend), and one of 2  TotalSeq Hashtag antibodies (TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, clones M1/42; 30-F11, Biolegend or TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody, clones M1/42; 30-F11, Biolegend), to allow pooling of 2 samples per experiment.
10x Genomics Chromium Next GEM Single Cell V(D)J Reagent Kit (v1.1)

treatment_protocol: mice were  untreated

tag: Sex

value: female

tag: concentration (ng/ul)

tag: volume (ul)

tag: i7 index

tag: tissue hto

value: Spleen=HTO tag1, Blood=HTO tag2


title: Batch1_Patient11600-15149_AE12_1

description:
AE12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_31


title: MUC26010

description:
HTO
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_B_CSP

source_name: J9 HTO LN lumbar+LN inguinal

value: LN lumbar=HTO tag1, LN inguinal=HTO tag2


title: Batch1_Patient11600-15149_AE11_2

description:
AE11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26009

description:
HTO
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_A_CSP

source_name: J9 HTO mRNA CSF+mELT

value: CSF=HTO tag1, mELT=HTO tag2


title: RB6891_29

value: OVX+Anastrozole


title: RB6891_28


title: MUC26008

description:
HTO
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_C_CSP

source_name: J119 HTO Spleen+Blood


title: Batch1_Patient11600-15149_AE11_1

description:
AE11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AE10_2

description:
AE10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_27


title: Batch1_Patient11600-15149_AE10_1

description:
AE10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AE09_2

description:
AE09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26007

description:
HTO
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_B_CSP

source_name: J119 HTO LN lumbar+LN inguinal


title: RB6891_26


title: MUC26006

description:
HTO
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_A_CSP

source_name: J119 HTO mRNA CSF+mELT


title: MUC26005

description:
HTO
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_C_CSP

source_name: I18 HTO Spleen+Blood

value: male


title: Batch1_Patient11600-15149_AE09_1

description:
AE09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_32


title: RB6891_25

value: OVX+Exemestane


title: MUC26004

description:
HTO
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_B_CSP

source_name: I18 HTO LN lumbar+LN inguinal


title: Batch1_Patient11600-15149_AE12_2

description:
AE12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_23


title: Batch1_Patient11600-15149_AE08_2

description:
AE08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AE08_1

description:
AE08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_24


title: RB6891_30


title: Batch1_Patient11600-15149_AE07_2

description:
AE07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PAMs, Infection 6hr replicate 2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) .
Assembly: Sscrofa11.1
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Sus scrofa

source_name: Porcine alveolar macrophage

extract_protocol:
For in vivo study, PAM cell were collected directly from infected or control pigs by lung lavage. For in vitro study, cells were collected from culture. All cells were washed, and resuspended in 1X PBS to a final concentration of about 1,200 cell/uL before performing library construction.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Porcine alveolar macrophage

tag: infection

value: PRRSV-FL12 GFP

tag: time


title: RB6891_21


title: RB6891_22


title: MUC26001

description:
GEX
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_B_GEX

data_processing:
cellranger-5.0.1 multi, refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0, refdata-gex-mm10-2020-A, default options
Hashtag Oligo used described in file Feature_mouse_10x.csv
Genome_build: GRCm38

source_name: J9 Total mRNA LN lumbar+LN inguinal


title: Batch1_Patient11600-15149_AE07_1

description:
AE07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26000

description:
GEX
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_A_GEX

source_name: J9 Total mRNA CSF+mELT


title: Batch1_Patient11600-15149_AE06_2

description:
AE06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC25999

description:
GEX
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_C_GEX

source_name: J119 Total mRNA Spleen+Blood


title: Batch1_Patient11600-15149_AE06_1

description:
AE06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_19

value: OVX+Raloxifene


title: RB6891_18


title: MUC25998

description:
GEX
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_B_GEX

source_name: J119 Total mRNA LN lumbar+LN inguinal


title: Batch1_Patient11600-15149_AE05_2

description:
AE05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_17


title: MUC25997

description:
GEX
J119_matrix.mtx.gz
J119_features.tsv.gz
J119_barcodes.tsv.gz
J119_A_GEX

source_name: J119 Total mRNA CSF+mELT


title: MUC26003

description:
HTO
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_A_CSP

source_name: I18 HTO mRNA CSF+mELT


title: RB6891_16

source_name: hippocampus


title: Batch1_Patient11600-15149_AE05_1

description:
AE05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube


title: Batch1_Patient11600-15149_AE04_2

description:
AE04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26002

description:
GEX
J9_matrix.mtx.gz
J9_features.tsv.gz
J9_barcodes.tsv.gz
J9_C_GEX

source_name: J9 Total mRNA Spleen+Blood


title: MUC25996

description:
GEX
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_C_GEX

source_name: I18 Total mRNA Spleen+Blood


title: Batch1_Patient11600-15149_AE04_1

description:
AE04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_14

value: OVX+Tamoxifen


title: Batch1_Patient11600-15149_AE03_2

description:
AE03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC25994

description:
GEX
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_A_GEX

source_name: I18 Total mRNA CSF+mELT


title: MUC25995

description:
GEX
I18_matrix.mtx.gz
I18_features.tsv.gz
I18_barcodes.tsv.gz
I18_B_GEX

source_name: I18 Total mRNA LN lumbar+LN inguinal


title: RB6891_15


title: RB6891_13


title: MUC25992

description:
VDJ-BCR
J9_filtered_contig_annotations.csv
J9_B_BCR

data_processing:
Library strategy: BCR-seq
cellranger-5.0.1 multi, refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0, refdata-gex-mm10-2020-A, default options
Hashtag Oligo used described in file Feature_mouse_10x.csv
Genome_build: GRCm38

source_name: J9 BCR LN lumbar+LN inguinal


title: RB6891_12


title: RB6891_20


title: Batch1_Patient11600-15149_AE02_2

description:
AE02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AE03_1

description:
AE03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_11


title: MUC25991

description:
VDJ-BCR
J9_filtered_contig_annotations.csv
J9_A_BCR

source_name: J9 BCR CSF+mELT


title: Batch1_Patient11600-15149_AE01_2

description:
AE01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_10

value: OVX+Estradiol


title: RB6891_9

value: hippocampus


title: MUC25989

description:
VDJ-BCR
J119_filtered_contig_annotations.csv
J119_B_BCR

source_name: J119 BCR LN lumbar+LN inguinal


title: Batch1_Patient11600-15149_AE01_1

description:
AE01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AE02_1

description:
AE02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_8

value: Sprague Dawley


title: RB6891_7


title: Batch1_Patient11600-15149_AD12_2

description:
AD12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC25988

description:
VDJ-BCR
J119_filtered_contig_annotations.csv
J119_A_BCR

source_name: J119 BCR CSF+mELT


title: MUC25987

description:
VDJ-BCR
I18_filtered_contig_annotations.csv
I18_C_BCR

source_name: I18 BCR Spleen+Blood


title: MUC25985

description:
VDJ-BCR
I18_filtered_contig_annotations.csv
I18_A_BCR

source_name: I18 BCR CSF+mELT


title: MUC25993

description:
VDJ-BCR
J9_filtered_contig_annotations.csv
J9_C_BCR

source_name: J9 BCR Spleen+Blood


title: RB6891_6


title: Batch1_Patient11600-15149_AD11_2

description:
AD11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PXB-tcps-monoculture-bio2

city: Bunkyo

first: Dhimas

middle: Agung

last: Kurniawan

state: Tokyo

address: Hongo

department: Chemical System Engineering

country: Japan

institute: The University of Tokyo

data_processing:
Galaxy (usegalaxy.org)
Reads were trimmed using Cutadapt module (parameters: -Minimum length (R1): 20 -Quality cutoff: 20)
Trimmed reads were aligned to hg38 reference genome using RNA STAR module, default settings (parameters: -Length of genomic sequence around annotated junctions: 149)
Alignment files were used to analyze read count using featureCounts module, default settings
Differential expression of count data performed using edgeR module (parameters: -filter lowly expressed genes: yes -minimum CPM: 6.0 -minimum samples: 2 -p-value adjusted threshold: 0.05 -p-value adjustment method: Benjamini and Hochberg -normalisation method: TMM -use robust settings: True -use likelihood ratio test: False)
Assembly: hg38

source_name: PXB-cells

extract_protocol:
RNA was extracted using the FastGene RNA Basic Kit (Nippon Genetics, Japan) according to the manufacturer’s protocol.
Prepared using NEBNext® Directional Ultra RNA Library Prep Kit for strand specific library.

