title: Sp140 KO Bystander and naïve cells, HTO-derived cDNA [RVDK002I]

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Raw sequencing reads for the mRNA libraries were processed into raw count matrices with CellRanger version 4.0.0 (10X Genomics). The ADT and HTO libraries were processed into raw count matrices with CITE-Seq-Count version 1.4.3.
The raw counts for mRNA, ADT, and HTO were analyzed using Seurat v4.1.1 using default settings for normalizing the data, finding variable features, and scaling the data. HTO demultiplexing was performed with the HTODemux function. Data was filtered to only include single cells with between 200 and 4500 genes and less than 5% mitochondrial reads. The resulting datasets were integrated together using 30 dimensions for the FindIntegrationAnchors function and 30 dimensions for the IntegrateData function. The data was then scaled and analyzed by PCA with 30 principal components followed by UMAP analysis with 30 dimensions. Clustering was performed by using 30 dimensions with the FindNeighbors function and a resolution of 0.8 for the FindClusters function.
To improve resolution for clustering innate immune cells, weighted nearest neighbor analysis was used to combine the protein data (ADTs) and the mRNA data when clustering cells. For this analysis, variable ADT features were identified and then normalized using centered log ratio transformation and a margin of 2. The normalized ADT data was then scaled and analyzed by PCA. The ADT and mRNA data was then combined with the FindMultiModalNeighbors function using 30 dimensions for the mRNA and 10 for the protein. The resulting dataset was analyzed by UMAP and clusters were identified with the FindClusters function using algorithm 3 and a resolution of 1.5.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Lung

extract_protocol:
FACS isolated cells were pooled and loaded into 3 different lanes on a Chromium Next GEM Chip. Lane 1 was loaded with Mtb-infected cells from all 3 B6 and 3 Sp140–/– lungs. Lane 2 was loaded with bystander myeloid cells from the 3 infected B6 lungs as well as the myeloid cell mixture from the 2 naïve B6 lungs. Lane 3 was loaded with bystander myeloid cells from the 3 infected Sp140–/– lungs as well as the myeloid cell mixture from the 2 naïve Sp140–/– lungs. All 3 lanes of the Chromium Next GEM Chip were super-loaded with 29000 cells with a target of 14800 single cells per lane,
The scRNA-sequencing libraries were generated using the v3.1 chemistry Chromium Single Cell 3’ Reagent Kit (10X Genomics) largely following this kits protocol and the CITE-seq protocol. 0.5 U/µL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen) was added to single cell RT master mix during the loading step and 1 µL of ADT and HTO additive primers (0.2 µM stock) were added during the cDNA amplification. Following cDNA, ADT, and HTO purification, samples were decontaminated by 2 rounds of centrifugation through 0.2 µM filter microcentrifuge tubes and then removed from the BSL3. Library preparations were completed outside of the BSL3 following the 10X Genomics protocol for the cDNA and the CITE-seq and Cell Hashing Protocol for the ADT and HTO libraries. Quality control of the libraries was performed with a Fragment Analyzer (Agilent). The mRNA, ADT, and HTO libraries were pooled at the following proportions: 85% mRNA, 9% ADT, and 6% HTO. Libraries were sequenced on a NovaSeq 6000 (Illumina) using two lanes of a S1 flow cell and the following cycles read 1 (28 cycles), i7 index (10 cycles), i5 index (10 cycles), read 2 (90 cycles).

value: Lung

value: myeloid cells

value: Mtb infected and naïve

value: Sp140 KO

tag: library type

value: HTO

tag: antibodies

value: Anti CD45 + Anti MHC classI :infected mice bystander--/TotalSeq-A0301 ; infected mice bystander--/TotalSeq-A0302 ; infected mice bystander--/TotalSeq-A0303 ; naive--/TotalSeq-A0304; naive--/TotalSeq-A0305;


title: DLD1 E545K only drug combination 1

status: Public on Jan 12 2024

type: SRA

city: cleveland heights

first: ZHENGHE

last: WANG

state: Ohio

address: 2103 CORNELL Road, WRB 3203

country: USA

institute: CASE WESTERN RESERVE UNIVERSITY

library_source: transcriptomic

data_processing:
Quality control was performed using FastQC
Read alignment was performed using HISAT2 (default parameters), mapping to the GRCh38/hg38 reference
Transcript Assembly and Abundance Quantification were performed using Stringtie (default parameteres)
FPKM Normalization was performed using Ballgown
Assembly: hg38
Supplementary files format and content: GTF files include raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes FPKM values for all Sample

molecule: total RNA

organism: Homo sapiens

source_name: colon

growth_protocol: DLD1 isogenic cells were maintained in DMEM/F12(1:1) with 10% FBS and antibiotic in 5% CO2 incubator

extract_protocol:
total RNA were extracted by Rnaesy mini kit (Qiagen)
RNA library were prepared using SMARTER mRNAseq

treatment_protocol: cells in 6 well plates treated with either DMSO or drug combination (5 μM CB839 plus 5 μM 5FU) for 16 hour

tag: tissue

value: colon

tag: cell line

tag: cell type

value: colon cancer cells

tag: genotype

value: PIK3CA E545K

tag: treatment

value: 5 μM CB839 plus 5 μM 5FU


title: DLD1 E545K only vehicle 1

value: DMSO


title: B6 and Sp140 KO Mtb infected cells, HTO-derived cDNA [RVDK002G]

city: Berkeley

first: Dmitri

middle: I

last: Kotov

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

organism: Mus musculus

value: Mtb infected

value: C57BL/6 and Sp140 KO

value: Anti CD45 + Anti MHC classI :B6--/TotalSeq-A0301 ; B6--/TotalSeq-A0302 ; B6--/TotalSeq-A0303 ; Sp140--/TotalSeq-A0304; Sp140--/TotalSeq-A0305; Sp140--/TotalSeq-A0306


title: Stool sRNA-Seq - Patient 24 T0

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Stool

extract_protocol:
Stool RNA was extracted from 200µl aliquots using stool total RNA purification kit (Norgen Biotek Corp.) following manufacturer’s protocol. RNA quality and quantity were verified following the MIQE guidelines (http://miqe.gene-quantification.info/). The RNA concentration was quantified with the Qubit microRNA assay kit (Invitrogen). The DNA was extracted with the DNeasy PowerSoil Pro Kit (Qiagen) following manufacturer's instructions with a higher final elution buffer volume (50µl) to increase DNA concentration which was quantified with Qubit DNA high sensitivity assay kit (Invitrogen).
Small RNA (sRNA) transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA).

value: Stool

tag: age

tag: Sex

value: F

tag: time

value: Time 0


title: phHep-derived iCCA_7

city: San Francisco

first: Cindy

middle: K

last: Pino

address: 400 Parnassus Ave.

institute: University of California, San Francisco

data_processing:
Sequencing reads were separated into human and mouse FASTQ files using xengsort v1.0.2 (https://gitlab.com/genomeinformatics/xengsort)
Ensembl Homo_sapiens.GRCh38.96 and Mus_musculus.GRCm38.96 were used as reference genomes
Mouse reads were discarded without further processing.
Human reads from tumors forming in mice and reads from patient-derived tumors were aligned to GRCh38.96 and reads per gene matrix were counted with the latest Ensembl annotation build using STAR_2.7.2b.
Read counts per gene were used as input to DESeq2
Assembly: Homo sapiens.GRCh38.96
Supplementary files format and content: tab-delimited text files include raw count matrix  for each Sample

source_name: Liver tumor

extract_protocol:
Quick-RNA FFPE Miniprep Kit (Zymo Research)
RNA sequencing was performed by BGI using a workflow optimized for FFPE samples

treatment_protocol: phHep-derived tumors were generated using different combinations of lentiviral vectors expressing simian virus 40 large T and small t antigens (SV40Tt), Harvey rat sarcoma viral oncogene homolog (HRAS) and human telomerase catalytic subunit (TERT). Because SV40T inhibits RB and TP53, patient-derived iCCAs with CDKN2A mutations or MDM2 amplifications were selected, including some with additional KRAS or NRAS mutations, and HCCs with TP53 mutations. All samples were fixed in formalin and embedded in paraffin (FFPE). Some mice were fed fed 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet to induce cholestasis.

value: Liver tumor

value: SV40Tt, TERT


title: Patient-derived HCC_G


title: Patient-derived iCCA_I

value: TP53, BRCA1


title: Stool sRNA-Seq - Patient 23 T2

value: Time 2


title: DLD1 E545K only drug combination 3


title: Patient-derived HCC_H

value: PIK3CA, TP53


title: DLD1 WT only drug combination 3

value: PIK3CA WT


title: Sp140 KO Bystander and naïve cells, ADT-derived cDNA [RVDK002F]

description: Antibody-derived oligonucleotide (ADT)

value: Lung

value: myeloid cells

value: Mtb infected and naïve

value: Sp140 KO

value: ADT

value: anti-Ly-6C (TotalSeq-A0013); CD44 (TotalSeq-A0073); Siglec F (TotalSeq-A0431); PD-L1 (TotalSeq-A0190); CD169 (TotalSeq-A0440); CSF-1R (TotalSeq-A0105); Ly-6G (TotalSeq-A0015); CD11b (TotalSeq-A0014); CD86 (TotalSeq-A0200); I-A/I-E (TotalSeq-A0117); CX3CR1 (TotalSeq-A0563)


title: B6 Bystander and naïve cells, mRNA-derived cDNA [RVDK002B]

description: polyA RNA

molecule: polyA RNA

value: mRNA


title: Stool sRNA-Seq - Patient 24 T2


title: Stool sRNA-Seq - Patient 24 T1

value: Time 1


title: phHep-derived iCCA_8


title: DLD1 E545K only vehicle 3

value: colon

value: colon cancer cells

value: PIK3CA E545K

value: DMSO


title: Patient-derived iCCA_J

value: Liver tumor

value: CDKN2A, BAP1


title: phHep-derived iCCA_9

value: SV40Tt, TERT


title: B6 Bystander and naïve cells, ADT-derived cDNA [RVDK002E]

