title: Sample 50_Mouse_CD4-T_polyA-RNA_Input_rep2

value: 7 weeks


title: Sample 45_Mouse_Bone-marrow_polyA-RNA_Input_rep1

status: Public on Sep 05 2022

type: SRA

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

country: USA

institute: The University of Chicago

description: Processed data file: GSE179798_Mouse_mRNA_12-Tissues_BID-seq.xlsx

library_source: transcriptomic

data_processing:
The sequencing data were all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73), 5-mer random barcodes at reads ends were trimmed and low-quality or short reads (less than 20 nt) were removed using cutadapt tool (v.1.15). Remaining reads were aligned to hg38 or mm10 genome using Tophat2 (v.2.1.1) and bowtie2 (v.2.4.0) allowing, at most, three mismatches. The generated.bam files were split into positive and negative strands and sorted using Samtools (v.1.9). Sequence variants were identified by measuring the base composition at each position using bam-readcount software (v.0.8.0). The generated bam-readcount results were parsed and analyzed by inhouse scripts. Internal deletion ratio at each Ψ candidate site suggested by Tophat2, was further calculated by data output from bam-readcount pipeline and confirmed by direct IGV visualization (v.2.8.0). In summary, one Ψ candidate site needs to satisfy the following criteria in its deletion profile: (1) deletion rate above 5% (with deletion count above five) in BID-seq libraries; (2) deletion rate below 1% in ‘Input’ libraries; (3) total reads coverage depth above 20 in both BID-seq and ‘Input’ libraries; (4) deletion rate above 1.5-fold over background in any given sequence motif (defined as the deletion rates detected from RNA probes containing 0% Ψ, as in Supplementary Fig. 1c); (5) we excluded uridine sites at the neighboring nucleotide 3′ or 5′ to known Ψ sites; (6) all deletion signatures must be from ‘U’ sites marked by hg38 or mm10 FASTA file, instead of from A or C or G. Under the current sequencing depth (around 80 M reads per library), we set RPKM = 1.5 as the lowest expression level for mRNA Ψ detection.
The ‘input’ samples of BID-seq, for both human cell lines and mouse tissues, are equivalent to regular RNA-seq; therefore, we quantified the gene-level read counts of input samples that aligned to hg38 or mm10 for gene expression analysis with Cufflinks software (v.2.2.1). GO analysis was performed using the online analysis software DAVID 2021 (https://david.ncifcrf.gov).

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Mice were housed in a virus-free facility at 21 ± 1 °C with a controlled 12-hour light cycle (Individually Ventilated Caging System (GM500)). The animals have access to standard chow and water ad libitum. The relative humidity was controlled at 55% ± 10%. The mice (Mus musculus) were fed an SD with 5.5% fat content (Rat and Mouse No. 3 breeding diet, Special Diet Services). All mice in this study were C57BL6/N background strain wild-type mice. All data were obtained from 7-week-old male mice.

extract_protocol:
(Note RNA 3′ SR Adapter: 5’rApp NNNNN ATCACG AGATCGGAAGAGCACACGTCT-3SpC3; 5′ SR Adapter: 5′-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3′)
Wild-type HeLa, HEK293T or A549 cells (three replicates for each sample, one 3.5-cm plate per replicate); HeLa shControl or PUS knockdown cells were prepared as described (two replicates for each sample, one 10-cm plate per replicate); mouse tissues, except immune cells, were collected from two replicates (one wild-type mouse per replicate), age- and sex-matched. To harvest enough material, mouse immune cells such as B cells, CD4 T cells and CD8 T cells were collected and combined from two replicates (eight wild-type mice per replicate), again age- and sex-matched. After extracting the polyA+ RNA from HeLa cells or mouse tissues, around 10–20 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with RNA Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by RNA Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water. To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (sequences listed above) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.
The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-sequences listed above-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.
A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

treatment_protocol: Wild-type mice are used for these RNA-seq libraries.

tag: tissue

value: Bone marrow

tag: genotype

value: WT

tag: strain

tag: Sex

value: Male

tag: age


title: Sample 42_Mouse_B-cell_polyA-RNA_Input_rep2

value: B cell


title: Sample 44_Mouse_B-cell_polyA-RNA_Treated_rep2


title: Sample 46_Mouse_Bone-marrow_polyA-RNA_Input_rep2


title: D19_TGFB2_SANCM_rep2

status: Public on Sep 01 2022

city: Amsterdam

first: Alexandra

last: Wiesinger

state: Amsterdam

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: late TGFB2-induced SAN cardiomyocytes at day 19 of differentiation

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on NextSeq500 using 1x75 bp read length kit
Mapping was performed using BWA-MEM against the (human) genome assembly GRCh38 (hg38). Count matrices were generated using MapAndGo, filtering reads with a minimum quality score of 60 and no alternative hits.
Assembly: hg38
Supplementary files format and content: transcript counts as .tsv files

organism: Homo sapiens

source_name: cell culture

growth_protocol: hiPSCs were maintained in mTeSR medium on growth factor reduced Matrigel

extract_protocol:
Cells at different stages during differentiation were singularzed and FACS sorted into 384-well plates (Muraro et al, 2016)
Preparation of single-cell libraries was performed using the CEL-Seq2 protocol (Muraro et al. 2016; Hashimshony et al., 2016)

treatment_protocol: Differentiation of hiPSCs towards MESP1+ mesoderm was initiated by activating Activin/Nodal, BMP and WNT signaling (Devalla et al., 2015; Devalla et al., 2016). To steer mesoderm towards a cardiomyocyte fate, WNT signaling was inhibited using XAV 939 for 96 hours, which resulted in predominantly ventricular-like cardiomyocytes (VCM). To direct mesoderm towards SANCM, we treated cultures with BMP4, RA, WNT inhibitor (XAV 939), TGFbR1/ALK5 inhibitor (SB431542) and FGF inhibitor (PD173074) for 48 hours (Protze et al., 2017).

value: cell culture

tag: cell line

tag: cell type

value: hiPSC

value: wild type

tag: treatment

value: SANCM protocol + TGFB2

tag: timepoint

value: Day 19


title: Sample 41_Mouse_B-cell_polyA-RNA_Input_rep1


title: D19_ACM_rep2

description: late atrial cardiomyocytes at day 19 of differentiation

value: ACM protocol


title: D19_TGFB2_SANCM_rep1


title: D19_ACM_rep3


title: Rat,PPH,C4-4

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

country: China

institute: Nanjing University of Chinese medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2 . P value < 0.05 and foldchange > 1.5 or foldchange < 0.67 was set as the threshold for significantly differential expression gene (DEGs) .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.
Supplementary files format and content: Excel file reports counts for each sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: tibia

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min.
B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube.
C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase.
D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.
E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.
F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.
G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube.
H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.
I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
1. Purify and Fragment mRNA
a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly.
b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperature for 5 min.
c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.
d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly.
e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.
f. Add 50 μL of Elution Buffer in each well and mix thoroughly.
g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature.
h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min.
i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.
j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly.
k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well.
l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly.
m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge.
2. Synthesize First Strand cDNA
a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly.
b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C.
3. Synthesize Second Strand cDNA
a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well.
b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. The mixture was incubated at 16°C for 60 min.
3.1 Purification
a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.
b. Place it on the magnetic stand at room temperature for 5 min.
c. Remove and discard all of the supernatant from each well.
d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.
e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.
f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.
g. Add 17.5 μL Resuspension Buffer and mix thoroughly.
h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.
i. Transfer 15 μL the supernatant from each well into the new PCR plate.
4. Adenylate 3’Ends
a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well.
b. Add 12.5 μL A-Tailing Mix and mix thoroughly.
c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C.
5. Ligate Adapters
a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well.
b. Add 2.5 μL Ligation Mix.
c. Add 2.5 μL RNA Adapter Index and mix thoroughly.
d. The mixture was incubated at 30°C for 10 min.
e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly.
5.1 Purification
a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.
b. Place it on the magnetic stand at room temperature for 15 min.
c. Remove and discard 79.5 μL of the supernatant from each well.
d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.
e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.
f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.
g. Add 52.5 μL Resuspension Buffer and mix thoroughly.
h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.
i. Transfer 50 μL the supernatant from each well into the new PCR plate.
j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.
k. Place it on the magnetic stand at room temperature for 15 min.
l. Remove and discard 95 μL of the supernatant from each well.
m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.
n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.
o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.
p. Add 22.5 μL Resuspension Buffer and mix thoroughly.
q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic
stand at room temperature for 5 min.
r. Transfer 20 μL the supernatant from each well into the new PCR plate.
6. Enrich DNA Fragments
a. Add 5 μL PCR Primer Cocktail.
b. Add 25 μL PCR Master Mix and mix thoroughly.
c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15
cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C.
7. Purification
a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min.
b. Place it on the magnetic stand at room temperature for 15 min.
c. Remove and discard 95 μL of the supernatant from each well.
d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well.
e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well.
f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand.
g. Add 32.5 μL Resuspension Buffer and mix thoroughly.
h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic
stand at room temperature for 5 min.
i. Transfer 30 μL the supernatant from each well into the new PCR plate.
8. Validate library
a. Load 1 μL sample on an Agilent 2100 Bioanalyzer.
b. Check the size and purity of the library.