tag: cell line

value: PXB-cells

value: monoculture in TCPS


title: Batch1_Patient11600-15149_AD11_1

description:
AD11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: PXB-tcps-coculture-bio2

value: coculture in TCPS


title: MUC25986

description:
VDJ-BCR
I18_filtered_contig_annotations.csv
I18_B_BCR

source_name: I18 BCR LN lumbar+LN inguinal


title: PXB-O2min-coculture-bio2

value: coculture in MPS O2[-]


title: RB6891_4

value: SHAM


title: Batch1_Patient11600-15149_AD10_2

description:
AD10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Mouse Mix Exposed replicate 1

city: Daejeon

first: Yoosik

last: Kim

state: Daejeon

address: Daejeon

country: South Korea

institute: KAIST

data_processing:
Basecalls performed using bcl2fastq
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with HISAT2 v2.1.0 using default parameters except with the option "--rna-strandness RF".
Only uniquely and concordantly mapped reads were then used in the further analyses.
featureCounts function of the Rsubread v2.4.2 R package was used by employing transcriptome information from the GENCODE v27 to assign and summarize reads to genomic features.
DESeq2 v.1.30.1 R package analyzed the differentially expressed genes with the summarized raw read counts for each gene.
ViSEAGO v1.4.0 was used to cluster biological functions using Gene Ontology and semantic similarity analysis.
GSEA v4.1.0 was performed using gene sets from Molecular Signatures Database (MSigDB) v7.4
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: csv of DESeq2 output containing log2 fold change upon ammonium nitrate and sulfate treatment

source_name: ICR WT lung

extract_protocol:
Total RNA was extracted using the Trizol reagent
2x101 paired-end RNA-seq library was constructed using TruSeq stranded mRNA LT sample prep kit and sequenced using the Illumina NovaSeq 6000 platform.

value: Ammonium nitrate/sulfate particle containing air exposure

value: ICR wild-type

value: lung


title: RB6891_3


title: MUC25990

description:
VDJ-BCR
J119_filtered_contig_annotations.csv
J119_C_BCR

source_name: J119 BCR Spleen+Blood

value: female

value: Spleen=HTO tag1, Blood=HTO tag2


title: Batch1_Patient11600-15149_AD10_1

description:
AD10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PXB-O2min-monoculture-bio2

value: monoculture in MPS O2[-]


title: RB6891_2

source_name: hippocampus


title: Mouse Mix NC replicate 2

value: Distilled water containing air exposure


title: Batch1_Patient11600-15149_AD09_2

description:
AD09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube


title: Mouse Mix NC replicate 1


title: Batch1_Patient11600-15149_AD09_1

description:
AD09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: RB6891_1


title: PXB-O2plus-monoculture-bio2

value: monoculture in MPS O2[+]


title: Batch1_Patient11600-15149_AD08_2

description:
AD08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: SE Rep2 IP

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie. Only uniquely mapped reads were retained.
Peaks were called us ing exomePeak2
Assembly: TAIR10
Supplementary files format and content: Peaks in CSV format
Library strategy: MeRIP-seq

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface sterilized and grown on 1/2MS plate under 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
7days seedling were collected and total RNA was extracted by Trizol. mRNA were isoloated with Dynabeads™ Oligo (dT)25 beads and were fragmented into about 100-nucleotide-long fragments. N6-methyladenosine antibody were then used to do the MeRIP and the the libraries from immunoprecipitated RNA and input were constructed with the RNANEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).
Illumina RNA library protocol

value: seedling

tag: ecotype

tag: antibody

value: N6-methyladenosine antibody


title: MUC26025

description: HTO

data_processing:
cellranger-5.0.1 multi using refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 (VDJ B and T cell receptors) and refdata-gex-mm10-2020-A (gene expression)
Hashtag Oligo used described in file Feature_mouse_10x.csv
Genome_build: mm10
Supplementary_files_format_and_content: contig_annotations.csv
Supplementary_files_format_and_content: count

source_name: H124 HTO

growth_protocol: Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 28±2 days after reaching an EAE score of 3.

extract_protocol:
Anesthetized mice underwent an intravascular staining procedure [20] with 0,75 µg of TotalSeq™-A0096 anti-mouse CD45 Antibody (clone 30-F11, Biolegend) in 300 µl PBS, 3-10 minutes before CSF aspiration from the cisterna magna, to be able to discriminate CSF from blood leukocytes. After thorough perfusion with PBS the spinal cord was dissected, and meninges were detached from the spinal cord using fine forceps. Meninges were passed through a cell strainer to collect mELT cells. Fc receptors were blocked and samples were incubatedwith DNA barcoded TotalSeq antibodies against CD4 (TotalSeq-C0001 anti-mouse CD4, clone RM4-5, Biolegend), CD8a (TotalSeq-C0002 anti-mouse CD8a , clone 53-6.7, Biolegend), CD19 (TotalSeq-C0093 anti-mouse CD19, clone 6D5, Biolegend), Ly6G (TotalSeq-C0015 anti-mouse Ly6G , clone 1A8, Biolegend), and NK1.1 (TotalSeq-C0118 anti-mouse NK-1.1, clone PK136, Biolegend), and one of 2  TotalSeq Hashtag antibodies (TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, clones M1/42; 30-F11, Biolegend or TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody, clones M1/42; 30-F11, Biolegend), to allow pooling of 2 samples per experiment.
10x Genomics Chromium Next GEM Single Cell V(D)J Reagent Kit (v1.1)
10x Genomics single cell sequencing, with feature barcoding

treatment_protocol: 100 µg of anti-CD20 mAb (clone 18B12, MTA with Roche) in a murine IgG2a Fc-format or anti-hen egg lysozyme (HEL) mouse IgG2a kappa isotype control (Crown bio, Cat: C0006) in 100 µl PBS was injected intraperitoneally (i.p.) at day 0 , 7, 14 and 21 after reaching an EAE score of 3, for a total of 4 doses.

tag: hto

value: CSF=HTO tag1, mELT=HTO tag2


title: Batch1_Patient11600-15149_AD12_1

description:
AD12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: SE Rep1  IP


title: PXB-tcps-coculture-bio1

value: PXB-cells


title: Mouse Mix Exposed replicate 2


title: PXB-tcps-monoculture-bio1

value: monoculture in TCPS


title: MUC26019

description: GEX

source_name: H124 Total mRNA CSF+mELT


title: SE Rep2 Input


title: Batch1_Patient11600-15149_AD07_2

description:
AD07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: PXB-O2min-coculture-bio1


title: SE Rep1  Input


title: MUC26024

description: HTO

source_name: H109 HTO


title: Batch1_Patient11600-15149_AD07_1

description:
AD07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Col WT Rep2 IP

value: WT


title: PXB-O2min-monoculture-bio1


title: PXB-O2plus-coculture-bio2

value: coculture in MPS O2[+]


title: PXB-O2plus-coculture-bio1


title: Batch1_Patient11600-15149_AD06_2

description:
AD06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Col WT Rep1  IP


title: MUC26018

description: GEX

source_name: H109 Total mRNA CSF+mELT


title: Batch1_Patient11600-15149_AD06_1

description:
AD06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26012

description: VDJ-BCR

source_name: H109 BCR CSF+mELT


title: PXB-O2plus-monoculture-bio1


title: MUC26027

description: HTO

source_name: I24 HTO

value: male


title: MUC26013

description: VDJ-BCR

source_name: H124 BCR CSF+mELT


title: Batch1_Patient11600-15149_AD05_1

description:
AD05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CTNNB1, Input, repl2

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Duplicate fasta files from the  replicates of the b-catenin chromatin immunoprecipitation and input samples were concatenated and aligned to hg19 using bowtie2 vesrsion 2.3.4.1  with default settings.
Peaks were called by MACS2 v.2.2.5 using the broad peak calling option (--broad) and p value=10-7 (-p 1e-7 ) adjusted to the larger dataset (--to-large) and the mfold parameter in between 5 and 50 (-m 5 50 ) 2. Thereby, 3386 highly significant peaks were determined.
To generate bedgraph files for UCSC genome browser visualization, we processed .sam files using standard commands of the Homer v.4.11 with parameters of the makeUCSCfile program ( -fsize 5e7 -res 10)
Assembly: hg19
Supplementary files format and content: .bedGraph files for ChIP and Input samples, except IgG, also, narrowPeak results from MACS2

source_name: Desmoid tumor

growth_protocol: Primary desmoid cell lines were grwon in DMEM with FBS media

extract_protocol: The cells were treated using CST SimpleChip enzymatic kit with following modifications. Four 150 mm dished of cells were crosslinked first by EGS 5mM, for 20 min followed by 1% formaldehyde for 10 min and washed with PBS. From here cells were treated with MNAse and sonicated  according to the kit instruction. We used 6ul of magnetic beads to pre-clear the chromatin and 0.18mkg of antibody to precipitate chromatin. In addition, we added the last washing step with 0.15% Sarcosin in 10mM Tris 1mM EDTA.  Experiments were conducted using β-catenin antibody D10A8 (6 μg, Cell Signaling Technology).

