title: PL292_v

description:
Library name: M20086
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Male


title: HPC-7, p42, LPS 2h, H3K27Ac, HiChIP, R1

status: Public on Mar 11 2025

type: SRA

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

library_source: genomic

data_processing:
HiChIP reads were mapped to the mm39 genome with the BWA-MEM software (v. 0.7.17) with specific settings to allow mapping of ligation events (bwa mem -5SP).
Alignment files were further processed with the ‘pairtools’ software to identify and record valid ligation events (pairtools parse) and to remove PCR duplicates (pairtools dedup).
Loop calling and differential loop analysis were performed with FitHiChIP.
Assembly: mm39
Supplementary files format and content: tab-delimited text files in bedpe format include predicted loops for each condition and common and condition-specific loops derived from differential loop analysis.
Library strategy: HiChIP

molecule: genomic DNA

organism: Mus musculus

growth_protocol: HPC-7 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco 12440-053) supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco 15140-122), 1% L-glutamine (Gibco 25030-024), 50μM b-mercaptoethanol (Gibco 31350-010), and 50 ng/mL murine SCF (Miltenyi Biotec, 130-101-697).

extract_protocol:
HiChIP was performed in duplicates using Dovetail Genomics’ HiChIP MNase kit and following manufacturer’s instructions. Briefly, 5x10^6 cells were pelleted to then be crosslinked, digested with MNase and lysed. After quality control, 1000ng of lysate were incubated with H3K27ac antibody.
Samples were then proximity ligated and DNA was purified for library preparation, followed by ligation capture and amplification.

treatment_protocol: For TLR4 stimulation, cells were exposed to LPS (Escherichia coli O111:B4, Sigma L2630) at a final concentration of 100 ng/mL

tag: cell line

tag: treatment

value: LPS 2h

tag: chip antibody

value: H3K27ac antibody (Cell Signaling, 8173)


title: G4: 400 µg QS-21 SMNP at week 12 2/2 HTO

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

description: Library name: SMNP_PBMC_W12_G4_2_HTO

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2.0 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Env-binding memory B cells at week 12 from 50 µg and 400 µg QS-21 SMNP groups were stained with tetramerized BG505 MD39 probes using fluorescent-SA and TotalSeq-C oligo-tagged fluorescent-SA, surface antibodies and six different TotalSeq-C oligo-tagged anti-b2M & CD298 antibodies to multiplex animal samples. Samples were sorted on a FACSymphony S6 (BD Biosciences) into 1.5 mL tubes with FBS supplemented RPMI media.
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v2.

tag: tissue

value: PBMC

tag: cell type

value: B cell


title: PBS 1hr treated BMDM, RNA-seq, replicate 2

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

country: South Korea

institute: Severance Hospital

description: Library name: WT_Control_R2

library_source: transcriptomic

data_processing:
RNA-seq : Sequencing yielded paired-end reads with a read length of 101 bp. Prepared bulk RNA-seq library quality was checked using FastQC (v0.11.9). Reads were aligned to the GRCm38 reference genome using HISAT2 (v2.1.0). The resulting SAM files were converted to BAM files and indexed using SAMtools (v1.17). A count matrix was constructed using featureCounts (v2.0.0) .
Assembly: mm10 (GRCm38)
Supplementary files format and content: RNA-seq : count matrix

source_name: Bone Marrow Derived Macrophages

growth_protocol: BMs were extracted from the femur and tibia of mice. To generate BMDMs, BM cells were cultured in Dulbecco’s Modified Eagle’s Medium (HyClone, SH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco, 10099141) and 20% L929-conditioned media. After 6 d in culture, cells were seeded and treated under the indicated conditions.

extract_protocol:
RNA-seq : Total RNA was extracted from samples using TRIzol reagent (Invitrogen, 15596018) following the manufacturer’s protocol. 500 ng of total RNA was used for library preparation.
RNA-seq : Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Globin Kit, following the manufacturer’s instructions.

value: Bone Marrow Derived Macrophages

tag: genotype

value: PBS

tag: batch


title: Sorted-DC2_5dpRT_2

type: RNA

city: Stanford

first: Sirimuvva

last: Tadepalli

state: CA

address: 299 Campus Drive

institute: Stanford University

data_processing: Data was analyzed by ROSALIND® with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Normalization, fold changes and p-values were calculated using criteria provided by NanoSTRING ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual

source_name: Sorted Myeloid cells

growth_protocol: B16F1 tumor cells were implanted into C57BL/6J mice and treated with radiationtherapy (20Gy) once the tumor reached 40-100 mm3.

extract_protocol: Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoSting nCounter® Mouse Myeloid Innate Immunity V2 Panel Standard Platform according to the manufacturer’s instructions.

treatment_protocol: Tumors were digested with collogenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for DC2s or TAMs

tag: treatement

value: Radiation (20Gy)

tag: timepoint


title: Sorted-DC2_5dpRT_1


title: HPC-7, p30, UT, H3K27Ac, HiChIP, R2


title: high-grade endometrial cancer-3

city: Fukuoka

first: Kazuhisa

last: Hachisuga

address: 1-1, Maidashi 3-chome

country: Japan

institute: Kyushu University Hospital

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.36) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

organism: Homo sapiens

source_name: endometrial cancer

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

tag: gender

value: female

value: endometrial cancer

tag: group

value: high-grade endometrial cancer


title: PBS 1hr treated BMDM, RNA-seq, replicate 1

description: Library name: WT_Control_R1


title: HPC-7, p30, UT, H3K27Ac, HiChIP, R1


title: Sorted-DC2_5dpRT_3


title: G4: 400 µg QS-21 SMNP at week 12 1/2 HTO

description: Library name: SMNP_PBMC_W12_G4_1_HTO


title: PL292_strom

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
Library name: M20084
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

data_processing:
Raw sequencing reads were trimmed to remove the UMI, Illumina TruSeq 3’ adapter sequence, and all nucleotides after the 3’ adapter. Pre-processed reads were aligned to the genome for seven small non-coding RNAs using the miRMaster2 online tool. Raw read counts were processed using R. Data was batch-corrected using COMBAT-seq. Low quality samples and sequences were removed, and data was normalized per sncRNA species separately using the Relative Log Expression (RLE) method and scaled by counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Raw count matrix of all samples before quality control and normalization

source_name: placenta

extract_protocol:
Sorted cells were isolated from fresh chorionic villi using FACS as described in GSE159526. Sorted cells and chorionic villi samples were extracted using the ZYMO Quick-RNA MiniPrep kit according to manufacturer’s instructions or using TRIzol (ThermoFisher Scientific, USA).
5.8S rRNA was masked during adapter ligation by a complementary oligonucleotide, while miRNAs underwent 3′ adapter ligation, digestion of unligated adapters, and 5′ adapter ligation sequentially. The 5′ adapter contains a unique molecular identifier (UMI), followed by two nucleotides (CA) prior to the miRNA sequence. Upon conversion to cDNA by reverse transcription, the cDNA was amplified by PCR to include the sequences required for Illumina cluster generation and sample indexing developed by the GSC. The number of PCR cycles was dependent on the amount of input RNA; samples with low and high input were subjected to 20 and 15 cycles of PCR, respectively. Quality of libraries was assessed using the Agilent Bioanalyzer 2100 HS DNA chip Assay, (Agilent, USA)

treatment_protocol: All samples were stored in RNAlater (ThermoFisher Scientific, USA) upon sampling and prior to extraction

tag: case id

value: placenta

value: Stromal

tag: gestational age

tag: trimester

tag: fetal sex

tag: plate

tag: extraction type

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: high-grade endometrial cancer-2


title: G2: 50 µg QS-21 SMNP at week 12 HTO

description: Library name: SMNP_PBMC_W12_G2_1_HTO


title: PM367_vc

description:
Library name: M20081
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi

value: Term

value: Female

value: Villi:TRIzol; Operator 2


title: high-grade endometrial cancer-1


title: PM367_hofb

description:
Library name: M20079
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Hofbauer


title: HPC-7, p30, LPS 2h, H3K27Ac, HiChIP, R1

tag: cell line

value: LPS 2h

value: H3K27ac antibody (Cell Signaling, 8173)


title: PM367_strom

description:
Library name: M20077
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette


