title: Smartseq2_Lipstic_TdLN_104


title: TB6Ag_D105_RM1

status: Public on Oct 04 2024

type: SRA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: G203_O14_RM1_F_B_D105_RNA1_Lib1_GL53_S17

library_source: transcriptomic

data_processing:
Raw sequence reads were processed to digitally remove residual adapters and low-quality bases by using Trim Galore v0.6.4 (powered by Cutadapt v3.7), along with quality check using FastQC v0.11.2.
Trimmed reads were then filtered to remove globin and ribosomal sequences using Bowtie2 v2.3.4.
Paired reads were aligned to the Mmul_10 Macaca mulatta genome (Ensembl v109) and gene expression was quantified with STAR v2.7.10b using the --quantMode GeneCounts flag to generate raw gene counts.
After removing lowly expressed genes with mean gene counts below 4, trimmed mean of M-values (TMM) normalization was performed using the calcNormFactors function in edgeR to calculate the scaling factor for the adjusted library sizes.
Gene counts were then transformed into log2-counts per million (log-CPM) values by limma package with the voom function for subsequent analyses.
Assembly: Mmul_10 Macaca mulatta genome (Ensembl v109)
Supplementary files format and content: count_matrix.txt; raw count data matrix file
Supplementary files format and content: 1.norm_matrix_HGNC.txt; voom normalized count data matrix file with HGNC symbol conversion

molecule: polyA RNA

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Longitudinal whole blood samples were collected into PAXgene RNA tubes (PreAnalytiX) following the manufacturer’s instructions. RNA was isolated using RNAdvance Blood Kit (Beckman) on a Biomek i7 Automated Workstation (Beckman) following the validated protocol provided with the kit that included an on-column DNase treatment.
mRNA-seq libraries were constructed using the KAPA HyperPrep Kit with RiboErase (HMR) Globin + mRNA Capture Kit (Roche Diagnostics) following the manufacturer’s recommended protocol that was adapted for the Biomek i7.

treatment_protocol: Each RM was given a prime and two boosts of one of the two vaccines: either 68-1 RhCMV/TB-6Ag or 68-1 RhCMV/Δpp71-TB-6Ag.

tag: tissue

value: Whole Blood

tag: animal

tag: animal age

tag: animal sex

value: Female

tag: treatment

value: 68-1 RhCMV/TB-6Ag

tag: time point

tag: colony of_origin

value: ONPRC


title: Smartseq2_Lipstic_TdLN_106

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

library_source: transcriptomic single cell

data_processing:
For 10x genomics sequencing, fastq files were aligned to the mouse genome (mm39) using the Cell Ranger pipeline (v. 7.0.1).
Data was processed using the Seurat package in R, with cells containing more than 5% mitochondrial reads excluded.
Normalization was performed using the SCTransform function.
Differential expression was analyzed using Wilcoxon-Rank-Test with Bonferroni correction.
For Smartseq2, reads were aligned to the mouse genome (GRCm38.p6) using STAR aligner.
Quantification matrices were generated using RSEM, processed in the Seurat pipeline, and filtered based on mitochondrial content.
Cells were clustered and visualized in t-SNE space using Seurat.
Assembly: mm39
Supplementary files format and content: Tab-separated matrix files for gene counts, normalized data.

molecule: total RNA

organism: Mus musculus

growth_protocol: All tumor cell lines were grown in DMEM supplemented with 1% L-Glutamine and 1% Penicillin/Streptomycin.

extract_protocol:
Freshly collected tumor-draining lymph nodes (tdLNs) and tumors were processed for single-cell isolation. Tumors were digested with collagenase D and DNase I, and lymph nodes were digested with collagenase D. Single-cell suspensions were then prepared, stained, and sorted by FACS based on surface markers, as detailed in the Methods section.
Single-cell RNA-seq libraries were constructed using the Chromium platform (10x Genomics) following the manufacturer’s instructions. The RNA from sorted cells was processed for library construction, aiming for specific read lengths for each segment of sequencing. Libraries for bulk RNA-seq were prepared using the Smart-Seq2 method.

treatment_protocol: Mice were injected with various tumor cell lines as described. Antibody treatments (e.g., anti-IL-27, anti-CD40L, anti-CTLA-4, anti-PD-1, or anti-MHC-II) were administered at specified doses and time points. LIPSTIC substrate biotin–LPETG was injected as described for labeling intratumoral APC-T cell interactions.

tag: mouse name

tag: cell line

tag: timepoint

tag: plate date

value: Tumor


title: pp71_D101_RM20

description: G178_O14_RM20_L_B_D101_RNA1_Lib1_GL53_S34

value: Male

value: 68-1 RhCMV/{delta}pp71-TB-6Ag


title: DNA from Kazakh individual 41

type: genomic

city: Astana

first: Ulykbek

last: Kairov

address: Kabanbay batyr ave.53

department: Center for Life Sciences

country: Kazakhstan

institute: National Laboratory Astana, Nazarbayev University

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 41

hyb_protocol: DNA was loaded onto BeadChips arrays

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Normalized signal intensity and genotype were computed using Illumina's GenomeStudio v.2 software. GSA MG v2 was used for genotyping
Genotype: AA,AB,BB,or NC (no call)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200 ng of Genomic DNA was amplified overnight at 37 degrees.  DNA was fragmented via FMS and precipitated with 2-propanol and PM1. Then DNA is resuspended

extract_protocol: DNA isolation from frozen blood was performed with Gentra Purgene Blood kit (Qiagen)