treatment_protocol: Cells were grown to approximately 80% confluency prior to harvest

value: Desmoid tumor

value: Desmoid tumor derived cell line

tag: chip antibody


title: Batch1_Patient11600-15149_AD08_1

description:
AD08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

tag: tissue


title: CTNNB1, Input, repl1


title: Batch1_Patient11600-15149_AD05_2

description:
AD05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Col WT Rep1  Input


title: Batch1_Patient11600-15149_AD04_2

description:
AD04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4T1-LM-2

city: Chongqing

first: Shaojie

last: Cheng

state: -- None selected --

address: No.1, Yi-Xue-Yuan Road, Yu-Zhong District

country: China

institute: Chongqing Medical University

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) or mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2. HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Human GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz. Mmouse GTF file:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 4T1 cell

growth_protocol: 4T1 cells were cultured in RPMI 1640 medium (Gibco, USA) with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Beyotime, Shanghai, China). MDA-MB-231 cells were cultured in DMEM medium (Gibco, USA) with 10% FBS and 1% penicillin/streptomycin. All cell lines were cultured in a 5% CO2 incubator at 37°C.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: 4T1 cell

value: TNBC

value: LM


title: 4T1-LM-3


title: MUC26021

description: GEX

source_name: I24 Total mRNA CSF+mELT


title: Batch1_Patient11600-15149_AD04_1

description:
AD04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26029

description: HTO

source_name: I105 HTO

value: female


title: CTNNB1, ChIP, repl2


title: MUC26015

description: VDJ-BCR

source_name: I24 BCR CSF+mELT


title: CTNNB1, ChIP, repl1


title: Batch1_Patient11600-15149_AD03_2

description:
AD03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4T1-LM-1


title: MUC26023

description: GEX

source_name: I105 Total mRNA CSF+mELT


title: MUC26017

description: VDJ-BCR

source_name: I105 BCR CSF+mELT


title: SKOV3 cells, placental nano-Evs, group3

city: Auckland

first: Xinyi

last: Sun

address: 85 Park Road, Grafton

country: New Zealand

institute: the university of auckland

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files includeTPM/counts for each Sample

growth_protocol: SKOV3 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum FBS and 1% antibiotics in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol
mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: treat SKOV3 cells with 200ug placental extracellular vesicles for 24h

value: ovarian cancer cells

tag: type

value: placental nano-Evs


title: Col WT Rep2 Input

value: seedling


title: Batch1_Patient11600-15149_AD02_2

description:
AD02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4T1-Pri-2

tag: treatment

value: Pri


title: SKOV3 cells, placental nano-Evs, group 2

tag: cell type


title: Batch1_Patient11600-15149_AD02_1

description:
AD02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: SKOV3 cells, Control, group 3

tag: genotype

value: Control


title: MUC26016

description: VDJ-BCR

source_name: I68 BCR CSF+mELT

tag: Sex

value: CSF=HTO tag1, mELT=HTO tag2


title: MUC26022

description: GEX

source_name: I68 Total mRNA CSF+mELT

tag: concentration (ng/ul)


title: MUC26026

description: HTO

source_name: H132 HTO

tag: volume (ul)


title: 4T1-Pri-1


title: Early_2cell_WT_2

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic. Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools. Duplicates were removed using picard to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values (average signal of all three biological replicates).
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.

source_name: 2-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 10-20 blastomeres (5 to 10 2-cell embryos) were collected in 2 μL DamID buffer (10mM TRIS acetate pH 7.5, 10mM magnesium acetate, 50mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.
Low-input LaminB1 DamID

treatment_protocol: For early 2-cell DamID, zygotes (18 h post hCG) were isolated and injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 and cultured in auxin (500μM)-containing medium. Auxin was removed just after mitosis for 4–6 h and early 2-cell embryos were collected at 34–36 h post hCG. For DamID in transcription inhibited late 2-cell embryos, zygotes (18 h post hCG) were injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 coding mRNA and cultured in KSOM containing 500 μM auxin and either 0.1 mg/mL alpha-amanitin (BioChemica) or 100 μM DRB (Santa Cruz). To allow methylation of LADs in the late 2-cell stage, auxin was washed out from 42 to 48 h post hCG and embryos were cultured in KSOM containing either 0.1mg/mL  alpha-amanitin or 100 μM DRB.

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: SKOV3 cells, placental nano-Evs, group 1

value: WT


title: Early_2cell_WT_1


title: SKOV3 cells, placental micro-Evs, group 2

value: placental micro-Evs


title: MUC26020

description: GEX

source_name: H132 Total mRNA CSF+mELT

value: male

tag: i7 index


title: Batch1_Patient11600-15149_AD03_1

description:
AD03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube

value: Fallopian tube


title: Batch1_Patient11600-15149_AC12_2

description:
AC12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26014

description: VDJ-BCR

source_name: H132 BCR CSF+mELT


title: SKOV3 cells, placental micro-Evs, group 3


title: RB6891_5

source_name: hippocampus

value: hippocampus

tag: strain

value: Sprague Dawley

value: SHAM


title: Batch1_Patient11600-15149_AD01_1

description:
AD01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: stim_2

city: Boston

first: Linden

last: Hu

state: MA

address: 136 Harrison Avenue

department: Microbiology

institute: Tufts University School of Medicine

data_processing:
Paired end reads were aligned to the mm10 mouse reference genome using STAR
Gene expression was summarized using RSEM version 1.3.0
Read counts for all samples were aggregated into a single matrix in R
Assembly: mm10
Supplementary files format and content: genes.results files are tab-delimited text file that includes the raw counts, FPKM and TPM for each sample
Supplementary files format and content: count_matrix.csv is a comma-seperated text file that has the aggregated raw counts for all samples

source_name: bone marrow

growth_protocol: Bone marrow cells were flushed from mouse femurs and tibiae with sterile DMEM and cultured for 5-7 days with DMEM supplemented with 30% L929 + 20% FBS + 1% streptomycin

extract_protocol:
Cells were harvested by asperating the cell culture surpernatant and adding TRIzol to the remaining cells. RNA was extracted.
Libraries were constructed by Genewiz using rRNA depletion. They were sequenced with approximately 25 million reads per sample

value: bone marrow

value: Bone marrow derived macrophages

value: Stimulation


title: Rhizome of cut explants after 4 days of  cutting

city: Ulaanbaatar

first: Bolortuya

last: Ulziibat

state: Tuv

address: 54b peace avenue

department: Institute of Biology

country: Mongolia

institute: Mongolian academy of sciences

data_processing:
Sequencing was performed on the BGISEQ-500 platform
the adapter sequences were trimmed and low-quality reads (more than 20% of the base qualities are lower than ten) and reads with unknown bases (N bases more than 5%) were removed, respectively.
Then, the high-quality reads were de novo assembled into unigenes by the Trinity program.
All the clean reads of each sample were mapped to the unigenes with Bowtie2 software
the gene expression levels were calculated with RSEM
Assembly: de-novo assembly
Supplementary files format and content: excel files include RPKM values for each Sample

organism: Acorus calamus

source_name: Rhizome

growth_protocol: Explants with cutting height of leaves (cut) and without cutting height of leaves (uncut) were cultured on the MS medium supplemented with 2 mg/l 2,4-D and 0.5 mg/l NAA for rhizome extension

extract_protocol:
Total RNA from each tissue was isolated using PureLink RNA mini kit (Invitrogen) following the manufacturer’s instructions.
Oligo dT selection or rRNA depletion was performed on the isolated total RNA. RNA was fragmented and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3′ adenylated. Adaptors were ligated to the ends of these 3′ adenylated cDNA fragments. The ligation products were purified and PCR amplification was performed to enrich the purified cDNA template using PCR primer. The PCR product was denatured by heat and the single-strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Cutting leaves (cut explants) dramatically increased rhizome extension and shoot proliferation was significantly high compared with uncut explants.

value: Rhizome

value: cut


title: SKOV3 cells, Control, group 2

value: ovarian cancer cells


title: Batch1_Patient11600-15149_AC12_1

description:
AC12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AC11_2

description:
AC11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4T1-Pri-3

value: 4T1 cell

value: TNBC

value: Pri


title: Batch1_Patient11600-15149_AD01_2

description:
AD01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MUC26028

description: HTO

source_name: I68 HTO

value: female

value: CSF=HTO tag1, mELT=HTO tag2


title: Early_2cell_WT_3

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: Leaves of cut explants after 4 days of  cutting

source_name: Leaf

value: Leaf


title: HEK293 cells with negative control mimics, sample on 9/18

city: AUGUSTA

first: Qingqing

last: Wei

state: Georgia

address: 1460 Laney Walker Blvd.

department: Cellular Biology & Anatomy

institute: Augusta University

data_processing:
Data mapping with STAR v2.5.
Quantification with HTSeq v0.6.1 to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of he gene and reads count mapped to this gene.
Differential Analysis with DESeq2 R package v2_1.6.3, padj<0.05
Assembly: Hg19
Supplementary files format and content: Raw read counts only
Supplementary files format and content: Raw counts, FPKM values, log2 fold change, P value

extract_protocol:
The RNA samples from the RISC-IP products were extracted with miVANA miRNA Isolation kit (Thermo Fisher Scientific, Carlsbad, CA)
The library was prepared with NEBnext Ultra II RNA library Prep Kit for Illumina folllowing the manufacturer's mannual.

treatment_protocol: HEK293 cells were cotransfected of Flag-Ago2 with negative control or mir-219 mimics. The cells were lysed and RNA-induced silencing complexes (RISC) were precipitated with anti-flag agarose.