value: Sprague Dawley

value: 10 weeks old

value: PPH

value: tibia


title: Rat,PPH,C4-3


title: D19_ACM_rep1


title: Rat,PPH,C4-2


title: Rat,Model,M5

value: Untreated model group


title: Rat,Model,M4


title: UiSomitoid, Day6

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Assembly: hg38
Supplementary files format and content: rsem_results.all.expected_count.csv, genes.results file

source_name: UiPSM

growth_protocol: 300-600 UiPSM cells in low-adherence 96-well plates (Corning, 7007) formed compact and spherical aggregations within 48 hours in DM medium, and then these aggregations elongated in CS medium (advanced DMEM/F12 supplemented with CHIR99021 and 5µM ALK5 inhibitor SB431542(PeproTech,301836-41-9)) for 7 days.

extract_protocol:
Extracted RNA using phenolic chloroform after pretreatment with Trizol
Purified total RNA was capture with magnetic bead with oligo-polyA, interrupt and reverse-transcribed into cDNA using the VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme), purified using VAHTS DNA Clean Beads (N411, Vazyme).
cDNAs ligated adapters and amplified libraries using the amplification mix (NR611, Vazyme). Finally, sequencing the cDNAs library to obtain 150bp paired-end reads.

value: Pax8+ Urine Cells

value: Reprogramming

tag: time

value: UiSomitoid


title: UiSomitoid, Day2


title: UiSomitoid, Day4


title: UiSomitoid, Day9


title: Sample 43_Mouse_B-cell_polyA-RNA_Treated_rep1

value: WT

value: 7 weeks


title: Rat,Model,M1

value: Male


title: IMM-feb20_M12_P46_24hpi

status: Public on Aug 31 2022

city: Modiin

first: Amichay

last: Afriat

state: non-US Resident

address: Nehar Hayarden Modiin

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description:
single_cell
MARSseq

data_processing:
bcl2fastq/2.20.0.422 Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2)). Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached).
STAR/2.7.3a & zUMI/0.0.6c alignment of data to a combined pseudo-genome of host + parasite
Assembly: host: GRCm38.p6
Assembly: parasite: PBANKA01.43
cleaning, and filtering: custom script on Python 3 using multiple packages. full script in Jupyter notebook at https://github.com/AmichayAfriat/SpatioTemporal_malaria_liver_stage_atlas/
Supplementary files format and content: single cell expression matrix
Supplementary files format and content: list of wells containing infected cells in each plate, wells corresponde to single_cell_384_barcodes_by_well.csv table
Supplementary files format and content: list of barcods used for demultiplexing the cells in the single cell RNAseq experiment

source_name: Hepatocytes single cells

growth_protocol: C57bl6 female mice were fed regular chow ad libitum

extract_protocol:
Isolation of hepatocytes was performed as previously decribed (Bahar-Halpern, K. et al. Nature 2017).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014).

value: post natal 1.5 month

tag: agent

value: infected with P. berghaei spz (injection)


title: IMM-Jan22_M32_P55_30hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M32_P57_30hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P49_24hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M32_P56_30hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M32_P54_30hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M31_P53_36hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P47_24hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P51_24hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P50_24hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P48_24hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M31_P50_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M31_P52_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M31_P49_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M30_P48_MB-36hpi

description:
single_cell
MARSseq

value: infected with P. berghaei spz (mosquito-bite)


title: IMM-Jan22_M30_P47_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M29_P45_12hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M31_P51_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M29_P44_12hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M29_P43_12hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M28_P40_MB-36hpi

description:
single_cell
MARSseq


title: IMM-feb20_M12_P45_24hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M28_P36_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M28_P39_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M28_P37_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M28_P38_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M27_P35_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M27_P41_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M27_P34_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M26_P30_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M26_P31_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M25_P27_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M26_P28_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M25_P26_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M30_P46_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M24_P23_NI

description:
single_cell
MARSseq


title: IMM-Jan22_M24_P24_NI

description:
single_cell
MARSseq


title: IMM-Dec21_M23_P19_NI

description:
single_cell
MARSseq


title: IMM-Jan22_M29_P42_12hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M23_P20_NI

description:
single_cell
MARSseq


title: IMM-Jan22_M24_P22_NI

description:
single_cell
MARSseq


title: IMM-Dec21_M23_P21_NI

description:
single_cell
MARSseq


title: IMM-Dec21_M22_P15_12hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M21_P13_12hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M21_P12_12hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M22_P14_12hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M20_P11_30hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M20_P10_30hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M20_P9_30hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M19_P7_36hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M19_P8_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M27_P32_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M19_P6_36hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M19_P5_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M26_P29_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M25_P25_MB-2hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M18_P4_36hpi

description:
single_cell
MARSseq


title: IMM-Jan22_M27_P33_MB-36hpi

description:
single_cell
MARSseq


title: IMM-Dec21_M22_P16_12hpi

description:
single_cell
MARSseq


title: CLIP_HEK293T-M3KO_rep2_input

status: Public on Aug 30 2022

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

description: M3KO replicate 2, paired input RNA

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
demultiplexing (Python 2.7.11)
alignment (Novoalign 3.09.00) to hg19
paired sample peak-calling (MACS2 2.1.1.20160309)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, hg19)
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
Assembly: UCSC homo sapiens (hg19)
Supplementary files format and content: bigwig (.bw), peak files (.bed), alignment (.bam)

source_name: HEK293T Mettl3 KO

growth_protocol: Dulbecco's Modified Essential Medium, 10% FBS, Penicillin/Streptamycin; cultured in vitro at 37˚C, 5.0% CO₂, humidified

extract_protocol:
CLIP RNA extraction performed according to iCLIP protocol (10.1016/j.ymeth.2013.10.011), size-matched input (SM input) RNA extraction performed in parallel as adapted from eCLIP protocol (10.1038/nmeth.3810)
libraries generated using iCLIP protocol with post-extraction input and CLIP RNA (10.1016/j.ymeth.2013.10.011)

treatment_protocol: cell lines transduced with lentivirus expressing FLAG-HA-tagged human RBM45 (HEK293T), subject to 300 mJ/cm2 UV irradiation (254 nm) in PBS prior to collection of cell culture

value: transformed human embryonic kidney cell

value: Mettl3 KO

tag: antibody

value: no antibody


title: IMM-Dec21_M18_P2_36hpi

description:
single_cell
MARSseq


title: CLIP_HEK293T-M3KO_rep1_input

description: M3KO replicate 1, paired input RNA


title: CLIP_mHippoE2-M3KO_rep2_input

description: M3KO replicate 2, paired input RNA

data_processing:
adapter removal (SeqAn 2.3.2, flexbar 3.0.3)
demultiplexing (Python 2.7.11)
alignment (Novoalign 3.09.00) to mm10
paired sample peak-calling (MACS2 2.1.1.20160309)
overlap of replicate peaksets (Bedtools 2.25.0)
de novo motif analysis (homer 4.11.1, MEME 5.0.5)
peak annotation (homer 4.11.1, mm10)
bam to bigwig conversion (Python 2.7.11, deeptools 3.2.1)
Assembly: UCSC mus musculus (mm10)
Supplementary files format and content: bigwig (.bw), peak files (.bed), alignment (.bam)

source_name: mHiPPoE-2 Mettl3 KO

extract_protocol:
CLIP RNA extraction performed according to iCLIP protocol (10.1016/j.ymeth.2013.10.011); size-matched input (SM input) RNA extraction performed in parallel as adapted from eCLIP protocol (10.1038/nmeth.3810)
libraries generated using iCLIP protocol with post-extraction input and CLIP RNA (10.1016/j.ymeth.2013.10.011)

treatment_protocol: cell lines transduced with lentivirus expressing FLAG-HA-tagged mouse RBM45 (mHippoE-2), expression confirmed by WB and RT-qPCR  crosslinked with UV irradiation using 2 doses of 150 mJ/cm2 at 85% confluency, prior to cell culture dissociation and collection for use in iCLIP library preparation protocol

value: transformed mouse hippocampal neuron cell


title: CLIP_mHippoE2-M3KO_rep2_CLIP

description: M3KO replicate 2, CLIP RNA

value: CST HA-Tag (C29F4) Rabbit mAb (#3724)


title: CLIP_HEK293T-M3KO_rep1_CLIP

description: M3KO replicate 1, CLIP RNA


title: CLIP_mHippoE2-M3KO_rep1_input

description: M3KO replicate 1, paired input RNA


title: Fibroid061919

status: Public on Aug 27 2022

city: San Francisco

first: Jyoti

last: Goad

state: California

address: 513 Parnassus

institute: University of California, San Francisco

description: 10X Genomics

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
GRCh38
Assembly: GRCh38
Supplementary files format and content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; features.tsv: gene ids per sample

source_name: Myomterium

extract_protocol:
Enzymatic and mechanical dissociation; 10X Genomics Single cell 5' gene expression V2
library constructiuon was carried out using Chromium Single cell 5' library and gel bead kit as per the manufacturer's instructions.