tag: health status

value: Healthy

value: blood


title: TB6Ag_D101_RM8

description: G176_O14_RM8_F_B_D101_RNA1_Lib1_GL52_S50

value: PR


title: pp71_D101_RM16

description: G182_O14_RM16_L_B_D101_RNA1_Lib1_GL53_S69


title: Smartseq2_Lipstic_TdLN_105

source_name: Biotin+

value: Biotin+


title: DNA from Kazakh individual 43

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 43


title: pp71_D101_RM14

description: G180_O14_RM14_L_B_D101_RNA1_Lib1_GL51_S27


title: DNA from Kazakh individual 38

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 38


title: DNA from Kazakh individual 39

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 39


title: pp71_D101_RM15

description: G181_O14_RM15_L_B_D101_RNA1_Lib1_GL51_S30


title: TB6Ag_D101_RM9

description: G177_O14_RM9_F_B_D101_RNA1_Lib1_GL53_S28


title: TB6Ag_D101_RM6

description: G174_O14_RM6_F_B_D101_RNA1_Lib1_GL50_S27


title: Smartseq2_Lipstic_TdLN_102


title: TB6Ag_D101_RM4

description: G173_O14_RM4_F_B_D101_RNA2_Lib1_GL62_S69


title: Smartseq2_Lipstic_TdLN_101


title: TB6Ag_D101_RM5

description: G175_O14_RM5_F_B_D101_RNA1_Lib1_GL53_S57


title: TB6Ag_D101_RM2

description: G171_O14_RM2_F_B_D101_RNA2_Lib1_GL62_S68


title: TB6Ag_D101_RM7

description: G172_O14_RM7_F_B_D101_RNA1_Lib1_GL51_S52


title: Smartseq2_Lipstic_TdLN_100


title: TB6Ag_D101_RM1

description: G170_O14_RM1_F_B_D101_RNA1_Lib1_GL51_S84


title: DNA from Kazakh individual 40

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 40


title: DNA from Kazakh individual 36

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 36


title: Smartseq2_Lipstic_TdLN_103


title: TB6Ag_D101_RM3

description: G169_O14_RM3_F_B_D101_RNA1_Lib1_GL52_S61


title: DNA from Kazakh individual 35

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 35


title: TB6Ag_D101_RM12

description: G168_O14_RM12_F_B_D101_RNA1_Lib1_GL53_S2


title: TB6Ag_D101_RM11

description: G167_O14_RM11_F_B_D101_RNA2_Lib1_GL50_S75


title: Smartseq2_Lipstic_TdLN_98


title: pp71_D98_RM17

description: G154_O14_RM17_L_B_D98_RNA1_Lib1_GL52_S84


title: DNA from Kazakh individual 34

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 34


title: TB6Ag_D101_RM10

description: G166_O14_RM10_F_B_D101_RNA2_Lib1_GL62_S67


title: Smartseq2_Lipstic_TdLN_97


title: pp71_D98_RM19

description: G153_O14_RM19_L_B_D98_RNA3_Lib1_GL57_S57


title: DNA from Kazakh individual 33

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 33


title: pp71_D98_RM18

description: G152_O14_RM18_L_B_D98_RNA1_Lib1_GL51_S28


title: pp71_D98_RM16

description: G149_O14_RM16_L_B_D98_RNA1_Lib1_GL50_S47


title: pp71_D98_RM15


title: Smartseq2_Lipstic_TdLN_96


title: DNA from Kazakh individual 32

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 32


title: DNA from Kazakh individual 37

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 37


title: Smartseq2_Lipstic_TdLN_95


title: DNA from Kazakh individual 31

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 31


title: pp71_D98_RM14

description: G147_O14_RM14_L_B_D98_RNA2_Lib1_GL57_S56


title: DNA from Kazakh individual 30

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 30


title: Smartseq2_Lipstic_TdLN_94


title: pp71_D98_RM20

description: G145_O14_RM20_L_B_D98_RNA1_Lib1_GL51_S35


title: Smartseq2_Lipstic_TdLN_99


title: pp71_D98_RM13

description: G146_O14_RM13_L_B_D98_RNA1_Lib1_GL52_S27


title: DNA from Kazakh individual 29

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 29


title: TB6Ag_D98_RM8


title: Smartseq2_Lipstic_TdLN_93


title: TB6Ag_D98_RM5


title: DNA from Kazakh individual 26

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 26


title: Smartseq2_Lipstic_TdLN_92


title: TB6Ag_D98_RM9


title: TB6Ag_D98_RM6


title: Smartseq2_Lipstic_TdLN_91


title: DNA from Kazakh individual 25

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 25


title: TB6Ag_D98_RM7


title: DNA from Kazakh individual 24

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 24


title: TB6Ag_D98_RM4


title: Smartseq2_Lipstic_TdLN_90


title: TB6Ag_D98_RM1


title: TB6Ag_D98_RM2


title: TB6Ag_D98_RM3


title: Smartseq2_Lipstic_TdLN_89


title: TB6Ag_D98_RM12

description: G135_O14_RM12_F_B_D98_RNA1_Lib1_GL50_S20


title: Smartseq2_Lipstic_TdLN_88


title: TB6Ag_D98_RM11


title: DNA from Kazakh individual 21

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 21


title: DNA from Kazakh individual 20

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 20


title: pp71_D14_RM19

description: G120_O14_RM19_L_B_D14_RNA1_Lib1_GL51_S42


title: pp71_D14_RM18

description: G119_O14_RM18_L_B_D14_RNA1_Lib1_GL52_S45


title: pp71_D14_RM17


title: Smartseq2_Lipstic_TdLN_87


title: DNA from Kazakh individual 18

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 18


title: Smartseq2_Lipstic_TdLN_86


title: DNA from Kazakh individual 17

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 17


title: pp71_D14_RM14

description: G114_O14_RM14_L_B_D14_RNA1_Lib1_GL51_S61


title: pp71_D14_RM13

description: G113_O14_RM13_L_B_D14_RNA1_Lib1_GL50_S58


title: Smartseq2_Lipstic_TdLN_85


title: pp71_D14_RM15


title: Smartseq2_Lipstic_TdLN_84


title: pp71_D14_RM20


title: DNA from Kazakh individual 15

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 15


title: DNA from Kazakh individual 22

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 22


title: TB6Ag_D14_RM8


title: TB6Ag_D14_RM9


title: TB6Ag_D14_RM5


title: TB6Ag_D98_RM10

description: G133_O14_RM10_F_B_D98_RNA1_Lib1_GL51_S25


title: Smartseq2_Lipstic_TdLN_83


title: DNA from Kazakh individual 8

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 8


title: Smartseq2_Lipstic_TdLN_82


title: TB6Ag_D14_RM4


title: Smartseq2_Lipstic_TdLN_81


title: DNA from Kazakh individual 6

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 6


title: TB6Ag_D14_RM7


title: pp71_D14_RM16

description: G116_O14_RM16_L_B_D14_RNA1_Lib1_GL50_S80


title: Smartseq2_Lipstic_TdLN_80

value: naïve


title: TB6Ag_D14_RM1


title: TB6Ag_D14_RM2


title: DNA from Kazakh individual 5

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 5


title: Smartseq2_Lipstic_TdLN_79


title: DNA from Kazakh individual 3

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 3


title: TB6Ag_D14_RM12

description: G102_O14_RM12_F_B_D14_RNA1_Lib1_GL53_S26


title: TB6Ag_D14_RM11

description: G101_O14_RM11_F_B_D14_RNA1_Lib1_GL51_S94


title: TB6Ag_D14_RM10

description: G100_O14_RM10_F_B_D14_RNA1_Lib1_GL53_S68


title: DNA from Kazakh individual 11

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 11


title: DNA from Kazakh individual 1

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 1


title: Smartseq2_Lipstic_TdLN_78


title: pp71_D7_RM17


title: pp71_D7_RM19


title: TB6Ag_D14_RM6


title: pp71_D7_RM18


title: pp71_D7_RM15


title: pp71_D7_RM16


title: APOEKO astrocytes

city: Rotselaar

first: Daan

last: Moechars

address: Catharinalaan 43

country: Belgium

institute: KULeuven

data_processing:
Raw BCL files were aligned to a modified GRCm39 mouse genome, which was appended with the human APOE gene. We used Bedtools 2.27.1 to extract the human APOE sequence and a thousand base buffer from GRCh38 (Quinlan and Hall, 2010). This was then appended to the murine GRCm39 genome in an artificial chromosome. The resulting genome was then filtered using the mkgtf function from Cellranger (6.1.2), in accordance with 10x guidelines (Zheng et al., 2017) and subsequently processed into a functional reference using cellranger mkref. Finally, each of the eight scRNAseq libraries were aligned to a custom genome using Cellranger’s count function which matches each transcript to its corresponding gene using the STAR aligner (Dobin et al., 2013). Raw count matrices were imported in R (v4.2.2) for data analysis.
Assembly: GRCm39  + human APOE
Supplementary files format and content: RDS encoded seurat file of astrocyte normalised counts and metadata
Supplementary files format and content: RDS encoded seurat file of microglia normalised counts and metadata

source_name: brain

extract_protocol:
6 months old mice were anaesthetized using CO2 chamber and perfused with ice-cold 1x DPBS (Gibco, #14190-144). Each mouse brain, excluding cerebellum and olfactory bulbs were dissected and placed in FACS buffer (1x DPBS, 2% FCS and 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, #A1410-5MG) for transcriptomics. Brains were mechanically and enzymatically dissociated using Miltenyi neural tissue dissociation kit P (Miltenyi, #130-092-628) supplemented with 5 μM ActD. Next, samples were passed through a 70 μm strainer (BD2 Falcon), washed in 10 ml of ice-cold FACS buffer + 5 μM ActD and spun at 300 rcf for 15 minutes at 4 °C. Note that 5 μM ActD was kept during collection and enzymatic dissociation of the tissue to preserve transcriptional state and prevent artificial induction stress-response genes during tissue dissociation (Perocchi et al., 2007; Marsh et al., 2022). ActD was removed from the myelin removal step to prevent toxicity derived from long-term exposure. Following dissociation, myelin was removed by resuspending pelleted cells into 30% isotonic Percoll (GE Healthcare, #17-5445-02) and centrifuging at 300 rcf for 15 minutes at 4 °C. Accumulating layers of myelin and cellular debris were discarded and Fc receptors were blocked in FcR blocking solution (1:10, Miltenyi, #130-092-575) in cold FACS buffer for 10 minutes at 4°C. Next, cells were washed in 5 ml of FACS buffer and pelleted cells split into two suspensions (one each for astrocyte and microglia sorting), and incubated with the following antibodies: for microglia- PE-CD11b (Miltenyi, #130-113-806, 1:50), BV421-CD45 (BD, #563890, 1:500); for astrocytes- APC-ACSA2 (Miltenyi, #130-116-142, 1:200), BV421-CD11b (BD, #562605, 1:500), PE-O4 (Miltenyi, #130-117-357, 1:50); in cold FACS buffer for 30 minutes at 4 °C. TotalSeq™-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, #65-0865-14) were also added to both fractions during the incubation step. After incubation, cells were washed, and the pellet was resuspended in 500 μl of FACS buffer and passed through 35 μm strainer prior sorting. For isolating microglia, cell suspension was loaded into the input chamber of MACSQuant Tyto Cartridge and cells were sorted on MACSQuant Tyto Cell Sorter at 4 °C, based on CD11b-positive and CD45-low populations. For isolating AAV-transduced astrocytes, cells were sorted on Aria Fusion, based on negative gating for O4 and CD11b populations, followed by positive gating for double-positive ACSA2 and mCherry populations.
20,000-30,000 cells of each cell type (astrocyte and microglia) from each mouse were diluted to a final concentration of 1000 cells/µl. All the samples were individually hashed using TotalSeq™-A cell hashing antibodies, 3000 cells/animal were pooled and loaded onto the Chromium Next GEM Chip G (PN #2000177). The DNA library preparations were generated following manufacturers’ instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). In parallel the hashtag oligo libraries were prepared according to manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3’ Reagent Kit v3 3.1 Protocol) using 16cycles for the index PCR. From the 4 experimental groups (APOEKO, APOE2, AOE3, and APOE4), a total of 8 libraries (APOEKO_astrocytes, APOE2_astrocytes, APOE3_astrocytes, APOE4_astrocytes, APOEKO_microglia, APOE2_microglia, APOE3_microglia, APOE4_microglia), containing 22 biological replicates (n(APOEKO)= 2, n(APOE2)= 3, n(APOE3)=3, n(APOE4)= 3), were sequenced (service provided by BGI Genomics, China) targeting 90% mRNA and 10% hashtag oligo library (50,000 reads/cell) on a DNBSEQ-G400 (MGI Tech) platform with the recommended read lengths by 10X Genomics workflow.

value: brain

tag: cell type

value: astrocyte

tag: genotype

value: APOEKO


title: Smartseq2_Lipstic_TdLN_75


title: APOEKO microglia

value: microglia


title: pp71_D7_RM14


title: APOE4 micrgolia


title: Smartseq2_Lipstic_TdLN_77


title: pp71_D7_RM13


title: TB6Ag_D14_RM3


title: Smartseq2_Lipstic_TdLN_74


title: APOE4 astrocytes


title: Smartseq2_Lipstic_TdLN_73


title: APOE2 microglia


title: TB6Ag_D7_RM9


title: TB6Ag_D7_RM5


title: Smartseq2_Lipstic_TdLN_72


title: APOE2 astrocytes


title: TB6Ag_D7_RM6


title: pp71_D7_RM20


title: Smartseq2_Lipstic_TdLN_71


title: TB6Ag_D7_RM7


title: TB6Ag_D7_RM4


title: TB6Ag_D7_RM2


title: Smartseq2_Lipstic_TdLN_76


title: Smartseq2_Lipstic_TdLN_70


title: TB6Ag_D7_RM1


title: APOE3 astrocytes


title: Smartseq2_Lipstic_TdLN_69


title: TB6Ag_D7_RM11


title: TB6Ag_D7_RM3


title: TB6Ag_D7_RM12


title: TB6Ag_D7_RM10


title: Smartseq2_Lipstic_TdLN_68


title: pp71_D3_RM17


title: TB6Ag_D7_RM8


title: Smartseq2_Lipstic_TdLN_67


title: pp71_D3_RM18


title: pp71_D3_RM15


title: pp71_D3_RM14


title: Smartseq2_Lipstic_TdLN_65


title: pp71_D3_RM13


title: APOE3 microglia


title: Smartseq2_Lipstic_TdLN_64


title: pp71_D3_RM20


title: TB6Ag_D3_RM9


title: 293Ttotal_SUPV3L1_RIP

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

country: China

description: RIP-seq

library_source: other

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
Assembly: hg38, mm10
Supplementary files format and content: csv or txt files include count values for each Sample

molecule: other

extract_protocol:
The isolated mitochondria, total cells were lysed in TRizol reagent (Life Technologies). RNA from  mitochondia, whole cell, mitochondrial fractions and RNA-IP were extracted by using TRizol reagent according to the manufacturer’s instructions.
For samll RNA seq, the small RNA bands in fractions 2-4 and the input were excised from the gel and RNAs were purified. Small RNA libraries were constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s protocol. For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs. For TRAP1 RIP and ATP5B RIP, sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. For other RIP-seq, NEB Next Ultra RNA Library Prep Kit was used for library construction of immunoprecipitated RNA. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: WT


title: TB6Ag_D3_RM8

value: Whole Blood


title: Platelets from HNSCC patient post-treatment_C44F1

type: RNA

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

hyb_protocol: Whole-genome gene expression profiling was performed using the Clariom S human gene expression array (Affymetrix) with Hybridization, Wash, and Stain Kit (Affymetrix) following manufacturer's instructions

scan_protocol: Clariom S chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Raw data was imported to Affymetrix software Transcriptome Analysis Console (TAC)  and quality control (QC) was performed as manufacturer's instructions (PCA, labeling controls, hybridization controls, Pos vs. Neg AUC, and Signal Box Plot). Normalization was performed with the Robust Multi-chip Analysis (RMA) approach with default analysis settings.