description: Antibody-derived oligonucleotide (ADT)


title: Stool sRNA-Seq - Patient 22 T2

value: Stool

value: F

value: Time 2


title: B6 and Sp140 KO Mtb infected cells, ADT-derived cDNA [RVDK002D]

description: Antibody-derived oligonucleotide (ADT)

value: Lung

value: myeloid cells

value: Mtb infected

value: C57BL/6 and Sp140 KO


title: DLD1 E545K only drug combination 2

value: 5 μM CB839 plus 5 μM 5FU


title: B6 Bystander and naïve cells, HTO-derived cDNA [RVDK002H]

description: Hashtag-derived oligonucleotide (HTO)

value: Mtb infected and naïve

value: HTO

value: Anti CD45 + Anti MHC classI :naive--/TotalSeq-A0301 ; naive--/TotalSeq-A0302 ;  infected mice bystander--/TotalSeq-A0304 ; infected mice bystander--/TotalSeq-A0305; infected mice bystander--/TotalSeq-A0306


title: Stool sRNA-Seq - Patient 23 T1

value: Time 1


title: Sp140 KO Bystander and naïve cells, mRNA-derived cDNA [RVDK002C]

description: polyA RNA

value: Sp140 KO

value: mRNA


title: Stool sRNA-Seq - Patient 23 T0

value: Time 0


title: Stool sRNA-Seq - Patient 25 T0


title: DLD1 WT only vehicle 4

value: colon

value: colon cancer cells

value: PIK3CA WT

value: DMSO


title: DLD1 E545K only vehicle 2

value: PIK3CA E545K


title: DLD1 WT only drug combination 2


title: Patient-derived iCCA_K

value: Liver tumor

value: BRAF


title: B6 and Sp140 KO Mtb infected cells, mRNA-derived cDNA [RVDK002A]

description: polyA RNA

value: Lung

value: myeloid cells

value: Mtb infected


title: Stool sRNA-Seq - Patient 22 T1

value: Stool

value: F


title: Stool sRNA-Seq - Patient 22 T0


title: DLD1 WT only vehicle 3


title: phHep-derived iCCA_10

value: SV40Tt, TERT

value: DDC


title: Stool sRNA-Seq - Patient 21 T2

value: M

value: Time 2


title: Stool sRNA-Seq - Patient 21 T1

value: Time 1


title: DLD1 WT only vehicle 1

value: colon


title: Patient-derived iCCA_N


title: phHep-derived iCCA_11


title: RNA-Seq SAP-30 Healthy T2

data_processing:
RNA-seq data were preprocessed using FastP (v.0.21) in default settings.
Read alignments Gencode v36 annotations was performed using Salmon (v.1.4) with options seqBias and gcBias to correct for hexamer priming and GC biases, respectively.
Read counts were normalized in transcripts per million (TPM) with the txImport R package (v.1.22) and paired differential expression analysis was performed with the DESeq2 package (v.1.28.1) using the Wald test.
Assembly: hg38
Supplementary files format and content: Matrix tables with the raw and TPM-normalized gene expression levels

source_name: Healthy mucosa

extract_protocol:
Total RNA was extracted from FFPE sections using MaxwellⓇ RSC RNA FFPE Kit (Promega, Japan). NA yields were determined by UV absorption on a NanoDrop 1000 spectrophotometer. RNA quality was evaluated using the Eukaryote Total RNA Nano assay on the 2100 Bioanalyzer, and the percentage of fragments longer than 200 nucleotides was determined with Agilent 2100 Expert Software.
Total RNA libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina Inc.). Library size and quality were assessed on the 2100 Bioanalyzer with a High Sensitivity DNA Chip, and individual library concentration with a High Sensitivity (HS) Assay on a Qubit 4 fluorometer. Libraries were pooled at 1.4nM and sequenced on NovaSeq6000 (Illumina Inc), on a S2 v1.5 flow cell, using the XP protocol with 1% PhiX (paired end, 100bp reads)

tag: individual

value: Healthy mucosa


title: RNA-Seq SAP-30 Healthy T0


title: DLD1 WT only vehicle 2

value: colon cancer cells

value: PIK3CA WT


title: Stool sRNA-Seq - Patient 21 T0

value: Time 0


title: phHep-derived iCCA_12

value: Liver tumor


title: Stool sRNA-Seq - Patient 20 T2


title: RNA-Seq SAP-30 Adenoma T0

source_name: Adenoma

value: Adenoma


title: Stool sRNA-Seq - Patient 20 T1


title: Patient-derived iCCA_O

value: NRAS, AKT3, ARID1A


title: Patient-derived iCCA_M

value: FRS2, PIK3CA, MDM2, ARID1A


title: DLD1 WT only drug combination 1

value: 5 μM CB839 plus 5 μM 5FU


title: Patient-derived iCCA_L

value: FRS2, MDM2, ARID2


title: Stool sRNA-Seq - Patient 20 T0

value: Stool

value: F


title: RNA-Seq SAP-10 Adenoma T2


title: Stool sRNA-Seq - Patient 19 T2


title: RNA-Seq SAP-10 Adenoma T0


title: RNA-Seq SAP-09 Adenoma T2


title: scrambled-injected mouse 10

type: RNA

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

hyb_protocol: Total RNA (130 ng) was added to a custom nCounter™ Elements TagSet in hybridization buffer and incubated for 20 hours at 67oC.

scan_protocol: The samples were processed on the nCounter™ Preparation Station and the cartridge scanned at 555 fields of view (high density) on the nCounter™ Digital Analyser (Nanostring Technologies). After background removal (based on the geometric mean of negative controls), raw counts were subjected to technical normalization to the geometric mean of counts obtained for positive control probe set within each sample.

data_processing: After removal of one outlier sample from the i-mir-709 group, results were analyzed using the nSolver 4.0 and nSolver Advanced Analysis Software v2.5 (NanoString Technologies). Ten housekeeping genes were included in the CodeSet: Cnot10, Aars, Lars, Asb7, Mto1, Ccdc127, Supt7l, Fam104a, Tada2b and Csnk2a2, selected from the standard housekeeping genes that are used in nCounter™ Neuropathology panels (Nanostring Technologies). Following evaluation of housekeeping gene stability with geNorm, the expression levels for each probe within a sample were scaled using the geometric mean of seven out of the ten housekeeping genes (Cnot10, Aars, Lars, Asb7, Mto1, Ccdc127, Supt7l). The fold change of signal intensity was derived by comparing the normalized means between the i-miR-709 group and the scrambled group

label: biotin

source_name: cortex

label_protocol: Followed NanoString nCounter gene expression assay protocol, using a Capture probe-3'biotin and a Reporter probe-5' barcode signal.

extract_protocol: At the day of the experiment, they were homogenized in QIAzol Lysis Reagent (Qiagen), using a tissue disruptor. RNA was extracted and purified using the RNEasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer guidelines. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific). RNA integrity was assessed by Qubit RNA HS Assay Kit (ThermoFisher Scientific).

treatment_protocol: Cortical tissues dissected from i-miR-709 and scrambled-ICV-injected mice (n=5 for each group) were snap frozen and stored in -80oC.

value: scrambled-injected

value: Cortical tissues


title: scrambled-injected mouse 09


title: scrambled-injected mouse 03


title: Stool sRNA-Seq - Patient 19 T1

value: M


title: 12_KCR007

city: Ottawa

first: Kristin

middle: L

last: Connor

state: Ontario

address: 1125 Colonel By Drive

country: Canada

institute: Carleton University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw expression files (.CEL files) were processed in Transcription Analysis Console software (version 4.0.2). Data were summarised using the signal space transformation algorithm and normalised using the robust multiple-array average method.

source_name: Whole placental homogenates

label_protocol: RNA was labelled using the GeneChip® WT Pico Labelling Kit.

extract_protocol: RNA was extracted from whole placental homogenates using the Qiagen RNeasy Plus Mini Kit (Qiagen, Toronto, Canada) according to the manufacturer’s protocol.

tag: study group

value: Control

value: fetus with no congenital anomalies


title: 17_KCR010


title: RNA-Seq SAP-09 Adenoma T0


title: Stool sRNA-Seq - Patient 18 T2

value: Time 2


title: 23_KCR011


title: scrambled-injected mouse 06


title: 9_KCR004


title: 15_KCR009


title: 11_KCR006


title: RNA-Seq SAP-28 Adenoma T2


title: 4_KCR002


title: 6_KCR003


title: Stool sRNA-Seq - Patient 19 T0


title: Stool sRNA-Seq - Patient 18 T1

value: Time 1


title: RNA-Seq SAP-28 Adenoma T0


title: RNA-Seq SAP-28 Healthy T2

value: Healthy mucosa


title: Stool sRNA-Seq - Patient 18 T0

value: Time 0


title: RNA-Seq SAP-25 Healthy T0


title: 2_KCR001


title: scrambled-injected mouse 01


title: miR-709-inhibitor injected mouse 07

value: i-miR-709 injected


title: miR-709-inhibitor injected mouse 05


title: 22952_KCR035D02D02

value: PT control


title: RNA-Seq SAP-25 Adenoma T0

value: Adenoma


title: Stool sRNA-Seq - Patient 17 T1


title: 21267_KCR032A02A02


title: miR-709-inhibitor injected mouse 04


title: 18520_KCR034C02C02


title: ABP278

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
Eightyfive-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0. Reads were aligned to the pig genome (Sus_scrofa_11.fa from the UCSC Genome Browser) with TopHat2 using Bowtie and Samtools, allowing 3 mismatches and 20 multihits. The REFseq gene annotation for Sus scrofa (susScr11.refGene.gtf) was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 10 in at least 25% of the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: Sus scrofa 11
Supplementary files format and content: A tab-delimited text file that includes normalized counts for each Sample

organism: Sus scrofa

source_name: Liver

extract_protocol:
RNA was extracted using Rneasy Mini kit (QIAGEN)
Total RNA samples (500ng; RQS/RIN average 7.4, range 6.9-7.8) were processed with the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR. This kit generates directional libraries stranded in the sense orientation, the read1 (the only read in single read format) has the sense orientation. cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols.