value: Myometrium

tag: disease state

value: Fibroid tumor

value: MED12 positive


title: CLIP_HEK293T-M3KO_rep2_CLIP

description: M3KO replicate 2, CLIP RNA


title: CLIP_mHippoE2-M3KO_rep1_CLIP

description: M3KO replicate 1, CLIP RNA


title: IMM-Dec21_M18_P1_36hpi

description:
single_cell
MARSseq


title: CRC19779 [Hi-C]

city: Palo ALto

first: Yizhou

last: Zhu

state: CA

address: 3165 Porter Dr, Rm 2260

department: Genetics

institute: Stanford University

library_source: genomic

data_processing:
Demultiplexed fastqs were processed using Distiller pipeline using default parameters (https://github.com/open2c/distiller-nf)
Deduplicated pairs.gz files were processed using Juicer pre to generate .hic with default parameters, before or after merging using pairtools (https://github.com/aidenlab/juicer, https://github.com/open2c/pairtools)
Stripes were called using MACS2 by identifying regions with significantly overrepresented distal interaction reads
Loops were called using combined .hic files using Juicer HiCCUPs at resolutions of 1k, 2k, 5k, and 10k (https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS)
Assembly: hg38
Supplementary files format and content: .hic (contact matrix), .bedpe (loop list), .bed (stripe list)

molecule: genomic DNA

source_name: colon cancer

extract_protocol:
5-10 mg of snap-frozen tissue was loaded in tissueTUBE-TT05 (Covaris 520071) and cryopulverized using the Covaris CP02 cryoPREP Automated Dry Pulverizer following manufacturer's procedure. Pulverized tissues were treated with freeze substitution40 by submerging in 1ml -80 oC 0.01% formaldehyde (ThermoFisher 28906), 97% ethanol, and 2% water. Samples were incubated in dry ice for 3 hours on a rotor with spinning speed around 100 rpm, and then placed in a CoolCell Container (Corning), transferred to a -20 oC freezer for overnight incubation. On day 2, the Container was transferred to a 4 oC cold room, spinning on a rotor around 100 rpm for 1 hour to bring the sample temperature above freezing point.
The tissue samples were separated from ethanol solution by centrifuging at 300 g for 5 min in a 4 oC microcentrifuge. Crosslinking was performed by incubating with 1ml 1% TBS-formaldehyde for 10 min at room temperature. The solution was quenched by adding 80 μl 2.5 M glycine and incubated for 5 min. Samples were centrifuged, washed once with 1 ml TBS (pH 7.5), and resuspended with 250 μl Hi-C lysis buffer (10 mM Tris-HCl, pH8.0, 10 mM NaCl, 0.2% Igepal CA630) plus 50 μl proteinase inhibitor cocktail (Sigma P8340). Nuclei extraction was performed on ice by squeezing the samples with 1.5 ml disposable pellet pestles (Fisher Scientific 12-141-368) for 15-20 times. The crude suspension was centrifuged at 1500 g, 4 oC for 5 min, resuspended in 800 μl Hi-C lysis buffer and passed through a 100 μm strainer (Sysmex). After centrifugation, purified nuclei were resuspended in 170 μl 10 mM Tris-HCl containing 0.5% Triton X-100 (Sigma 93443), and incubated at room temperature with rotation for 15 min. Ten microliter of 1% SDS, 20 μl Cutsmart buffer (NEB), 3 μl HinP1I (NEB R0124S), 3 μl DdeI (NEB R0175L), 3 μl CviAII (NEB R0640L), 3 μl FspBI (ThermoFisher ER1762), and 0.6 μl MseI (NEB R0525M), were added to the suspension in the indicated order. The mixture was incubated at 25 oC and then 37 oC for 2 hours each with rotation. To stop restriction digestion, the suspension was incubated in a 62 oC heating block for 20 min followed by cool down. End repair was carried out by adding a 30 μl solution containing 0.5 mM biotin-14-dATP (Active Motif 14138), 0.5 mM biotin-14-dCTP (AAT bio 17019), 0.5 mM dTTP, 0.5 mM dGTP, and 4 μl Klenow DNA polymerase (NEB M0210L) to the mixture, and incubated for 1 hour at 37 oC with rotation. For ligation, a 750 μl solution containing 1x NEB T4 DNA ligase buffer (NEB B0202), 120 μg BSA (ThermoFisher AM2616), and 2000 U T4 DNA ligase (NEB M0202M) was added. The mixture was incubated at room temperature for 90 min, then 4 oC overnight, and then room temperature for 60 min with rotation.To perform reverse crosslinking, the mixture was centrifuged at 1500 g for 5 min. Supernatant was replaced with a mixture of 300 μl 1x T4 ligase buffer, 30 μl 20 mg/ml proteinase K (ThermoFisher 25530049), 30 μl 10% SDS, and 40 μl 5 M NaCl. The suspension was then incubated at 66 oC for 4 hours. DNA content was then purified in 20 μl 10 mM Tris-HCl by phenol-chloroform extraction.To generate mHi-C sequencing library, 300 ng of purified DNA was tagmented with 2.5 μl Tn5 transposase (APExBIO K1155, discontinued) loaded with equimolar Mosaic Ends containing Illumina Nextera i5 and i7 extensions following the manufacturer's protocol. Tagmentation was performed in a 100 μl buffer containing 10% DMF, 10 mM Tris-HCl, and 150 mM NaCl, at 55 oC for 10 min. The product was column purified (Zymo D4014) and PCR amplified for 2 cycles using the NEBNext master mix (NEB M0544L) with Illumina Nextera primers and conditions. Biotin enrichment was then performed by adding 20 μl Dynabeads MyOne Streptavidin C1 (ThermoFisher 65001) and incubating at room temperature for 30 min with rotation. The magnetic beads were washed three times with 1x wash buffer (10 mM Tris-HCl pH7.5, 1 mM NaCl, 0.5 mM EDTA) and one time with 10 mM Tris-HCl. Final libraries were obtained by amplifying the beads with additional 8 cycles of PCR, followed by purification with SPRI (Beckman B23318) size selection at 0.5x-1.1x range. The 33 samples were combined to 2 pools and sequenced with 2 NovaSeq (Illumina) S4 200 cycle flow cells.
multi-RE digested in situ Hi-C

value: colon cancer

tag: Stage

value: AdeCa

tag: donor


title: CRC26616 [Hi-C]


title: CRC8396 [Hi-C]


title: CRC25135 [Hi-C]


title: A015C010 [Hi-C]

source_name: colon

value: colon

value: Mucosa


title: A014C040 [Hi-C]

value: Polyp


title: A014C053 [Hi-C]


title: A014C038 [Hi-C]


title: A014C046 [Hi-C]


title: A014C004 [Hi-C]


title: A014C012 [Hi-C]


title: A014C045 [Hi-C]


title: A014C054 [Hi-C]


title: A014C041 [Hi-C]


title: A002C122 [Hi-C]


title: A015C006 [Hi-C]


title: A002C212 [Hi-C]


title: A002C006 [Hi-C]


title: A002C013 [Hi-C]


title: A002C012 [Hi-C]


title: A002C010 [Hi-C]


title: CRC25988 [Hi-C]


title: A002C002 [Hi-C]


title: A002C001 [Hi-C]


title: A001C024 [Hi-C]


title: CRC15157 [Hi-C]


title: A001C019 [Hi-C]


title: A015C004 [Hi-C]


title: A001C023 [Hi-C]


title: A001C008 [Hi-C]


title: A001C011 [Hi-C]


title: A001C013 [Hi-C]


title: A001C007 [Hi-C]


title: CRC25988 [ATAC-Seq]