title: low-grade endometrial cancer with p53 abnormal expression-3


title: G2: 50 µg QS-21 SMNP at week 12 VDJ

description: Library name: SMNP_PBMC_W12_G2_1_VDJ

value: PBMC

value: B cell


title: HPC-7, p42, UT, INPUT

data_processing:
ChIP-seq reads were pre-processed with TrimGalore v0.6.6 for quality and adapter trimming.
Trimmed reads were aligned to mouse genome mm39 using Bowtie2 v. 2.4.4 with ‘--very-sensitive’ flag set and a minimum fragment length (-X flag) of 1000bp, all other parameters set to default.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis.
ChIP-seq peaks were identified by MACS2 v. 2.2.5 for individual replicates and pooled replicates for each condition, using input libraries as control. Peaks identified in each condition were merged with bedtools merge (v. 2.31.1) to generate a common peak set.
Reads from each sample were quantified over the common peak set using the regionCounts function from the csaw R package and differential binding analysis was performed with DESeq2
Assembly: mm39
Supplementary files format and content: bigWig files for each sample, generated with deeptools bamCoverage and normalized by counts per million mapped reads (CPM)
Supplementary files format and content: tab-delimited text files include narrowPeak files from MACS2 and merged peaks in bed format.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and lysed (1% Triton, 0.1% sodium deoxycholate, 0.1% SDS, 0.2M NaCl, 10mM Tris pH 7.5, 10mM EDTA and 1X protease inhibitor cocktail (Roche 11836170001)). Sonication was performed in the same buffer with 0.5% SDS in a Bioruptor (Diagenode) for 60 cycles (30s ON 30s OFF), vortexing every 20 minutes. Sodium butyrate 5mM was added to the buffers in the cells for the H3K27ac ChIP to inhibit deacetylases. For H3K4me1 ChIP-seq, DNA was digested in 50mM Tris pH 7.5, 4mM MgCl2 and 2mM CaCl2 with 10U micrococcal nuclease (Thermo Scientific EN0181) for 15 min at 22ºC. Lysates were incubated with 4 µg of H3K27ac antibody (Abcam ab4729), 8µg of anti-ERa (sc-8002X) or 3µg anti-H3K4me1 (Diagenode, C15410194) overnight at 4ºC. Antibody-bound chromatin was pulled down with protein G Dynabeads (Invitrogen 10003D). Samples were washed, RNase-treated and reverse cross-linked by incubation at 65°C in 1% SDS, 0.1M NaHCO3 and proteinase K. DNA was purified using ChIP DNA Clean & Concentrator Kit (Zymo D5205)
Libraries were prepared using the NEBNext Ultra DNA Library Prep kit (E7645, New England Biolabs).

tag: treatment


title: PM367_troph

description:
Library name: M20075
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Cytotrophoblast


title: low-grade endometrial cancer with p53 abnormal expression-2


title: Sorted-DC2_0dpRT_1

value: nontreated control


title: PM367_endo

description:
Library name: M20074
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Endothelial


title: G4: 400 µg QS-21 SMNP at week 12 2/2 GEX

description: Library name: SMNP_PBMC_W12_G4_2_GEX


title: HPC-7, p30, UT, INPUT

tag: chip antibody


title: low-grade endometrial cancer with p53 wild-type expression-3

value: female

tag: tissue

value: endometrial cancer


title: G4: 400 µg QS-21 SMNP at week 12 1/2 GEX

description: Library name: SMNP_PBMC_W12_G4_1_GEX

tag: cell type


title: HPC-7, p42, UT, ER, ChIP

value: ERα (sc-8002, Santa Cruz Biotechnology)


title: PL289_strom

description:
Library name: M20070
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: placenta

value: Stromal

value: Male


title: HPC-7, p30, LPS 2h, H3K27Ac, HiChIP, R2


title: G4: 400 µg QS-21 SMNP at week 12 2/2 VDJ

description: Library name: SMNP_PBMC_W12_G4_2_VDJ


title: PL289_v

description:
Library name: M20072
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

value: Villi


title: HPC-7, p30, UT, ER, ChIP


title: HPC-7, p30, UT, H3K4me1, INPUT


title: HPC-7, p42, UT, H3K4me1, INPUT


title: G2: 50 µg QS-21 SMNP at week 12 GEX

description: Library name: SMNP_PBMC_W12_G2_1_GEX


title: low-grade endometrial cancer with p53 wild-type expression-2


title: low-grade endometrial cancer with p53 wild-type expression-1


title: Cowc_MicroC

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

institute: Centre for Genomic Regulation (CRG)

data_processing:
*library strategy: Micro-C
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1; Ephydatia muelleri genome assembly Emue_v2; Trichoplax adhaerens genome assembly TadhH1_v1
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedGraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedGraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops

organism: Capsaspora owczarzaki

growth_protocol: Capsaspora owczarzaki strain ATCC30864 was maintained in axenic culture at 23 ºC in the ATCC medium 1034 (modified PYNFH medium). Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.  Trichoplax adhaerens colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
Capsaspora owczarzaki cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392).  Mnemiopsis leidyi specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water by triturating every 2 min for a total of 10 min. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. Seven days post hatching sponges Ephydatia muelleri were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Next, animal tissues were dissociated into cells and double crosslinked with 1% formaldehyde and 3 mM DSG. Crosslinked cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate choanocytes. Trichoplax adhaerens specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).

treatment_protocol: To synchronize cells in G1/early S phase, C. owczarzaki cells were treated with 100 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours. Synchronised cells were scraped off the surface and pelleted at 2,200 g for 5 min at room temperature (RT).

value: filopodial cells

tag: genotype

value: wild type

value: 100 mM hydroxyurea for 18 hours


title: PL289_endo

description:
Library name: M20069
Size selection for small RNAs (upto 30 nucleotides) was conducted using the Blue Pippin 3% agarose gel cassette

tag: batch

value: Sorted-cells:Zymo Quick-RNA Miniprep


title: G4: 400 µg QS-21 SMNP at week 12 1/2 VDJ

description: Library name: SMNP_PBMC_W12_G4_1_VDJ


title: HPC-7, p42, UT, H3K4me1, ChIP, R2

value: H3K4me1 (Diagenode, C15410194)


title: Emue_MicroC

organism: Ephydatia muelleri

source_name: choanocytes

value: choanocytes


title: Spheroid_Spk-hAAT-GFP

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: 10x Genomics

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvain algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Assembly: GRCh38
Supplementary files format and content: Sparse Cellranger matrix

source_name: hiPSC-derived brain spheroids

growth_protocol: Generation of 3D spheroids was performed as previously described (Marton et al., 2019). hiPSCs were plated as single cells on AggreWell-800 plates (StemCell Technologies) in Essential 8 medium (Thermo Fisher Scientific) in the presence of 10 μM of Rock inhibitor Y-27632. After 24h, hiPSC-derived embryoid bodies (EBs) were transferred in low attachment 10-cm dishes and cultured in Essential 6 medium (Thermo Fisher Scientific) with 10 μM SB431542 and 2.5 μM dorsomorphin (Sigma-Aldrich), by adding 5 μM IWP-2 (Selleckchem) at day 4 of differentiation. At day 5, culture medium was changed in Differentiation and Maintenance Medium (DMM) containing DMEM/F12 1:1 media (Thermo Fisher Scientific), B-27 supplement without vitamin A (1:50), N2 supplement (1:100), minimum essential media (MEM) non-essential amino acids (1:100; Thermo Fisher Scientific), GlutaMax (1:100; Thermo Fisher Scientific), 25 μg/ml human insulin (Sigma-Aldrich), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), and penicillin/streptomycin. The DMM was supplemented with 20 ng/ml EGF, 20 ng/ml bFGF and 5 μ M IWP-2 from day 5 to 24, by adding 1 μ M SAG (smoothened agonist, Sigma-Aldrich) at day 12. At day 25, the culture medium was switched in DMM supplemented with 60 ng/ml T3, 100 ng/ml biotin (Sigma-Aldrich), 20 ng/ml NT-3, 20 ng/ml BDNF (PeproTech), 1 μM cAMP (Sigma-Aldrich), 5 ng/ml HGF, 10 ng/ml human IGF-1, and 10 ng/ml PDGF-AA to induce glia differentiation. To favor glia maturation, the DMM medium was supplemented with 60 ng/ml T3, 100 ng/ml biotin, 1 μM cAMP and 20 μg/ml ascorbic acid from day 37 to 150.

extract_protocol:
Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12-14 cycles, according to the available cDNA quantity).
scRNA-Seq libraries were prepared according to the manufacturer’s instructions

treatment_protocol: Brain spheroids of 150 days were individually transduced with the different vectors, 2 spheroids per condition. Organoids were harvested after 2 or 5 days of transduction for library preparation.