source_name: blood platelet tumour free

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Leucocyte kit (Norgen, Canada) as per manufacturer's instructions

treatment_protocol: not applicable

tag: blood

value: platelet

tag: condition

value: tumour free

tag: histology

tag: tnm

tag: Sex

tag: age


title: Platelets from HNSCC patient pre-treatment_C45F0

source_name: blood platelet in tumour presence

value: tumour presence

value: Orofaringynx squamous cell carcinoma


title: Platelets from HNSCC patient post-treatment_C45F1

value: Male


title: TB6Ag_D3_RM5

tag: tissue

tag: animal

tag: animal age

tag: animal sex

value: 68-1 RhCMV/TB-6Ag


title: Platelets from HNSCC patient pre-treatment_C44F0

value: Larynx squamous cell carcinoma


title: Smartseq2_Lipstic_TdLN_62

tag: mouse name

tag: treatment


title: pp71_D3_RM19

value: 68-1 RhCMV/{delta}pp71-TB-6Ag

tag: time point

tag: colony of_origin


title: Smartseq2_Lipstic_TdLN_63

tag: cell line

tag: timepoint

tag: plate date


title: Smartseq2_Lipstic_TdLN_66


title: pp71_D3_RM16

value: PR


title: TB6Ag_D3_RM6


title: 293Tmito_SUPV3L1_RIP

institute: University of Science and Technology of China

description: RIP-seq

tag: genotype


title: T47D, H, sgMETTL3_2, input

city: wuhan

first: Jingjing

last: Xiong

state: Hubei

address: Shuiguohu Street

institute: Wuhan University

data_processing:
Raw sequencing files were filtered using cutadapt (v1.18), and then aligned against the human reference genome (GRCh38/hg38) using tophat (v2.1.1).
The m6A-enriched regions in each m6A-immunoprecipitation sample were identified by MACS2 (v2.2.6) with the option of “--nomodel” with corresponding input library as control.
Peaks identified with p < 1e-10 were used for downstream analysis. Tracks of signal were computed using MACS2 bdgcmp module with parameter ‘-m FE’, and then visualized using the Integrative Genomics Viewer (IGV) visualization tool.
Assembly: hg38
Supplementary files format and content: bed, bw

growth_protocol: T47D cell were cultured in RPMI-1640 (Sigma-Aldrich) containing 10% fetal bovine serum with 1% penicillin–streptomycin. Cell was maintained in an incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Following purification with poly-T oligo attached magnetic beads (Invitrogen), the poly(A) mRNA fractions is fragmented
mRNA was subjected to incubated for 2 h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany). Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. Then we performed the paired-end 2×150 bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.
m6A-seq

treatment_protocol: T47D cells in control group and METTL3 knockout group were treated in hypoxic work station(5% CO2,1% O2,37°C) for 24 hours.

tag: cell type

value: Human breast cancer

tag: rip antibody

value: METTL3 knockout

value: hypoxia


title: Platelets from HNSCC patient post-treatment_C40F1

tag: blood

tag: condition

tag: histology

tag: tnm


title: Platelets from HNSCC patient post-treatment_C39F1

tag: Sex

tag: age


title: Platelets from HNSCC patient pre-treatment_C40F0


title: T47D, H, sgControl_2, input


title: Platelets from HNSCC patient pre-treatment_C39F0


title: Smartseq2_Lipstic_TdLN_60

value: Tumor


title: TB6Ag_D3_RM4

tag: tissue

tag: animal

tag: animal age

tag: animal sex


title: Platelets from HNSCC patient post-treatment_C38F1


title: Smartseq2_Lipstic_TdLN_59

tag: mouse name

value: Biotin+

tag: treatment


title: TB6Ag_D3_RM7

tag: time point

tag: colony of_origin


title: Smartseq2_Lipstic_TdLN_61

value: naïve

tag: cell line

tag: timepoint

tag: plate date


title: T47D, N, sgControl_2, input

tag: cell type

tag: rip antibody

tag: genotype

value: WT

value: normoxia


title: TB6Ag_D3_RM1

value: Whole Blood

value: Female

value: ONPRC


title: T47D, H, sgMETTL3_2, m6A

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: T47D, N, sgMETTL3_2, input


title: T47D, H, sgControl_2, m6A


title: Smartseq2_Lipstic_TdLN_56


title: Smartseq2_Lipstic_TdLN_58


title: TB6Ag_D3_RM3


title: Platelets from HNSCC patient post-treatment_C37F1

tag: blood

value: platelet

tag: condition

value: tumour free

tag: histology

tag: tnm

value: Male


title: TB6Ag_D3_RM2

tag: tissue

tag: animal

value: 68-1 RhCMV/TB-6Ag


title: Smartseq2_Lipstic_TdLN_57


title: Smartseq2_Lipstic_TdLN_55


title: Platelets from HNSCC patient pre-treatment_C38F0

value: tumour presence

value: Larynx squamous cell carcinoma

tag: Sex

tag: age


title: T47D, N, sgMETTL3_2, m6A

value: Human breast cancer

value: METTL3 knockout

tag: treatment


title: TB6Ag_D3_RM12

tag: animal age

tag: animal sex

tag: time point


title: T47D, N, sgControl_2, m6A

tag: cell line


title: Smartseq2_Lipstic_TdLN_54

tag: mouse name

tag: timepoint

tag: plate date

value: Tumor


title: TB6Ag_D3_RM11

tag: colony of_origin


title: Platelets from HNSCC patient post-treatment_C36F1

tag: blood


title: Platelets from HNSCC patient pre-treatment_C36F0

tag: condition

value: Orofaringynx squamous cell carcinoma


title: Smartseq2_Lipstic_TdLN_53


title: T47D, H, sgMETTL3_1, input

tag: cell type

tag: rip antibody

tag: genotype

value: hypoxia


title: TB6Ag_D3_RM10

tag: tissue

tag: animal


title: T47D, H, sgControl_1, input

value: WT


title: Platelets from HNSCC patient post-treatment_C33F1

tag: histology

tag: tnm

tag: Sex

tag: age


title: Smartseq2_Lipstic_TdLN_52

value: Biotin+

tag: treatment


title: pp71_D0_RM17

value: Whole Blood

tag: animal age

tag: animal sex

value: 68-1 RhCMV/{delta}pp71-TB-6Ag

tag: time point

value: PR


title: Smartseq2_Lipstic_TdLN_51

tag: mouse name

tag: cell line

tag: timepoint

tag: plate date


title: T47D, N, sgMETTL3_1, input

tag: cell type

value: normoxia


title: Platelets from HNSCC patient pre-treatment_C33F0

tag: blood

value: platelet

tag: condition


title: Platelets from HNSCC patient pre-treatment_C37F0


title: Smartseq2_Lipstic_TdLN_50


title: pp71_D0_RM19

tag: tissue

tag: colony of_origin


title: Platelets from HNSCC patient post-treatment_C32F1

value: tumour free

tag: histology

value: Female


title: pp71_D0_RM18

tag: animal

value: Male


title: T47D, N, sgControl_1, input

tag: rip antibody

tag: genotype


title: pp71_D0_RM16

tag: treatment


title: T47D, H, sgMETTL3_1, m6A

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: Platelets from HNSCC patient pre-treatment_C32F0

value: tumour presence

tag: tnm

tag: Sex

tag: age


title: T47D, H, sgControl_1, m6A

value: Human breast cancer


title: Smartseq2_Lipstic_TdLN_48

tag: mouse name


title: pp71_D0_RM15

tag: animal age

tag: animal sex

tag: time point

value: ONPRC


title: T47D, N, sgMETTL3_1, m6A

tag: cell line

tag: cell type

value: METTL3 knockout


title: pp71_D0_RM14


title: Smartseq2_Lipstic_TdLN_46

tag: timepoint

tag: plate date

value: Tumor


title: T47D, N, sgControl_1, m6A


title: pp71_D0_RM13

tag: tissue

tag: colony of_origin


title: Smartseq2_Lipstic_TdLN_45


title: Platelets from HNSCC patient pre-treatment_C29F0

tag: blood

tag: condition

tag: histology

value: Orofaringynx squamous cell carcinoma


title: Platelets from HNSCC patient post-treatment_C30F1


title: Platelets from HNSCC patient pre-treatment_C30F0


title: T47D, Hypoxia_3, input

data_processing:
Raw sequencing files were filtered using cutadapt (v1.18), and then aligned against the human reference genome (GRCh38/hg38) using tophat (v2.1.1).
The m6A-enriched regions in each m6A-immunoprecipitation sample were identified by MACS2 (v2.2.6) with the option of “--nomodel” with corresponding input library as control.
Peaks identified with p < 1e-10 were used for downstream analysis. Tracks of signal were computed using MACS2 bdgcmp module with parameter ‘-m FE’, and then visualized using the Integrative Genomics Viewer (IGV) visualization tool.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

treatment_protocol: T47D cells were treated in hypoxic work station(5% CO2,1% O2,37°C) for 24 hours.