data_processing:
Demultiplexed Fastqs were processed using the ENCODE pipeline with default parameters (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Assembly: hg38
Supplementary files format and content: .bigwig (p value, fold change) .bed (combined peak sites)

extract_protocol:
5-10 mg of snap-frozen tissue was loaded in tissueTUBE-TT05 (Covaris 520071) and cryopulverized using the Covaris CP02 cryoPREP Automated Dry Pulverizer following manufacturer's procedure.
Assay was performed following ENCODE's most recent protocol (https://www.encodeproject.org/documents/ce0b7d60-8043-4fd8-9a2e-fd6df4127c76/@@download/attachment/ENCODE4_ATAC_TissueProcessing_v1.pdf)


title: A014C054 [ATAC-Seq]


title: A014C053 [ATAC-Seq]


title: A015C004 [ATAC-Seq]


title: A002C010 [ATAC-Seq]


title: CRC15157 [ATAC-Seq]


title: A014C057 [ATAC-Seq]


title: A014C041 [ATAC-Seq]


title: A002C002 [ATAC-Seq]


title: A014C046 [ATAC-Seq]


title: A001C019 [ATAC-Seq]


title: A002C212 [ATAC-Seq]


title: CRC19779 [ATAC-Seq]


title: CRC26616 [ATAC-Seq]


title: A015C010 [ATAC-Seq]


title: A015C008 [ATAC-Seq]


title: CRC8396 [ATAC-Seq]


title: A001C007 [ATAC-Seq]


title: CRC25135 [ATAC-Seq]


title: A002C001 [ATAC-Seq]


title: CRC25135

data_processing:
RNA seq results were processed using Tomas Bencomo’s pipeline (https://github.com/tjbencomo/bulk-rnaseq),
Assembly: hg38
Supplementary files format and content: .sf (expression level per transcript), .csv (DESeq2 differential expression)

extract_protocol:
Total RNA was extracted from ~5mg frozen tissue using zymo extraction kit (R1054)
Assay was performed using NEB E7775S,E7490S following manufacturer's protocol. 1000 ng of DNase I-treated initial total RNA input was used


title: CRC26616


title: CRC8396


title: A002C006 [ATAC-Seq]


title: A002C122 [ATAC-Seq]


title: CRC19779


title: A015C010


title: A015C004


title: A001C013 [ATAC-Seq]


title: CRC15157


title: A014C046


title: A014C040


title: A002C013


title: A014C054


title: A002C002


title: A002C006


title: A001C019


title: A014C012


title: A002C010


title: A014C053


title: A002C212


title: A014C041


title: A002C001


title: A002C122


title: A001C011


title: A001C013


title: A001C007


title: MAOC01893-6-9

status: Public on Aug 26 2022

type: genomic

city: Melbourne

first: Dale

middle: W

last: Garsed

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
MAOC01893-6-9
relapse tumor not used in batch corrected file

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina Infinium HD Methylation protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.

data_processing: Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated for each EPIC and 450k arrays separately. The beta values for each array were then merged by the probe ID into file "betaVals.all.txt.gz" file (i.e., union of the two arrays). To generate file "betaVals.platform_corrected_by_combat.txt.gz" (i.e., intersection of the two arrays), first only probes present in both arrays were kept and then batch corrected for platform differences using the "ComBat" function in the R package sva (v3.34.0).

label: Cy5 and Cy3

source_name: Relapse Tumor

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: DNA was isolated from frozen tissue sections using either the Gentra Puregene Tissue Kit (Qiagen), DNeasy Blood and Tissue Kit (Qiagen), or AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