value: hiPSC-derived brain spheroids

value: Spk100-hAAT-GFP 5 days


title: Cowc_ChIP_H3K4me3

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
peaks were called with MACS2.
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1; Ephydatia muelleri genome assembly Emue_v2; Trichoplax adhaerens genome assembly TadhH1_v1
Supplementary files format and content: BigWig

growth_protocol: Capsaspora owczarzaki strain ATCC30864 was maintained in axenic culture at 23 ºC in the ATCC medium 1034 (modified PYNFH medium). Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. For experiments we used adult lobate animals that were starved for 2 days.  Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.  Trichoplax adhaerens colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
Capsaspora owczarzaki cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392).  Mnemiopsis leidyi specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water by triturating every 2 min for a total of 10 min. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. Seven days post hatching sponges Ephydatia muelleri were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Next, animal tissues were dissociated into cells and double crosslinked with 1% formaldehyde and 3 mM DSG. Crosslinked cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate choanocytes. Trichoplax adhaerens specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation. The pool of chromatin was incubated for 14 - 16 hours at 4 ºC with 6 µL (3.4 µg) anti-H3K4me2 (Abcam, ab32356), 2.5 µL anti-H3K4me3 (Millipore, 07-473), 5 µL (5 µg) anti-SMC1 (ThermoFisher , A300-055A) or 2 µL (2 µg) anti-H3 (Abcam, ab1791).

value: H3K4me3, Millipore, 07-473


title: Spheroid_Spk-CAG-LUC

description: 10x Genomics

value: Spk100-CAG-LUC 5 days


title: Cowc_ChIP_H3

value: H3, Abcam ab1791


title: Nvec_MicroC

data_processing:
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedgraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedgraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops
Supplementary files format and content: domains.bed includes genomic coordinates of identified chromatin domains
Library strategy: Micro-C

organism: Nematostella vectensis

source_name: Nematostella vectensis

growth_protocol: Sphaeroforma arctica culture was grown in Marine Broth (37.4 g/L) at 12 ºC. Salpingoeca rosetta culture was kept in artificial sea water with salinity 33 ppt supplemented with 4 % CGM3 and 4 % SWC at 23 ºC. Nematostella vectensis specimens were grown in 1/3 artificial sea water with salinity 14 ppt at 25 ºC. Cladtertia collaboinventa colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).

treatment_protocol: To synchronize cells in G1/early S phase, S. arctica cells were treated with 200 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours, S. rosetta culture was treated with 0.05 mM aphidicolin for 18 hours.

value: neuronal ELAV+ cells


title: HPC-7, p42, UT, H3K4me1, ChIP, R1


title: Spheroid_Spk-CAG-GFP

description: 10x Genomics

value: Spk100-CAG-GFP 5 days


title: Cowc_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: low-grade endometrial cancer with p53 abnormal expression-1

value: female

value: endometrial cancer


title: HPC-7, p30, UT, H3K4me1, ChIP, R2


title: Chicken 7 Tissue

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

description: Library name: Sample 2

data_processing:
Read quality was assessed using FastQC, and high-quality reads were mapped to the galgal5.0.91 transcriptome. CellRanger was used to conduct read alignment and gene expression counts for single-nuclei RNA sequencing. Single-nuclei RNA sequencing data was normalized and log transformed using R package Seurat. R and corresponding R scripts were then used for data preparation procedures, analysis procedures, and visualization. Data was stored on GitHub and figshare respositories, and Zenodo was used to create Digital Object Identifiers (DOIs) for publication citations. Gene Set Enrichment Analysis with the fgsea package was used for pathway analysis, and gene signatures were acquired from the Molecular Signatures Database (MSigDB).
Assembly: galgal5.0.91 transcriptome
Supplementary files format and content: snRNAseq_cellTypes_CLEAN.RData

molecule: nuclear RNA

organism: Gallus gallus

source_name: lung tissue

extract_protocol:
Organoids were harvested for single-nuclei RNA sequencing via collection from the Matrigel matrix using the cleaning protocol previously described. Organoids were resuspended in 500 µL DMEM/F12 and transferred to a cryovial. After centrifuging at 100 x g (4°C) for 5 minutes, the supernatant was removed, and the sample was flash-frozen in liquid nitrogen for 30 seconds. Samples were stored in a -80°C freezer and sent to Genewiz from Azenta Life Sciences (South Plainfield, NJ, USA) on dry ice for analysis.
Upon arrival, tissue and organoid samples were stored in liquid nitrogen for further processing. Using the manufacturer’s instructions, nuclei were extracted from both samples using Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec, Auburn, CA, USA), in addition to gentle MACS Dissociation and C tubes. Once isolated, AO/PI dye was used on the Nexcelom Cellaca MX to count the nuclei, and a Chromium Single Cell 3’ kit (10X Genomics, CA, USA) was used to create single nuclei RNA libraries. Following the manufacturer’s guidelines, the nuclei were loaded and processed on the Chromium X, targeting approximately 6,000 gel bead-in-emulsions (GEMs) per sample. An Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) evaluated quality of the sequencing libraries, and a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) quantified them. qPCR (Applied Biosystems, Carlsbad, CA, USA) was also used to quantify libraries before loading the samples on an Illumina HiSeq 4000 (or equivalent) instrument. Then, samples were sequenced using the 10X Genomics recommended guidelines. The raw sequence data (.bcl files) were converted to fastq files before being de-multiplexed with the Genomics’ cellranger mkfastq command.

value: lung tissue


title: HPC-7, p30, UT, H3K4me1, ChIP, R1


title: Chicken_Day2_Rep2_scRNAseq

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

institute: Achucarro BCN

description: 10X Chronium v3.7

data_processing:
For both species, 10X CellRangerv6.0.2 was employed for alignment and demultiplexing of FASTQ files to obtain feature-barcode matrices. The genomes used as reference for each species alignment were mm10-2020-A for mouse and Gallus_gallus6_98for chicken. The quality control statistics related to this alignment steps and others are summarized in Supplementary Table S4. Afterwards, data matrices were imported to R(v4.1.0), where Seurat (v4.1.0) (60)was employed to further analysis, as describe in their vignettes (https://satijalab.org/seurat/).
Assembly: mm10-2020-Afor mouse and Gallus_gallus6_98for chicken
Supplementary files format and content: Output folder of 10X CellRanger v6.0.2 (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

molecule: polyA RNA

source_name: Brain

extract_protocol:
Isolation of birthdated cells for scRNAseq was performed as previously described(28). Briefly, chick and mouse embryos were birthdated at early neurogenic timepoints (E4 or E12, respectively) and sacrificed either two or eleven days after EdU injection. P3 postnatal mouse pups and E15 chick embryos were anesthetized by hypothermia after immersion of either pup or the chick egg in ice. Brains were extracted in ice-cold HBSS. Then, the pallial region was microdissected under a stereomicroscope, collected in ice-cold HBSS, pooled and cut into small pieces. Tissue was dissociated in a species and stage specific manner, according to Supplementary Table S3.Following enzymatic digestion, chick (both E6 and E15) and mouse P3 tissue was manually homogenized by carefully pipetting and tissue clogs were removed by filtering the cell suspension through a 40 μm nylon strainer to a 15 ml Falcon tube containing 4 mlof 25% fetal bovine serum (FBS) in HBSS. After mouse E14 tissue digestion, FBS was added to the mix, cells were manually dissociated by pipetting and tissue clogs were removed by filtering the cell suspension though a 40 μm nylon strainer. Dissociated cells were then centrifuged at 200g for 10 min at room temperature (RT) and EdU molecule was detected in the pelleted cells. Following reaction, cells were washed thrice by centrifugation at 200g for 10 min and suspended in 1 ml of HBSS then passed on a 50 μm cell strainer. PI-/EdU+ cells, gated to include only the top 10% brightest cells, were finally FAC-sorted: for the E6 chick E6 a Synergy 3200 2L sorter (Sony) was used; for the E15 chick sample a FACSAria (BD Biosciences) was used; and for both mice samples a FACS Jazz (BD Biosciences) was used.
Cells were processed for single cell GEM formation following the standard Chromium Single Cell 3’ v3.1. Briefly cells were placed at the Chromium chip with the beads and reagents for the RNA capture and cDNA amplification. After the emulsion were obtained, the cDNA was amplificated in a thermocycler. Post amplificated cDNA, now marked with individual cell barcode, were fragmented, ligated the sequencing adapters and amplified. After that, the PCR product were purified and quantified.
Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) User Guide” (Document number CG000315). Resulting libraries were sequenced on a Novaseq 6000 for an approximated 50.000 reads per cell.