value: Liver

value: TPN


title: Stool sRNA-Seq - Patient 17 T2


title: miR-709-inhibitor injected mouse 02


title: Stool sRNA-Seq - Patient 17 T0


title: RNA-Seq SAP-23 Healthy T2


title: 17667_KCR030G01G01


title: RNA-Seq SAP-23 Adenoma T2


title: Stool sRNA-Seq - Patient 15 T1


title: 17433_KCR033B02B02


title: ABP277


title: 11999_KCR029F01F01


title: RNA-Seq SAP-23 Healthy T0


title: ABP276


title: ABP275


title: RNA-Seq SAP-21 Healthy T2


title: Stool sRNA-Seq - Patient 15 T0


title: Stool sRNA-Seq - Patient 14 T2


title: 11499_KCR027D01D01


title: ABP274


title: 11847_KCR028E01E01


title: Stool sRNA-Seq - Patient 15 T2


title: ABP272

value: milk


title: Stool sRNA-Seq - Patient 14 T1

value: Stool


title: RNA-Seq SAP-21 Adenoma T2


title: RNA-Seq SAP-21 Healthy T0


title: ABP271


title: RNA-Seq SAP-19 Adenoma T2


title: Stool sRNA-Seq - Patient 13 T2

value: F


title: ABP269


title: RNA-Seq SAP-19 Healthy T2


title: 11055_KCR025B01B01


title: Stool sRNA-Seq - Patient 13 T1


title: 10736_KCR024A01A01


title: 11261_KCR026C01C01


title: RNA-Seq SAP-19 Healthy T0


title: ABP268


title: Stool sRNA-Seq - Patient 14 T0


title: ABP267


title: RNA-Seq SAP-15 Healthy T2


title: 49_KCR023

value: Case

value: fetus with spina bifida


title: RNA-Seq SAP-15 Healthy T0

value: M


title: Stool sRNA-Seq - Patient 11 T2


title: Stool sRNA-Seq - Patient 11 T1


title: 48_KCR022


title: HK3 [scRNA-seq]

city: Ås

first: Adriana Magalhaes

middle: Santos

last: Andresen

state: Other

address: Elizabeth Stephansens v. 1

country: Norway

institute: Veterinærinstituttet

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, mapping of the raw reads and quatification of per-cell gene expression were done using STARsolo (2.7.10a). Cellbender was used for infer and remove ambient RNA. Seurat (4.1.0) was used for downstream analysis and scDblFinder (1.14.0) used to find and exclude doublets.
Assembly: Ssal_v3.1; GCA_905237065.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Salmo salar

source_name: head kidney

extract_protocol:
ScRNA-seq: Head kidney was sampled and placed in L15 (Leibovitz-15 + 5% FBS + 4 mM L-glutamine + 1% penicillin/streptomycin/amphotericin) and kept on ice. Head kidney tissue was passed through strainer (70 µm) in 10 mL PBS. Cell suspension filtered through a 30-µm strainer and centrifuged. Cells collected from the interface after Percoll gradient were washed and prepared in DPBS with BSA for subsequent sequencing.
SnRNA-seq: Flash frozen head kidney tissue was minced in 1 mL TST buffer (2 mL of 2X ST buffer, 120 µL of 1% Tween, 20 µL of 2% BSA, 1.86 mL nuclease-free water). The homogenate was filtered through a 40-µm cell strainer and 3 mL of 1X ST solution (2X ST buffer [146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 21 mM MgCl2, brought up to 10 mL with nuclease-free water]) was added. The samples were ready for sequencing after centrifugation, re-suspension in 1X ST buffer and filtration.
Single Cell 3′ Reagent Kit v3.1 from 10X Genomics

value: head kidney


title: 45_KCR021


title: 9693_KCR031H01H01

value: fetus with no congenital anomalies


title: RNA-Seq SAP-15 Adenoma T0


title: Stool sRNA-Seq - Patient 11 T0


title: HK5 [scRNA-seq]

description: 10x Genomics


title: Endochondral bone, E18.5, scRNAseq

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

description: 10x Genomics

data_processing:
Alignment, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: forelimb long bones (humerus, radius, ulna)

extract_protocol:
Forelimb long bones (humerus, radius and ulna) were dissected from fetuses at embryonic day E18.5 and pups at postnatal day 1 and carefully cleaned of surrounding tissue.  Cell suspensions for sorting were prepared according to Houlihan et al., 2012 (PMID 23154782) with the following specific modifications. Bones were cut in small pieces with a scalpel and all tissue was processed (bone marrow cells were not washed out or flushed) for enzymatic digestion using collagenase D (2mg/ml in DMEM [high glucose]).  Red cell lysis was not performed. The time of digestion was 45-50 minutes in a water bath at 37ºC with 3 rounds of gentle pipetting every 10 min to help disaggregation. Collagenase digestion was stopped in ice and by addition of ice-cold 10%FBS/HBSS+ (HBSS, 10mM HEPES, 1% Penicillin-Streptomycin). Cells in suspension were recovered to a new tube and any remaining bone pieces were transferred to a ceramic mortar and 2 steps of very gentle tapping with the pestle (20-30 times) was applied to increase cell recovery. Cells in the mortar were recovered with the addition of 10%FBS/HBSS+, filtered through a 100µm strainer and pooled with the cell suspension set aside.  After centrifugation (350g for 10 min at 4°C), cells were resuspended in 2%FBS/HBSS+ for FACS. Before antibody staining, blocking of FcγR II/III was performed by incubation in ice with anti-CD16/CD32 antibodies for 15 min (1mg  per million cells). The gates were defined by the use of a mix of pan-antibodies to mesenchymal (CD140a/PDGFR-a) and endothelial cells (CD31/PECAM), together with CD9, a marker highly expressed in early hematopoietic progenitors and stromal cells. Collection tubes for sorting were precoated for 15 minutes with 10% FBS/HBSS+ in ice, and kept at 4º C during sorting.  Samples were analyzed and sorted in a SONY MA900 (lasers: 488/561 and 405/638nm). 7AAD (7-amino actinomycin D) was the only dye used to discriminate dead cells.  Dead cells and multiplets were excluded by gating, and no lineage labeling was used to prevent the loss of any cell subsets. The following four gates were used: CD9hi, PDGFRa/CD31hi; CD9hi, PDGFRa/CD31low; CD9low, PDGFRa/CD31hi; CD9low, PDGFRa/CD31low and sorted cells were mixed using a 10:1:1:2 ratio to represent both abundant and minor populations and processed for scRNAseq.
scRNAseq libraries were constructed according to the manufacter’s protocol (Chromium Next GEM Single Cell 3' Kit v3.1; 10x Genomics). Cells suspensions representing all heterogeneity within the perinatal endochondral bone 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 DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

tag: strain

value: wild-type

value: embryonic day E18.5


title: Stool sRNA-Seq - Patient 10 T2

value: Time 2


title: Endochondral bone, postnatal day 1, scRNAseq

description: 10x Genomics

value: forelimb long bones (humerus, radius, ulna)

value: postnatal day 1


title: Stool sRNA-Seq - Patient 13 T0

value: Time 0


title: Stool sRNA-Seq - Patient 10 T1

value: Time 1


title: RNA-Seq SAP-12 Adenoma T2

value: Adenoma


title: RNA-Seq SAP-12 Adenoma T0


title: 44_KCR020


title: 43_KCR019


title: 38_KCR017


title: RNA-Seq SAP-08 Healthy T2

value: Healthy mucosa


title: 40_KCR018


title: Stool sRNA-Seq - Patient 10 T0


title: 35_KCR016


title: RNA-MBD2-ZF108-rep1

city: Los Angeles

first: Shuya

last: Wang

state: California

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
ChIP-seq: Quality control was initially run to filter out the low-quality reads. Trim Galore (Babraham Institute) was used to remove the Illumina adapters. Then the reads were aligned to the Arabidopsis reference genome (TAIR10) using the bowtie2, allowing only uniquely mapped reads with perfect matches. MarkDuplicates.jar (picard-tools suite, Broad Institute) was used to remove the PCR duplicates. Bigwig files were generated using deeptools (v 3.0.2) bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. For correlation analysis between the ChIP-seq signal and mCG density, the samples were normalized to the no-FLAG control using bamCompare with the options --scaleFactorsMethod readCount, --binSize 10, and --operation log2. The normalized ChIP-seq signal and CG methylation percentages were summarized into 400 bp bins. We took a random subset covering 10% of all genomic regions for the correlation analysis. The data were plotted using the R package ggplot with the option geom_smooth. ChIP-seq peaks were called using MACS2 (v2.1.1) using an FDR cutoff of 0.05. The FLAG-associated hyperchipable regions, defined as peaks called in the anti-FLAG Col-0 controls, were removed from the peak files. Heterochromatin peaks were defined as peaks intersecting with TAIR10 pericentromeric regions using bedtools intersect55 function from deeptools (v 3.0.2).
Mnase-seq: The reads of low quality were fileterd out and the adaptors were trimmed with Trim Galore (Babraham Institute). Next the processed reads were aligned to TAIR10 using bowtie2 keeping reads smaller than 2000 bp and allowing only uniquely mapped reads with perfect matches. Then PCR duplicates were removes using MarkDuplicate (picard-tools suit, Broad Institute) and bigwig files were generated using bamCoverage.
RNA-seq: RNAs-seq reads were filtered according to quality score and were trimmed out Illumina adaptors using Trim Galore (Babraham Institute). Then the filtered reads were mapped to the Arabidopsis reference genome (TAIR10) using STAR. We allowed only uniquely mapped reads with less than 5% of mismatches. Bigwig files for genome browser visualization were generated using bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. HTSeq was used to obtain the read counts for TE and our previously reannotated pollen transcripts. DESeq2 was used to perform the differential analysis with the cutoff padj < 0.05 and |log2FC| > 1. We used ggplot to generate all the related plots.
snRNA-seq: The analysis was performed following the published pipeline (Ichino et. al). In brief, Cell Ranger 6.1.1 was used to process the raw data following the published pollen transcriptome reannotations. With Cell Ranger results, SoupX and Seurat were used to remove the ambient RNA and filter out the cells detected with less than 200 genes. The data were normalized and scaled following the published settings. After the normalization, PCA analysis was performed (npc=20). DoubletFinder v3 was used to identify doublets and find.pK was used to obtain the ideal pK parameters for each sample. The percentage of doublets removed and the pK values were summarized in Table S1. Col-0 and mbd2 datasets were integrated with Seurat v4 FindIntegrationAnchors and IntegrateData using default settings. The data was scaled, and PCA analysis was performed (npcs=40). Then clustering analysis was done using FindNeighbors and FindClusters functions. The number of cells per cluster is summarized in Table S1. In addition, the markers for each cluster were obtained with FindAllMarker using the integrated dataset. Finally, DEG analysis was performed on individual clusters. We specifically focused on activated TEs using the cutoff padj < 0.05 & |avg_log2FC| > 0.25. In this analysis, the following clusters were groups: VN_bi and VN_late_bi, VN_tri and VAN_mature. The TE expression heatmap was generated using Seurat function AverageExpression.
WGBS: WGBS were filtered and removed with Illumina adaptors using Trim Galore (Babraham Institute). Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. Bismark51 was used to map the reads to the Arabidopsis reference genome (TAIR10) and obtain the methylation percentages for each cytosine. We used ViewBS to generate the plots showing the genome-wide methylation information across genotypes.
Assembly: TAIR10
Supplementary files format and content: bigwig: ChIP-seq, RNA-seq, and MNase-seq intensity
Supplementary files format and content: narrowPeak: peak file
Supplementary files format and content: tsv.gz and matrix.gz: tab-seprated values files and matrix files
Supplementary files format and content: bed and bedGraph for WGBS: methylation ratio