tag: gender

value: Female

value: Relapse Tumor

tag: case id

value: high grade serous ovarian cancer


title: MWMH00552-6-8

description:
MWMH00552-6-8
relapse tumor not used in batch corrected file

tag: tissue


title: AOCS_171_1_0

description: Re-analysis of GSM1606967

source_name: Primary Tumor

value: Primary Tumor


title: MWMH00758-8-2

description:
MWMH00758-8-2
relapse tumor not used in batch corrected file


title: MWMH00758-6-3

description:
MWMH00758-6-3
relapse tumor not used in batch corrected file


title: AOCS_164_1_7

description: Re-analysis of GSM1606957


title: AOCS_169_1_0

description: Re-analysis of GSM1606964


title: AOCS_168_1_8

description: Re-analysis of GSM1606963


title: AOCS_161_1_9

description: Re-analysis of GSM1606954


title: AOCS_165_1_X

description: Re-analysis of GSM1606958


title: AOCS_160_1_6

description: Re-analysis of GSM1606953


title: AOCS_157_1_3

description: Re-analysis of GSM1606950


title: AOCS_149_1_7

description: Re-analysis of GSM1606944


title: AOCS_153_1_2

description: Re-analysis of GSM1606948


title: AOCS_147_1_1

description: Re-analysis of GSM1606942


title: AOCS_148_1_4

description: Re-analysis of GSM1606943


title: AOCS_145_1_6

description: Re-analysis of GSM1606940


title: AOCS_158_1_6

description: Re-analysis of GSM1606951


title: AOCS_144_1_3

description: Re-analysis of GSM1606939


title: AOCS_139_1_5

description: Re-analysis of GSM1606931


title: AOCS_163_1_4

description: Re-analysis of GSM1606956


title: AOCS_143_1_0

description: Re-analysis of GSM1606938


title: MAOC00944-6-X

description:
MAOC00944-6-X
relapse tumor not used in batch corrected file


title: AOCS_132_1_6

description: Re-analysis of GSM1606923


title: AOCS_133_1_9

description: Re-analysis of GSM1606924


title: AOCS_128_1_0

description: Re-analysis of GSM1606920


title: AOCS_126_1_5

description: Re-analysis of GSM1606919


title: AOCS_131_1_3

description: Re-analysis of GSM1606922


title: AOCS_130_1_0

description: Re-analysis of GSM1606921


title: AOCS_159_1_9

description: Re-analysis of GSM1606952


title: AOCS_116_1_3

description: Re-analysis of GSM1606911


title: AOCS_125_1_2

description: Re-analysis of GSM1606918


title: AOCS_115_1_0

description: Re-analysis of GSM1606910


title: AOCS_123_1_7

description: Re-analysis of GSM1606916


title: AOCS_124_1_X

description: Re-analysis of GSM1606917


title: AOCS_122_1_4

description: Re-analysis of GSM1606915


title: AOCS_113_1_5

description: Re-analysis of GSM1606908


title: AOCS_114_1_8

description: Re-analysis of GSM1606909


title: AOCS_111_1_X

description: Re-analysis of GSM1606906


title: AOCS_152_1_X

description: Re-analysis of GSM1606947


title: AOCS_108_1_7

description: Re-analysis of GSM1606904


title: AOCS_107_1_4

description: Re-analysis of GSM1606903


title: AOCS_105_1_9

description: Re-analysis of GSM1606901


title: AOCS_097_1_X

description: Re-analysis of GSM1606899


title: AOCS_096_1_7

description: Re-analysis of GSM1606898


title: AOCS_104_1_6

description: Re-analysis of GSM1606900


title: AOCS_093_1_9

description: Re-analysis of GSM1606893


title: AOCS_106_1_1

description: Re-analysis of GSM1606902


title: AOCS_091_1_3

description: Re-analysis of GSM1606888


title: AOCS_092_1_6

description: Re-analysis of GSM1606890


title: AOCS_090_1_0

description: Re-analysis of GSM1606886


title: AOCS_088_1_0

description: Re-analysis of GSM1606884


title: AOCS_083_1_7

description: Re-analysis of GSM1606879


title: AOCS_085_1_2

description: Re-analysis of GSM1606881


title: AOCS_081_1_1

description: Re-analysis of GSM1606878


title: AOCS_080_1_9

description: Re-analysis of GSM1606877


title: AOCS_077_1_6

description: Re-analysis of GSM1606874


title: AOCS_084_1_X

description: Re-analysis of GSM1606880


title: AOCS_064_1_6

description: Re-analysis of GSM1606869


title: AOCS_112_1_2

description: Re-analysis of GSM1606907


title: AOCS_079_1_1

description: Re-analysis of GSM1606876


title: AOCS_075_1_0

description: Re-analysis of GSM1606872


title: AOCS_086_1_5

description: Re-analysis of GSM1606883


title: AOCS_063_1_3

description: Re-analysis of GSM1606867


title: AOCS_061_1_8

description: Re-analysis of GSM1606866


title: AOCS_059_1_8

description: Re-analysis of GSM1606864


title: AOCS_056_1_X

description: Re-analysis of GSM1606861


title: AOCS_057_1_2

description: Re-analysis of GSM1606862


title: AOCS_034_1_0

description: Re-analysis of GSM1606859


title: AOCS_055_1_7

description: Re-analysis of GSM1606860


title: AOCS_058_1_5

description: Re-analysis of GSM1606863


title: AOCS_109_1_X

description: Re-analysis of GSM1606905


title: AOCS_005_1_8

description: Re-analysis of GSM1606857


title: AOCS_001_1_7

description: Re-analysis of GSM1606855


title: AOCS_004_1_5

description: Re-analysis of GSM1606856


title: AOCS_065_1_9

description: Re-analysis of GSM1606870


title: AOCS-168

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411733

data_processing:
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Assembly: hg19
Supplementary files format and content: Raw counts, gene by sample matrix. The GeneID column is in the format "EnsemblID|Chromosome|Start|End|Strand|Whole_Gene_Length|Exon_Only_Length|Gene_Symbol|Gene_Biotype", eg.. "ENSG00000000003|X|99883667|99894988|-|11322|2968|TSPAN6|protein_coding"
Supplementary files format and content: TMM normalized log2 counts, gene by sample matrix. The raw counts were first filtered to only contain protein coding genes. Genes were further filtered to only contain genes with a CPM of > 0.5 in at least 10 samples. The data was then TMM normalized using edgeR (v3.28.1) and batch corrected for strand orientation differences (library_strand_orientation) while retaining comparison survival group differences (survival_group_LTS) by limma's (v3.42.2) removeBatchEffect function [i.e. limma::removeBatchEffect(log2_tmm_data, batch = library_strand_orientation, design = model.matrix(~survival_group_LTS))].

extract_protocol:
RNA was isolated from frozen tissue sections using either the miRNeasy Mini Kit (Qiagen), AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), or mirVana miRNA Isolation Kit (Ambion/Life Technologies)
Quality assessment was performed using the Bioanalyzer RNA 6000 Nano assay (Agilent), finding a median RNA integrity number of 9.0 (range 4.7 to 10). Total RNA (1 ug) was used for library preparation using Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments at the AGRF in accordance with the manufacturer’s instructions.

value: High Grade Serous Ovarian Cancer

tag: survival group

value: STS

tag: survival group_lts

value: no

tag: library strand_orientation

value: unstranded


title: AOCS-169

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411734


title: AOCS-171

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411737

value: MTS


title: AOCS_060_1_5

description: Re-analysis of GSM1606865


title: AOCS-165

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411726


title: AOCS-164

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411725


title: AOCS-166

description:
MSI, very high somatic mutation rate detected in WGS
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411727


title: AOCS-158

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411719


title: AOCS-159

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411720


title: AOCS-161

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411722


title: AOCS-163

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411724


title: AOCS-160

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411721


title: AOCS-152

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411715


title: AOCS-153

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411716


title: AOCS-148

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411711

value: LTS

value: yes


title: AOCS-145

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411708


title: AOCS-144

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411707


title: AOCS-147

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411710


title: AOCS-143

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411706


title: AOCS-139

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411700


title: AOCS-132

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411688


title: AOCS-126

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411684


title: AOCS-128

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411685


title: AOCS-133

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411689


title: AOCS-131

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411687


title: AOCS-149

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411712


title: AOCS-157

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411718


title: AOCS-125

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411683


title: AOCS-116

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411676


title: AOCS-122

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411680


title: AOCS-123

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411681


title: AOCS-115

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411675


title: AOCS-113

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411673


title: AOCS-124

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411682


title: AOCS-109

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411670


title: AOCS-112

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411672


title: AOCS-111

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411671


title: AOCS-104

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411665


title: AOCS-105

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411666


title: AOCS-107

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411668


title: AOCS-106

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411667


title: AOCS-108

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411669


title: AOCS-130

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411686


title: AOCS_095_1_4

description: Re-analysis of GSM1606897


title: AOCS-097

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411664


title: AOCS-096

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411663


title: AOCS-093

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411656


title: AOCS-092

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411654


title: AOCS-095

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411661


title: AOCS-090

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411650


title: AOCS-091

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411652


title: AOCS-086

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411646


title: AOCS-085

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411645


title: AOCS-084

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411644


title: AOCS-088

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411648


title: AOCS-114

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411674


title: AOCS-083

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411643


title: AOCS-079

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411640


title: AOCS-080

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411641


title: AOCS-075

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411636


title: AOCS-081

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411642


title: AOCS-065

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411634


title: AOCS-064

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411632


title: AOCS-063

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411631


title: AOCS-076

description:
cross sample contamination detected in WGS
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411637


title: AOCS-058

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411627


title: AOCS-001

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411618


title: AOCS-060

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411629


title: AOCS-004

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411620


title: AOCS-056

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411625


title: AOCS-055

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411624


title: AOCS-005

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411621


title: MWMH00758_7_8

description: Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001008537

value: reverse stranded


title: MWMH00758_9_7


title: MWMH00758_4_4


title: MWMH00475_4_3


title: MWMH00507_4_3


title: MWMH00351_4_1


title: MWMH00552_4_9


title: MMAY00981_4_0


title: AOCS-077

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411638


title: AOCS-061

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411630


title: MWMH00083_4_1


title: AOCS-059

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411628


title: MMAY00758_4_4


title: MMAY00761_4_1


title: AOCS-057

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411626


title: MMAY00753_4_6


title: MMAY00738_4_9


title: AOCS-034

description:
Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877
Re-analysis of GSM6411622


title: MMAY00631_4_1


title: MMAY00711_4_8


title: MWMH00851_4_0


title: MMAY00594_4_7


title: MMAY00621_4_9


title: MMAY00627_4_0


title: MMAY00566_4_6


title: MMAY00507_4_3


title: MMAY00010_4_1


title: MAOC02427_4_9


title: MAOC02417_4_6


title: MMAC00102_4_8


title: MMAY00149_4_4


title: MMAY00176_4_1


title: MAOC02541_4_4


title: MAOC02278_4_2


title: MAOC02410_4_0


title: MAOC01893_7_3


title: MAOC01847_4_0


title: MAOC02193_4_8


title: MAOC01783_4_5


title: MAOC02145_4_1


title: MAOC01893_4_X


title: MAOC01370_4_4


title: MAOC01064_4_0


title: MAOC01262_4_7


title: MAOC01315_4_6


title: MAOC00944_4_0


title: MAOC01491_4_5


title: MAOC00682_4_9


title: MAOC00673_4_X


title: MAOC01475_4_4


title: MMAY00363_4_1


title: MAOC01138_4_9


title: MAOC02394_4_5


title: MAOC02444_4_3


title: MAOC00037_4_2


title: MAOC00287_4_X


title: MAOC00602_4_7


title: MAOC00562_4_1


title: MAOC00357_4_3


title: MAOC00623_4_6


title: PREP0031_CHaas10169A_H02v1_P_DsR_20200310_S4

status: Public on Aug 25 2022

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
SMART-seq2 sequencing data were aligned with hisat2 using genome reference mm10. featureCounts was used to generate count matrix.
Assembly: GRCm38/mm10
Supplementary files format and content: count matrix in csv

growth_protocol: 8wk-old C57Bl6/J mice (#000664) were ordered from the Jackson Laboratory, housed in our animal facility for at least 2 weeks and used for experiments between 10-12 weeks of age

extract_protocol:
To remove contaminating RBCs prior to sample isolation, all mice were first perfused with 10ml of 5mM EDTA/PBS at a flow rate of 5ml/min and then with 10ml PBS (without Ca/Mg) at a flow rate of 5ml/min. Samples were isolated from distinct proliferative microenvironments in the calvarium by a combination of plasma mediated laser ablation and micropipette aspiration (Image-seq samples, see manuscript for details).
Dissociation of tissues into single cells: All Image-seq and control samples were collected in Media 199 supplemented with 2% (v/v) FBS. Samples were pipetted up and down to generate a single cell suspension and 1ml of PBS (no Ca/Mg) was added to the cell suspension. Samples were incubated for 10min with 0.1µg of DAPI, and AML cells were sorted into individual wells of a 96well PCR plate filled with lysis buffer based on their GFP fluorescence. Samples were sealed and spun down immediately after sorting, flash frozen and stored at -80deg Celsius. Libraries were prepared using the MANTIS Liquid Handler (Formulatrix) and the Biomek FXP Single Arm System with Span-8 Pipettor (Beckman Coulter, A31843). Full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.) and sequencing libraries prepared using the Nextera XT DNA library preparation kit (Illumina).

treatment_protocol: Image-seq mice were injected with 3 million HoxA9/Meis1 leukemia cells 3 days prior to the experiment, calcium binding dye alizarin red (AR) 2 days prior to the experiment and calcein blue (CB) on the day of the experiment.