value: co-transfection of negative control mimics and Flag-Ago2, followed by Flag-IP


title: untreated_2

value: WT

value: Untreated


title: restim_2

value: bone marrow

value: Re-stimulation


title: Rhizome of uncut explants after 4 days of  cutting

value: uncut


title: SKOV3 cells, placental micro-Evs, group 1

value: placental micro-Evs


title: HEK293 cells with negative control mimics, sample on 9/5


title: Batch1_Patient11600-15149_AC10_1

description:
AC10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Leaves of uncut explants after 4 days of cutting


title: restim_1

value: Bone marrow derived macrophages


title: Batch1_Patient11600-15149_AC10_2

description:
AC10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HEK293 cells with mir-219 mimics, sample on 9/18

value: co-transfection of mir-219 mimics and Flag-Ago2, followed by Flag-IP.


title: HEK293 cells with negative control mimics, sample on 8/22


title: SKOV3 cells, Control, group 1

value: ovarian cancer cells

value: Control


title: Batch1_Patient11600-15149_AC09_1

description:
AC09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: untreated_1


title: Il17aCre_IMM

city: St. Louis

first: Brian

middle: Todd

last: Edelson

state: MO

address: 660 S. Euclid Ave., Box 8118

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Cell Ranger Single-cell Software Suite was used for demultiplexing and alignment.
Seurat package was used for dimensionality reduction, tSNE clustering, identification of cluster-specific genes, and differential expression analysis.
See detailed methods in Cook et al.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: central nervous system

extract_protocol:
10x Genomics protocols
Single cell libraries were prepared using standard 10x Genomics protocols with the v2 Chromium Single Cell 3' Library Kit.

treatment_protocol: Live CD45+ central nervous system cells were FACS sorted from either naïve mice or immunized Bhlhe40fl/fl, Cd4-Cre+ Bhlhe40fl/fl, or Il17a-Cre+ Bhlhe40fl/fl mice.

value: central nervous system

value: FACS sorted live CD45+

value: Il17a-Cre+ Bhlhe40fl/fl

value: Day 14 EAE


title: HEK293 cells with mir-219 mimics, sample on 9/5


title: Batch1_Patient11600-15149_AC08_2

description:
AC08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2


title: Rhizome of uncut explants after a month of cutting

value: Rhizome


title: Cd4Cre_IMM

description: 10x Genomics

value: Cd4-Cre+ Bhlhe40fl/fl


title: HEK293 cells with mir-219 mimics, sample on 8/22


title: Batch1_Patient11600-15149_AC08_1

description:
AC08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: FL_IMM

description: 10x Genomics


title: Leaves of uncut explants after a month of cutting

value: Leaf


title: Batch1_Patient11600-15149_AC11_1

description:
AC11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: stim_1

value: WT

value: Stimulation


title: day 62, 4X

city: Aarhus

first: Mark

last: Denham

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

description:
S6
10X genomics

data_processing:
The Cell Ranger Single-Cell Software Suite (v 3.1.0) was used for sample demultiplexing, barcode processing, and single-cell 3′ gene counting. The reads were aligned to the human GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes, features, matrix)

source_name: hESCs

extract_protocol:
On 16, 28, and 62 days in vitro (DIV), cultured cells were dissociated into single cells using Accutase. On 16 DIV, neurospheres (n = 10 biological replicates per cell line) were pooled together, on 28 DIV, four biological replicates per cell line were pooled together, and on 62 DIV, four biological replicates per cell line were pooled together.
To construct the library, the 10X Genomics Chromium Next GEM Single Cell 3’ kit v 3.1 was used according to a standard protocol. Each of the four groups (H9 DIV16, 4X DIV16, H9 DIV28, 4X DIV28, H9 DIV62, and 4X DIV62) was run in separate lanes of the Chromium controller, and a total of 8,000 cells were loaded per lane.

value: hESCs

value: GBX2,CDX1,CDX2,CDX4 knockout

value: Day 62 of differentiation


title: FL_NAIVE

description: 10x Genomics

value: Naïve


title: day 28, 4X

description:
S4
10X genomics

value: day 28 of differentiation


title: Rhizome of cut explants after a month of cutting

value: cut


title: mCLC 40hr rep2

city: Rochester

first: Ryan

last: Watkins

state: MN

address: 200 First St SW

department: Surgery

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using FastQC
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: mm10
Supplementary files format and content: tab-delimited files with RNA-Seq gene expression

source_name: Liver

extract_protocol:
Livers were lysed in Trizol followed by chloroform precipitation. RNA was then applied to Qiagen RNAeasy column and processed according to manufacturer protocol
Illumina TruSeq Stranded mRNA library prep protocol

treatment_protocol: Mice were treated with vehicle or mCLC846 7.5 mg/kg/dose twice daily starting 12 hours prior to 70% partial hepatectomy and continued until euthanasia at 40 hours.

value: Liver

value: Hour 40


title: Batch1_Patient11600-15149_AC07_1

description:
AC07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.

value: Fallopian tube


title: Batch1_Patient11600-15149_AC07_2

description:
AC07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: LPP3_input

city: Meizhou

first: Congjun

last: Jia

address: xueyuan road

institute: Guangdong Meizhou Vocational and Technical College

data_processing:
Trimmomatic (v 0.39)  software to obtain clean reads
clean reads were then aligned to the chicken reference genome GRCg7b using the HISAT2 (v 2.1.0)
MeTDiff (v 1.1.0)  was used to call the peaks of m6A modification in each group with the input data as control (P value < = 0.05, fold change > = 0.05)
annotation of the identified m6A peaks in each group and differential m6A peaks between groups was conducted by ChIPseeker (v 1.12.1)
Assembly: GRCg7b
Supplementary files format and content: txt format,BLP.m6A_site
Supplementary files format and content: txt format, LPP.m6A_site

organism: Gallus gallus

source_name: ovary

extract_protocol:
The total RNA was isolated from each ovary sample using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The concentration and purity of the RNA were measured using the NanoDrop 2000 (NanoDrop, Wilmington, DE, USA).
The mRNA was enriched from the total RNA using the Dynabeads Oligo (dT) and then fragmented. The fragmented RNAs were then divided into two parts, one for isolation of m6A enriched mRNA and the other used for RNA-seq as the input background. The former part of fragmented RNAs was incubated with the m6A-Dynabeads at room temperature for 1 hour to allow them binding to the beads. Eluted m6A-containing fragments (IP) and untreated input control fragments (the latter part) were then concentrated to generate the final cDNA library.

value: ovary

tag: breed

value: Wuhua yellow-feathered chicken

tag: developmental stage

value: after sexual maturity


title: mCLC 40hr rep3

tag: time


title: LPP3_RIP


title: Leaves of cut explants after a month of cutting


title: day 16, 4X

description:
S2
10X genomics

tag: cell line

value: neural progenitors

value: Day 16 of differentiation


title: Batch1_Patient11600-15149_AC06_2

description:
AC06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: mCLC 40hr rep1


title: day 62, H9

description:
S5
10X genomics


title: Batch1_Patient11600-15149_AC09_2

description:
AC09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: LPP2_input


title: Vehicle 40hr rep3

value: vehicle


title: Batch1_Patient11600-15149_AC05_2

description:
AC05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: LPP2_RIP


title: Vehicle 40hr rep2


title: LPP1_RIP


title: day 16, H9

description:
S1
10X genomics

value: WT


title: Batch1_Patient11600-15149_AC05_1

description:
AC05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Vehicle 40hr rep1


title: BCs of IPF patient

city: Shanghai

first: Tao

last: Ren

address: No. 600, Yi Shan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

description: 10x Genomics

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: human bronchial epithelia

extract_protocol:
fibroblast and BCs were resuspended and  flash frozen on dry ice,  RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BD Rhapsody Analysis pipeline (Version: 1.8) protocols

value: Airway basal cells

value: human bronchial epithelia

tag: diagnosis

value: IPF


title: Batch1_Patient11600-15149_AC04_2

first: Ahmed

last: Ahmed

address: John Radcliffe Hospital, Headley way

institute: University of Oxford

description:
AC04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Fibroblast of IPF patient

description: 10x Genomics

value: Fibroblast


title: Vehicle 0hr rep3

value: Hour 0


title: BLP3_input

value: before sexual maturity


title: Batch1_Patient11600-15149_AC04_1

description:
AC04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: After

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

description: cen0005.TCATGAGGAG-TGTGGAGAGG.HVHYGDSX2_TCATGAGGAG-TGTGGAGAGG

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCh38.76
Supplementary files format and content: The counts per million (CPM) reads were log-transformed (attached processed data file) and used to select genes that were significantly (P<0.005) positively and negatively associated with AT pO2 by using Pearson’s correlation.

source_name: Subcutaneous adipose tissue

growth_protocol: RNA was isolated from frozen subcutaneous adipose tissue samples obtained from an individual before and after weight gain (32%).