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under long-day condition (16h light and 8h dark).

extract_protocol:
For ChIP-seq experiments, 1~2 g of unopen flower buds or 2~4 g rosette leaves from the T2 lines were collected. For RNA-seq, rosette leaf tissues from 4- to 5-week-old plants, 500 uL of open flowers, 1 inflorescence, or 3 individuals of 10-day-old seedlings were harvested. For WGBS, rosette leaf tissues from 4- to 5-week-old plants, 1000 uL of open flowers, or 5 individuals of 10-day-old seedlings were pooled as one biological replicate. For snRNA-seq, 5 mL of unopen flower buds and open flowers from the same inflorescence were harvested. For MNase-seq, 0.5 g of unopen flower buds were freshly harvested.
ChIP-seq and Mnase-seq libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN, 0344NB-A01) following the manufacturer’s instructions. Whole genome bisulfite sequencing libraries were prepared using the Nugen Ultralow Methyl Kit. RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina). SnRNA-seq libraries were prepared with 10x Genomics Chromium Single Cell 30 Reagent Kit v3.
ChIP-seq, RNA-seq, snRNA-seq, WGBS, and MNase-seq

treatment_protocol: For 5AZA treatment, 100mg of 5AZA (Sigma) was first dissolved in 10ml of DMSO. Then the 5AZA stock was added to MS agar plates to reach 100uM final concentration. Control plates were only added with the same volume of DMSO. Seedlings of the Col-0 and mbd2 CRISPR mutant were harvested after 10-day incubation under long-day conditions.

value: rosette leaf

value: fwa

tag: ecotype


title: RNA-Seq SAP-08 Adenoma T2


title: RNA-fwa-rep3


title: RNA-Seq SAP-08 Adenoma T0


title: RNA-Seq SAP-08 Healthy T0


title: RNA-Seq SAP-07 Healthy T2

value: F


title: RNA-MBD2-ZF108-rep3


title: hippocampus_sleepdeprived_8

hyb_protocol: The labeled RNAs were hybridized to a Mouse miRNA Microarray (G4472B, Agilent Technologies) for 20h at 55°C with rotation. Samples were pooled per group of 2 animals for each condition (SD/control) and for each brain region (cortex/hippocampus), resulting in a total of 8 arrays.

scan_protocol: After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer. Agilent Feature Extraction Software was used to extract the data.

data_processing: Data were normalized by a quantile normalization approach implemented in-house in the R programming language, as described in S. Pradervand et al., 2009, doi: 10.1261/rna.1295509.

source_name: hippocampus, sleep deprived

label_protocol: Total RNA (100ng) was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH), denaturated with dimethyl sulfoxide, and labeled with pCd-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH).

extract_protocol: Brain tissues dissected from SD and control mice were homogenized in QIAzol Lysis Reagent (Qiagen). RNA was extracted and purified using the QIAGEN miRNeasy mini kit 50 (Qiagen) according to the manufacturer instructions. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and the quality of RNA samples was verified on Agilent 2100 bioanalyzer chips (Agilent technologies).

treatment_protocol: Half of the mice were submitted to a 6 hour SD performed by the so-called “gentle handling protocol”, starting at light onset (Zeitgeber Time 0). The other half was left undisturbed and used as control. At the end of the SD (ZT6), animals from both groups were sacrificed and brains were dissected and collected.For cortex and hippocampus dissection, two 2mm-thick sagittal slices taken 1mm lateral from the inter-hemispheric fissure were cut using a sagittal slicer matrix (Alto Stainless Matrices) in PBS (Life Technologies Europe). From the two resulting slices, hippocampi and cortex were dissected according to the Mouse Brain Atlas (Paxinos and Franklin, 2001).

value: hippocampus

value: sleep-deprived


title: hippocampus_sleepdeprived_7


title: 34_KCR015

value: Case

value: fetus with spina bifida


title: mesentery_M

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description: 10x Genomics

data_processing:
cellranger pipeline using default parameters with forced recovery of 10000 cells for each library
Assembly: PRJNA667495 from Zimmerman et al 2023 doi:10.1038/s41467-023-44080-7
Supplementary files format and content: extracted barcodes representing captured cells: XX_barcodes
Supplementary files format and content: gene designation: XX_features
Supplementary files format and content: extracted count matrix: XX_matrix

organism: Nematostella vectensis

source_name: mesentery of mature male, post-spawning

extract_protocol:
Whole embryos or dissected tissues were dissociated with collagenase (24hr_rep4 and mesentery_male) or tripleE (2day_rep2, interparietal bodywall).  Mechanical force was used to disrupt the tissues and obtain single-cell suspensions. Cell suspensions were washed with 0.1% BSA (bovine serum albumin), and cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted to 1000 cells/ microliter and loaded into a 10x Genomics single cell platform using vs3 reagents.
10X Genomics Chromium v2/v3 chemistry according to manufacturer protocols

value: mesentery of mature male, post-spawning

value: wildtype


title: RNA-fwa-rep2


title: RNA-MBD2-ZF108-rep2


title: 32_KCR014


title: 31_KCR013


title: 30_KCR012


title: 24hr_rep4

description: 10x Genomics

source_name: 50-100 whole embryos

value: 50-100 whole embryos


title: cortex_sleepdeprived_6

source_name: cortex, control condition

value: cortex

value: control


title: 2day_rep2

description: 10x Genomics


title: RNA-Seq SAP-07 Adenoma T0


title: RNA-Seq SAP-02 microAdenoma T2

source_name: microAdenoma

value: microAdenoma


title: hippocampus_control_4


title: pbs9 [snRNA-seq]

description: 10x Genomics

molecule: nuclear RNA

value: head kidney


title: hippocampus_control_3


title: RNA-Seq SAP-07 Adenoma T2


title: RNA-fwa-rep1


title: cortex_sleepdeprived_5


title: pbs3 [snRNA-seq]

description: 10x Genomics


title: WGBS-fwa

library_source: genomic

molecule: genomic DNA


title: WGBS-MBD2-ZF108-T2-fwa


title: Tet_induced, mut, rep2

status: Public on Jan 11 2024

first: Yeon

last: Lee

address: 1 Barker Hall

institute: UC Berkeley

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 D262V mut rep 2

data_processing:
Pre-mRNA splicing analysis using JUM.2.0.2 software to detect pre-mRNA splicing patterns was performed as described before (Lee et al. 2018). AP-value of 0.05 was used as the statistical cutoff for differentially spliced AS events. Expressed genes for GO-terminology enrichment analysis was generated using cufflinks.v2.1.1(Trapnell et al. 2009) using the following parameters: --library-type fr-firststrand -m 100 -s 10, then filtered for FPKM > 1.
For Differential expression analysis, uniquely mapped reads were mapped to hg38 using STAR_2.5.3a_modified version using --outFilterMultimapNmax 1. Read counts were calculated using HTSeq script htseq-count with the following specifications: -s yes -r pos -f. Differential gene expression analysis was performed using DESeq2 (Love et al. 2014) using CPM cutoff. The expression cutoff (CPM) value was determined according to the library size and normalization factors, roughly equal to 10/LwhereLis the minimum library size in millions (Chen et al. 2016).
The Quick irCLIP-seq reads were preprocessed prior to mapping using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Reads were quality-filtered based on quality score (fastq_quality_filter -q 25 -p 80), and PCR duplicates were collapsed (fastx_collapser). Only uniquely mapped reads were used for further analysis. The reads were mapped tohg38using STAR using the following parameters: --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped fastx --outSAMtype BAM SortedByCoordinate. Uniquely mapped reads were filtered and then used for cluster identification using pycrac/1.2.3.0 (Webb et al. 2014). irCLIP clusters were generated using at least ten overlapping unique cDNA reads generated after removal of PCR duplicates (pyClusterReads.py --cic=10). pyCalculateFDRs were used to filter out statistically significant clusters over the regions with a read coverage of at least 5 (--min=10) and FDRp< 0.05. De novo binding motifs for hnRNPA1 wild type and mutant protein were determined using STREME (Bailey 2021) using the following parameter: streme --verbosity 1 --oc --rna --minw 8 --maxw 15 --pvt 0.05.
Assembly: hg38
Supplementary files format and content: counts.txt files, significant_clusters.bed files

source_name: embryonickidney

growth_protocol: Human SH-SY5Y cells (American Type Culture Collection) were maintained at 37°C in DMEM/F-12 (Gibco™, 11320082) medium supplemented with 10% FBS, 1% Pen-Strep. Human FLP-In™ T-REx™ 293 (Invitrogen™, R78007) cells were maintained in D-MEM™ (high glucose), 10% FBS, 2mM L-glutamine, and 1% Pen-Strep.