tag: strain

tag: phenotype

value: Endothelial


title: PREP0031_CHaas10169A_H02v1_P_DsR_20200312_S4


title: PREP0031_CHaas10169A_G02v1_P_DsR_20200312_S4


title: PREP0031_CHaas10169A_H03v1_P_DsR_20200310_S4


title: PREP0031_CHaas10169A_G05v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_F02v1_P_DsR_20200312_S4

value: Mesenchymal Stromal


title: PREP0031_CHaas10169A_G06v1_P_DsR_20200312_S3


title: MAOC00665_4_4

tag: cell type


title: PREP0031_CHaas10169A_F01v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_E05v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_D06v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_D04v1_P_DsR_20200312_S2


title: PREP0031_CHaas10169A_E07v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_E01v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_D02v1_P_DsR_20200310_S4


title: PREP0031_CHaas10169A_D01v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_G01v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_C05v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_C04v1_P_DsR_20200312_S2


title: PREP0031_CHaas10169A_C03v1_NP_DsR_20200305_S3


title: PREP0031_CHaas10169A_G07v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_C01v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_C02v1_P_DsR_20200310_S4


title: PREP0031_CHaas10169A_B03v1_NP_DsR_20200305_S3


title: PREP0031_CHaas10169A_B06v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_B04v1_NP_DsR_20200305_S1


title: PREP0031_CHaas10169A_B01v1_NP_DsR_20200317_P1_1


title: PREP0031_CHaas10169A_A03v1_P_DsR_20200312_S4


title: PREP0031_CHaas10169A_A06v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_A04v1_P_DsR_20200310_S3


title: PREP0031_CHaas10169A_D03v1_NP_DsR_20200305_S3


title: PREP0031_CHaas10169A_E03v1_NP_DsR_20200305_S3


title: PREP0031_CHaas10169A_D02v1_NP_DsR_20200303_S2


title: PREP0020_CHaas09906A_G07v1_20200123_1_Sample2_RFP


title: PREP0031_CHaas10169A_A02v1_NP_DsR_20200303_S2


title: PREP0031_CHaas10169A_A01v1_NP_DsR_20200305_S1


title: PREP0020_CHaas09906A_G03v1_20200123_2_Sample4_RFP


title: PREP0031_CHaas10169A_A01v1_NP_DsR_20200317_P1_1


title: PREP0031_CHaas10169A_C06v1_P_DsR_20200312_S3


title: PREP0031_CHaas10169A_B02v1_P_DsR_20200312_S4


title: PREP0031_CHaas10169A_A02v1_NP_DsR_20200305_S4


title: PREP0031_CHaas10169A_A03v1_NP_DsR_20200305_S3


title: PREP0020_CHaas09906A_C07v1_20200123_1_Sample2_RFP


title: MDA-MB-231_week4_tumor2

status: Public on Aug 24 2022

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

description: Last collection. EPIKOL-transduced MDA-MB-231 cells first implanted into Nude mice and tumors were collected after 4 weeks.

data_processing:
Base calling was performed with Illumina HiSeq platforms (Genewiz, USA)
For analysis of CRISPR screens, sgRNA counting, gene summarization and comparative analyses between samples were performed using MAGeCK version 0.5.8 (Li, W., et al., 2014) using median normalization and the RRA method. R1 fastq files were used in counting.
Assembly: For analysis of CRISPR screens, sgRNA counted by matching to custom CRISPR Screen library; Epigenetic Knock-out Library (EPIKOL).
Supplementary files format and content: CRISPR screen data files include txt files containing MAGeCK outputs; normalized counts, gene summary and sgRNA summary.
Library strategy: CRISPR Amplicon Sequencing

source_name: breast adenocarcinoma cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum and %1 Penicillin/Streptomycin.

extract_protocol:
Genomic DNA (gDNA) from tumor samples was isolated by NucleoSpin Tissue kit (Macherey-Nagel, Germany) according to manufacturer's instructions.
Library was constructed with Illumina-compatible adapters. sgRNA cassettes were amplified from genomic DNA using pLentiGuide specific forward and reverse primers in the first PCR. For second PCR, %1-2.5 of the first PCR product was amplified with forward stagger and reverse index primers (specific to sample). Final library fragments of ~350 bp were agarose gel purified. Fragments were quality checked with fragment analyzer and sequenced with Illumina Hiseq (Genewiz, USA)

treatment_protocol: Cells were transduced with EPIKOL at low MOI (0.3-0.4) with 1000x coverage for in vivo screen. Following three days of puromycin selection, initial reference point pellets were collected as 8 million cells. Later, 8 million cells were mixed with matrigel 1:1 and injected subcutaneously into both flanks of six nude mice. After 2 and 4 weeks tumors were collected.

tag: cell line

value: breast adenocarcinoma cells


title: PREP0020_CHaas09906A_C01v1_20200123_2_Sample4_RFP


title: MDA-MB-231_week2_tumor3

description: Last collection. EPIKOL-transduced MDA-MB-231 cells first implanted into Nude mice and tumors were collected after 2 weeks.


title: MDA-MB-231_week4_tumor1


title: MDA-MB-231_week2_tumor2


title: MDA-MB-231_in vivo_initial

description: Initial collection (reference point). EPIKOL-transduced MDA-MB-231 cells were collected right after puromycin selection.


title: MDA-MB-231_SS18L2KO_rep1

description: SS18L2 knockout sample. Transduced with SS18L2 sgRNA carrying virus. Cells were collected from 10 cm plates on day 6 post-transduction.

data_processing:
Base calling was performed with Illumina HiSeq platforms (Genewiz, USA)
For RNAseq, the output from STAR was sorted by co-ordinate transcriptome BAM file. Further quality control of the sample BAM files was performed using RSeQC and Picard, with several quality metrics collected for assessment and comparison using MultiQC. SALMON was then used to quantify the transcripts for each sample based on the Transcripts Per Million (TPM) method. The SALMON transcript quantification files are read and summarized at the gene-level using the R package tximport. DESeq2 was used to identify differentially expressed genes between cells infected with NT1 carrying or SS18L2 sgRNA carrying lentiviruses. Differentially expressed genes (DEGs) were defined with a threshold for Log2FoldChange>1 (up-regulated) or Log2FoldChange<-1 (down-regulated) and false discovery rate (FDR)<0.05.
Assembly: For RNAseq analysis, GENCODE human transcriptome reference (GRCh38) was used with STAR alignment
Supplementary files format and content: RNAseq data files include TPM and VST counts and Differentially Expressed Genes as xls files.

extract_protocol:
MN Nucleospin RNA isolation kit was used according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit (New England Biolabs). RNA quality was assessed using High Sensitivity RNA Screentape and an Agilent 4200 Tapestation. Single-indexed and multiplexed samples were run on an Illumina Next Seq 500 sequencer using a NextSeq 500 v2 kit (FC-404–2005; Illumina, Can Diago, CA) for paired-end sequencing. Sequencing length was 42 bp.


title: MDA-MB-231_week2_tumor1


title: WT_B (RNA-seq)

status: Public on Aug 22 2022

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
Signal per gene was normalized by the number of all S. pombe reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: acCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Processed CSV files contain normalized signal for all analyzed features (5797 mRNA coding genes).

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Newly synthesized RNA molecules were labeled for 5 minute with 4-thioU.