extract_protocol:
RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

tag: time point

value: after weight gain

value: Subcutaneous adipose tissue


title: Vehicle 0hr rep2

value: Liver


title: Batch1_Patient11600-15149_AC03_2

city: Oxford

description:
AC03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: BLP2_input

value: ovary


title: day 28, H9

description:
S3
10X genomics

value: hESCs

value: day 28 of differentiation


title: BLP1_input

value: Wuhua yellow-feathered chicken


title: Sox9-GFP high, biological replicate 4

city: Bronx

first: Jihong

last: Cui

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

data_processing:
Base calling were conducted by illumina HiSeq Control Software.
After investigating the quality of raw data by FASTQC, RNA-seq reads were aligned using Hisat2 to the reference mouse genome (GRCm38) using the M14 Gencode Basic CHR Annotations.
Stringtie and the prepDE.py script were used to generate raw counts from aligned reads.
Differential expression was determined using DESeq2 (from Galaxy Version 2.11.40.7+galaxy2).
Matrix table with raw gene counts for every gene and every sample.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cell

growth_protocol: The tumors were grew spontaneously.

extract_protocol:
Cells were sorted based on the level of Sox9-GFP. RNA was extracted using Quick-RNA microprep kit (Cat# R1050).
RNA libraries were prepared using the NEBNext Ultra II Directional library prep kit (New England Biolabs, E7765) and sequenced by Genewiz.

treatment_protocol: No treatment

value: Basal-like breast cancer (Primary tumor)

value: Breast

value: Sox9-GFP high


title: Vehicle 0hr rep1

value: vehicle


title: Batch1_Patient11600-15149_AC02_2

description:
AC02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Before

description: psq0004.AACGGATCGC-TATCCAGTTC.HVHYGDSX2_AACGGATCGC-TATCCAGTTC

value: before weight gain


title: BLP3_RIP


title: Batch1_Patient11600-15149_AC03_1

description:
AC03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: BLP2_RIP


title: Sox9-GFP low, biological replicate 4

value: Sox9-GFP low


title: Sox9-GFP negative, biological replicate 4

value: Sox9-GFP negative


title: Batch1_Patient11600-15149_AC01_2

description:
AC01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A10 rep 2

first: Charles

last: Kaufman

address: 4518 McKinley Ave. McDonnell Science BuidinRM 558

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
Read count  normalization and differential expresion analysis were performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2-normalized values for each Sample, and results from DESeq2 differential expression analysis

growth_protocol: WT and CDC20 promoter indel A375 cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1C Pen/Step in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 5-`0 ug of total RNA was used for the construction of sequencing libraries.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: human melanoma cell line

value: CDC20 promoter indel


title: A3 rep 1


title: Sox9-GFP high, biological replicate 3


title: A3 rep 2


title: A10 rep 1


title: Batch1_Patient11600-15149_AC02_1

description:
AC02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AB12_2

description:
AB12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: WT A375 Cas9 Control 2

value: WT


title: Sox9-GFP negative, biological replicate 3


title: WT plus apyrase

city: Madison

first: Robert

last: Landick

state: Wisconsin

address: 1550 Linden drive

department: Department of Biochemistry

institute: University of Wisconsin–Madison

description: nascent RNA

data_processing:
NET-seq data analysis was performed using open-sourced packages in Python and custom scripts written in R 4.1.0. Adaptor sequence in raw NET-seq reads was removed with Cutadapt and aligned to E. coli MG1655 reference genome (NCBI Reference Sequence: NC_000913.3) with Bowtie. Unwanted reads in ribosomal RNA regions and t-RNA regions were removed with SAMtools and converted to BED format with BEDTools. Full length NET-seq reads were then trimmed to 15 nt from 3' ends. The total read numbers and 3' end read numbers in genome positions were quantified with BEDTools. To scale reads among strains and replicates, 3' end read numbers (R(raw)) were normalized according to the E. coli cell genomic DNA amount in cell harvested (M(E. coli)), the B. subtilis spike-in cell number (N(spike-in)) and the reads (R(spike-in)) specifically aligned to B. subtilis genome (NCBI Reference Sequence: NC_000964.3): scaled 3' end read R(scaled) = 2.5 * 10^8 * R(raw) * N(spike-in) / ( M(E. coli) * R(spike-in)). M(E. coli) was calculated with pre-determined equation for the two NET-seq strains: for WT NET-seq strain, M(E. coli) = (7.24 * OD + 3.98) * 500; for ∆SI3* NET-seq strain, M(E. coli) = (9.83 * OD + 9.34) * 500.
For pause calling, we used a multi-round sliding window strategy: for each position in a transcription unit, if its 3' end read number is larger than the mean + 4*standard deviation of the non-zero read pool containing this position, 100 bp upstream and 99 bp downstream, then it is classified as a pause signal. The pause reads defined in the first round is removed from the pool and the remaining sites were subjected to pause calling in the next round. Four rounds of pause calling in total were conducted and common pause positions from 3 biological replicates were used as the final pause positions. Detected pause signals located in several tRNA and sRNA genes were filtered due to their high probability of contamination during NET-seq library preparation. In addition, pause signals matching mature RNA 3' ends were also removed based on the published E. coli SEnd-seq results.
Assembly: E. coli: NC_000913.3, B. sub: NC_000964.3
Supplementary files format and content: Tab-delimited text files recording normalized nascent RNA 3' end reads and total reads (read trimmed to 15 nt) covering each genomic position.
Library strategy: NET-seq

organism:
Escherichia coli
Bacillus subtilis

source_name: F- λ- ilvG468+ rfb-50 rph+ ybhJ(L54->I) yebN(G25xxx->D) ycfK::97bp  ∆InsB-5 ∆InsA-5 ∆InsAB-5 rpoC::3XFLAG; B. subtilis 168 trpC2 rpoC::3XFLAG

growth_protocol: A single colony of E. coli NET-seq strains was inoculated into MOPS rich defined medium with 0.2% (w/v) glucose (RDM) and 50 µg/mL kanamycin for overnight growth at 37 °C. 2.5 mL of the overnight culture was inoculated into 0.5 L RDM with 50 µg/mL kanamycin (freshly prepared and sterilized with 0.22 µM filter) in Erlenmeyer flasks and culture with 200 revolution per minute orbital shaking at 37 °C until cell density reached early log-phase (OD~0.4, record OD value at harvesting). At 37 °C, quickly filter cells through a 0.22 µM cellulose filter unit and transform all cell pellets into liquid nitrogen with a spatula. Frozen cells were stored at –80 °C before homogenizing. Biological triplicate samples were collected for each NET-seq strain. As for B. subtilis spike-in cells (RL3116), a single colony was inoculated into 5 mL LB with 7.5 µg/mL kanamycin for overnight growth at 37 °C. 2.5 mL of the overnight culture was inoculated into 0.5 L LB with 7.5 µg/mL kanamycin at 37 °C until cell density reached early log-phase (OD~0.4, record OD value at harvesting). Spin down cells with centrifugation at 4,000 Xg for 10 min for the cell pellet. Resuspend cells with 10 mL ice cold sterile PBS (with 20% (v/v) glycerol and 0.5 mL 1X protease inhibitor cocktail) and flash frozen in liquid nitrogen.