extract_protocol: RNA isolation was performed using the RNeasy Minikit (Qiagen, 74104), followed by 30 min. of DNase treatment (Ambion, AM2238) at 37°C, poly(A)+ RNA transcripts were isolated [NEBNext poly(A) mRNA magnetic isolation module; New England Biolabs, E7490] from 1 µg of total RNA for RNA library preparation and sequencing using NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (New England Biolabs, E7420S) according to the manufacturer’s instruction.

treatment_protocol: Tetracycline (Tet)-inducible 293 FLP-In hnRNPA1 wild type and hnRNPA1 mutant (D262V) cells were induced with 1 µg/mL Tetracycline (Tet) for 72 hr prior to harvest. SH-SY5Y cells were differentiated accordingly to a published a protocol (Shipley et al. 2016) with the following modification. F12/DMEM media with 10% FBS was used in place of EMEM media with 15% FBS as basic growth media. 2.5% FBS F12/DMEM with 1X Pen/Strep, 2 mM Glutamine, 10 uM RA was used as Differentiation Media 1. 1% FBS F12/DMEB with 1X Pen/Strep, 2 mM Glutamine, 10 µM RA was used as Differentiation Media 2. F12/DMEM with 1X B-27, 20 mM KCl, 1X Pen/Strep, 2 mM GlutamaxI, 50 ng/mL BDNF, 2 mM dibutyryl cyclic AMP (db-cAMP), 10 uM RA was used as Differentiation Media 3. SH-SY5Y cells were differentiated as described previously (Shipley et al. 2016), and harvested on day 18 for imaging experiments and RNA-seq library preparation.

value: embryonickidney

value: Flp-In™ T-REx™ 293

value: immortalized human embryonic kidney cells

value: mutant


title: RNA-Seq SAP-07 Healthy T0

value: Healthy mucosa


title: Tet_induced, WT, rep3

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 WT rep 3

value: induced with 1 µg/mL Tetracycline (Tet) for 72 hr prior to harvest


title: WGBS-MBD2-ZF108-T3-fwa

value: rosette leaf

value: fwa


title: RNA-Seq SAP-02 Adenoma T0

value: F

value: Adenoma


title: Tet_induced, WT, rep2

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 WT rep 2


title: Tet_induced, WT, rep1

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 WT rep 1


title: cortex_control_2


title: Tet_induced, mut, rep3

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 D262V mut rep 3


title: Tet_induced, mut, rep1

description:
RNA-seq
Flp_In_293.D262V.merged.counts.txt
Sh-SY_WT_merged_count_output_reads.cic10.gtf.significant_clusters.bed
Flp-In Tet-induced hnRNPA1 D262V mut rep 1


title: interP_BW

description: 10x Genomics

source_name: interparietal bodywall, 2 month old non-sexed animal


title: cortex_control_1


title: Tsu0_G14_L6

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
When applicable, different files corresponding to the same sample were merged at the BAM stage using “samtools merge -n” (Samtools version 1.11).
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute

source_name: leaf tissue

growth_protocol: For the MA-accessions, seeds were planted and grown in 16-h-day lengths.

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end or single-end 150bp format.

value: leaf tissue

tag: generation

tag: lineage


title: Ler0_G8_L8


title: Tsu0_G13_L6


title: Mt0_G16_L11


title: Tsu0_G10_L6


title: Mt0_G8_L11


title: Og0_G11_L1


title: Tsu0_G0


title: Ler0_G8_L4


title: Og0_G4_L2


title: Mt0_G4_L11


title: Mt0_G4_L8


title: Og0_G8_L1


title: Tsu0_G16_L7


title: Ler0_G5_L8


title: Tsu0_G8_L6


title: Tsu0_G4_L7


title: Mt0_G0


title: Og0_G10_L2


title: Mt0_G14_L11


title: Tsu0_G8_L7


title: Mt0_G12_L11


title: Og0_G0


title: Tsu0_G4_L6


title: Tsu0_G12_L7


title: Og0_G14_L1


title: Og0_G8_L2


title: Og0_G5_L1


title: Ler0_G4_L4


title: Ler0_G15_L4


title: Ler0_G13_L8


title: Ler0_G0


title: Ler0_G12_L4


title: Col0_G5_L2


title: Col0_G11_L2


title: Hi0_G4_L1


title: Kn0_G14_L5


title: Kn0_G0


title: Hi0_G0


title: Col0_G11_L8


title: Col0_G2_L8


title: Hi0_G10_L5


title: Col0_G5_L8


title: Kn0_G15_L10


title: Col0_G8_L2


title: Col0_G4_L8


title: Kn0_G4_L5


title: Hi0_G8_L1


title: Hi0_G4_L12


title: Col0_G8_L8


title: Col0_G4_L2


title: Kn0_G11_L5


title: Col0_G1_L8


title: Kn0_G6_L5


title: Kn0_G4_L10


title: Col0_G2_L2


title: Hi0_G12_L1


title: Kn0_G8_L10


title: Hi0_G15_L1


title: Hi0_G12_L5


title: Col0_G1_L2


title: Col0_G0


title: Liver_6dpf_Lipofermata_rep1

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome, and counted using FeatureCounts. For normalization, differential gene expression analysis, and GO analysis, iDEP version 0.951 was utilized with default parameters. For differential gene expression, a fold-change of 2 and false-discovery rate of 0.1 was used for cut-off.
Assembly: GRCz11
Supplementary files format and content: comma-separate file (csv) with raw counts for all samples.

organism: Danio rerio

growth_protocol: Zebrafish larvae at 6 dpf.

extract_protocol:
For RNA-Seq, mRNA was isolated from livers at 6 dpf. For this, livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems (Promega, Z6110). mRNA was isolated from the lysed tissue by following the manufacture’s instruction.
cDNA synthesis, library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods, e.g. measurement of volume and quantity, gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology, using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation, after first strand synthesis, the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next, the sequencing adapters were ligated to the DNA fragments, and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.

treatment_protocol: Lipofermata or DMSO treatment for 48 hours

value: Liver

value: AB

value: Lipofermata


title: Liver_6dpf_Lipofermata_rep2


title: in vivo passaged ICB sensitive CT26 cells, IFNγ untreated [WT-3minus]

city: Cambridge

first: Danish

last: Memon

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
ATAC-Seq raw data was trimmed using Trimmomatic 0.3873 to remove sequencing adapters and low-quality bases. Cleaned reads were next aligned to reference genome mm10 using bowtie278.
Aligned reads were filtered using samtools 1.979 to keep alignments that have a minimum mapping quality of 30 and are aligned concordantly. Peak calling was performed using MACS2 2.1.280 to identify open chromatin regions.
For each pair-wise comparison, peaks from the relevant conditions are merged and peaks found in either condition are kept for downstream analyses. Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
Assembly: Mus Musculus GRCm38
Supplementary files format and content: Peak calls from MACS2 2.1.2 for each sample

growth_protocol: BALB/C mice were acquired from The Jackson Laboratory, after several days of acclimation, mice were inoculated with 500k CT26 on the rear flank. When the average tumor volume reached 80-100 mm3 (indicating day 0), mice were given a series of intraperitoneal injections of anti-PD-1 (clone RMP1-14; BioXcell), consisting of 100 μg each on days 0, 3, and 6. Tumors were excised from mice that did not respond to anti-PD-1 therapy, approximately 10-14 days following the initial treatment. Tumors were dissociated using collagenase (Stemcell Technologies), washed in 1X PBS, and plated in IMDM culture media supplemented in 10% fetal bovine serum, 1% GLUTiMAX, and 1% Antibiotic-Antimycotic (all GIBCO). Cells were passaged at least 5 times and then inoculated into new recipient mice according to the same protocol as above. Again, when tumors reached 80-100 mm3, another treatment course of anti-PD-1 began. This process was repeated for a total of four rounds, at which point none of the treated mice responded to anti-PD-1 therapy. The cell lines generated after two rounds of anti-PD1 selection are referred to throughout this manuscript as ‘2nd round’, ‘2nd generation’ or ‘F2 generation’, and the cell line generated after four rounds of anti-PD1 selection are referred to as ‘4th round’, ‘4th generation’, or ‘F4 generation’.

treatment_protocol: For ATACSeq, CT26 cell pellets from two distinct vials of parental CT26 cells, five independently isolated tumors from mice, and five independently isolated tumors from ‘4th round’ mice were collected according to the same procedure as described above for RNA isolation, and pellets were sent to Genewiz (www.genewiz.com) for nuclei isolation, library generation, and sequencing. Nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples. Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: CT26 cells

value: murine colorectal carcinoma cell line


title: Liver_6dpf_DMSO_rep2

value: DMSO


title: Liver_6dpf_DMSO_rep1


title: parental CT26 cells, IFNγ untreated [Cells-1minus]

source_name: parental CT26 cells, IFNγ untreated

extract_protocol:
Nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: parental CT26 cells, IFNγ untreated


title: in vivo passaged ICB sensitive CT26 cells, IFNγ untreated [WT-2minus]


title: in vivo passaged ICB sensitive CT26 cells, IFNγ untreated [WT-5minus]


title: in vivo passaged ICB sensitive CT26 cells, IFNγ untreated [WT-1minus]


title: 4th round ICB resistant CT26 cells, IFNγ untreated [Mut-3minus]


title: 4th round ICB resistant CT26 cells, IFNγ untreated [Mut-2minus]


title: 4th round ICB resistant CT26 cells, IFNγ untreated [Mut-4minus]


title: 4th round ICB resistant CT26 cells, IFNγ untreated [Mut-5minus]


title: Senescent FAPs replicate 2

city: Rochester

first: Xu

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

data_processing:
Libraries weresequenced using the Illumina cBot and HiSeq 3000/4000 PE Cluster kit on an Illumina HiSeq 4000. Differentially expressed genes were analyzed using EdgeR (V3.10) in R (V3.6.0). Gene Set Enrichment Analysis was performed using software GSEA (v.4.0.3).
Assembly: mm10

source_name: Senescent FAPs

extract_protocol: For RNAseq, libraries were prepared using TruSeq Stranded mRNA Sample Prep kit.