value: Brain

value: Wild-type

tag: Stage


title: Spheroid_AAV9-CAG-GAA

description: 10x Genomics

value: AAV9-CAG-GAA 5 days


title: Spheroid_AAV9-CAG-GFP

description: 10x Genomics

value: AAV9-CAG-GFP 5 days


title: HPC-7, p42, UT, INPUT, R3


title: Chicken 7 Tissue_rep3 [RO-33]

description: Library name: Chicken 7 Tissue_rep3

data_processing:
Read quality was assessed using FastQC, and high-quality reads were mapped to the galgal5.0.91 transcriptome. Kallisto was used to conduct read alignment and gene expression counts for bulk RNA sequencing. R and corresponding R scripts were then used for data preparation procedures, analysis procedures, and visualization. Data was stored on GitHub and figshare respositories, and Zenodo was used to create Digital Object Identifiers (DOIs) for publication citations. Gene Set Enrichment Analysis with the fgsea package was used for pathway analysis, and gene signatures were acquired from the Molecular Signatures Database (MSigDB).
Assembly: galgal5.0.91 transcriptome
Supplementary files format and content: .xlsx includes TPM for all samples

extract_protocol:
After at least 4 passages, organoids were preserved for bulk RNA-sequencing by following the cleaning protocol described in the development and maintenance of organoid cultures section. After removing 6 mL of DMEM/F12 supernatant, the cell pellet was resuspended in 100 µL PBS, moved to a cryovial containing 900 µL RNAlater (Invitrogen; AM7021), and stored at -80°C. For RNA extractions, the organoids samples were thawed and transferred to 15 mL tubes, washed with 2 mL of PBS, and centrifuged at 1,200 x g (4°C) for 5 minutes. The supernatant was removed, the cell pellet was resuspended in 1 mL of Trizol (Invitrogen; 15596026), and each sample was briefly vortexed. Flash frozen tissues were transferred from cryovials to microcentrifuge tubes, 800 µL of Trizol were added to each tube, and tissues were pestled until homogenized. Both tissue and organoid samples were left at room temperature for five minutes before centrifuging at 12,000 x g (4°C) for 10 minutes. The supernatant was transferred to a microcentrifuge tube, and 160 µL or 200 µL of chloroform (Alfa Aesar; J67241) were added for tissues and organoids, respectively. The samples were vigorously mixed by shaking for 20 seconds. After sitting at room temperature for 2-3 minutes, samples were spun at 10,000 x g for 18 minutes (4°C). The aqueous top layer was collected and moved to a sterile RNase-free tube before adding an equal amount of 100% RNA-free ethanol. Up to 700 µL were loaded in a Qiagen RNeasy column and collection tube (RNeasy Mini kit; Qiagen; 74104). Samples were centrifuged at 8,000 x g for 30 seconds, the waste in the collection tube was discarded, and DNase treatment was performed according to Qiagen’s protocol (Qiagen; 79254). In a new collection tube, 500 µL buffer RPE was added to the column, and the samples were spun at the same settings as before. After discarding the flow-through, this step was repeated, but samples were now spun for 2 minutes at 8,000 x g. The flow-through was discarded again, and the samples were centrifuged at the same settings for 1 minute. 50 µL of RNase-free water (Sigma; W4502-50ML) was added to the column and incubated for 2 minutes. Samples were centrifuged twice at 8,000 x g for 1 minute. RNA concentration was determined with a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and samples were kept at -80°C until shipped.
All samples were sent to Azenta Life Sciences (South Plainfield, NJ, USA) for preparation of the RNA library and bulk RNA sequencing. A Quibit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) was first used to quantify RNA, followed by assessment of the RNA integrity with an Agilent TapeStation 4200 instrument (Agilent Technologies, Palo Alto, CA, USA). A NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was used to prepare the RNA sequencing libraries, using the manufacturer's instructions. Then the mRNA was enriched with Oligo(dT) beads and fragmented for 15 minutes (94°C). Both cDNA strands were synthesized, and at the 3’ ends, fragments were end-repaired and adenylated. The cDNA fragments were ligated with universal adapters, and limited-cycle PCR was used for index addition and library enrichment. An Aligent TapeStation (Agilent Technologies, Palo Alto, CA, USA) was utilized to confirm the sequencing libraries, and both a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA) were used for quantification. Sequencing libraries were multiplexed and clustered onto one flow cell. Using the manufacturer’s protocol, an Illumina instrument was then used to sequence the samples with 2x150bp Paired End (PE) configuration. Control Software (HCS) was used for image analysis and base calling. Illumina HiSeq created raw sequence data (.bcl files), which were converted to fastq files and de-multiplexed with Illumina's bcl2fastq 2.17 software. For index sequence identification, one mismatch was allowed.

value: SPF White Leghorn chicken


title: Chicken_Day2_Rep3_scRNAseq

description: 10X Chronium v3.8


title: Chicken_Day1_Rep1_scRNAseq

description: 10X Chronium v3.5


title: Chicken_Day2_Rep1_scRNAseq

description: 10X Chronium v3.6


title: Chicken 7 Tissue_rep1 [RO-31]

description: Library name: Chicken 7 Tissue_rep1


title: Spheroid_AAV2_Day 5

description: 10x Genomics

value: AAV2-CAG-GFP 5 days


title: Chicken 7 Tissue_rep2 [RO-32]

description: Library name: Chicken 7 Tissue_rep2


title: HPC-7, p42, UT, INPUT, R2


title: Spheroid_UT

description: 10x Genomics

value: hiPSC-derived brain spheroids

value: Untreated 5 days


title: Chicken 7 Organoids_rep3 [RO-42]

description: Library name: Chicken 7 Organoids_rep3

source_name: lung organoid

value: lung organoid


title: Spheroid_Spk_Day 5

description: 10x Genomics

value: AAV Spk100-CAG-GFP 5 days


title: GC41_cx_GACamk

city: Munich

first: Ali

last: Rezaei

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU

description: Library name: GC41_cx

data_processing:
The raw data was quality checked using fastqc (version 0.11.8) and then trimmed of poly(A) tails using Cutadapt (version 1.12). Following trimming, the zUMIs pipeline (version 2.9.4) was used to filter the data, with a Phred quality score threshold of 20 for 2 BC bases and 3 UMI bases. After demultiplexing using demultiplex (v 1.2.2), fastq files were processed using zUMIs (v 2.9.7e) with default settings and a provided barcode listto map to the mouse genome (mm39) with STAR. The count tables were analyzed using the DESeq2 (v 1.44) pipeline in R.
Assembly: mm39
Supplementary files format and content: count table as CSV file; rows are gene names while each column corresponds to a unique sample in the study