tag: rip antibody

tag: treatment

value: hypoxia


title: Smartseq2_Lipstic_TdLN_44

value: Biotin+


title: Platelets from HNSCC patient post-treatment_C27F1

tag: tnm

tag: Sex


title: pp71_D0_RM20

value: Whole Blood

tag: animal


title: Platelets from HNSCC patient post-treatment_C28F1

tag: age


title: Smartseq2_Lipstic_TdLN_49

tag: mouse name


title: T47D, Hypoxia_3, m6A


title: TB6Ag_D0_RM9

tag: animal age

tag: animal sex

value: 68-1 RhCMV/TB-6Ag

tag: time point


title: T47D, Normoxia_3, input

tag: cell line

tag: cell type


title: Smartseq2_Lipstic_TdLN_47

tag: timepoint

tag: plate date


title: T47D, Normoxia_3, m6A


title: Smartseq2_Lipstic_TdLN_42

value: naïve


title: Platelets from HNSCC patient pre-treatment_C27F0

tag: blood


title: TB6Ag_D0_RM5

tag: tissue

tag: colony of_origin

value: PR


title: Smartseq2_Lipstic_TdLN_41


title: T47D, Hypoxia_2, input

tag: rip antibody


title: TB6Ag_D0_RM6

tag: treatment


title: Smartseq2_Lipstic_TdLN_40


title: Platelets from HNSCC patient pre-treatment_C26F0

value: platelet

tag: condition

tag: histology

tag: tnm


title: T47D, Normoxia_2, input

value: normoxia


title: TB6Ag_D0_RM4

tag: animal


title: Smartseq2_Lipstic_TdLN_39

tag: mouse name


title: T47D, Hypoxia_2, m6A


title: TB6Ag_D0_RM8

tag: animal age


title: Platelets from HNSCC patient pre-treatment_C23F0

value: Larynx squamous cell carcinoma

tag: Sex

tag: age


title: Smartseq2_Lipstic_TdLN_43

tag: cell line


title: T47D, Normoxia_2, m6A

tag: cell type


title: Smartseq2_Lipstic_TdLN_38

tag: timepoint


title: TB6Ag_D0_RM2

tag: animal sex

value: Female

tag: time point


title: Platelets from HNSCC patient post-treatment_C21F1

tag: blood

value: tumour free

value: Male


title: Smartseq2_Lipstic_TdLN_36

tag: plate date


title: T47D, Hypoxia_1, input

value: Human breast cancer

tag: rip antibody


title: TB6Ag_D0_RM1

tag: tissue

tag: treatment

tag: colony of_origin

value: ONPRC


title: TB6Ag_D0_RM3


title: Platelets from HNSCC patient pre-treatment_C21F0

tag: condition

value: tumour presence

tag: histology

tag: tnm


title: Platelets from HNSCC patient post-treatment_C19F1


title: TB6Ag_D0_RM12

tag: animal

tag: animal age


title: Platelets from HNSCC patient pre-treatment_C19F0

tag: Sex

tag: age


title: Platelets from HNSCC patient post-treatment_C18F1


title: Smartseq2_Lipstic_TdLN_34

tag: mouse name

tag: cell line


title: TB6Ag_D0_RM7

tag: animal sex


title: TB6Ag_D0_RM11

tag: time point


title: Smartseq2_Lipstic_TdLN_37

tag: timepoint


title: Platelets from HNSCC patient post-treatment_C17F1

tag: blood


title: Whole blood, Male, CARD_Negative_5

city: Baltimore

first: Monica

last: Mugnier

state: MD

address: 615 N Wolfe St

department: MMI

institute: Johns Hopkins University

description:
H754
CHAVArawcounts.txt

data_processing:
Paired reads were adapter- and quality-trimmed using Trimmomatic (v. 0.38)
Reads were aligned to the human genome GRCh38 ensembl release 84 using HiSAT2 (v. 2.1.0)
read counts per gene were obtained using featureCounts (v 2.0.1)
Assembly: GRCh38 ensembl release 84
Supplementary files format and content: tab-delimited txt file of raw read counts

source_name: Whole blood

extract_protocol:
RNA was extracted using Quick-RNA Whole Blood Kit (Zymo Research, Irvine, CA, USA) and treated with TURBO DNAse (Thermo Fisher Scientific, Waltham, MA, USA) to remove remaining DNA contamination. Samples were then rRNA and globin depleted using the Ribo-Zero™ kit (Illumina, San Diego, CA, USA) and the GLOBINclear™ kit (Invitrogen, Waltham, MA, USA) respectively.
Non-directional libraries were then constructed using Novogene’s proprietary kit

value: Whole blood

tag: cardiac stage

value: CARD

tag: chagas serostatus

value: Negative


title: Whole blood, Male, CARD_Positive_4

description:
H524
CHAVArawcounts.txt

tag: tissue

value: Positive


title: Smartseq2_Lipstic_TdLN_33

tag: plate date

tag: treatment


title: TB6Ag_D0_RM10

value: Whole Blood

tag: colony of_origin


title: T47D, Normoxia_1, input

tag: cell type

tag: rip antibody


title: Platelets from HNSCC patient pre-treatment_C17F0

tag: condition

tag: histology

tag: tnm


title: Platelets from HNSCC patient pre-treatment_C28F0

tag: Sex

tag: age


title: Whole blood, Male, non-CARD_Negative_4

description:
H093
CHAVArawcounts.txt

value: non-CARD


title: Smartseq2_Lipstic_TdLN_35

tag: mouse name

value: naïve

tag: cell line


title: T47D, Hypoxia_1, m6A

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)

value: hypoxia


title: Smartseq2_Lipstic_TdLN_31

tag: timepoint


title: Platelets from HNSCC patient pre-treatment_C13F0

tag: blood

value: platelet


title: Smartseq2_Lipstic_TdLN_30


title: Whole blood, Female, non-CARD_Negative_9

description:
G756
CHAVArawcounts.txt

tag: cardiac stage


title: Platelets_NSCLC patient post-treatment_P32F1_miRNA

hyb_protocol: Labeled RNA were hybridizaded in miRNA 4.0 chips with  Hybridization, Wash, and Stain Kit (Affymetrix) following manufacturer's instructions

scan_protocol: miRNA 4.0 chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Raw data was imported to Affymetrix Transcriptome Analysis Console (TAC) and analyzed with RMA method using Affymetrix default parameters.

label: Biotin

source_name: Blood platelet tumour free

label_protocol: 200ng total RNA for each sample was labeled with FlashTag Biotin HSR RNA Labeling Kit (Affymetrix) following manufacturer's instructions

extract_protocol: Total RNA was extracted using Leucocyte kit (Norgen, Canada) as manufacturer's instructions