tag: stain

value: FAPs


title: non-senescent FAPs replicate 2

source_name: non-senescent FAPs


title: non-senescent FAPs replicate 3


title: non-senescent FAPs replicate 1


title: Senescent FAPs replicate 3


title: in vivo passaged ICB sensitive CT26 cells, IFNγ untreated [WT-4minus]


title: Senescent FAPs replicate 1


title: XV0001C1_Orthotopic PDAC tumor Replicate 1 (ROI1)

city: Singapore

first: Melissa

last: Ng

address: 8A Biomedical Grove, #03-06 Immunos Building, Singapore

country: Singapore

institute: Singapore Immunology Network

description: Fresh Frozen Spatial Transcriptome Sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm 10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors _json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: PDAC tumor

growth_protocol: The luciferase-stable pancreatic ductal adenocarcinoma FC1242L cell line was generated as described in Leong et al., and was derived from the FC1242 cell line (kind gift from Dr Dannielle Engle, Tuveson lab, Cold Spring Harbour Laboratory) derived from Pdx1Cre; KrasG12D/+; Trp53R172H/+ (KPC) mice. FC1242L was culturecultured in complete media (cDMEM) comprising Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal calf serum (FCS), 1% Penicillin-Streptomycin (Gibco) and seeded at a density of 2 X 10^5 cells/mL in T75 cell culture flask. Cells were grown at 37°C in 5% CO2 incubator until they reached 80% confluency. Upon reaching confluency, cells were trypsinized with pre-warmed 0.25% Trypsin with Ethylenediaminetetraacetic acid (EDTA), phenol red (Gibco) for 5 minutes at 37°C in 5% CO2 incubator, washed with pre-warmed cDMEM and counted, before seeding at a density of 2 X 10^5 cells/mL for the next passage.

extract_protocol:
At 6 weeks post injection, tumors were excised from tumor-bearing mice and weighed before mincing into smaller pieces using surgical scissors. Frech frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Mice were administered intrapancreatic injections of FC1242L tumor cells. The mice were anaesthetized, the pancreas was exposed by surgical excision, and 10,000 FC1242L cels were re-suspended in 1X phosphate buffered saline (PBS) and mixed with Matrigel (BD) in a 1:1 ratio, and were injected as a volume of 50 µL into the body of the pancreas to form a visible bolus.

value: PDAC tumor

tag: tumor stage

value: 6wk post surgery

tag: model

value: Orthotopic KPC


title: 4th round ICB resistant CT26 cells, IFNγ untreated [Mut-1minus]


title: 187R-NIC/p66High (Aggressive)

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: tab separated file containing the raw exonic counts for each sample using the mm10 Ensembl annotation set.

source_name: Mammary fat pad

extract_protocol:
Total RNA was extracted using RNeasy Midi Kit (QIAGEN).
Library preparation was performed using the rRNA-depleted stranded (HMR) kit according to instruction from the manufacturer

treatment_protocol: Orthotopic injections were performed in 8- to 12-week-old FVB/N mice for NIC cells, using 250,000 NIC cells per mouse suspended in a 1:1 mixture of PBS and matrigel (VWR, CACB354234). The area of the fourth mammary fat pad was depilated and sterilized before suspended cells were injected into the fat pad itself through a small incision. Subcutaneous carpofen and topical lidocaine were applied as analgesics.

tag: tissue

value: Mammary fat pad

value: FVB/N

tag: disease state

value: mammary tumor

tag: phenotype

value: Aggressive

value: female


title: 185L-NIC/p66High (Aggressive)

tag: genotype


title: XV0001D1_Orthotopic PDAC tumor Replicate 2 (ROI2)


title: 183L-NIC/p66Low (Aggressive)


title: 182L-NIC/p66Low (Aggressive)


title: parental CT26 cells, IFNγ untreated [Cells-2minus]

tag: cell line

tag: cell type

tag: treatment


title: 185R-NIC/p66High (Aggressive)

tag: Sex


title: 176R-NIC/p66High (Parental)

value: Parental


title: 181R-NIC/p66Low (Aggressive)


title: 173R-NIC/p66High (Parental)


title: 173L-NIC/p66High (Parental)


title: 171R-NIC/p66Low (Parental)


title: 172R-NIC/p66Low (Parental)


title: Subject 100467, P+7D

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

description: Column name in processed data file: 340

data_processing:
raw counts were normalized as Log2 counts per million
Assembly: hg18
Supplementary files format and content: normalized_counts_050523.csv, corresponding to 59 subjects

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the NEBNext single cell/low input RNA library prep kit for Illumina. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform

tag: subject

tag: timepoint

value: Blood

tag: group

value: Prime


title: Subject 100472, P+7D

description: Column name in processed data file: 344


title: Subject 100467, P+3H

description: Column name in processed data file: 342


title: Subject 100380, P+1D

description: Column name in processed data file: 337


title: periosteum_day0

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

country: China

institute: the First Affiliated Hospital of China Medical University

data_processing:
cell ranger 6.01
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol: 10X Single Cell 3' v3


title: Subject 100418, P+1D

description: Column name in processed data file: 332


title: 169L-NIC/p66Low (Parental)