extract_protocol:
Frozen cells were pulverized on a Retsch MM400 Mixer Mill (canisters pre-cooled in liquid nitrogen) 6 times at 15 Hz for 3 min in the presence of 400 µL frozen lysis buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 100 mM NH4Cl, 10 mM MnCl2, 250 Unit RNaseIn (Promega), 1X protease inhibitor cocktail, 0.4 mg/mL puromycin). Spike-in cells were thawed on ice and added proportional to the E. coli cell amount (500 µL*OD E.coli) to homogenize with E. coli cells. The lysate was resuspended on ice with extra 5 mL of lysis buffer by gentle pipetting. RQ1 DNase I (110 Unit total, Promega) was added and incubated for 15 min on ice. For apyrase treatment, 15 unit of apyrase (Sigma-Aldrich) was added together with DNase. The reaction was quenched with EDTA (25 mM final), which releases ribosomes from the transcript. The lysate was clarified at 4 °C by centrifugation at 25,000 xg for 10 min and incubated with 0.5 mL anti-FLAG M2 affinity resin (Sigma-Aldrich) for 3 hours at 4 °C. The resin was washed with 10 mL Wash Buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 300 mM KCl, 1 mM EDTA) 4 times at 4 °C and the RNAP was eluted with 600 µL Elution Buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 2 mg/mL FLAG peptide (Sigma-Aldrich)). Nascent RNA was extracted from the eluate with miRNeasy Mini Kit (Qiagen) following manufacturer’s instructions. The nascent RNA sample was further purified by EtOH precipitation, dissolved in DEPC-treated water and store at –80 °C.
The adaptor oligo(/5Phos/CTGTAGGCACCATCAAT/3ddC/, 6 µM) was 5' adenylated by incubating with 80 µM ATP, 6 µM Mth RNA ligase (NEB), 25% (v/v) PEG 8000 in 1X NEB Buffer 1 at 65 °C for 4 hours, then 85 °C for 5 min. Nascent RNA (16.7 ng/µL, normally 1.5 µg for each sample) was ligated to the adaptor by incubating with 1X T4 RNA ligase buffer (NEB), 25% PEG 8000, 6.7 Unit/µL T4 RNA ligase 2, truncated (NEB), 2 µM adaptor, 1.3 Unit/µL RNaseIn at 37 °C for 3 hours. The ligation was stopped by adding 16 mM EDTA. The adaptor-ligated RNA was alkaline fragmented by incubating with 6 mM Na2CO3, 44 mM NaHCO3, 1 mM EDTA at 95 °C for 35 min (time may vary depending on the freshness of the alkaline solution) and the RNA was precipitated by isopropanol precipitation with NaOAc (pH=5.5) and GlycoBlue coprecipitant (Thermo Fisher). The fragmented, adaptor-ligated RNA was run on a 15% TBE urea polyacrylamide gel (Novex, Thermo Fisher) and RNA species ranging from 50 to 100 nt was excised and gel extracted. The RNA was reversely transcribed into cDNA by mixing with 1X First Strand Buffer (Thermo Fisher), 0.5 mM dNTPs, 0.3 µM RT adaptor (/5Phos/AGATCGGAAGAGCACACGTCTGAAC/iSp18/CACTCA/iSp18/CCTACACGACGCTCTTCCGATCTTCCGACGATCATTGATGGTGCCTACAG), 0.6 Unit/µL SuperaseIn, 5 mM DTT, 10 Unit/µL Superscript III (Thermo Fisher) and incubating at 50 °C for 60 min. The RNA template in the cDNA was eliminated by adding 0.1 M NaOH and incubating at 95 °C for 20 min followed by adding 0.1 M HCl. The cDNA was run on a 10% TBE urea polyacrylamide gel (Novex, Thermo Fisher) and DNA species ranging from 100 to 200 nt was excised and gel extracted. The cDNA library was circularized by incubating with 1X Reaction Buffer (Lucigen), 50 µM ATP, 2.5 µM MnCl2, 5 Unit/µL CircLigase (Lucigen) at 60 °C for 1 hour followed by 80 °C for 10 min. The cDNA libraries were amplified with Q5 DNA polymerase (NEB) PCR system using dual indexed primers for NovaSeq 6000 (Illumina) sequencing platform using 150-nt paired-end sequencing.

value: bacterial cell

value: Mixing with spike-in control cells


title: Batch1_Patient11600-15149_AC01_1

description:
AC01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Sox9-GFP low, biological replicate 3


title: WT A375 rep 2


title: Sensitive_09

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using HISAT2 with default parameters.
StringTie was used to quantify gene expression levels
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Ovary

extract_protocol:
Total RNA was collected using TRIzol Reagent (Invitrogen); then, rRNAs were removed by using the RiboMinus Eukaryote Kit (QIAGEN, Valencia, CA, USA). We next prepared the RNA-seq libraries using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Beverly, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovary

tag: disease

value: Ovarian cancer

tag: phenotype

value: Platinum sensitive patient


title: Sensitive_10

tag: tissue


title: Batch1_Patient11600-15149_AB12_1

description:
AB12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: BLP1_RIP

value: ovary

value: Wuhua yellow-feathered chicken

value: before sexual maturity


title: Batch1_Patient11600-15149_AB11_2

description:
AB11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Sox9-GFP high, biological replicate 2

value: Basal-like breast cancer (Primary tumor)

value: Breast

value: Sox9-GFP high

tag: treatment


title: Sensitive_08


title: WT A375 rep 1

tag: cell type


title: Sox9-GFP low, biological replicate 2

tag: genotype

value: Sox9-GFP low


title: Sox9-GFP negative, biological replicate 2

value: Sox9-GFP negative


title: Sensitive_07


title: Batch1_Patient11600-15149_AB11_1

description:
AB11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: ADC9010, 2B

first: Or

last: Yaacov

department: Center of Human Genetics and Genomics

institute: NYU School of Medicine

data_processing:
Adapter sequences, CTGTCTCTTATACACATCT, were trimmed from the raw reads using cutadapt (V2.10 with Python 3.6.5) with parameters “-e 0.1 -O 1 -q 20,20 -m 35”.
The trimmed reads were mapped to hg38 with Bowtie2 (version 2.4.1), with the options “-X 2000 --dovetail --no-mixed --no-discordant –t”
Duplicated reads were marked and removed using picard (V2.26.10) MarkDuplicates with "REMOVE_DUPLICATES=true".
All reads mapping to the + strand were offset by +5bp and all reads mapping to the - strand were offset by -4bp, to account for the 9bp duplication of the target site by Tn5 transposase
Peaks and read density signals were calculated using MACS2 (ver. 2.1.2) with the parameters “–nomodel –shift -50 –extsize 100 --keep-dup all"
Assembly: hg38
Supplementary files format and content: narrowPeak for ATAC-seq peaks

source_name: Kidney (cortex)

extract_protocol:
Tissue samples were finely chopped on ice and homogenized in an Accumax solution (Sigma-Aldrich) using a Dounce homogenizer. The samples were then passed through a 100um cell strainer followed by a 40um cell strainer. The cells were pelleted in a cold centrifuge at 2,000 rpm and washed with cold PBS twice. We resuspended the pellet in 125uL of ATAC-Resuspension Buffer (RSB) containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin, and incubated on ice for 3 minutes. We washed the lysis with 5ml ATAC wash buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20) and counted nuclei using trypan blue (1:9). We kept 50K nuclei from each sample, and centrifuged at 500 RCF (10 minutes, 4C). Later samples were using an improved protocol that includes sorting: These samples were homogenized in Nuclei EZ lysis buffer (NUC-101, Sigma-Aldrich) as recommended in presence of 0.25U/ul RNAse inhibitor. Lysis was promoted by gentle mixing of homogenate using bore tips, followed by incubation for 5 minutes on ice and passing of homogenate through 70um cell strainer. Nuclei were then pelleted by centrifugation of the filtered homogenate at 500g for 5 minutes at 4 degrees. Nuclei was washed two times with 500ul Nuclei Wash and Resuspension Buffer (1x PBS, 1% BSA, 0.25ul RNAse) for 5 minutes on ice (first wash without resuspending nuclei, second wash with resuspending nuclei). After each wash, nuclei were pelleted by centrifugation at 500g for 5 minutes at 4 degrees. Pelleted nuclei were further resuspended in 100-500ul Nuclei Wash and Resuspension Buffer with DAPI (10ug/ml) and nuclei were sorted to eliminate cellular debris. Sorted nuclei were then pelleted at 500g for 5 minutes at 4 degrees and 500ul ATAC wash buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20) was gently added and incubated for 5 minutes on ice without resuspending nuclei. Washed nuclei were then pelleted by centrifugation at 500g for 5 minutes at 4 degrees and nuclei was gently resuspended in 500ul ATAC wash buffer and incubated for 5 minutes. Nuclei pellet was obtained by centrifugation at 500g for 5 minutes at 4 degrees and resuspended in 100ul 1x TD buffer (20034198, Illumina). About 10K nuclei was used for transposition reaction.
Nuclei were resuspended in 50ul transposition mixture, containing 2.5uL transposase in 1x TD buffer (20034198, Illumina) with 0.001% Digitonin and 0.01% Tween 20, and incubated for 30 minutes on a thermomixer at 1000RPM and 37C. DNA was extracted using MinElute Reaction Cleanup Kit (Qiagen).

value: Kidney (cortex)


title: WT minus apyrase

description: nascent RNA


title: ADC9009, 13A, S17


title: Sox9-GFP high, biological replicate 1


title: Batch1_Patient11600-15149_AB10_2

description:
AB10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube


title: Sensitive_05


title: Sensitive_06


title: WT A375 Cas9 Control 1

value: human melanoma cell line


title: Batch1_Patient11600-15149_AB10_1

description:
AB10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: T1-Unsort, S14


title: Sensitive_04


title: Batch1_Patient11600-15149_AB09_2

description:
AB09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Sox9-GFP low, biological replicate 1


title: Sensitive_03


title: Batch1_Patient11600-15149_AB09_1

description:
AB09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Sensitive_02


title: Sox9-GFP negative, biological replicate 1


title: T1-Sort, S13


title: GEX of Z3_F21_LN

city: Munich

first: Gildas

last: Lepennetier

address: Ismaninger Straße 22

institute: Klinikum Rechts der Isar

description: GEX

data_processing:
Cellranger-4.0.0 with vdj_GRCm38_alts_ensembl-4.0.0 for the VDJ B and T cell analysis, default options
Cellranger-5.0.0 with mm10-2020-A for the gene expression count, default options
Genome_build: mm10
Supplementary_files_format_and_content: count
Supplementary_files_format_and_content: contig_annotations.csv

source_name: LN lumbar

growth_protocol: Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 23±3 days after disease onset.