value: Tumour free


title: Smartseq2_Lipstic_TdLN_29


title: Platelets_NSCLC patient pre-treatment_P32F0_miRNA

source_name: Blood platelet in tumour presence

value: Tumour presence

value: Lung adenocarcinoma

value: Female


title: T47D, Normoxia_1, m6A

value: Human breast cancer

value: normoxia


title: Whole blood, Female, CARD_Negative_5

description:
G282
CHAVArawcounts.txt

tag: chagas serostatus


title: Platelets from HNSCC patient pre-treatment_C11F0

value: tumour presence

value: Larynx squamous cell carcinoma

value: Male


title: Platelets from HNSCC patient post-treatment_C11F1

value: tumour free


title: Platelets_NSCLC patient post-treatment_P31F1_miRNA


title: Smartseq2_Lipstic_TdLN_32


title: Platelets from HNSCC patient post-treatment_C10F1


title: Smartseq2_Lipstic_TdLN_27


title: Platelets from HNSCC patient post-treatment_C23F1


title: Platelets_NSCLC patient pre-treatment_P31F0_miRNA


title: Smartseq2_Lipstic_TdLN_28


title: Whole blood, Male, CARD_Negative_4

description:
G026
CHAVArawcounts.txt

tag: tissue

value: Whole blood

value: CARD

value: Negative


title: Whole blood, Female, non-CARD_Negative_7

description:
E375
CHAVArawcounts.txt

value: non-CARD


title: Platelets from HNSCC patient pre-treatment_C10F0

value: Orofaringynx squamous cell carcinoma


title: Smartseq2_Lipstic_TdLN_25

value: naïve

tag: plate date


title: Whole blood, Female, CARD_Negative_4

description:
E054
CHAVArawcounts.txt


title: Platelets from HNSCC patient post-treatment_C5F1

value: platelet


title: Smartseq2_Lipstic_TdLN_24

tag: treatment


title: Platelets_NSCLC patient pre-treatment_P27F0_miRNA


title: Platelets from NSCLC patient post-treatment_P32F1


title: Whole blood, Male, CARD_Positive_3

description:
B621
CHAVArawcounts.txt

value: Positive


title: Platelets_NSCLC patient post-treatment_P21F1_miRNA

value: Tumour free


title: Platelets from HNSCC patient post-treatment_C2F1


title: Whole blood, Female, non-CARD_Negative_8

description:
G028
CHAVArawcounts.txt


title: Platelets_NSCLC patient post-treatment_P20F1_miRNA


title: Smartseq2_Lipstic_TdLN_22


title: Platelets from NSCLC patient post-treatment_P31F1


title: Platelets from NSCLC patient pre-treatment_P32F0

value: Lung adenocarcinoma


title: Platelets_NSCLC patient pre-treatment_P20F0_miRNA

value: Tumour presence

value: Lung squamous cell carcinoma


title: Platelets_NSCLC patient post-treatment_P27F1_miRNA

value: Female


title: Smartseq2_Lipstic_TdLN_26


title: Smartseq2_Lipstic_TdLN_23


title: Whole blood, Male, non-CARD_Negative_3

description:
B430
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_21


title: Platelets from NSCLC patient pre-treatment_P31F0

value: tumour presence


title: Whole blood, Male, non-CARD_Negative_2

description:
B429
CHAVArawcounts.txt


title: Whole blood, Female, non-CARD_Negative_6

description:
B412
CHAVArawcounts.txt


title: Platelets_NSCLC patient post-treatment_P19F1_miRNA


title: Smartseq2_Lipstic_TdLN_20


title: Platelets from NSCLC patient post-treatment_P30F1


title: Platelets_NSCLC patient pre-treatment_P19F0_miRNA

value: no information


title: Smartseq2_Lipstic_TdLN_19


title: Platelets_NSCLC patient pre-treatment_P21F0_miRNA


title: Whole blood, Female, non-CARD_Positive_3

description:
B383
CHAVArawcounts.txt


title: Platelets from NSCLC patient pre-treatment_P30F0


title: Platelets from NSCLC patient post-treatment_P28F1

value: Male


title: Smartseq2_Lipstic_TdLN_18


title: Platelets_NSCLC patient post-treatment_P13F1_miRNA


title: Whole blood, Male, CARD_Positive_2

description:
B340
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_17


title: Platelets_NSCLC patient pre-treatment_P13F0_miRNA


title: Whole blood, Female, CARD_Negative_3

description:
B339
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_16


title: Platelets from NSCLC patient pre-treatment_P28F0


title: Platelets_NSCLC patient post-treatment_P9F1_miRNA


title: Whole blood, Male, CARD_Negative_3

description:
B284
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_15


title: Whole blood, Female, CARD_Negative_2

description:
B213
CHAVArawcounts.txt


title: Platelets from NSCLC patient pre-treatment_P27F0


title: Platelets_NSCLC patient pre-treatment_P9F0_miRNA


title: Platelets_NSCLC patient post-treatment_P8F1_miRNA


title: Platelets from NSCLC patient post-treatment_P27F1

value: tumour free


title: Smartseq2_Lipstic_TdLN_14


title: Whole blood, Female, non-CARD_Positive_2

description:
B209
CHAVArawcounts.txt

value: Whole blood


title: Platelets from NSCLC patient post-treatment_P26F1


title: Platelets_NSCLC patient pre-treatment_P8F0_miRNA


title: Smartseq2_Lipstic_TdLN_13


title: Whole blood, Male, non-CARD_Positive_1

description:
B207
CHAVArawcounts.txt


title: Platelets_NSCLC patient pre-treatment_P7F0_miRNA


title: Smartseq2_Lipstic_TdLN_12


title: Whole blood, Female, non-CARD_Negative_5

description:
B200
CHAVArawcounts.txt


title: B73 CK, 7 days, rep3

city: Beijing

first: Qianqian

last: Zhang

address: 2 West, Yuanmingyuan Road, Haidian District

institute: China Agricultural University

data_processing:
The raw data (raw reads) in FASTQ format were subjected to quality control, with the removal of adaptor sequences and low-quality reads to get clean reads.
These clean reads were then aligned to the Maize genome (B73 RefGen_v4, AGPv4) using HISAT (2.0.4) with default parameters.
FPKM (fragments per kilobase of transcript per million mapped reads) values of each gene were calculated using HTSeq (version 0.6.1) software.
Differentially expressed genes (DEGs) were analyzed using DESeq (1.12.0) software, with significant DEGs defined based on a p-value threshold (log2 fold change > 1, p < 0.05). The z-score scale represents the mean-subtracted, regularized log-transformed FPKM values.
The abundance of reads was visualized using the Integrative Genomics Viewer (2.16.1). Gene ontology (GO) enrichment analysis was performed using the accession numbers of significant DEGs via GOseq (version 2.12). Pathway enrichment analysis of DEGs was conducted using KOBAS (version 2.0).
Assembly: Maize genome (B73 RefGen_v4, AGPv4)
Supplementary files format and content: Tab-delimited file includes raw counts for each samples.
Supplementary files format and content: Tab-delimited files include FPKM values for each samples.

organism: Zea mays

source_name: mesocotyls

growth_protocol: Seedings of  ZmWRKY53-KO and B73 were germinated in vermiculite soil with/without  teliospores in pots in a greenhouse at 20℃ (16h/light, 8h/dark).

extract_protocol:
Total RNA was extracted from maize mesocotyls with a PLANTpure plant RNA Kit (Aidlab, China), following the manufacturer's protocol.
RNA libraries were constructed and sequenced on an Illumina Hiseq platform, generating 125 bp/150 bp paired-end reads.

treatment_protocol: The uncoated seeds were artificially inoculated with a thin layer of soil containing 0.2% teliospores and placed in the greenhouse for 7 days and collected the maize mesocotyls.

value: mesocotyls

tag: genotype

value: WT

value: Normal condition


title: B73 CK, 7 days, rep2


title: Smartseq2_Lipstic_TdLN_11


title: Whole blood, Female, CARD_Positive_1

description:
B189
CHAVArawcounts.txt

value: CARD


title: Whole blood, Female, CARD_Positive_2

description:
E053
CHAVArawcounts.txt


title: Whole blood, Female, non-CARD_Negative_4

description:
B182
CHAVArawcounts.txt

value: non-CARD

value: Negative


title: Platelets from NSCLC patient pre-treatment_P24F0

value: platelet


title: B73 CK, 7 days, rep1


title: ZmWRKY53-KO CK, 7 days, rep3

value: CRISPR


title: Smartseq2_Lipstic_TdLN_9

value: naïve


title: Smartseq2_Lipstic_TdLN_10


title: Smartseq2_Lipstic_TdLN_8


title: Platelets from NSCLC patient pre-treatment_P26F0

value: Lung adenocarcinoma


title: Platelets from NSCLC patient pre-treatment_P21F0


title: Platelets from NSCLC patient post-treatment_P19F1


title: ZmWRKY53-KO CK, 7 days, rep2


title: ZmWRKY53-KO CK, 7 days, rep1


title: Smartseq2_Lipstic_TdLN_7


title: Platelets from NSCLC patient pre-treatment_P14F0


title: Platelets from NSCLC patient pre-treatment_P19F0


title: Platelets from NSCLC patient post-treatment_P13F1


title: Whole blood, Male, CARD_Positive_1

description:
B180
CHAVArawcounts.txt

value: Positive


title: B73 Sporisorium reilianum, 7 days, rep3

value: Infected with Sporisorium reilianum


title: Whole blood, Female, CARD_Negative_1

description:
B118
CHAVArawcounts.txt

value: Female


title: Platelets from NSCLC patient post-treatment_P14F1


title: Whole blood, Female, non-CARD_Negative_2

description:
B100
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_5


title: B73 Sporisorium reilianum, 7 days, rep2


title: Platelets from HNSCC patient post-treatment_C26F1


title: Platelets from NSCLC patient pre-treatment_P13F0

value: tumour presence


title: Smartseq2_Lipstic_TdLN_4


title: ZmWRKY53-KO Sporisorium reilianum, 7 days, rep3


title: Platelets from NSCLC patient post-treatment_P9F1


title: Whole blood, Male, CARD_Negative_1

description:
B097
CHAVArawcounts.txt

value: Male


title: Whole blood, Female, non-CARD_Negative_3

description:
B160
CHAVArawcounts.txt


title: Smartseq2_Lipstic_TdLN_3


title: ZmWRKY53-KO Sporisorium reilianum, 7 days, rep2


title: Whole blood, Male, non-CARD_Negative_1

description:
B087
CHAVArawcounts.txt


title: Whole blood, Female, non-CARD_Negative_1

description:
B083
CHAVArawcounts.txt


title: Whole blood, Male, CARD_Negative_2

description:
B146
CHAVArawcounts.txt


title: Platelets from NSCLC patient pre-treatment_P9F0


title: Smartseq2_Lipstic_TdLN_2


title: Smartseq2_Lipstic_TdLN_1


title: ZmWRKY53-KO Sporisorium reilianum, 7 days, rep1


title: Platelets from NSCLC patient post-treatment_P8F1

value: tumour free


title: Smartseq2_Lipstic_TdLN_6


title: M66

status: Public on Oct 03 2024

city: Cape Coast

first: Nicholas

middle: Ekow

last: Thomford

state: Central

address: PMB, University of Cape Coast School of Medical Sciences, Coast Coast, Ghana

department: Dept. of Med. Biochem.,SMS, CoHAS,

country: Ghana

institute: University of Cape Coast, Ghana

description:
HBV_Gh_2.xml
DNA was extracted and used to undertake genotyping

scan_protocol: Plate is placed on the MassARRAY System.with Chip Prep Module or Mass ARRAY Nanodispenser and MAssARRAY analyzer

data_processing:
MassARRAY TyperAnalyzer is used to capture and process datasets.Post processing parameters are set and autolcuster used for cluster plots. PGx Reprot v3 is then generated after post processing using the software
Traffic Light pane with call rates of >/= 85% are good data calls and indcated as green

source_name: Blood

label_protocol: Genomic DNA would be amplified using supplied PGx PCR primers in a final reaction volume of 5uL

extract_protocol: not provided

value: Blood

tag: subject status

value: non-HBV infected patients

tag: well id


title: M65


title: M62


title: M67


title: Platelets from NSCLC patient pre-treatment_P8F0

tag: condition


title: M58


title: M53


title: M52


title: Platelets from NSCLC patient pre-treatment_P5F0

tag: histology


title: M23


title: M21


title: M26


title: M19


title: M25


title: M20


title: Platelets from NSCLC patient pre-treatment_P7F0

tag: tnm


title: M17


title: M14


title: M16


title: Whole blood, Female, non-CARD_Positive_1

description:
B052
CHAVArawcounts.txt

value: Whole blood

tag: Sex


title: M68


title: HBV_194

value: Hepatitis B patients


title: HBV_180


title: HBV_178


title: HBV_162


title: HBV_176


title: HBV_153


title: HBV_059


title: HBV_050


title: HBV_082


title: HBV_123


title: HBV_045


title: M57


title: HBV_129


title: 99


title: 98


title: 95


title: 94


title: 97


title: M15


title: 91


title: 93


title: 96


title: 90


title: 88


title: 89


title: 87


title: 85


title: 86


title: HBV_111


title: 83


title: 81


title: 80


title: 76


title: 17873_T

city: Dallas

first: Kenneth

middle: S

last: Chen

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: UT Southwestern

data_processing:
Read from each sample were mapped to the reference genome using STAR
Read counts were generated using featureCounts
Assembly: mm10
Supplementary files format and content: raw counts

source_name: tumor

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen). Strand-specific whole transcriptome sequencing was performed at the UT Southwestern McDermott NGS Core.
NEBNext Ultra RNA Library Prep Kit

value: tumor


title: 77


title: 14644_T


title: 79


title: 92


title: M11


title: 14649_T


title: 75


title: Mouose WT rep3

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: Mouose WT rep3

data_processing:
Salmon software
Reads were trimmed for adapters and low-quality bases using Trimmomatic software.
The transcript level raw counts were computed with the salmon quant method from Salmon software
DESeq2 Bioconductor package was used for normalization, summarization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: Raw read counts computed by salmon quant method from Salmon software
Supplementary files format and content: Normalized TPM values computed byu salmon tpm method from Salmon software

source_name: uterus

extract_protocol:
Illumina standard mRNA sample prep protocol
Illumina strandard mRNA library prep protocol for paired-end sequencing

value: uterus

value: WT


title: Mouose WT rep2

description: Mouose WT rep2


title: 74


title: Mouose WT rep1

description: Mouose WT rep1


title: Mouse mutant  rep4

description: Mouse mutant  rep4


title: 71


title: Mouse mutant  rep3

description: Mouse mutant  rep3


title: 70


title: 82


title: 69


title: Mouse mutant  rep2

description: Mouse mutant  rep2


title: 84


title: Mouse mutant  rep1

description: Mouse mutant  rep1


title: 67


title: X11918_T_Rb

description:
X11918_T_Rb_R1_001_trimmed
small RNA

data_processing:
Trimmed, filtered reads were aligned and counted using miRge3.0
Assembly: mm10
Supplementary files format and content: raw miRNA counts

extract_protocol:
Total RNA was prepared using the Qiagen miRNeasy kit. Sequencing was performed at the UT Southwestern McDermott NGS Core using the NEBNext Small RNA kit (New England Biolabs, cat. E7330), with size selection between 15bp and 30bp
NEBNext small RNA kit


title: 66


title: X12092_T_Rb

description:
X12092_T_Rb_R1_001_trimmed
small RNA


title: 65


title: X11710_T_Rb

description:
X11710_T_Rb_R1_001_trimmed
small RNA


title: X11626_T_Dro

description:
X11626_T_Dro_R1_001_trimmed
small RNA

value: IPDrosha


title: 68


title: 73


title: 63


title: X10166_T_Dro

description:
X10166_T_Dro_R1_001_trimmed
small RNA


title: X10028_T_Dro

description:
X10028_T_Dro_R1_001_trimmed
small RNA


title: 72


title: 62


title: 64


title: 78


title: 12092_T


title: 61


title: 60


title: B73 Sporisorium reilianum, 7 days, rep1

value: mesocotyls


title: 11918_T


title: 48


title: 44


title: 11710_T


title: 10166_T


title: 10047_T


title: Mouose WT rep4

description: Mouose WT rep4


title: 10028_T


title: 39


title: 34


title: mP16734_V17929

source_name: allograft tumor

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen). Strand-specific mRNA sequencing was performed at the UT Southwestern McDermott NGS Core.
NEBNext Ultra RNA Library Prep Kit

treatment_protocol: Tumor cells were injected into the flanks of NSG mice. Once tumors reached 150 mm3, mice were administered either ceritinib (50 mg/kg) or an equivalent volume of vehicle (0.5% methylcellulose/ 0.5% Tween80) by oral gavage, five days a week for up to 3 weeks. When tumors reached 1000 mm3, they were harvested and rinsed in PBS before flash freezing or fixation in formalin.