tag: strain


title: Subject 100467, D0

description: Column name in processed data file: 343

value: Control


title: Subject 100380, D0

description: Column name in processed data file: 339


title: Subject 100380, P+3H

description: Column name in processed data file: 338


title: Subject 100380, P+7D

description: Column name in processed data file: 336


title: Subject 100418, P+7D

description: Column name in processed data file: 331


title: fracture_day10


title: Subject 100562, P+7D

description: Column name in processed data file: 335


title: Subject 100562, D0

description: Column name in processed data file: 334


title: Subject 100418, D0

description: Column name in processed data file: 330


title: Subject 100435, P+3H

description: Column name in processed data file: 328


title: Subject 100418, P+3H

description: Column name in processed data file: 329


title: Subject 100435, P+1D

description: Column name in processed data file: 327


title: Subject 100435, P+7D

description: Column name in processed data file: 326


title: Subject 100435, D0

description: Column name in processed data file: 325


title: fracture_day5


title: Subject 100417, D0

description: Column name in processed data file: 324


title: Subject 100467, P+1D

description: Column name in processed data file: 341


title: Subject 100417, P+1D

description: Column name in processed data file: 322


title: Subject 100566, P+7D

description: Column name in processed data file: 320


title: Subject 100562, P+3H

description: Column name in processed data file: 333


title: Subject 100566, D0

description: Column name in processed data file: 319


title: Subject 100566, P+3H

description: Column name in processed data file: 318


title: Subject 100563, P+1D

description: Column name in processed data file: 316


title: Subject 100552, P+3H

description: Column name in processed data file: 314


title: Subject 100563, P+7D

description: Column name in processed data file: 315


title: Subject 100552, P+1D

description: Column name in processed data file: 312


title: Subject 100558, P+7D

description: Column name in processed data file: 310


title: Subject 100552, D0

description: Column name in processed data file: 311


title: Subject 100552, P+7D

description: Column name in processed data file: 313


title: Subject 100566, P+1D

description: Column name in processed data file: 317


title: Subject 100495, P+1D

description: Column name in processed data file: 306


title: Subject 100540, P+3H

description: Column name in processed data file: 303


title: Subject 100495, P+3H

description: Column name in processed data file: 307


title: Subject 100495, D0

description: Column name in processed data file: 309


title: Subject 100495, P+7D

description: Column name in processed data file: 308


title: Subject 100540, P+7D

description: Column name in processed data file: 302


title: Subject 100540, D0

description: Column name in processed data file: 304


title: Subject 100540, P+1D

description: Column name in processed data file: 305


title: Subject 100559, P+1D

description: Column name in processed data file: 301


title: Subject 100510, P+3H

description: Column name in processed data file: 297


title: Subject 100510, P+1D

description: Column name in processed data file: 295


title: Subject 100510, P+7D

description: Column name in processed data file: 296


title: Subject 100559, D0

description: Column name in processed data file: 300


title: Subject 100510, D0

description: Column name in processed data file: 298


title: Subject 100417, P+3H

description: Column name in processed data file: 323


title: Subject 100559, P+3H

description: Column name in processed data file: 299


title: Subject 100417, P+7D

description: Column name in processed data file: 321


title: Subject 100494, D0

description: Column name in processed data file: 294


title: Subject 100494, P+7D

description: Column name in processed data file: 293


title: Subject 100494, P+3H

description: Column name in processed data file: 291


title: Subject 100473, P+3H

description: Column name in processed data file: 287


title: Subject 100470, D0

description: Column name in processed data file: 283


title: Subject 100450, P+3H

description: Column name in processed data file: 289


title: Subject 100473, P+7D

description: Column name in processed data file: 285


title: Subject 100473, P+1D

description: Column name in processed data file: 284


title: Subject 100470, P+1D

description: Column name in processed data file: 282


title: Subject 100494, P+1D

description: Column name in processed data file: 292


title: Subject 100450, D0

description: Column name in processed data file: 288


title: Subject 100473, D0

description: Column name in processed data file: 286


title: Subject 100443, P+3H

description: Column name in processed data file: 277


title: Subject 100503, P+3H

description: Column name in processed data file: 279


title: Subject 100470, P+3H

description: Column name in processed data file: 281


title: Subject 100450, P+1D

description: Column name in processed data file: 290


title: Subject 100443, P+7D

description: Column name in processed data file: 274


title: Subject 100443, P+1D

description: Column name in processed data file: 276


title: Subject 100354, P+7D

description: Column name in processed data file: 271


title: Subject 100354, P+1D

description: Column name in processed data file: 270


title: Subject 100443, D0

description: Column name in processed data file: 275


title: Subject 100354, P+3H

description: Column name in processed data file: 272


title: Subject 100428, P+7D

description: Column name in processed data file: 269


title: Subject 100399, P+7D

description: Column name in processed data file: 265


title: Subject 100503, P+1D

description: Column name in processed data file: 280


title: Subject 100428, P+1D

description: Column name in processed data file: 268


title: Subject 100503, D0

description: Column name in processed data file: 278


title: Subject 100428, P+3H

description: Column name in processed data file: 267


title: Subject 100399, P+1D

description: Column name in processed data file: 266


title: Subject 100223, D0

description: Column name in processed data file: 262


title: Subject 100223, B+1D

description: Column name in processed data file: 263

value: MVA-BN-Filo

value: Boost


title: Subject 100223, P+1D

description: Column name in processed data file: 261


title: Subject 100223, P+29D

description: Column name in processed data file: 259


title: Subject 100399, P+3H

description: Column name in processed data file: 264


title: Subject 100439, P+1D

description: Column name in processed data file: 254


title: Subject 100223, P+7D

description: Column name in processed data file: 257


title: Subject 100439, P+3H

description: Column name in processed data file: 253


title: Subject 100223, B+3H

description: Column name in processed data file: 260


title: Subject 100223, P+3H

description: Column name in processed data file: 256


title: Subject 100439, P+7D

description: Column name in processed data file: 250


title: Subject 100354, D0

description: Column name in processed data file: 273


title: Subject 100439, D0

description: Column name in processed data file: 249


title: Subject 100283, D0

description: Column name in processed data file: 248


title: Subject 100283, P+7D

description: Column name in processed data file: 247


title: Subject 100283, P+1D

description: Column name in processed data file: 246


title: Subject 100283, B+7D

description: Column name in processed data file: 245


title: Subject 100283, B+1D

description: Column name in processed data file: 244


title: Subject 100439, B+3H

description: Column name in processed data file: 255


title: Subject 100283, P+3H

description: Column name in processed data file: 243


title: Subject 100223, B+7D

description: Column name in processed data file: 258


title: Subject 100341, B+3H

description: Column name in processed data file: 241


title: Subject 100341, P+7D

description: Column name in processed data file: 236


title: Subject 100341, B+1D

description: Column name in processed data file: 239


title: Subject 100341, D0

description: Column name in processed data file: 240


title: Subject 100341, P+29D

description: Column name in processed data file: 237


title: Subject 100341, B+7D

description: Column name in processed data file: 238


title: Subject 100439, P+29D

description: Column name in processed data file: 251


title: Subject 100304, D0

description: Column name in processed data file: 228


title: Subject 100304, B+1D

description: Column name in processed data file: 233


title: Subject 100304, P+1D

description: Column name in processed data file: 229


title: Subject 100341, P+1D

description: Column name in processed data file: 234


title: Subject 100304, P+7D

description: Column name in processed data file: 230


title: Subject 100341, P+3H

description: Column name in processed data file: 235


title: Subject 100439, B+1D

description: Column name in processed data file: 252


title: Subject 100304, P+29D

description: Column name in processed data file: 232


title: Subject 100304, B+7D

description: Column name in processed data file: 226


title: Subject 100284, B+3H

description: Column name in processed data file: 225


title: Subject 100284, D0

description: Column name in processed data file: 221


title: Subject 100284, P+1D

description: Column name in processed data file: 224


title: Subject 100284, P+3H

description: Column name in processed data file: 222


title: Subject 100284, P+29D

description: Column name in processed data file: 220


title: Subject 100284, B+7D

description: Column name in processed data file: 223


title: Subject 100283, P+29D

description: Column name in processed data file: 242


title: Subject 100401, B+3H

description: Column name in processed data file: 217


title: Subject 100401, P+7D

description: Column name in processed data file: 216


title: Subject 100258, P+3H

description: Column name in processed data file: 214


title: Subject 100284, B+1D

description: Column name in processed data file: 218


title: Subject 100401, P+3H

description: Column name in processed data file: 211


title: Subject 100401, P+1D

description: Column name in processed data file: 213


title: Subject 100258, D0

description: Column name in processed data file: 210


title: Subject 100401, D0

description: Column name in processed data file: 215


title: Subject 100258, B+1D

description: Column name in processed data file: 212


title: Subject 100304, B+3H

description: Column name in processed data file: 227


title: Subject 100304, P+3H

description: Column name in processed data file: 231


title: Subject 100401, B+1D

description: Column name in processed data file: 207


title: Subject 100401, P+57D

description: Column name in processed data file: 209


title: Subject 100258, P+1D

description: Column name in processed data file: 202


title: Subject 100249, P+1D

description: Column name in processed data file: 205


title: Subject 100258, B+7D

description: Column name in processed data file: 208


title: Subject 100258, P+7D

description: Column name in processed data file: 206


title: Subject 100258, B+3H

description: Column name in processed data file: 200


title: Subject 100284, P+7D

description: Column name in processed data file: 219


title: Subject 100506, D0

description: Column name in processed data file: 198


title: Subject 100258, P+29D

description: Column name in processed data file: 204


title: Subject 100249, P+57D

description: Column name in processed data file: 203


title: Subject 100249, B+1D

description: Column name in processed data file: 201


title: Subject 100506, P+1D

description: Column name in processed data file: 190


title: Subject 100506, B+3H

description: Column name in processed data file: 196


title: Subject 100249, D0

description: Column name in processed data file: 197


title: Subject 100249, B+7D

description: Column name in processed data file: 195


title: Subject 100506, B+7D

description: Column name in processed data file: 194


title: Subject 100465, B+3H

description: Column name in processed data file: 189


title: Subject 100506, B+1D

description: Column name in processed data file: 192


title: Subject 100249, P+7D

description: Column name in processed data file: 191


title: Subject 100465, P+7D

description: Column name in processed data file: 187


title: Subject 100506, P+7D

description: Column name in processed data file: 188


title: Subject 100506, P+3H

description: Column name in processed data file: 186


title: HSV1_virus_B

city: Utrecht

first: Marie

last: Bannier-Hélaouët

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Sequencing was performed at Single Cell Discoveries, a sequencing service provider located in the Netherlands using an adapted version of the CEL-seq protocol. In brief:
Total RNA was extracted using thestandard Qiagen RNAeasy kit according to the manufacturer's instructions and used for library preparation and sequencing. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq [Hashimshony et al. 2012; PMID: 22939981 and Simini et al, 2014; PMID: 25500896]. In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on anIllumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).
Reads were mapped to a human genome (hg38) using STAR (version 2.7.8a), reads with multiple mapping positions were excluded. Reads were associated with genes if they were mapped to an exon. Reads were collapsed into UMI tables using umi_tools (version 1.1.1).
Assembly: hg38
Supplementary files format and content: tab-delimited csv file including read counts for all samples

source_name: human conjunctiva air-liquid interface

growth_protocol: WT and KO organoids were grown in expansion medium (EM) for 7 days.

extract_protocol:
After a week, organoids were retrieved from BME and resuspended in 350 µL of RLT buffer (Qiagen). RNA was extracted using the RNeasy extraction kit (Qiagen).
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (Hashimshony et al., 2016; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.

value: human conjunctiva air-liquid interface

tag: virus

value: HSV1 infection for 3 hours

tag: ali age_at_infection

value: 17 days

tag: collection time_point

value: 96h after infection


title: HCT116 GNAS R201C/+, rep4

city: Helsinki

first: Pirjo

last: Nummela

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCh38.p12 whole genome using STAR aligner with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.v32.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric means, using negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance)  to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: GRCh38.p12 genome and annotations from GENCODE Release v.32
Supplementary files format and content: Raw gene expression matrix in MS  .xlsx -format

source_name: HCT116 GNAS R201C/+

growth_protocol: The cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany)
NEBNext Ultra II Directional RNA

value: HCT116 GNAS R201C/+

value: colon cancer cell line

value: GNAS R201C/+


title: HSV1_Ctrl_A

value: uninfected


title: Subject 100249, B+3H

description: Column name in processed data file: 193


title: Subject 100249, P+3H

description: Column name in processed data file: 199


title: HSV1_virus_A


title: two-month GTF2I-KO organoids, rep 1

city: La Jolla

first: Alysson

middle: R.

last: Muotri

address: 2880 Torrey Pines Scenic Road MC 0695

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio)
reads were trimmed using cutadapt
quality scores were assessed using Fast QC
reads were aligned to Homo sapiens genome build hg19 using STAR
individual sample reads were quantified using HTseq and normalized via Relative Log Expression using DESeq2 R library
DESeq2 was used to calculate fold changes and p-values and perform optional covariate correction
Assembly: hg19
Supplementary files format and content: raw counts.csv
Supplementary files format and content: normalized counts.csv

source_name: hiPSC-derived cortical organoids

growth_protocol: hiPSCs were cultured in mTeSR. Organoids were grown in neurobasal formulation supplemented with growth factors to promote proliferation and neuronal differentiation and maturation.