source_name: cortex

growth_protocol: mice were sacrificed at 30-40 weeks of age

extract_protocol:
as explained in LaClair et al.: "Tissues were homogenized in Trizol using homogenizer (Precellys). Total RNA was isolated using Direct-zol-96 RNA isolation kit (ZymoResearch) following the manufacturer’s instructions. RNA quantity and quality were controlled on Agilent 2100 BioAnalyzer using Agilent RNA 6000 Nano Kit"
Following extraction and QC, samples were transferred to 96-well plates and RNA-sequencing was performed with 20ng of total RNA using the prime-seq protocol as described in Janjic et al., 2022.  Briefly, reverse transcription was carried out in a 10 uL reaction consisting of 20 ng to total RNA, 30 units Maxima H- enzyme (Thermo Fisher, EP0753), 1x Maxima H- Buffer (Thermo Fisher), 1 mM each dNTPs (Thermo Fisher), 1 uM template-switching oligo (IDT), 1 uM barcoded oligo(dT) primers (IDT). The reaction was incubated at 42 C for 90 minutes. Following cDNA synthesis, the samples were pooled, cleaned, and concentrated with cleanup beads at a 1:1 ratio and eluted in 17 uL of ddH20. Residual primers were digested using Exonuclease I (Thermo Fisher, EN0581) at 37 C for 20 minutes followed by a heat inactivation step at 80 C for 10 minutes. The samples were cleaned once more using cleanup beads at a 1:1 ratio, and eluted in 20 L of ddH2O.  Second strand synthesis and pre-amplification were performed in a 50 uL reaction, consisting of 1x KAPA HiFi Ready Mix (Roche, 7958935001) and 0.6 uM SingV6 primer (IDT), with the following PCR setup: initial denaturation at 98 C for 3 minutes, denaturation at 98 C for 15 seconds, annealing at 65 C for 30 seconds, elongation at 68 C for 4 minutes, and a final elongation at 72 C for 10 minutes. Denaturation, annealing, and elongation were repeated for 5-15 cycles depending on the initial input.  The DNA was cleaned using cleanup beads at a ratio of 1:0.8 of DNA to beads and eluted with 10 uL of ddH2O. The quantity was assessed using a quant-iT PicoGreen dsDNA assay kit (Thermo Fisher, P11496) and the quality was assessed using an Agilent 2100 Bioanalyzer with a High Sensitivity DNA analysis kit (Agilent, 5067-4626).  Libraries were prepared with the NEBNext Ultra II FS Library Preparation Kit (NEB, E6177S) according to manufacturer instructions in most steps, with the exception of adapter sequence and reaction volumes. Fragmentation was performed on 2.5 uL of cDNA (generally 2 - 20 ng) using Enzyme Mix and Reaction buffer in a 6 uL reaction. A custom prime-seq adapter (1.5 uM, IDT) was ligated using the Ligation Master Mix and Ligation Enhancer in a reaction volume of 12.7 uL. The samples were then double-size selected using SPRI-select Beads (Beckman Coulter, B23317), with a high cutoff of 0.5 and a low cutoff of 0.7. The samples were then amplified using Q5 Master Mix (NEB, M0544L), 1 uL i7 Index primer (Sigma-Aldrich), and 1 uL i5 Index primer (IDT) using the following setup: 98 C for 30 seconds; 10-12 cycles of 98 C for 10 seconds, 65 C for 1 minute 15 seconds, 65 C for 5 minutes and 65C for 4 minutes. Double-size selection was performed once more as before using SPRI-select Beads. The quantity and quality of the libraries were assessed as before.  Sequencing was performed on an Illumina HiSeq 1500 flow cell with Read 1 (barcode & UMI): 28 bp, Read 2 (cDNA): 50bp.

value: cortex

value: GACamk


title: GC41_hp_GACamk

description: Library name: GC41_hp

source_name: hippocampus

value: hippocampus


title: HPC-7, p42, LPS 2h, INPUT, R2

value: LPS 2h


title: Spheroid_AAV9_Day 5

description: 10x Genomics


title: Chicken 7 Organoids_rep2 [RO-41]

description: Library name: Chicken 7 Organoids_rep2


title: Chicken 7 Organoids_rep1 [RO-40]

description: Library name: Chicken 7 Organoids_rep1


title: HPC-7, p42, LPS 2h, INPUT, R1


title: Chicken 7 Organoids

description: Library name: Sample 1


title: GC37_hp_ctrl

description: Library name: GC37_hp

value: ctrl


title: GC37_cx_ctrl

description: Library name: GC37_cx


title: HPC-7, p30, UT, INPUT, R3


title: HPC-7, p30, UT, INPUT, R2


title: Spheroid_AAV2_Day 2

description: 10x Genomics

value: AAV2-CAG-GFP 2 days


title: GC35_hp_GACamk

description: Library name: GC35_hp


title: Spheroid_Spk_Day 2

description: 10x Genomics

value: AAV Spk100-CAG-GFP 2 days


title: HPC-7, p42, UT, INPUT, R1


title: Chicken 3 Tissue_rep2 [RO-29]

description: Library name: Chicken 3 Tissue_rep2

value: lung tissue


title: Chicken 3 Tissue_rep1 [RO-28]

description: Library name: Chicken 3 Tissue_rep1


title: HPC-7, p30, UT, INPUT, R1


title: GC35_cx_GACamk

description: Library name: GC35_cx


title: Spheroid_AAV9_Day 2

description: 10x Genomics

value: AAV9-CAG-GFP 2 days


title: HPC-7, p42, LPS 2h, INPUT, R3


title: Chicken 3 Organoids_rep3 [RO-39]

description: Library name: Chicken 3 Organoids_rep3


title: GC34_hp_GACamk

description: Library name: GC34_hp


title: HPC-7, p30, LPS 2h, INPUT, R3


title: GC38_cx_ctrl

description: Library name: GC38_cx


title: Mixed-AAV2-day4

description: 10x Genomics

source_name: hiPSC-derived neural cultures

growth_protocol: Human healthy donor derived iPSC were firstly differentiated into Neural Stem Cells  (NSCs), according to the published Dual Smad inhibition protocol (Chambers et al, 2009).  NSCs were then further differentiated into more committed neural cell types reaching a mixed neural population following a protocol adapted from  Giordano et al, 2023 and Santos et al, 2017. Briefly, NSCs were plated on 48-well plates coated with Matrigel (20,000 cells/cm2) in NSC medium. During the initial 4 days after plating, NSC medium was gradually replaced by an increasing ratio of glial differentiation medium, consisting of NSC basal medium supplemented with 10 ng/ml platelet-derived growth factor AA, 10 ng/ml NT3, 10 ng/ml IGF-1, 5 ng/ml hepatocyte growth factor, and 60 ng/ml T3. For the induction of glial cell maturation, from days 14 to 34 the medium was switched to DMEM/F-12 Glutamax (Thermo Fisher Scientific) supplemented with N2 and B27 (both from Thermo Fisher Scientific), 10% FBS and 10 ng/ml leukemia inhibitory factor (LIF).  Cells were transduced on day 24 of the differentiation protocol, in which neurons, astrocytes and oligodendrocytes are present at different stages of maturation.

treatment_protocol: Mixed cultures grown on 48-well plates were transduced with different AAV serotypes encoding for GFP under the CAG promoter. Cells were harvested after 2 or 4 days of transduction for library preparation.

value: hiPSC-derived neural cultures

value: AAV2-CAG-GFP 4 days


title: GC34_cx_GACamk

description: Library name: GC34_cx


title: Chicken 3 Organoids_rep1 [RO-37]

description: Library name: Chicken 3 Organoids_rep1

value: SPF White Leghorn chicken


title: Spheroid_UT_Day 5

description: 10x Genomics


title: Mixed-Spk-day4

description: 10x Genomics

value: AAV Spk100-CAG-GFP 4 days


title: HPC-7, p30, LPS 2h, INPUT, R2


title: Chicken 3 Tissue_rep3 [RO-30]

description: Library name: Chicken 3 Tissue_rep3


title: GC30_hp_GACamk

description: Library name: GC30_hp


title: Chicken 1 Tissue_rep3 [RO-27]

description: Library name: Chicken 1 Tissue_rep3


title: Mixed-AAV9-day4

description: 10x Genomics

value: AAV9-CAG-GFP 4 days


title: GC31_hp_ctrl

description: Library name: GC31_hp


title: Chicken 1 Tissue_rep1 [RO-25]

description: Library name: Chicken 1 Tissue_rep1


title: Mixed-AAV2-day2

description: 10x Genomics


title: Chicken 1 Organoids_rep3 [RO-36]

description: Library name: Chicken 1 Organoids_rep3


title: GC23_hp_GACamk

description: Library name: GC23_hp


title: GC30_cx_GACamk

description: Library name: GC30_cx


title: Mixed-Spk-day2

description: 10x Genomics


title: HPC-7, p30, LPS 2h, INPUT, R1


title: GC31_cx_ctrl

description: Library name: GC31_cx


title: Mixed-UT-day4

description: 10x Genomics

value: Untreated 4 days


title: HPC-7, p42, UT, H3K27Ac, ChIP, R3

value: H3K27Ac (Abcam ab4729)


title: Chicken 1 Organoids_rep2 [RO-35]

description: Library name: Chicken 1 Organoids_rep2

value: lung organoid


title: Mixed-AAV9-day2

description: 10x Genomics


title: HPC-7, p42, UT, H3K27Ac, ChIP, R2


title: HPC-7, p42, UT, H3K27Ac, ChIP, R1


title: Chicken 1 Organoids_rep1 [RO-34]

description: Library name: Chicken 1 Organoids_rep1


title: Mixed-UT-day2

description: 10x Genomics

value: Untreated 2 days


title: HPC-7, p42, LPS 2h, H3K27Ac, ChIP, R3


title: Spheroid_UT_Day 2

description: 10x Genomics

value: hiPSC-derived brain spheroids


title: HPC-7, p42, LPS 2h, H3K27Ac, ChIP, R2


title: GC20_hp_ctrl

description: Library name: GC20_hp

value: hippocampus


title: HPC-7, p42, LPS 2h, H3K27Ac, ChIP, R1

value: LPS 2h


title: Sheep IgG size matched input

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

country: United Kingdom

institute: University of Dundee

description: Sheep IgG size matched input seCLIP library

data_processing:
Libraries were sequenced using the Illumina MiSeq v3 150 instrument to yield 2x75bp reads. Only read 1 was processed further for analysis as read 2 does not contain additional information (consistent with single-end (se) CLIP protocol).
Barcodes were extracted using umi_tools in extract mode, then adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) trimmed from the extracted reads using cutadapt.
Reads were aligned to the mouse genome (mm10) with gencode vM12 basic annotation using STAR version 2.5.2b, then demultiplexed using umi_tools in dedup mode to remove PCR duplicates.
Bedgraph files were generated using deeptools, options -bs 10 --Offset 1 1  -of bedgraph
Assembly: mm10
Supplementary files format and content: Bedgraph files have the counts of reads starting within the 10bp windows, read start sites should be 1 nt downstream of crosslinked nucleotides.