value: allograft tumor

value: vehicle


title: mP16734_V17928


title: 29


title: 28


title: mP16734_C17914

value: ceritinib


title: 17


title: R17466-IgG

description: CUT&RUN

library_source: genomic

data_processing:
CUT&RUN reads were analyzed using the nf-core/cutandrun bioinformatic pipeline v2.0
Trimmed reads are aligned to the target genome and the spike-in using Bowtie2
Assembly: mm10
Supplementary files format and content: bigWig files of aligned reads
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN libraries were prepared using the ChIC/CUT&RUN Kit (EpiCypher) according to manufacturer recommendations. Briefly, tumors in single-cell suspension were immobilized onto solid beads, permeabilized, and incubated in the antibody of interest. Target-DNA complexes were cleaved using pAG-MNase and purified.
NEBNext Ultra II DNA Library Prep Kit

tag: antibody

value: IgG


title: 120


title: R17466-H3K4me3

description: CUT&RUN


title: 12


title: R17466-H3K27me3

description: CUT&RUN


title: 118


title: 117


title: 41


title: R17466-H3K27ac

description: CUT&RUN


title: 115


title: R17466-CTCF

description: CUT&RUN

value: CTCF


title: D16383-IgG

description: CUT&RUN


title: D16383-H3K27me3

description: CUT&RUN


title: 114


title: 113


title: D16383-H3K27ac

description: CUT&RUN


title: 116


title: D16383-H3K4me3

description: CUT&RUN


title: 112


title: D16383-CTCF

description: CUT&RUN


title: 109


title: 111


title: mP16451_V2B

source_name: Allograft tumor

treatment_protocol: Tumor cells were injected into the flanks of NSG mice. When tumors reached 150 mm3, mice were administered either palbociclib (150 mg/kg) or an equivalent volume of vehicle (50 mM sodium L-lactate) by oral gavage, five days a week for up to 3 weeks. When tumors reached 1000 mm3, they were harvested.

value: Allograft tumor


title: 110


title: mP16734_C17913


title: mP16451_V2R


title: mP16451_P4B

value: palbociclib


title: 108


title: 107


title: 10477_480_P

data_processing:
Read from each sample were mapped to the reference genome using STAR
Read counts were generated using featureCounts
Assembly: mm10
Supplementary files format and content: FPKM

source_name: pineal

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen). Whole transcriptome sequencing was performed at the UT Southwestern McDermott NGS Core.
NEBNext Ultra RNA Library Prep Kit

value: pineal

value: control


title: 106

value: Blood


title: 119


title: 10369_333_P


title: 10242_247_P


title: 103


title: 104


title: 10166_T


title: 10047_T


title: 101


title: 102


title: 10166_B

source_name: normal brain

value: normal brain


title: 100

value: Hepatitis B patients


title: HBV-205


title: 10047_B


title: 10028_B


title: HBV-204


title: 17159_T_Di

description: ATAC-seq

data_processing:
Trimmed, filtered reads were aligned to the mm10 genome using BWA (v0.7.12)
Peaks were called using MACS2 (v2.1.0), followed by removal of blacklisted regions
Assembly: mm10
Supplementary files format and content: narrowPeak output from MACS2 after removal of blacklisted regions

extract_protocol:
ATAC-seq libraries were prepared using the ATAC-seq kit from ActiveMotif. Nuclei were prepared from minced flash-frozen tissue in a dounce homogenizer. Tagmentation was performed with Tn5 transposase, followed by PCR amplification using indexed sequencing primers.
Libraries were prepared using the ATAC-seq kit from ActiveMotif per manufacturer guidelines.

value: tumor


title: HBV-199


title: 15127_T_Dro

description: ATAC-seq


title: 105


title: 15525_T_Di

description: ATAC-seq


title: HBV-198


title: HBV-197


title: 11118_B

description: ATAC-seq

value: brain


title: mP16451_P3R


title: HBV-195


title: HBV-193


title: 13674_B

description: ATAC-seq


title: 10028_T


title: HBV-190


title: 10444_B

description: ATAC-seq


title: HBV-196


title: lymph node S13530_s1309520 scRNA targeted resequencing

city: Leiden

first: Cornelis

last: van Bergen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

description:
PacBio
full length ccs fastq

data_processing:
cellranger-6.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references
BCR comma separated cellranger output files
Supplementary files format and content: all_contig.fasta: cellranger VDJ analysis fasta output
Supplementary files format and content: all_contig_annotations.csv: cellranger VDJ analysis annotation output
GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix: cellranger GEX count table output
Assembly: GRCh38-2020-A
Supplementary files format and content: processed PacBio csv.gz: barcode and gene aligned with read genotype

source_name: lymph node

extract_protocol:
Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: lymph node

value: tissue

tag: cell type

value: B cell

value: fresh


title: HBV-192


title: YDFR-CB3-inhibitor-2-III_S13

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Partek Flow (build 7.20. 0831).
Trim bases based on quality score, min Phred score 20.
STAR - 2.7.8a aligned to hg38.
Quantify to annotation model (Partek E/M). Gene level qualntifiaction, Median ratio normalization.
Assembly: hg38
Supplementary files format and content: Normalized (DESeq2 Median ratio normalization) gene expression data, Excel.

source_name: Brain-metastasizing melanoma cell (BMMC) line

growth_protocol: In short, human MBM cells were inoculated subdermally into nude mice to establish the cutaneous (C) variants. Cells from these cultures were inoculated intracardially and passaged in the brain for two or three passages yielding the brain metastatic variants (CB2 or CB3, respectively). Melanoma cells were maintained in RPMI-1640 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 10% fetal calf serum (FCS), 2 mmol/mL L-glutamine, 100 units/mL penicillin, 0.1 mg/mL streptomycin, and 12.5 units/mL nystatin.

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen, Valencia, CA, USA).
mRNA libraries were prepared with the KitKAPA mRNA HyperPrep kit (Roche Diagnostics, Basel, Switzerland).
The quality and quantity of final libraries were assessed by High Sensitivity D1000 assay (Agilent Technologies) and Qubit dsDNA HS ScreenTape (Agilent Technologies), followed by KAPA Library Quant Kit (Illumina Inc., San Diego, CA, USA)

treatment_protocol: Cells were treated with 2.5 microM of NT157, 5microM of JQ1, or with a combination of both 2.5 microM of NT157 and 5 microM of JQ1 for three h.

tag: cell line

value: YDFR CB3

value: inhibitor 2 (JQ1 (BRD4 inhibitor))


title: HBV-191


title: HBV-189


title: YDFR-CB3-inhibitor-2-II_S12

value: Brain-metastasizing melanoma cell (BMMC) line


title: lymph node S10000_s1095790 scRNA targeted resequencing

description:
full length ccs fastq
PacBio

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references
BCR comma separated cellranger output files
Assembly: GRCh38-2020-A
Supplementary files format and content: all_contig.fasta (cellranger VDJ analysis fasta output)
Supplementary files format and content: all_contig_annotations.csv (cellranger VDJ analysis annotation output)
Supplementary files format and content: GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix (cellranger GEX count table output)
Supplementary files format and content: processed PacBio csv.gz (barcode and gene aligned with read genotype)

growth_protocol: Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).
cellranger-6.0.1


title: HBV-203


title: YDFR-CB3-inhibitor-1-III_S10

value: inhibitor 1 (NT157 (IRS2 inhibitor))