extract_protocol:
Total RNA was isolated using a Qiagen Rneasy Mini kit
TruSeq RNA Sample Preparation Kit

treatment_protocol: Cells were supplemented with growth factors including FGF, EGF, BDNF, GDNF, NT-3 as well as ascorbic acid and cAMP

value: hiPSC-derived cortical organoids

value: CVB

value: genetic modification


title: two-month GTF2I-KO organoids, rep 2


title: two-month control organoids, rep 2

value: control


title: two-month control organoids, rep 1


title: Subject 100465, D0

description: Column name in processed data file: 183

value: Blood


title: Subject 100506, P+29D

description: Column name in processed data file: 184

value: Prime


title: Subject 100531, P+7D

description: Column name in processed data file: 180


title: Subject 100465, P+1D

description: Column name in processed data file: 179


title: Subject 100465, P+3H

description: Column name in processed data file: 181


title: Subject 100531, B+3H

description: Column name in processed data file: 178


title: HCT116 GNAS R201C/+, rep1


title: HCT116 parental, rep3

value: GNAS wt

value: Ctrl


title: Subject 100465, B+1D

description: Column name in processed data file: 177

value: MVA-BN-Filo

value: Boost


title: MTX-3937_1

city: Jinan

first: Rong

last: Xiao

address: Lixia strict Wenhuaxi street No. 44

institute: Shandong University

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2)
Removing reads containing adapters (adapter contamination) using SOAPnuke
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%;  using SOAPunke
Removing reads whose unknown base ('N' base) ratio is more than 5% using SOAPunke
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each SAMPLE

source_name: Peripheral NK cells

extract_protocol:
Cells were lysed in TRIzol Reagent (TIANGEN) for extracting total RNA.
RNA llibraries were prepared by the Beijing Genomics Institute (BGI) following protocols.

value: Peripheral NK cells

value: WT


title: HCT116 parental, rep4


title: MTX-3937_2


title: Subject 100465, P+57D

description: Column name in processed data file: 185


title: Subject 100531, P+29D

description: Column name in processed data file: 176


title: HSV1_Ctrl_B

value: human conjunctiva air-liquid interface

value: 17 days

value: 96h after infection


title: DMSO_2

value: DMSO


title: Subject 100531, D0

description: Column name in processed data file: 182

value: Control


title: DMSO_1


title: HCT116 GNAS R201C/+, rep3

value: HCT116 GNAS R201C/+

value: colon cancer cell line

value: GNAS R201C/+


title: HCT116 GNAS R201C/+, rep2


title: Subject 100465, B+7D

description: Column name in processed data file: 175


title: HCT116 parental, rep1


title: HCT116 parental, rep2


title: Subject 100531, B+1D

description: Column name in processed data file: 174


title: BM_REL_123

city: Heidelberg

first: Anna

last: Mathioudaki

state: None / N/A

address: Meyerhofstraße 1, 1

institute: EMBL Heidelberg

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Sample demultiplexing based on genotypes was performed using souporcell (https://www.nature.com/articles/s41592-020-0820-1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow aspirates

extract_protocol:
Ficoll-processed primary BM samples were sorted into CD34+ and CD3+ fractions.
Library was performed according to the manufacter’s protocol CG000204 (single cell 3’ v2 protocol, 10x Genomics).

value: T cells & HSPCs

value: Bone marrow aspirates

tag: patient diagnosis

value: acute myeloid leukemia

value: relapse (REL)


title: Subject 100302, B+1D

description: Column name in processed data file: 173

value: Blood


title: hAdV8_virus_C

data_processing:
Sequencing was performed at Single Cell Discoveries, a sequencing service provider located in the Netherlands using an adapted version of the CEL-seq protocol. In brief:
Total RNA was extracted using the standard Qiagen RNAeasy kit according to the manufacturer's instructions and used for library preparation and sequencing. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq [Hashimshony et al. 2012; PMID: 22939981 and Simini et al, 2014; PMID: 25500896]. In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the reference transcriptome using BWA MEM [Li and Durbin, 2009; PMID 20080505]. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script.
Assembly: hg19
Supplementary files format and content: tab-delimited csv file including read counts for all samples

value: hAdV8 infection for 3 hours


title: Subject 100302, P+57D

description: Column name in processed data file: 171

value: Prime


title: Subject 100531, B+7D

description: Column name in processed data file: 172

value: MVA-BN-Filo

value: Boost


title: hAdV8_virus_B

value: human conjunctiva air-liquid interface


title: Subject 100531, P+3H

description: Column name in processed data file: 170


title: hAdV8_virus_A

value: 17 days


title: hAdV8_Ctrl_C

value: uninfected

value: 96h after infection


title: Subject 100302, D0

description: Column name in processed data file: 169

value: Control


title: Subject 100531, P+1D

description: Column name in processed data file: 168


title: Subject 100302, P+1D

description: Column name in processed data file: 167


title: hAdV8_Ctrl_B


title: hAdV8_Ctrl_A


title: Tumor sample from Patient 27, post-immunotherapy treatment

description: RMA expression value derived from Affymetrix Expression Console software

hyb_protocol: Hybridization was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays".

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing.

data_processing: The RNA samples quantification on Affymetrix Arrays was performed in two separate batches. Samples from each batch were processed independently using Affymetrix Expression Console Software version 1.4.1.46. Initially the samples were normalized using the SST-RMA algorithm and outlier samples were excluded. Samples from the two batches were then combined into a single dataset and subject to batch normalization using ComBat. Finally all the samples were further normalized together using LOESS normalization. For genes with multiple measurements, we selected the measurement with the highest coefficient of variation. Here we provide the CHP files with the SST-RMA normalization alone, but we can provide the SST-RMA+loess normalize gene expression values upon request.   affymetrix-algorithm-name = sst-rma-gene-full  affymetrix-algorithm-version = 1.0  affymetrix-array-type = Clariom_D_Human  program-name = Expression Console  program-version = 1.4.1.46

source_name: NSCLC patient

label_protocol: Labeling was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Trascript Expression Arrays".

extract_protocol: RNA was extracted from FFPE samples using the RecoverAll Total Nucleic Acid Isolation from Thermo Fisher Scientific (Catalog Number: AM1975).

tag: gender

value: Female

tag: tumor site

value: Lymph node

tag: tumor type

value: Non-Small Cell Lung Cancer (NSCLC)

value: Post-treatment

tag: sample type

value: FFPE


title: Tumor sample from Patient 29, post-immunotherapy treatment

value: Spine


title: Subject 100458, P+29D

description: Column name in processed data file: 166

tag: tissue


title: Jurkat cells - control IP

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

institute: CIB-CSIC

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human/mouse genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak calling was done with MACS2 v.2.2.7.1: broad peaks mode with a cutoff for the broad region of 0.1; q-value (minimum FDR) cutoff to call significant regions was 0.05.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: peak files; BW = signal map in bigWIG format (UCSC) normalized by a scaling factor determined from the sequencing depth

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol:
Cells were washed, strained and fixed with 1% formaldehyde for 4 min and quenched with 0.125 M glycine.  Lysates were sonicated with a Diogenode Bioruptor to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4º C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Jurkat cells were cultured in suspension or in 3D conditions (a type I collagen matrix of 1,7 mg/mL) for 3 hours.

value: Jurkat

value: untreated


title: Tumor sample from Patient 26, post-immunotherapy treatment

value: Male


title: Tumor sample from Patient 25, post-immunotherapy treatment

value: Sternum


title: Tumor sample from Patient 29, pre-immunotherapy treatment

value: Lung

value: Pre-treatment


title: Subject 100302, B+7D

description: Column name in processed data file: 165

value: Blood

value: MVA-BN-Filo

value: Boost


title: Tumor sample from Patient 25, pre-immunotherapy treatment


title: Jurkat cells - H3K4me3 - 3D - rep3

tag: chip antibody

value: H3K4me3 (Cell signaling, Cat 9751S, Lot 14)

value: cultured in 3D conditions for 3 hours


title: Tumor sample from Patient 26, pre-immunotherapy treatment


title: Tumor sample from Patient 23, pre-immunotherapy treatment


title: Tumor sample from Patient 21, post-immunotherapy treatment


title: Subject 100458, D0

description: Column name in processed data file: 164

value: Control


title: Tumor sample from Patient 19, post-immunotherapy treatment

value: Female

value: Adrenal


title: Tumor sample from Patient 23, post-immunotherapy treatment

value: Lymph node

value: Non-Small Cell Lung Cancer (NSCLC)

value: Post-treatment


title: Tumor sample from Patient 22, post-immunotherapy treatment

value: Kidney

value: FFPE


title: Tumor sample from Patient 24, post-immunotherapy treatment

value: Male


title: Tumor sample from Patient 27, pre-immunotherapy treatment


title: Subject 100302, B+3H

description: Column name in processed data file: 163


title: Jurkat cells - H3K4me3 - 3D - rep2

tag: cell type

value: Jurkat


title: Tumor sample from Patient 28, post-immunotherapy treatment

value: Femor


title: Tumor sample from Patient 20, post-immunotherapy treatment

value: Lung


title: Tumor sample from Patient 17, post-immunotherapy treatment


title: Jurkat cells - H3K4me3 - 3D - rep1

tag: treatment


title: Tumor sample from Patient 19, pre-immunotherapy treatment

value: Pre-treatment


title: Tumor sample from Patient 16, post-immunotherapy treatment


title: Subject 100458, B+3H

description: Column name in processed data file: 162

value: Blood

value: MVA-BN-Filo


title: Tumor sample from Patient 15, post-immunotherapy treatment


title: Jurkat cells - H3K4me3 - control - rep3

value: H3K4me3 (Cell signaling, Cat 9751S, Lot 14)

value: untreated


title: Tumor sample from Patient 18, post-immunotherapy treatment


title: Tumor sample from Patient 14, post-immunotherapy treatment


title: Subject 100302, P+7D

description: Column name in processed data file: 161

value: Prime


title: Subject 100458, B+1D

description: Column name in processed data file: 160

value: Boost


title: Tumor sample from Patient 20, pre-immunotherapy treatment

value: Female


title: Jurkat cells - H3K4me3 - control - rep2


title: Tumor sample from Patient 13, post-immunotherapy treatment


title: Tumor sample from Patient 14, pre-immunotherapy treatment

value: Brain


title: Jurkat cells - H3K4me3 - control - rep1