source_name: Sox1-GFP mouse ES cells

growth_protocol: Sox1-GFP mouse ES cells were cultured on gelatin coated dishes in the presence of LIF. 5x10cm dishes of cells at 80% confluency were used per sample.

extract_protocol:
Lysis steps for seCLIP were performed as described previously (Van Nostrand et al, 2017). Samples were digested with optimised high (1:20) and low (1:200) concentrations of RNase1 as indicated.
Lysates were precleared with protein G dynabeads (Thermo Fisher Scientific) at 4°C for 1hour, prior to immunoprecipitation with 50µl of protein G dynabeads preincubated with 5 µg of either RNMT, or isotype control antibody overnight at 4°C. 10% of each sample was subsequently removed to serve as the size-matched input control. IP samples were were washed three times for 5 minutes with high salt wash buffer supplemented with 2M urea. Downstream library preparation was performed as described previously (Van Nostrand et al, 2017). Libraries underwent sequencing using the Illumina MiSeq v3 150 flow cell (2x75bp reads).

treatment_protocol: Cells were washed once with cold PBS and either crosslinked using 254nm UV light (400mJ/cm2) or non-crosslinked prior to snap freezing on dry ice.

tag: antibody

tag: rnase treament

value: high

tag: uv treatment

value: Non-crosslinked


title: Chicken 3 Organoids_rep2 [RO-38]

description: Library name: Chicken 3 Organoids_rep2


title: Chicken 1 Tissue_rep2 [RO-26]

description: Library name: Chicken 1 Tissue_rep2


title: RNMT 2 size matched input

description: RNMT 2 size matched input seCLIP library

value: low

value: 254nm UV crosslinked (400mJ/cm2)


title: GC20_cx_ctrl

description: Library name: GC20_cx

value: cortex

value: ctrl


title: HPC-7, p30, UT, H3K27Ac, ChIP, R3


title: choloepus didactylus, blood sample #2-3

city: Shibuya-ku

first: David

middle: D

last: Ordinario

state: Tokyo

address: 26F Yebisu Garden Place Tower, 4-20-3 Ebisu

institute: Genesis Healthcare Co.

data_processing:
Illumina DRAGEN
Assembly: mChoDid1.pri
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Choloepus didactylus

source_name: blood sample

extract_protocol:
Total RNA for the mononuclear cells was isolated using ISOGEN (NIPPON GENE, Tokyo, Japan) based on the phenol-chloroform extraction method.
RNA libraries were prepared using an MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd., Shenzhen, China).

value: blood sample

value: peripheral blood mononuclear cells (PBMC)


title: choloepus didactylus, blood sample #2-2


title: GC23_cx_GACamk

description: Library name: GC23_cx

value: GACamk


title: RNMT 1 size matched input

description: RNMT 1 size matched input seCLIP library


title: GC16_hp_GACamk

description: Library name: GC16_hp


title: choloepus didactylus, blood sample #2-1


title: Sheep IgG IP

description: Sheep IgG IP seCLIP library

value: Sheep IgG (Fisher, 31243)


title: choloepus didactylus, blood sample #1-3


title: HPC-7, p30, LPS 2h, H3K27Ac, ChIP, R3


title: HPC-7, p30, UT, H3K27Ac, ChIP, R1


title: GC11_hp_ctrl

description: Library name: GC11_hp


title: choloepus didactylus, blood sample #1-2


title: HPC-7, p30, LPS 2h, H3K27Ac, ChIP, R2


title: RNMT 2 IP

description: RNMT 2 IP seCLIP library

value: RNMT (anti-sheep, in house)


title: choloepus didactylus, blood sample #1-1


title: Control_5d_Rep1

status: Public on Mar 10 2025

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCm38.p6
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

source_name: dorsal hippocampus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Mice were injected with rAAV to either express GFP or exogenous Dnmt3a2 in dorsal hippocampus. 3 weeks later, they were trained in contextual fear conditioning and 1 day or 5 days after that sacrificed by decapitation and hippocampal tissue dissected.

value: dorsal hippocampus

tag: time

value: Control

value: GFP


title: HPC-7, p30, LPS 2h, H3K27Ac, ChIP, R1

value: H3K27Ac (Abcam ab4729)


title: Control_5d_Rep3


title: Control_5d_Rep4


title: Control_1d_Rep4


title: Control_1d_Rep2


title: HPC-7, p30, UT, H3K27Ac, ChIP, R2


title: Dnmt3a2_5d_Rep4

value: overexpressed Dnmt3a2


title: Control_1d_Rep3


title: Dnmt3a2_5d_Rep2


title: GC16_cx_GACamk

description: Library name: GC16_cx


title: Dnmt3a2_5d_Rep1


title: Dnmt3a2_5d_Rep3


title: Control_1d_Rep1


title: Dnmt3a2_1d_Rep4


title: Dnmt3a2_1d_Rep3


title: GC11_cx_ctrl

description: Library name: GC11_cx


title: RNMT 1 IP

description: RNMT 1 IP seCLIP library


title: Dnmt3a2_1d_Rep1


title: LLC cells, PBS, 48 hours, rep 3

city: Jinan

first: Xianglei

last: Fu

address: Wenhuaxi Road

country: China

institute: Shandong University

description:
Library name: Sample 6
control_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.  Hisat2 was selected as the mapping tool.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: FPKM(Fragments Per Kilobase of transcript per Million mapped reads) was used as gene expression data. The processed data files are provided in tab-delimited text format.

source_name: Lung

growth_protocol: Lewis lung cancer cells were maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% PS and were cultivated in an environment with a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent for RNA sequencing.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Lewis lung cancer cells  were seeded overnight and treated with MPDOLs (2 μM of OST and 1 μg/mL of DNA) or PBS for 48 hours.

value: Lung

value: Lewis lung carcinoma (LLC)

value: Wild type

value: PBS (Phosphate-buffered saline, same volume as MPDOLs) for 48 hours


title: LLC cells, PBS, 48 hours, rep 1

description:
Library name: Sample 4
control_1


title: LLC cells, MPDOLs, 48 hours, rep 3

description:
Library name: Sample 3
MPDOL_3

value: MPDOLs (2 μM Osimertinib, co-delivered with DNA plasmids targeting IGF2BP3) for 48 hours


title: Dnmt3a2_1d_Rep2


title: LLC cells, MPDOLs, 48 hours, rep 1

description:
Library name: Sample 1
MPDOL_1


title: Control_5d_Rep2


title: oncogene negative tumor, Rasa1 guide2 site1, 9 weeks, Sample_ID LA75_63

first: Haiqing

last: Xu

address: 327 Campus Drive

department: Biology

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site1_9_weeks_Sample_ID_LA75_63

data_processing:
Paired-end reads were processed with regular expressions to identify the crRNA arrays and clonal barcodes. When identifying guide sequences, we strictly required a perfect match with the designed sequences.
For the same crRNA array, when we encountered low-frequency clonal barcodes within a 1-hamming distance of high-frequency clonal barcodes, we attributed them to sequencing or PCR errors. These low-frequency barcodes were merged with barcodes of higher frequencies
After extracting barcode and crRNA information, we converted the read counts associated with clonal tumors into absolute neoplastic cell numbers. This conversion was accomplished by normalizing the reads of the clonal tumor to the number of reads of the "spike-in" benchmark cell lines added to each sample prior to lung lysis and DNA extraction
Assembly: GRCm39
Supplementary files format and content: PDAC_Batch1.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch1.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch1.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: PDAC_Batch2.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch2.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch2.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Efficiency.txt: This file contains processed Tuba-seq data for tumors from the Cas12a efficiency experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Triple_TSG_KO.txt: This file contains processed Tuba-seq data for tumors from the triple TSG knockout experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: off_target_summary.csv: This file contains the indel sequencing results for three samples of oncogene-negative tumors. It includes the designed guide sequence, the chromosome, position, and sequence of predicted off-target sites (with lowercase letters indicating mismatches with the designed guide sequence), as well as the indel percentage.