title: YDFR-CB3-inhibitor-2-I_S11


title: HBV-194


title: 14042_T_Rb

description: ATAC-seq


title: HBV-186


title: 15459_T_Rb

description: ATAC-seq


title: YDFR-CB3-inhibitor-1-II_S9


title: HBV-185


title: 12493_T_Dro

description: ATAC-seq

value: IPDrosha


title: HBV-184


title: YDFR-CB3-Control-III_S7

value: Control


title: YDFR-CB3-Control-I_S5


title: HBV-181


title: HBV-183


title: YDFR-CB3-Control-II_S6


title: HBV-179

description:
HBV_Gh_1.xml
DNA was extracted and used to undertake genotyping


title: HBV-178


title: HBV-180


title: YDFR-CB3-1-2-III_S16

value: inhibitor 1+2


title: M16-CB3-inhibitor-2-II_S4

value: M16 CB3


title: HBV-177

value: Blood


title: HBV-188


title: HBV-176


title: M16-CB3-inhibitor-2-III_S5


title: HBV-174


title: M16-CB3-inhibitor-1-III_S2


title: HBV-173


title: HBV-187


title: HBV-172


title: M16-CB3-inhibitor-1-II_S1


title: YDFR-CB3-inhibitor-1-I_S8


title: M16-CB3-inhibitor-1-I_S16


title: HBV-171


title: M16-CB3-inhibitor-2-I_S3


title: HBV-170


title: HBV-169


title: M16-CB3-Control-II_S14


title: M16-CB3-Control-I_S13


title: M16-CB3-Control-III_S15


title: YDFR-CB3-1-2-II_S15


title: YDFR-CB3-1-2-I_S14


title: HBV-168


title: HBV-167


title: M16-CB3-1-2-I_S6


title: HBV-165


title: HBV-164


title: M16-CB3-1-2-II_S7


title: HBV-163


title: M12-CB3-inhibitor-2-II_S8

value: M12 CB3


title: HBV-159

value: Hepatitis B patients


title: HBV-158


title: HBV-162


title: HBV-160


title: M12-CB3-inhibitor-2-I_S7


title: M12-CB3-inhibitor-1-III_S6


title: M12-CB3-inhibitor-1-I_S4


title: M12-CB3-inhibitor-1-II_S5


title: M12-CB3-Control-III_S3


title: HBV-156


title: HBV-154


title: HBV-155


title: M12-CB3-Control-I_S1


title: HBV-153


title: HBV-152


title: M16-CB3-1-2-III_S8


title: M12-CB3-Control-II_S2


title: M12-CB3-1plus2-II_S11


title: HBV-150


title: HBV-151


title: HBV-149


title: M12-CB3-1plus2-III_S12


title: M12-CB3-1plus2-I_S10


title: DP-CB2-inhibitor-2-III_S1

value: DP CB2


title: HBV-148


title: DP-CB2-inhibitor-2-II_S16


title: HBV-147


title: HBV-144


title: HBV-145


title: DP-CB2-inhibitor-1-III_S14


title: HBV-146


title: DP-CB2-inhibitor-1-II_S13


title: DP-CB2-inhibitor-1-I_S12


title: DP-CB2-Control-II_S10


title: DP-CB2-Control-III_S11


title: DP-CB2-Control-I_S9


title: HBV-143


title: HBV-142


title: HBV-141


title: HBV-140


title: HBV-138


title: HBV-139


title: DP-CB2-1-2-III_S4


title: DP-CB2-1-2-I_S2


title: DP-CB2-1-2-II_S3


title: HBV-137


title: HBV-135


title: DP-CB2-inhibitor-2-I_S15


title: HBV-133


title: HBV-134


title: HBV-132


title: HBV-129


title: HBV-126


title: HBV-124


title: HBV-130


title: HBV-131


title: HBV-123


title: HBV-121


title: HBV-122


title: STAT1_YAP1_Rep_D

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

description: Gene expression data from HCT116 STAT1_YAP1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HCT116 cells were cultured in Dulbecco’s Modified Eagle Medium (Wisent) supplemented with 10% fetal calf serum (Wisent) and 100 U/mL penicillin-streptomycin (Wisent)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: human colon cancer cells


title: HBV-046


title: Control_Rep_C

description: Gene expression data from HCT116 Control

source_name: Control


title: STAT1_Rep_D

description: Gene expression data from HCT116 STAT1


title: Control_Rep_D


title: STAT1_YAP1_Rep_C


title: YAP1_Rep_D

description: Gene expression data from HCT116 YAP1


title: STAT1_Rep_B

description: Gene expression data from HCT116 STAT1


title: YAP1_Rep_B

description: Gene expression data from HCT116 YAP1


title: M12-CB3-inhibitor-2-III_S9


title: DCLPB,Stress_CAN,Slevel_LOW,T24,REPLICATE_5

city: Amherst

first: Peter

last: Chien

state: MA

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

institute: University of Massachusetts Amherst

data_processing:
Samples were de-multiplexed, and unique molecular identifiers (UMIs) were added during PCR steps removed using Je
The clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC011916.1) using bwa and sorted with samtools.
Duplicate transposon reads removed by Je and indexed with samtools.
Genome positions are assigned to the 5′ position of transposon insertions using bedtools genomecov.
bedtools map is used to count either the total number of transposon insertions per gene using the bedtools map -o sum argument or the unique number of insertions using the bedtools map -o count argument
Assembly: NCBI Reference Sequence: NC011916.1
Supplementary files format and content: tab delimited text files include raw total or unique insertion counts for each gene.
Library strategy: Tn-seq

organism: Caulobacter vibrioides

source_name: DCLPB RB-TN Library

growth_protocol: Transposon mutagenesis libraries were thawed and recovered in PYE or PYE + %0.2 Xylose overnight at saturating concentrations to minimize growth during recovery. Only for dnaK-NI library, overnights were recovered in saturating Xylose concentrations (%0.2), and treatment and T24 control conditions were grown in minimal Xylose concentrations. (%0.002)

extract_protocol:
Following overnight growth, 1 ml of saturated culture from each Tn library was pelleted at 8000xg for 2 minutes. Genomic DNA was extracted by Monarch Genomics DNA Preparation Kit (NEB) according to the manufacturer’s protocol.
The sequencing libraries for Next-generation sequencing were prepared using a customized three-step PCR protocol. Genomic DNA input was normalized to a concentration of 100 ng/μl. The initial transposon junction amplification (PCR1) was carried out using an arbitrary PCR amplification method. This step utilized a forward primer designed to align with one end of the transposon and three reverse arbitrary primers. The PCR1 process employed a 2-step cycling protocol with annealing temperatures set at 42°C and 58°C, and number of cycles at 6 and 15, respectively.  Subsequently, the second PCR step (PCR2) involved the addition of 16S adapters for Illumina indexing, along with unique molecular identifiers (UMI), and amplification of the library for 36 cycles. Post-PCR2 cleanup was performed using Aline PCRClean DX magnetic beads. The final PCR step (PCR3) incorporated NexteraXT indexing in accordance with the manufacturer's protocol. Post-indexed library (PCR3) cleanup was carried out using Aline PCRClean DX magnetic beads.

treatment_protocol:
Control condition: Libraries were back diluted to OD 0.008 into 7 ml of PYE or PYE+0.002% xylose and grown overnight until they reached saturation at OD ∼1.6.
Heat stress: Libraries diluted to OD of 1 and heat-stressed at low, medium, or high (37, 42, 43.8◦C, respectively) for 45 minutes in a Biorad Thermocycler. After 45 minutes, cells diluted back to a final OD of 0.008 in 7 ml media for 24-hour growth.
Oxidative stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (0.025mM, 0.05mM, 0.1mM) level hydrogen peroxide. Cells were grown for 24 hours in these chronic stress conditions.
L-canavanine stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (25ug/ml, 50ug/ml, 100ug/ml) levels of L-canavanine. Cells were grown for 24 hours in these chronic stress conditions.

value: DCLPB RB-TN Library

value: transposon mutagenesis library

value: DCLPB


title: HBV-042


title: DCLPB,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_5


title: Control_Rep_B


title: HBV-036


title: STAT1_Rep_A

description: Gene expression data from HCT116 STAT1


title: STAT1_Rep_C

description: Gene expression data from HCT116 STAT1


title: DCLPB,Stress_OS,Slevel_LOW,T24,REPLICATE_4


title: DCLPB,Stress_CAN,Slevel_HIGH,T24,REPLICATE_5


title: YAP1_Rep_C

description: Gene expression data from HCT116 YAP1


title: Control_Rep_A


title: STAT1_YAP1_Rep_B


title: HBV-066


title: HBV-032


title: HBV-045


title: HBV-037


title: DCLPB,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_4


title: YAP1_Rep_A

description: Gene expression data from HCT116 YAP1


title: DCLPB,Stress_OS,Slevel_HIGH,T24,REPLICATE_4


title: Aged02

city: Los Angeles

first: Kay

last: Linker

state: California

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

description: A panel of 383 genes for massively multiplexed FISH, for subcellular resolution for each gene of interest. Each cell has counts for each gene of interest

hyb_protocol: Once adhered to the coverslip the tissue was fixed (4% PFA in 1x PBS, 15 min, room temperature) followed by three washes with 1x PBS. After aspiration, 70% ethanol was added to permeabilize the tissue for 24 h. After a wash with Formamide Wash Buffer (30% formamide in 2x saline sodium citrate (SSC)), the sample was incubated with a custom MERFISH probe library (Vizgen) and left to hybridize for 48 h. The sample was then washed and incubated at 47 °C with formamide wash buffer twice, and then the tissue was embedded in a polyacrylamide gel followed by incubation with tissue clearing solution (2x SSC, 2% SDS, 0.5% v/v Triton X-100, and 1:100 proteinase K) overnight at 37°C. Then, the tissue was washed and hybridized for 15 min with the first hybridization buffer, which contained the readout probes associated with the first round of imaging. After washing, the coverslip was assembled into the imaging chamber and placed into the microscope for imaging.

scan_protocol: MERFISH imaging was performed on an automated Vizgen Alpha Instrument using imaging buffers, hybridization buffers and parameter files provided by Vizgen. Briefly, the sample was loaded into a flow chamber connected to the Vizgen Alpha Instrument. First, a low-resolution mosaic image was acquired (DAPI channel) with a low magnification objective (10X). Then the microscope was switched to a high magnification objective (60X) and seven 1.5 μm z-stack images of each field of view position were generated in 750 nm, 650 nm, and 560 nm channels. A single image of the fiducial beads on the surface of the coverslip was acquired and used as a spatial reference. After each round of imaging, the readout probes were extinguished, and the sample was hybridized with another set of readout probes.

data_processing:
. Raw data were decoded using the MERLIN pipeline (v.0.1.6, provided by Vizgen) with the codebook for the library. Each Id_
Values in the matrix show the genes (ID_Ref) and mean RNA expression. Individual raw files have transcripts and count for each cell for each gene in ID_Ref.

source_name: Bilateral Striatal Slice

label_protocol: not applicable

extract_protocol: mice were euthanized and brains were immediately placed in cold OCT. Embedded brains were then frozen at −20°C and transferred to −80°C for storage. Ten micrometer coronal slices of the striatum were sectioned and placed upon a functionalized coverslip covered with fluorescent beads.

tag: age

tag: group

value: Aged


title: Aged01


title: DCLPB,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_4


title: Young02

value: Young


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_4


title: STAT1_YAP1_Rep_A


title: Young01


title: DCLPB,Stress_HS,Slevel_LOW,T24,REPLICATE_4


title: DCLPB,Stress_OS,Slevel_LOW,T24,REPLICATE_3


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_4


title: DCLPB,Stress_CAN,Slevel_LOW,T24,REPLICATE_4


title: DCLPB,Stress_HS,Slevel_HIGH,T24,REPLICATE_4


title: Patient Brazil 55

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

institute: Universidade de São Paulo

description: RNA was isolated from tissues with tumor-rich areas previously marked by a pathologist (FPS) which represent the highest Gleason pattern. Sections were processed at the Ontario Institute for Cancer Research, Toronto, Canada (OICR) using a dual DNA and RNA extraction. Briefly, hematoxylin and eosin slides were prepared for all the formalin-fixed paraffin-embedded (FFPE) tissues. Histologic analysis of all the slides was performed in the pathology department, and all tumor areas were carefully marked by an experienced pathologist (FPS). Within each marked tumor-rich area, the percentage of tumor cells (range 70-95% tumor-rich) was estimated and recorded. Adjacent slides for each tumor were prepared, and the same areas of interest were macrodissected for RNA extraction.