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0


title: MDA-MB-231_NT1_rep1

description: Control sample. Transduced with non-targeting (NT1) sgRNA carrying virus. Cells were collected from 10 cm plates on day 6 post-transduction.


title: WT_C (RNA-seq)


title: MDA-MB-231_SS18L2KO_rep2


title: PREP0020_CHaas09906A_B01v1_20200123_2_Sample4_RFP


title: MDA-MB-231_NT1_rep2


title: MDA-MB-231_SS18L2KO_rep3


title: Med15_DMSO_SM_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED15-3xV5 IAA7::KanMX


title: Med15_IAA_HS_C (RNA-seq)


title: med16del_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 Dsin4::TRP1


title: med16del_B (RNA-seq)


title: Med15_IAA_SM_B (RNA-seq)


title: Med15_IAA_HS_B (RNA-seq)


title: Med15_IAA_SM_C (RNA-seq)


title: Med15_IAA_HS_A (RNA-seq)


title: Med15_IAA_SM_A (RNA-seq)


title: WT_A (RNA-seq)


title: Med15_DMSO_SM_B (RNA-seq)


title: Med15_DMSO_SM_A (RNA-seq)


title: Med15_DMSO_HS_B (RNA-seq)


title: Med15_DMSO_HS_C (RNA-seq)


title: Med15_DMSO_no_stress_B (RNA-seq)


title: Med15_DMSO_no_stress_A (RNA-seq)


title: MDA-MB-231_NT1_rep3


title: Med15_DMSO_HS_A (RNA-seq)


title: med15del_C (RNA-seq)

value: MAT{alpha} Dade2::hisG D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 Dgal11::HPH


title: med16del_A (RNA-seq)


title: med15del_B (RNA-seq)


title: med15del_A (RNA-seq)


title: Med15_DMSO_no_stress_C (RNA-seq)


title: MDA-MB-231_week4_tumor3


title: exvivo_PNT_S5_vg9vd2_G, TCR

status: Public on Aug 19 2022

city: Brussels

first: David

last: Vermijlen

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

description:
bulk TCR-seq
PT6_g.csv

data_processing:
Data processing of single-cell RNA sequencing libraries: Cell Ranger v3.0.2 was used to demultiplex and map sequencing reads against the GRCh38 genome. The resulting count matrices were loaded into R using read10x function form Seurat R package. All downstream analyses were implemented using R v4.0.3 and the package Seurat v3.2.3 (Stuart et al., 2019). Low-quality and doublet cells were filtered. Percentage of mitochondrial genes were plotted as well, and outliers were removed to filter out dead cells. Cell cycle score was calculated for all cells and regressed out. Integration vignette from Seurat v3.0 was followed to generate merged Seurat objects using the SCTransform function and regressing mitochondrial genes and trdv & trgv genes. PCA component was performed using pca Seurat function with 20 dimensions. RunUMAP function was used to obtain bidimensional coordinates for each cell. We determined the k-nearest neighbors of each cell using the FindNeighbors function and used this knn graph to construct the SNN graph by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. Finally, we used the FindClusters function to cluster cells using the Louvain algorithm based on the same PCs as RunUMAP function.
Single-cell TCR sequencing analysis: Sc TCR libraries were generated by using CellRanger vdj pipeline (v3.0.2). Human genome GRCh38 was used as reference for alignment. Integrated FT and PNT Seurat objects (gene expression data) were combined with their respective sc TCR-seq (TCR sequence) data based on shared 10× cell barcodes and following the script provided here (https://www.biostars.org/p/384640/). Only those cells expressing productive TCR sequences (γ and/or δ chain) from the ‘filtered_contig_annotations’ file were retained for data integration in the Seurat objects.
RNA-Seq samples: Approximately 30 million paired-end reads (2x101 bases) /sample were collected on a NovaSeq 6000 (Illumina). Paired-end reads with variable trimming (minimum size 36 bases) were mapped against the human reference genome (GRCh38) using STAR_2.5.3a software to generate read alignments for each sample. Annotations Homo_sapiens.GRCh38.90.gtf were obtained from ftp.Ensembl.org. After transcripts assembling, gene level counts were obtained using HTSeq, followed by a library size normalization data processing step. Supplementary_files_format_and_content: CSV file include CPM (count per million) values for each Sample.
Bulk TCR-seq samples: Raw sequencing reads from fastq files (read 1 and read 2) were aligned to reference V, D and J genes from GenBank database specifically for ‘TRG’ or ‘TRD’ to build CDR3 sequences using the MiXCR software version 2.1.1. Default parameters were used except to assemble TRDD gene segment where 3 instead of 5 consecutive nucleotides were applied as assemble parameter. CDR3 sequences were then exported and analyzed using VDJtools software version 1.2.1 using default settings. Sequences out of frame and containing stop codons were excluded from the analysis. Finally data from both files, sorted Vg9Vd2 and nonVg9Vd2, were combined in a same csv file to analysis publicity levels in the single cell dataset.
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. // matrix files include transcript count from each single-cell GEX library, barcodes tsv files includes the barcodes present in that single-cell GEX library and features tsv file includes the ID of the genes detected in that single-cell GEX library. /-/ scTCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv. // CSV files include single-cell barcoded CDR3 sequences. /-/ bulk RNA-seq file: CPM_FT_PNT_Vg9Vd2.csv // CSV file include CPM (count per million) transcript values for each sample. /-/ bulk TCR-seq files: FT17_d.csv,FT17_g.csv,FT19_d.csv,FT19_g.csv,FT3_d.csv,FT3_g.csv,PT3_d.csv,PT3_g.csv,PT4_d.csv,PT4_g.csv,PT5_d.csv,PT5_g.csv,PT6_d.csv,PT6_g.csv,PT7_d.csv,PT7_g.csv,PT8_d.csvPT8_g.csv // Each csv file contains CDR3 sequences (gamma for files with a g in the name and delta for files with a d in the name) of sorted gamma delta T cells.
Library strategy: TCR-seq

source_name: ϒδ thymocytes

extract_protocol:
Cell suspension from FT and PNT samples was obtained as previously described (McGovern et al., 2017; Van Coppernolle et al., 2009). γδ T cells from postnatal suspensions were isolated by positive selection using anti-TCRγδ magnetic activated cell sorting beads (Miltenyi Biotec) according to the manufacturer’s instruction. Thus, the γδ+ fraction was further sorted into CD3+TCRγδ+Vγ9+Vδ2+ subset (all around 10,000 cells) on a FACS Aria III cell sorter (BD Biosciences), snap-frozen in liquid nitrogen, and stored at −80°C for later RNA extraction. The mean purity was 95.0% (percentage of living cells). .RNA was extracted using RNeasy Plus Micro kit according to manufacturer’s instructions.
Prior steps before TCRγ (TRG) and TCRδ (TRD) high-throughput sequencing were performed as previously described (Tieppo et al. JEM 2020 and Papadopoulou et al. JI 2019). High-throughput sequencing of the generated amplicon products containing the TRG and TRD sequences was performed on an Illumina MiSeq platform using the V2 300 kit
RNA-Seq (RACE)

value: Gamma delta T cell

tag: age

value: 3 years and 2 months

value: pediatric thymus


title: exvivo_PNT_S4_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT5_g.csv

value: 3 years


title: exvivo_PNT_S5_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT6_g.csv


title: exvivo_PNT_S4_vg9vd2_G, TCR

description:
bulk TCR-seq
PT5_g.csv


title: TEAD4 ChIP liver YAP Tg biol rep 1

status: Public on Aug 20 2022

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

institute: UT Southwestern Medical Center

data_processing:
Reads were aligned with Bowtie2 to the mm10 mouse genome and duplicates were removed from the mapped data using PICARD.  Aligned results were normalized with ChipSeqSpike R package and visualized by uploading normalized Bigwig files into mm10 assembly of USCS genome browser. TET1 and TEAD4 peaks were called against mm10 background using MACS2 default parameters.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
For ChIP-seq, ChIP was performed with Magna ChIP HiSens chromatin immunoprecipitation kit (Millipore Sigma) according to the manufacturer’s protocols. Briefly, 100 mg mouse liver was pulverized with liquid nitrogen, and cross-linked in 1% methanol-free formaldehyde at room temperature for 10 minutes. Fixed cells were collected and lysed in Nuclei Isolation Buffer for 15 minutes. Then, cells were homogenized 10 times in a Dounce homogenizer (loose pestle). Extracted nuclei were fragmented by sonication to an average size of 200-700 bp (S2 Focused-ultrasonicator, Covaris). 10 μg fragmented chromatin was subjected to overnight incubation at 4 °C with specific antibody pre-conjugated beads. For ChIP normalization, 10 ng spike-in Drosophila chromatin (Active Motif, 53083) and 1 ug spike-in antibody (Active Motif, 61686) were added in each reaction before overnight incubation. After serial washing, the beads were incubated with ChIP elution buffer, Proteinase K at 65 °C for 2 hours and at 95°C for 15 minutes. The released DNA was purified using MinElute PCR Purification Kit (Qiagen).
5 ng of ChIP eluent were prepared using KAPA HTP Library Preparation Kit according to the manufacturer’s protocols. PCR amplified libraries were purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer for quality control.