extract_protocol:
Bulk tumor-bearing tissues were homogenized in 6 mL of cell lysis buffer (Puregene, 158063, Qiagen) using a FastPrep-24 5G tissue homogenizer (116005500, MP Biomedicals) and digested overnight with proteinase K (AM2544, Life Technologies). Benchmark control cell lines containing unique barcodes (50,000 or 100,000 cells each) were added to each lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumor.
Q5 High-Fidelity 2x Master Mix (M0494X, New England Biolabs) was used to amplify the U6-BC-crRNA region from 32 μg of genomic DNA in a total reaction volume of 800 μL per sample using unique dual-indexed primers.


title: oncogene negative tumor, Rasa1 guide3 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide2 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide2 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide3 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide1 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site3_9_weeks_Sample_ID_LA75_63


title: ChIPbis_AtT_ERPax7_Tam10d_NoTam20d_rep1

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

institute: IRCM

description: Library name: ChIPbis_AtT_ERPax7_Tam10d_NoTam20d_rep1

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept and six to twelve independent ChIPs were pooled. Bisulfite conversion was done with EZ DNA Methylation-Lightning (Zymo Research).
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Corticotrope

value: Tam 9d


title: ChIPbis_AtT_ERPax7_Tam10d_NoTam20d_rep2

description: Library name: ChIPbis_AtT_ERPax7_Tam10d_NoTam20d_rep2


title: oncogene negative tumor, Rasa1 guide1 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide3 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide3_site3_9_weeks_Sample_ID_LA75_63


title: LLC cells, PBS, 48 hours, rep 2

description:
Library name: Sample 5
control_2


title: oncogene negative tumor, Pten guide2 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide2_site1_9_weeks_Sample_ID_LA75_63


title: LLC cells, MPDOLs, 48 hours, rep 2

description:
Library name: Sample 2
MPDOL_2


title: oncogene negative tumor, Pten guide2 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide2_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide3 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide3_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide2 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide2_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide1 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide1_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide1 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide1_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide3 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide3_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide3 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide3_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide1 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Pten_guide1_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide3 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide3_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide3 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide2 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide2_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide2 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide2_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide3 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide3_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide1 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide1_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Nf1 guide1 site2, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide1_site2_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide3 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide3 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide1 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide1_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide3 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide1 site1, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site1_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Rasa1 guide2 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide2 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide1 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide1 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide2 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide3 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide3_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide1 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide2 site3, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_Nf1_guide2_site3_9_weeks_Sample_ID_LA75_63


title: oncogene negative tumor, Pten guide3 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide3_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide2 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide2_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide3 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide3_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide2 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide2_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide2 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide2_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide3 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide3_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide1 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide1_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide3 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide3_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide1 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide1_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide2 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide2_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide1 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Pten_guide1_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide2 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide2_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide2 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide2_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide1 site3, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide1_site3_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide1 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide1_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Nf1 guide1 site1, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide1_site1_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Rasa1 guide3 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide3 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide3 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide3_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide2 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide2 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide2 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide2_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide1 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide1 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide3 site2, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_Nf1_guide3_site2_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, Pten guide3 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide3_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Rasa1 guide1 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Rasa1_guide1_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide2 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide2_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide2 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide2_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide3 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide3_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide1 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide1_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide1 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide1_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide3 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide3_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide3 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide3_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide3 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide3_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide1 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide1_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Pten guide2 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide2_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide2 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide2_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide2 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide2_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide2 site2, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide2_site2_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide1 site1, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide1_site1_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, Nf1 guide1 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Nf1_guide1_site3_9_weeks_Sample_ID_LA75_60


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_09

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_09


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_01

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_01


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_03

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_03


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_11

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_11


title: oncogene negative tumor, Pten guide3 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide3_site3_9_weeks_Sample_ID_LA75_60


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_07

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_07


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_66

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_66

value: KT


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_65

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_65


title: oncogene negative tumor, Pten guide1 site3, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_Pten_guide1_site3_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_67

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_67


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_68

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_68


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_60


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_61


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_69

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_69


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_64

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_64


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_63


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_79

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_79

source_name: Pancreas

value: Pancreas


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_77

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_77


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_70

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_70


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_75

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_75


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_73

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_73


title: SCLC tumor, PE150, 18 weeks, Sample_ID LA77_05

description: Library name: SCLC_tumor_PE150_18_weeks_Sample_ID_LA77_05


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_74

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_74


title: PDAC tumor, PE150, 7 weeks, Sample_ID LA75_72

description: Library name: PDAC_tumor_PE150_7_weeks_Sample_ID_LA75_72


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_76

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_76


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_81

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_81


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_80

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_80


title: MC38_aPD1_R_m16_sec1_spatial

city: Cambridge

first: Andrew

middle: J

last: Kavran

state: MA

address: 250 Water Street

institute: Bristol Myers Squibb

description:
Library name: MC38_aPD1_R_m16_sec1_spatial
FFPE Spatial Transcriptomic Sequencing

library_source: other

data_processing:
Raw sequencing data were processed using 10X Genomics Space ranger pipeline to generate FASTQ files
Sequences were aligned to the visium mouse probeset v1 using space ranger to quantify gene expression
Assembly: Visium mouse probeset v2
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_positions_list.csv
Supplementary files format and content: scalefactors_json.json
Library strategy: Spatial Transcriptomics

molecule: other

source_name: MC38 Tumor

growth_protocol: Syngeneic tumors were grown by injecting 1 million MC38 cells subcutaneously in the right flank of 6–8-week-old female C57BL/6 mice. Sixteen mice were enrolled for study if their tumor reached 150-250 mm3 on day 16.

extract_protocol:
5 uM FFPE sections were cut on a microtome and placed on 10X Genomics Visium gene expression capture slides, and followed the Visium for FFPE manufacturer's protocol (10X Genomics CG000407|Rev D, non-cytassist) for the sample labeled "base_protocol". For the rest of the samples, there was an added permeabilization step during RNA Digestion. A blend of collagenase B and dispase enzymes (EMD Millipore Sigma #SCR140) resuspended in Hank’s Buffered Salt Solution (ThermoFisher Scientific cat# 14175095) was added to the RNase buffer and enzyme mix to a concentration of 0.4 CDU/uL in step 3.1 to improve the permeabilization of the tissue. Then, after permeabilization at step 3.1.n, the slide was washed with 2X saline-sodium citrate buffer (Millipore Sigma S6639) with 0.1% sodium dodecyl sulfate (Millipore Sigma 71736).
Libraries were constructed according to the Visium for FFPE mouse probeset manufacturer's protocol (non-cytassist)

treatment_protocol: Mice were randomly assigned to control IgG or aPD-1 treatments (n=8 per treatment) and were dosed with 200ug, on days 16 and 20 (Q4Dx2). Mice were euthanized by CO2, and tumors were harvested on day 21 and stored in ice cold PBS before processing. Each tumor was cut in half and processed by either FFPE or fresh-frozen tissue embedding. For FFPE blocks, the tumors were placed in 10% Neutral Buffered Formalin for 24-h fixation. The tumors were then processed for paraffin embedding in a Sakura VIP automated system with vacuum/pressure cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning

value: MC38 Tumor

value: Colorectal Carcinoma


title: oncogene negative tumor, PE150, 9 weeks, Sample_ID LA75_62

description: Library name: oncogene_negative_tumor_PE150_9_weeks_Sample_ID_LA75_62


title: MC38_aPD1_NR_m13_spatial

description:
Library name: MC38_aPD1_NR_m13_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m10_spatial

description:
Library name: MC38_aPD1_NR_m10_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m12_spatial

description:
Library name: MC38_aPD1_NR_m12_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m14_spatial

description:
Library name: MC38_aPD1_NR_m14_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m11_spatial

description:
Library name: MC38_aPD1_NR_m11_spatial
FFPE Spatial Transcriptomic Sequencing