extract_protocol:
Blood was collected by cardiac puncture. After thorough perfusion with PBS lumbar lymph nodes, and spinal cord were dissected, and meninges were detached from the spinal cord using fine forceps. Organs were passed through cell strainers. Samples were enriched for CD45+ cells using a MACS (Miltenyi Biotech) with anti‐CD45 mouse MAb‐conjugated microbeads (Miltenyi Biotech, #130-052-301).
10x Genomics Chromium Single Cell Immune Profiling (v1)
10x Genomics single cell sequencing, without feature barcoding

treatment_protocol: mice were untreated

tag: Sex

value: male

tag: model

value: Thx2D2 EAE (experimental autoimmune encephalomyelitis)

value: Lumbar lymph node

tag: concentration (nm)

value: SI-GA-B4 (8nt)


title: GEX of Z3_F21_mELT

description: GEX

source_name: mELT from spinal cord

value: Meningeal Ectopic Lymphoid Tissue from spinal cord

tag: volume (ul)

tag: i7 index

value: SI-GA-B3 (8nt)


title: Batch1_Patient11600-15149_AB08_2

description:
AB08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Sensitive_01

value: Ovary

value: Ovarian cancer

value: Platinum sensitive patient


title: 10xspatial_GW17_05

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger-atac(v1.0)
Filtered count matrix was merged by Seurat R Package(v3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: human embryonic cerebellum

extract_protocol:
Fetal cerebellum tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF)
Chromium Single Cell ATAC Reagent Kits v1.0,Visium Spatial Gene Expression Slide & Reagent Kit

tag: gestational week

value: cerebellum

tag: tag


title: 10xspatial_GW17_04


title: Batch1_Patient11600-15149_AB08_1

description:
AB08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 10xspatial_GW17_02


title: GEX of Z3_E72_LN

description: GEX

value: SI-GA-B2 (8nt)


title: Batch1_Patient11600-15149_AB07_2

description:
AB07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GEX of Z3_E72_mELT

description: GEX

value: SI-GA-B1 (8nt)


title: Resistance_08

value: Platinum resistant patient


title: Resistance_09


title: Batch1_Patient11600-15149_AB06_2

description:
AB06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AB07_1

description:
AB07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 10xspatial_GW17_03


title: Batch1_Patient11600-15149_AB06_1

description:
AB06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Resistance_07


title: GEX of Z3_E21_LN

description: GEX

value: SI-GA-A6 (8nt)


title: 10xspatial_GW17_01


title: Resistance_06


title: GEX of Z3_E21_mELT

description: GEX

value: SI-GA-A5 (8nt)


title: 10xspatial_GW12_03


title: LPP1_input

value: ovary

tag: breed

value: Wuhua yellow-feathered chicken

tag: developmental stage

value: after sexual maturity


title: PE_H2BGFP_low_5

city: TOULOUSE

first: Vincent

last: Fregona

state: Terres australes françaises

address: 2 avenue hubert curien

country: France

institute: INSERM

data_processing:
Fastq was cleaned using Fastp.
Read alignment was performed on the mm10 assembly of the mouse genome using the genome mappers STAR in two pass mode.
Reads was counted with featurecounts
Normalization and differential expression of RNAseq data sets was performed by DeSeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw reads values for each Sample

source_name: Bone marrow B-cells

extract_protocol:
RNA was harvested using Quiagen Micro-kit.
RNA libraries for RNA-seq were prepared SMART-Seq® v4 Ultra® Low Input RNA Kit following manufacturer's protocols.

value: Bone marrow B-cells

value: PAX5-ELN H2B-GFP

value: Doxycycline

value: proliferating

tag: time

value: 35 days


title: Resistance_05

value: Ovary


title: Batch1_Patient11600-15149_AB05_2

description:
AB05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: PE_H2BGFP_low_4


title: 10xspatial_GW12_01


title: PE_H2BGFP_low_3


title: Batch1_Patient11600-15149_AC06_1

description:
AC06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 200 uM Sul 0 uM replicate 3

city: Daejeon

first: Yoosik

last: Kim

address: Daejeon

institute: KAIST

data_processing:
Basecalls performed using bcl2fastq
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with HISAT2 v2.1.0 using default parameters except with the option "--rna-strandness RF".
Only uniquely and concordantly mapped reads were then used in the further analyses.
featureCounts function of the Rsubread v2.4.2 R package was used by employing transcriptome information from the GENCODE v27 to assign and summarize reads to genomic features.
DESeq2 v.1.30.1 R package analyzed the differentially expressed genes with the summarized raw read counts for each gene.
ViSEAGO v1.4.0 was used to cluster biological functions using Gene Ontology and semantic similarity analysis.
GSEA v4.1.0 was performed using gene sets from Molecular Signatures Database (MSigDB) v7.4
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: res_comp.csv: csv of DESeq2 output containing log2 fold change upon ammonium nitrate and sulfate treatment
Supplementary_files_format_and_content: comp_GO.csv: csv of ViSEAGO output

extract_protocol:
Total RNA was extracted using the Trizol reagent
2x101 paired-end RNA-seq library was constructed using TruSeq stranded mRNA LT sample prep kit and sequenced using the Illumina NovaSeq 6000 platform.

value: Ammonium nitrate 0 uM sulfate 200 uM


title: Batch1_Patient11600-15149_AB05_1

description:
AB05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Resistance_03

value: Ovarian cancer


title: A549 comp Nit 200 uM Sul 0 uM replicate 2


title: PE_H2BGFP_low_2


title: Batch1_Patient11600-15149_AB04_2

description:
AB04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 200 uM Sul 0 uM replicate 1


title: PE_H2BGFP_low_1


title: Normal_08

value: Normal ovary


title: Batch1_Patient11600-15149_AB03_2

description:
AB03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AB03_1

description:
AB03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AB02_2

description:
AB02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PE_H2BGFP_high_4

value: quiescent


title: 10xspatial_GW12_02

value: cerebellum


title: PE_H2BGFP_high_5


title: A549 comp Nit 150 uM Sul 50 uM replicate 3

value: Ammonium nitrate 150 uM sulfate 50 uM


title: A549 comp Nit 150 uM Sul 50 uM replicate 2


title: Normal_07


title: Normal_05


title: A549 comp Nit 150 uM Sul 50 uM replicate 1


title: PE_H2BGFP_high_3


title: Normal_06


title: Batch1_Patient11600-15149_AB02_1

description:
AB02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Resistance_04

value: Platinum resistant patient


title: A549 comp Nit 100 uM Sul 100 uM replicate 3

value: Ammonium nitrate 100 uM sulfate 100 uM


title: Batch1_Patient11600-15149_AB01_2

description:
AB01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PE_H2BGFP_high_1


title: Normal_02


title: PE_H2BGFP_high_2


title: Batch1_Patient11600-15149_AB01_1

description:
AB01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Resistance_01


title: Batch1_Patient11600-15149_AB04_1

description:
AB04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 100 uM Sul 100 uM replicate 1


title: A549 comp Nit 50 uM Sul 150 uM replicate 3

value: Ammonium nitrate 50 uM sulfate 150 uM


title: WT_CTV_low_2

growth_protocol: B-cell progenitors was maintained in co-culture of MS5 in medium composed of IMDM 5% FBS with penicilin-streptavidin, L-glutamine and Beta-mercaptoethanol. Cytokine was added in the medium : Il7  (5ng/ml), SCF (10ng/ml) and Flt3 (10ng/ml).

extract_protocol:
RNA was harvested using Quiagen Micro-kit.
RNA libraries for RNA-seq were prepared using Trueseq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: After purification of total bone marrow cells with column Cd19+, the cells was treated by CTV and cell sort after overnight resting.

value: WT

value: Cell trace violet

value: 3 days in vitro


title: Batch1_Patient11600-15149_AA12_2

description:
AA12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: WT_CTV_low_1

value: Bone marrow B-cells


title: PE_CTV_low_2

value: proliferating


title: Batch1_Patient11600-15149_AA12_1

description:
AA12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 50 uM Sul 150 uM replicate 2


title: Batch1_Patient11600-15149_AA11_2

description:
AA11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 50 uM Sul 150 uM replicate 1


title: Normal_03


title: PE_CTV_low_1


title: A549 comp Nit 0 uM Sul 200 uM replicate 2


title: Batch1_Patient11600-15149_AA11_1

description:
AA11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 comp Nit 100 uM Sul 100 uM replicate 2


title: A549 comp Nit 0 uM Sul 200 uM replicate 3


title: Normal_01


title: Batch1_Patient11600-15149_AA10_2

description:
AA10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PE_CTV_high_2


title: Batch1_Patient11600-15149_AA10_1

description:
AA10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PE_CTV_high_1


title: HV4_KU55_2: Huvec Isolate #4 - KU55933 (R2)

city: San Antonio

first: Henry

last: Miller

state: TX

address: 8403 Floyd Curl Drive

department: Cell Systems and Anatomy

institute: UT Health San Antonio

description: Cell Isolate: Huvec Isolate #4, Treatment: KU55933, Replicate: R2

data_processing:
Fastq files were trimmed and filtered automatically using fastp v0.20.0  with default settings
Filtered reads were mapped to the Gencode v30 hg38 transcriptome and quantified using Salmon v0.14.1 with the following settings: -l A --validateMappings --gcBias
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix was generated using the tximport R package to summarize transcript-level counts to the gene level. Matrix contains counts for each gene (rows) by sample (column). First column contains gene symbol, and first row contains sample name.