value: liver

value: YAP Tg

tag: treatment

value: Doxycycline


title: TEAD4 ChIP  liver Control biol rep 2

value: wild type


title: TET1 ChIP liver YAP Tg biol rep 2


title: TEAD4 ChIP liver Control biol rep 1


title: TET1 ChIP  liver Control biol rep 2


title: TET1 ChIP liver YAP Tg biol rep 1


title: TEAD4 ChIP liver YAP Tg biol rep 2


title: TEAD4 ChIP liver Tet1 KO YAP Tg biol rep 1

value: Tet1 -/- YAP Tg


title: TET1 ChIP liver Control biol rep 1


title: exvivo_PNT_S5_vg9vd2_D, TCR

description:
bulk TCR-seq
PT6_d.csv


title: exvivo_PNT_S3_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT3_g.csv

value: 1 year and 1 month


title: exvivo_PNT_S4_vg9vd2_D, TCR

description:
bulk TCR-seq
PT5_d.csv


title: exvivo_FT_S3_nonvg9vd2_D, TCR

description:
bulk TCR-seq
FT3_d.csv

value: 17 wk gestation time

value: fetal thymus


title: exvivo_FT_S3_nonvg9vd2_G, TCR

description:
bulk TCR-seq
FT3_g.csv


title: exvivo_PNT_S3_vg9vd2_D, TCR

description:
bulk TCR-seq
PT3_d.csv


title: exvivo_PNT_S3_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT3_d.csv


title: exvivo_PNT_S6_vg9vd2_G, TCR

description:
bulk TCR-seq
PT7_g.csv

value: 3 years and 10 months


title: exvivo_FT_S3_vg9vd2_D, TCR

description:
bulk TCR-seq
FT3_d.csv


title: exvivo_PNT_S6_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT7_g.csv


title: exvivo_PNT_S6_vg9vd2_D, TCR

description:
bulk TCR-seq
PT7_d.csv


title: exvivo_PNT_S2_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT4_d.csv

value: 4 months


title: exvivo_FT_S2_vg9vd2_D, TCR

description:
bulk TCR-seq
FT17_d.csv


title: exvivo_PNT_S5_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT6_d.csv


title: exvivo_PNT_S6_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT7_d.csv


title: exvivo_PNT_S4_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT5_d.csv


title: TEAD4 ChIP liver Tet1 KO YAP Tg biol rep 2


title: exvivo_PNT_S3_vg9vd2_G, TCR

description:
bulk TCR-seq
PT3_g.csv


title: exvivo_PNT_S2_vg9vd2_D, TCR

description:
bulk TCR-seq
PT4_d.csv


title: exvivo_FT_S3_vg9vd2_G, TCR

description:
bulk TCR-seq
FT3_g.csv


title: exvivo_FT_S2_nonvg9vd2_D, TCR

description:
bulk TCR-seq
FT17_d.csv


title: exvivo_PNT_S2_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT4_g.csv


title: exvivo_PNT_S1_nonvg9vd2_D, TCR

description:
bulk TCR-seq
PT8_d.csv

value: 8 years and 4 months


title: exvivo_PNT_S2_vg9vd2_G, TCR

description:
bulk TCR-seq
PT4_g.csv


title: exvivo_FT_S2_nonvg9vd2_G, TCR

description:
bulk TCR-seq
FT17_g.csv


title: exvivo_FT_S2_vg9vd2_G, TCR

description:
bulk TCR-seq
FT17_g.csv


title: exvivo_PNT_S1_vg9vd2_D, TCR

description:
bulk TCR-seq
PT8_d.csv


title: exvivo_FT_S1_nonvg9vd2_D, TCR

description:
bulk TCR-seq
FT19_d.csv

value: 19 wk gestation time


title: exvivo_PNT_S1_nonvg9vd2_G, TCR

description:
bulk TCR-seq
PT8_g.csv


title: exvivo_FT_S1_vg9vd2_G, TCR

description:
bulk TCR-seq
FT19_g.csv


title: exvivo_FT_S1_vg9vd2, GEX

description:
bulk RNA-seq
CPM_FT_PNT_Vg9Vd2.csv

data_processing:
Data processing of single-cell RNA sequencing libraries: Cell Ranger v3.0.2 was used to demultiplex and map sequencing reads against the GRCh38 genome. The resulting count matrices were loaded into R using read10x function form Seurat R package. All downstream analyses were implemented using R v4.0.3 and the package Seurat v3.2.3 (Stuart et al., 2019). Low-quality and doublet cells were filtered. Percentage of mitochondrial genes were plotted as well, and outliers were removed to filter out dead cells. Cell cycle score was calculated for all cells and regressed out. Integration vignette from Seurat v3.0 was followed to generate merged Seurat objects using the SCTransform function and regressing mitochondrial genes and trdv & trgv genes. PCA component was performed using pca Seurat function with 20 dimensions. RunUMAP function was used to obtain bidimensional coordinates for each cell. We determined the k-nearest neighbors of each cell using the FindNeighbors function and used this knn graph to construct the SNN graph by calculating the neighborhood overlap (Jaccard index) between every cell and its k.param nearest neighbors. Finally, we used the FindClusters function to cluster cells using the Louvain algorithm based on the same PCs as RunUMAP function.
Single-cell TCR sequencing analysis: Sc TCR libraries were generated by using CellRanger vdj pipeline (v3.0.2). Human genome GRCh38 was used as reference for alignment. Integrated FT and PNT Seurat objects (gene expression data) were combined with their respective sc TCR-seq (TCR sequence) data based on shared 10× cell barcodes and following the script provided here (https://www.biostars.org/p/384640/). Only those cells expressing productive TCR sequences (γ and/or δ chain) from the ‘filtered_contig_annotations’ file were retained for data integration in the Seurat objects.
RNA-Seq samples: Approximately 30 million paired-end reads (2x101 bases) /sample were collected on a NovaSeq 6000 (Illumina). Paired-end reads with variable trimming (minimum size 36 bases) were mapped against the human reference genome (GRCh38) using STAR_2.5.3a software to generate read alignments for each sample. Annotations Homo_sapiens.GRCh38.90.gtf were obtained from ftp.Ensembl.org. After transcripts assembling, gene level counts were obtained using HTSeq, followed by a library size normalization data processing step. Supplementary_files_format_and_content: CSV file include CPM (count per million) values for each Sample.
Bulk TCR-seq samples: Raw sequencing reads from fastq files (read 1 and read 2) were aligned to reference V, D and J genes from GenBank database specifically for ‘TRG’ or ‘TRD’ to build CDR3 sequences using the MiXCR software version 2.1.1. Default parameters were used except to assemble TRDD gene segment where 3 instead of 5 consecutive nucleotides were applied as assemble parameter. CDR3 sequences were then exported and analyzed using VDJtools software version 1.2.1 using default settings. Sequences out of frame and containing stop codons were excluded from the analysis. Finally data from both files, sorted Vg9Vd2 and nonVg9Vd2, were combined in a same csv file to analysis publicity levels in the single cell dataset.
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. // matrix files include transcript count from each single-cell GEX library, barcodes tsv files includes the barcodes present in that single-cell GEX library and features tsv file includes the ID of the genes detected in that single-cell GEX library. /-/ scTCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv. // CSV files include single-cell barcoded CDR3 sequences. /-/ bulk RNA-seq file: CPM_FT_PNT_Vg9Vd2.csv // CSV file include CPM (count per million) transcript values for each sample. /-/ bulk TCR-seq files: FT17_d.csv,FT17_g.csv,FT19_d.csv,FT19_g.csv,FT3_d.csv,FT3_g.csv,PT3_d.csv,PT3_g.csv,PT4_d.csv,PT4_g.csv,PT5_d.csv,PT5_g.csv,PT6_d.csv,PT6_g.csv,PT7_d.csv,PT7_g.csv,PT8_d.csvPT8_g.csv // Each csv file contains CDR3 sequences (gamma for files with a g in the name and delta for files with a d in the name) of sorted gamma delta T cells.

extract_protocol:
Cell suspension from FT and PNT samples was obtained as previously described (McGovern et al., 2017; Van Coppernolle et al., 2009). γδ T cells from postnatal suspensions were isolated by positive selection using anti-TCRγδ magnetic activated cell sorting beads (Miltenyi Biotec) according to the manufacturer’s instruction. Thus, the γδ+ fraction was further sorted into CD3+TCRγδ+Vγ9+Vδ2+ subset (all around 10,000 cells) on a FACS Aria III cell sorter (BD Biosciences), snap-frozen in liquid nitrogen, and stored at −80°C for later RNA extraction. The mean purity was 95.0% (percentage of living cells). .RNA was extracted using RNeasy Plus Micro kit according to manufacturer’s instructions.
Library was obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer's instruction


title: exvivo_PNT_S2_vg9vd2, GEX

description:
bulk RNA-seq
CPM_FT_PNT_Vg9Vd2.csv


title: exvivo_FT_S2_vg9vd2, GEX

description:
bulk RNA-seq
CPM_FT_PNT_Vg9Vd2.csv


title: exvivo_PNT_S1_vg9vd2, GEX

description:
bulk RNA-seq
CPM_FT_PNT_Vg9Vd2.csv


title: exvivo_PNT_S1_vg9vd2_G, TCR

description:
bulk TCR-seq
PT8_g.csv