title: PDAC tumor, PE150, 6 weeks, Sample_ID LA75_71

description: Library name: PDAC_tumor_PE150_6_weeks_Sample_ID_LA75_71


title: MC38_IgG_m07_spatial

description:
Library name: MC38_IgG_m07_spatial
FFPE Spatial Transcriptomic Sequencing

value: IgG Control


title: MC38_IgG_m06_spatial

description:
Library name: MC38_IgG_m06_spatial
FFPE Spatial Transcriptomic Sequencing


title: PDAC tumor, PE150, 10 weeks, Sample_ID LA75_78

description: Library name: PDAC_tumor_PE150_10_weeks_Sample_ID_LA75_78


title: MC38_aPD1_NR_m09_spatial

description:
Library name: MC38_aPD1_NR_m09_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m08_spatial

description:
Library name: MC38_IgG_m08_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m05_spatial

description:
Library name: MC38_IgG_m05_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m02_spatial

description:
Library name: MC38_IgG_m02_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m09_bulk

description:
Library name: MC38_aPD1_NR_m09_bulk
Bulk RNA Sequencicng

data_processing:
Reads were aligned to GRCm38 Mus Musculus genome using STAR v2.6.
Counts were quantified for Ensembl 91 annotated genes using RSEM v1.3.0
Assembly: GRCm38
Supplementary files format and content: tab delimited .txt file contaning raw counts for all genes and samples

extract_protocol:
Two sections measuring 100 microns of each fresh frozen tumor block were collected in microcentrifuge tubes. The tubes were kept on dry ice and shipped to Azenta Life Sciences (South Plainfield, New Jersey, USA) for downstream RNA sequencing. Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit (Qiagen cat# 73404), followed by poly(A) enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs cat# E7490).
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs cat# E7760S) following manufacturer’s instructions.

treatment_protocol: Mice were randomly assigned to control IgG or aPD-1 treatments (n=8 per treatment) and were dosed with 200ug, on days 16 and 20 (Q4Dx2). Mice were euthanized by CO2, and tumors were harvested on day 21 and stored in ice cold PBS before processing. Each tumor was cut in half and processed by either FFPE or fresh-frozen tissue embedding. For fresh frozen blocks, the tumors were placed in cryomolds with ice-cold TissueTek O.C.T. Compound (VWR, 25608-930) on a pre-cooled aluminum block that was placed in a dry ice and ethanol mixture. Additional O.C.T. was added to ensure the entire tissue was covered. Blocks were stored sealed at -80°C.

tag: treatment response_status

value: aPD-1 Non-Responder


title: MC38_IgG_m08_bulk

description:
Library name: MC38_IgG_m08_bulk
Bulk RNA Sequencicng

value: IgG


title: MC38_IgG_m04_sec1_spatial

description:
Library name: MC38_IgG_m04_sec1_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m01_spatial

description:
Library name: MC38_IgG_m01_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m04_sec2_spatial

description:
Library name: MC38_IgG_m04_sec2_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_IgG_m03_spatial

description:
Library name: MC38_IgG_m03_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m10_bulk

description:
Library name: MC38_aPD1_NR_m10_bulk
Bulk RNA Sequencicng


title: MC38_IgG_m04_sec3_spatial

description:
Library name: MC38_IgG_m04_sec3_spatial
FFPE Spatial Transcriptomic Sequencing


title: MC38_aPD1_NR_m13_bulk

description:
Library name: MC38_aPD1_NR_m13_bulk
Bulk RNA Sequencicng


title: MC38_aPD1_NR_m12_bulk

description:
Library name: MC38_aPD1_NR_m12_bulk
Bulk RNA Sequencicng


title: MC38_aPD1_R_m16_bulk

description:
Library name: MC38_aPD1_R_m16_bulk
Bulk RNA Sequencicng

value: aPD-1 Responder


title: MC38_aPD1_R_m15_bulk

description:
Library name: MC38_aPD1_R_m15_bulk
Bulk RNA Sequencicng


title: MC38_aPD1_NR_m14_bulk

description:
Library name: MC38_aPD1_NR_m14_bulk
Bulk RNA Sequencicng


title: MC38_aPD1_NR_m11_bulk

description:
Library name: MC38_aPD1_NR_m11_bulk
Bulk RNA Sequencicng


title: MC38_IgG_m04_bulk

description:
Library name: MC38_IgG_m04_bulk
Bulk RNA Sequencicng


title: MC38_IgG_m05_bulk

description:
Library name: MC38_IgG_m05_bulk
Bulk RNA Sequencicng


title: MC38_IgG_m02_bulk

description:
Library name: MC38_IgG_m02_bulk
Bulk RNA Sequencicng


title: MC38_IgG_m01_bulk

description:
Library name: MC38_IgG_m01_bulk
Bulk RNA Sequencicng


title: ChIP_AtT_ERPax7_Flag_Tam30min

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing RPKM/BPM) from deepTools/3.3.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: fragments per million over 10 bp bins (fpkm) or counts per million (cpm)

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept for library preparation.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Tam 30min


title: MC38_IgG_m07_bulk

description:
Library name: MC38_IgG_m07_bulk
Bulk RNA Sequencicng


title: WGBS_AtT_ERPax7_Tam48h_Mim60h

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

extract_protocol:
Genomic DNA was extracted from 1,000,000 cells with a Qiagen DNeasy Blood & Tissue. Bisulfite conversion was done with EZ DNA Methylation-Lightning (Zymo Research).
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Tam 48h, Mim 60h


title: WGBS_AtT_ERPax7_Tam0h


title: RNAseq_AtT_ERPax7_Tam72h_rep2

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 / GRCm38 reference genome using Hisat 2.2 (--no-unal --no-mixed --no-discordant).
Bam files were created using view (-b) from SAMtools 1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Gene expression was assessed by integrating reads mapped to exons over transcripts length and normalized across samples with the median of ratios method.
Assembly: mm10
Supplementary files format and content: Bigwig (unit: counts per million) and tsv (unit: normalized gene expression)

extract_protocol:
RNA was extracted from 1,000,000 cells in culture using Qiagen RNeasy Plus Mini. Ribosomal depletion was performed by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Tam 72h


title: MC38_IgG_m03_bulk

description:
Library name: MC38_IgG_m03_bulk
Bulk RNA Sequencicng


title: ChIP_AtT_ERPax7_Flag_Tam4h

value: Tam 4h


title: RNAseq_AtT_ERPax7_Tam48h_rep2

value: Tam 48h


title: MC38_IgG_m06_bulk

description:
Library name: MC38_IgG_m06_bulk
Bulk RNA Sequencicng


title: WGBS_AtT_ERPax7_Tam48h


title: RNAseq_AtT_ERPax7_Tam72h_rep1


title: RNAseq_AtT_ERPax7_Tam48h_rep1


title: RNAseq_AtT_ERPax7_Tam24h_rep1

value: Tam 24h


title: ChIPbis_AtT_ERPax7_Tam9d


title: ChIPbis_AtT_ERPax7_Tam30min


title: ChIP_AtT_ERPax7_Flag_Tam10d

value: Tam 10d


title: ChIP_AtT_ERPax7_Flag_Tam24h

value: Corticotrope


title: RNAseq_AtT_ERPax7_Tam0h_rep1


title: RNAseq_AtT_ERPax7_Tam0h_rep2


title: ChIP_AtT_ERPax7_Flag_Tam1h

value: Tam 1h


title: ChIP_AtT_ERPax7_Flag_Tam12h

value: Tam 12h


title: ChIP_AtT_ERPax7_5hmC_Tam10d


title: ChIP_AtT_ERPax7_5hmC_Tam72h


title: ChIP_AtT_ERPax7_Flag_Tam0h


title: ChIP_AtT_ERPax7_5hmC_Tam48h


title: ChIP_AtT_ERPax7_5hmC_Tam24h


title: ChIP_AtT_ERPax7_5hmC_Tam12h


title: ChIP_AtT_ERPax7_5hmC_Tam0h


title: ATAC_AtT_ERPax7_Tam10d_rep2

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing RPKM) from deepTools/3.3.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: fragments per million over 10 bp bins

extract_protocol:
Nuclei from 50,000 cells were isolated and transposition was performed using Tagment DNA kit following Illumina’s recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation


title: ATAC_AtT_ERPax7_Tam1h


title: ATAC_AtT_ERPax7_Tam10d_rep1


title: ATAC_AtT_ERPax7_Tam6h

value: Tam 6h