source_name: Human umbilical vein endothelial cells

growth_protocol: Medium 199 (Earle’s Salts, GIBCOTM) supplemented with 1mM sodium pyruvate, 1.82mM glutamine, 10mM HEPES, 2% LSGS, 8% FBS and 1% PS (to keep physiologically relevant glucose and glutamine levels, 5.5mM and 2mM respectively). 16-20h before experiments, cells were washed twice with HBSS (Corning) and media changed to low serum (2% LSGS only). HUVECs were kept at 3% Oxygen and 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented using divalent cautions under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final RNA-seq library. After RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequent 50bp single read sequencing run with Illumina HiSeq 3000 platform.

treatment_protocol: Cells were treated with either 5uM KU60019, 10uM KU55933, or vehicle (DMSO) for 8 hours.

value: Human umbilical vein endothelial cells

tag: cell isolate

value: Huvec Isolate #4

tag: replicate


title: HV4_KU60_1: Huvec Isolate #4 - KU60019 (R1)

description: Cell Isolate: Huvec Isolate #4, Treatment: KU60019, Replicate: R1


title: HV4_KU60_2: Huvec Isolate #4 - KU60019 (R2)

description: Cell Isolate: Huvec Isolate #4, Treatment: KU60019, Replicate: R2


title: HV4_KU60_3: Huvec Isolate #4 - KU60019 (R3)

description: Cell Isolate: Huvec Isolate #4, Treatment: KU60019, Replicate: R3


title: A549 comp Nit 0 uM Sul 200 uM replicate 1


title: Batch1_Patient11600-15149_AA09_2

description:
AA09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

growth_protocol: Fallopian tube WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

value: Fallopian tube


title: HV4_KU55_1: Huvec Isolate #4 - KU55933 (R1)

description: Cell Isolate: Huvec Isolate #4, Treatment: KU55933, Replicate: R1


title: Atac_PE_H2BGFP_low_3

data_processing:
ATAC-seq reads were trimmed (qualilty threshold >20 and lenght >20) using Sickle
ATAC-seq reads were aligned to the mm10 genome using Bowtie2 (paired-end, maxsize of 2000, -fr, and very sensitive local parameters).
ATAC-seq BAMs was cleaned for mtc, duplicated, unmmated and low-quality mapped reads.
ATAC-seq BAMs was cleaned of backlisted regions reads using Samtools.
ATAC-seq reads was shifted using Alignmentsieve (-4 -5).
ATAC-seq reads was corrected for their GC biais using computeGCbiais and CorrectGCBiais.
Peaks calling was performed using MACS2 (SE, 200, 100, lambdafix).
Normalization and differential expression ofATAC-seq data sets was performed by DiffTF
Assembly: mm10

source_name: Primary sample

extract_protocol:
Cells were lysed and prepared following ATAC-seq kit (Active motif) recommandations
ATAC-seq libraries were prepared using theATAC-seq Kit. Libraries were validated using the Agilent High Sensitivity DNA Kit. 2 independant run of sequencing was used for each sample to increase the depth.

tag: cell line

value: Primary sample

tag: phenotype


title: A549 comp NC replicate 3

tag: treatment

value: Media


title: Atac_PE_H2BGFP_low_2

tag: cell type


title: HV4_CTR_3: Huvec Isolate #4 - DMSO (R3)

description: Cell Isolate: Huvec Isolate #4, Treatment: DMSO, Replicate: R3

tag: tissue

value: DMSO


title: A549 comp NC replicate 2


title: Atac_PE_H2BGFP_low_1


title: Batch1_Patient11600-15149_AA08_2

description:
AA08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2


title: A549 comp NC replicate 1


title: HV4_KU55_3: Huvec Isolate #4 - KU55933 (R3)

description: Cell Isolate: Huvec Isolate #4, Treatment: KU55933, Replicate: R3


title: HV4_CTR_1: Huvec Isolate #4 - DMSO (R1)

description: Cell Isolate: Huvec Isolate #4, Treatment: DMSO, Replicate: R1


title: Atac_PE_H2BGFP_high_3

value: quiescent


title: A549 Mix moderate 100 uM replicate 2

data_processing:
Basecalls performed using bcl2fastq
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with HISAT2 v2.1.0 using default parameters except with the option "--rna-strandness RF".
Only uniquely and concordantly mapped reads were then used in the further analyses.
featureCounts function of the Rsubread v2.4.2 R package was used by employing transcriptome information from the GENCODE v27 to assign and summarize reads to genomic features.
DESeq2 v.1.30.1 R package analyzed the differentially expressed genes with the summarized raw read counts for each gene.
ViSEAGO v1.4.0 was used to cluster biological functions using Gene Ontology and semantic similarity analysis.
GSEA v4.1.0 was performed using gene sets from Molecular Signatures Database (MSigDB) v7.4
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: csv of DESeq2 output containing log2 fold change upon ammonium nitrate and sulfate treatment

value: Ammonium nitrate/sulfate 100 uM


title: Batch1_Patient11600-15149_AA08_1

description:
AA08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HV4_CTR_2: Huvec Isolate #4 - DMSO (R2)

description: Cell Isolate: Huvec Isolate #4, Treatment: DMSO, Replicate: R2


title: Batch1_Patient11600-15149_AA07_2

description:
AA07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 Mix moderate 100 uM replicate 1


title: Atac_PE_H2BGFP_high_2


title: HV1_KU60_2: Huvec Isolate #1 - KU60019 (R2)

description: Cell Isolate: Huvec Isolate #1, Treatment: KU60019, Replicate: R2

value: Huvec Isolate #1


title: Batch1_Patient11600-15149_AA07_1

description:
AA07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 Mix moderate 10 uM replicate 2

value: Ammonium nitrate/sulfate 10 uM


title: HV1_KU60_3: Huvec Isolate #1 - KU60019 (R3)

description: Cell Isolate: Huvec Isolate #1, Treatment: KU60019, Replicate: R3


title: Atac_PE_H2BGFP_high_1


title: Batch1_Patient11600-15149_AA06_2

description:
AA06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HV1_KU60_1: Huvec Isolate #1 - KU60019 (R1)

description: Cell Isolate: Huvec Isolate #1, Treatment: KU60019, Replicate: R1


title: A549 Mix moderate 1 uM replicate 2

value: Ammonium nitrate/sulfate 1 uM


title: Batch1_Patient11600-15149_AA06_1

description:
AA06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: HV1_CTR_3: Huvec Isolate #1 - DMSO (R3)

description: Cell Isolate: Huvec Isolate #1, Treatment: DMSO, Replicate: R3


title: A549 Mix moderate 10 uM replicate 1


title: Batch1_Patient11600-15149_AA09_1

description:
AA09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: intracolorectal and intrahepatic injection - Low ME-score

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

description: Single-cell RNA

data_processing:
The Cell Ranger output of single-cell RNA sequencing data were analyzed using Seurat in R-program (https://satijalab.org/seurat/).
Genome_build: mm10
Supplementary_files_format_and_content: Archive with barcodes, features and matrix of each sample

source_name: Liver metastases

growth_protocol: 250 000 MC38-luciferase (luc) expressing cells (colorectal (CRC) tumor cell line, from c57Black/6 mice background, that express luciferase reporter gene for in vivo tumor growth monitoring) were injected intra-hepatic (IH) in the liver of B6 mice (by microsurgery procedure). Only IH implantation were performed in the mice (group IH alone) or they were performed concomitantly with intra-colon(IC) injection of 500 000 MC38 (parental) cells (by microsurgery procedure) (group IH+IC). At day 10, IH tumors were harvested and an immune-score (or MicroEnvironment (ME)-score; % CD8+ T cells*% dendritic cells/ % macrophages infiltrating IH tumors) was determined by flow cytometry analyses. Than IH tumor samples were segregated depending on their low, intermediate or high ME-score and 7 low ME-score tumors were pooled, 7 intermediate ME-score were pooled and 7 low ME-score were pooled for scRNA-seq analyses.

extract_protocol:
CD45+ cells were enriched by positive selection from tumor cell suspension by magnetic cell sorting.
3’ gene expression single-cell libraries were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 3′ Kit v3 and Dual Index TT Set A, according to the manufacturer’s instructions starting with 16500 cells per sample pool. Library size and quality were confirmed on Fragment analyzer. KAPA quantification kit for Illumina platforms was used to quantify libraries. Samples were pooled in equimolar fashion. The libraries were sequenced on a NextSeq 550 in pair end sequencing 28 bp (read1) x 90 bp (read2) and dual index 10 bp.

value: Liver metastases

value: day 10 of in vivo tumor development

tag: microenvironment (me)-score

value: Low ME-score


title: A549 Mix moderate 1 uM replicate 1


title: HV1_CTR_2: Huvec Isolate #1 - DMSO (R2)

description: Cell Isolate: Huvec Isolate #1, Treatment: DMSO, Replicate: R2