hyb_protocol: The Human nCounter Breast Cancer 360 (NanoString Technologies Inc., Seattle, WA, USA) is a 776 gene panel designed to characterize breast cancer-specific gene expression patterns associated with breast cancer tumor progression. The panel contains several proprietary signatures generated by NanoString, describing key aspects of breast cancer biology and immune oncology to aid tumor classification. Among these signatures is the PAM50 Signature, which classifies tumors into one of four molecular subtypes (Luminal A, Luminal B, HER2-Enriched, and Basal-like) associated with tumor biology and patient prognosis as well as a Genomic Risk Score. The panel also includes the Tumor Inflammation Signature, which measures the tumor's pre-existing, peripherally suppressed adaptive immune responses. A description of the NanoString proprietary signatures and the genes comprising these signatures is found in Supplementary Table S3. The generation of scores for these proprietary signatures was performed by NanoString.

data_processing: For prognostic biomarker discovery, raw expression data from the BC360 was loaded onto the nSolver software v4.0 (NanoString Technologies) to perform the quality control (QC analysis) and to build the transcript matrix for downstream analysis.

label: NanoString

source_name: primary prostate cancer

extract_protocol: RNA was isolated from tissues with tumor-rich areas previously marked by a pathologist (FPS) which represent the highest Gleason pattern. Sections were processed at the Ontario Institute for Cancer Research, Toronto, Canada (OICR) using a dual DNA and RNA extraction. Briefly, hematoxylin and eosin slides were prepared for all the formalin-fixed paraffin-embedded (FFPE) tissues. Histologic analysis of all the slides was performed in the pathology department, and all tumor areas were carefully marked by an experienced pathologist (FPS). Within each marked tumor-rich area, the percentage of tumor cells (range 70-95% tumor-rich) was estimated and recorded (Table S2). Adjacent slides for each tumor were prepared, and the same areas of interest were macrodissected for RNA extraction.

tag: bcr

value: no

tag: capra-s

value: low Capra-S

tag: months to brc

tag: preoperatory psa

tag: psa at last followup/recurrence

tag: gleason

tag: isup

value: pT2c; pN0; pMx


title: DCLPB,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_4

tag: genotype

tag: treatment


title: DCLPB,Stress_CAN,Slevel_HIGH,T24,REPLICATE_4


title: DNAK-NI,Stress_CAN,Slevel_LOW,T24,REPLICATE_4

source_name: DNAK-NI RB-TN Library

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: Patient Brazil 53

value: intermediate Capra-S

value: pT2 pN0 pMx


title: Patient Brazil 54

value: yes

value: pT2c pN0 pMx


title: Patient Brazil 51


title: HBV-021

tag: tissue

value: Blood

tag: subject status

value: Hepatitis B patients

tag: well id


title: DNAK-NI,Stress_OS,Slevel_LOW,T24,REPLICATE_4


title: DNAK-NI,Stress_CAN,Slevel_HIGH,T24,REPLICATE_4


title: DNAK-NI,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_4


title: DNAK-NI,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_4


title: Patient Brazil 50

tag: tnm

value: pT2b; pN0


title: Patient Brazil 49

value: pT2c, pN0, pMX


title: Patient Brazil 47

value: pT2b pN0


title: Patient Brazil 46


title: DNAK-NI,Stress_OS,Slevel_HIGH,T24,REPLICATE_4

tag: cell type

value: transposon mutagenesis library


title: Patient Brazil 45

value: pT2c, pN0


title: DNAK-NI,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_4

tag: cell line


title: DNAK-NI,Stress_HS,Slevel_HIGH,T24,REPLICATE_4


title: Patient Brazil 41

tag: age


title: Patient Brazil 44


title: DNAK-NI,Stress_HS,Slevel_LOW,T24,REPLICATE_4


title: Patient Brazil 39

value: pT2a, pN0, pMX


title: Patient Brazil 40


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_4


title: HBV-035


title: DCLPA,Stress_CAN,Slevel_LOW,T24,REPLICATE_4

source_name: DCLPA RB-TN Library

value: DCLPA RB-TN Library

value: DCLPA


title: DCLPA,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_4


title: DCLPA,Stress_CAN,Slevel_HIGH,T24,REPLICATE_4


title: DCLPA,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_4


title: Patient Brazil 35

value: no

value: pT2c pN0


title: DCLPA,Stress_OS,Slevel_HIGH,T24,REPLICATE_4


title: Patient Brazil 34

value: pT2c pNx pMx


title: DCLPA,Stress_HS,Slevel_LOW,T24,REPLICATE_4


title: Patient Brazil 33

value: intermediate Capra-S


title: DCLPA,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_4


title: DCLPA,Stress_HS,Slevel_HIGH,T24,REPLICATE_4


title: DLON,Stress_CAN,Slevel_LOW,T24,REPLICATE_4

source_name: DLON RB-TN Library

value: DLON RB-TN Library

value: DLON


title: Patient Brazil 32

value: low Capra-S

value: pT2a pN0 pMx


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_4


title: Patient Brazil 30

value: pT2c, pN0.


title: Patient Brazil 31


title: DLON,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_4


title: Patient Brazil 37

value: yes


title: Patient Brazil 27


title: Patient Brazil 29


title: DLON,Stress_CAN,Slevel_HIGH,T24,REPLICATE_4


title: DLON,Stress_OS,Slevel_LOW,T24,REPLICATE_4


title: DLON,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_4


title: Patient Brazil 38


title: Patient Brazil 26


title: Patient Brazil 36

value: pT2c pNx pMx


title: Patient Brazil 24


title: Patient Brazil 25


title: Patient Brazil 28


title: DCLPA,Stress_OS,Slevel_LOW,T24,REPLICATE_4


title: Patient Brazil 22

value: high Capra-S


title: Patient Brazil 21

value: pT2c, pN0, pMX


title: Patient Brazil 23

value: pT3b, pN0


title: DLON,Stress_OS,Slevel_HIGH,T24,REPLICATE_4

value: transposon mutagenesis library


title: DLON,Stress_HS,Slevel_HIGH,T24,REPLICATE_4


title: DLON,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_4


title: Patient Brazil 19

value: pT3a, pN0


title: Patient Brazil 20

value: pT3a, pNx


title: WT,Stress_CAN,Slevel_LOW,T24,REPLICATE_4

source_name: WT RB-TN Library

value: WT RB-TN Library

value: WT


title: Patient Brazil 18

value: pT2c, pN0


title: WT,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_4


title: DLON,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_4


title: DLON,Stress_HS,Slevel_LOW,T24,REPLICATE_4


title: WT,Stress_CAN,Slevel_HIGH,T24,REPLICATE_4


title: Patient Brazil 17

value: pT3b, pNx, pMx


title: WT,Stress_OS,Slevel_HIGH,T24,REPLICATE_4


title: WT,Stress_OS,Slevel_LOW,T24,REPLICATE_4


title: Patient Brazil 14

value: no

value: pT3a PN0


title: Patient Brazil 15

value: low Capra-S


title: Patient Brazil 13

value: intermediate Capra-S

value: pT3a pN0 pMx


title: WT,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_4


title: Patient Brazil 11

value: yes

value: pT3a, pN1


title: WT,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_4


title: WT,Stress_HS,Slevel_LOW,T24,REPLICATE_4


title: Patient Brazil 10

value: high Capra-S

value: pT3b, pN0, pMX


title: Patient Brazil 12


title: WT,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_4


title: DCLPB,Stress_CAN,Slevel_LOW,T24,REPLICATE_3

value: DCLPB RB-TN Library

value: DCLPB


title: DCLPB,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_3

value: transposon mutagenesis library


title: DCLPB,Stress_CAN,Slevel_HIGH,T24,REPLICATE_3


title: DCLPB,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_3


title: DCLPB,Stress_OS,Slevel_HIGH,T24,REPLICATE_3


title: DCLPB,Stress_HS,Slevel_LOW,T24,REPLICATE_3


title: Patient Brazil 8


title: DCLPB,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_3


title: WT,Stress_HS,Slevel_HIGH,T24,REPLICATE_4


title: Patient Brazil 9

value: pT3b pN0 pMx


title: ATAC, Spleen, FB

city: Murfreesboro

first: Rafet

last: Al-Tobasei

state: TN

address: 358 KOM

department: Computer Science Department

institute: Middle Tennessee State University

data_processing:
The raw sequencing data was subjected to quality control using FastQC (version v0.11.8). Adapter sequences were removed from the reads using trim galore (version 0.6.4) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the rainbow trout reference genome using Bowtie2 (version 2.3.5.1) with the "--end-to-end" and "--very-sensitive" parameters.
The aligned reads were stored in BAM format for subsequent analysis. MACS3 (Model-based Analysis of ChIP-Seq 3) (version 3.0.0a6) was used for peak calling. The aligned reads in BAM format were utilized as input, and specific parameters were adjusted for each histone modification. For H3K27me3, which represents broad peaks, we set the q-value threshold to 0.05. For the rest of the histone modifications, which represent narrow peaks, we set the q-value threshold to 0.01.
Assembly: GCF_013265735.2
Supplementary files format and content: bed, narrowPeak (except for Input sample)

organism: Oncorhynchus mykiss

source_name: Rainbow trout Spleen

extract_protocol:
20–30 mg of tissue powder was cross-linked with 1% formaldehyde for 8 minutes, and quenched for 10 minutes with 100 μl of glycine. Centrifugation at 2000 g for 5 min yielded the nuclei, which were then resuspended in 600 μl of iS1 buffer and incubated for 30 min on ice. Depending on the tissues, the Bioruptor Pico sheared chromatin between 10 and 15 cycles.
Libraries were constructed using the NEBNext Ultra DNA library prep kit (New England Biolabs #E7645L, Ipswich, MA)

value: Rainbow trout Spleen


title: DCLPB,Stress_HS,Slevel_HIGH,T24,REPLICATE_3


title: ATAC, Liver, FB

source_name: Rainbow trout Liver

value: Rainbow trout Liver


title: DCLPB,Stress_CAN,Slevel_LOW,T24,REPLICATE_2


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_3


title: ATAC, Liver, FA


title: DCLPB,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_2


title: ATAC, Brain, FB

source_name: Rainbow trout Brain

value: Rainbow trout Brain


title: ATAC, Spleen, FA


title: Patient Brazil 3

value: pT2c, pN0


title: Patient Brazil 2

value: no

value: pT2c pN0 pMx


title: Patient Brazil 5

value: pT3b pNX pMX


title: Patient Brazil 7

value: low Capra-S


title: Patient Brazil 6

value: pT3b, pN0


title: Patient Brazil 4

value: yes

value: pT2c; pN0; pMx


title: DCLPB,Stress_CAN,Slevel_HIGH,T24,REPLICATE_2


title: Patient Brazil 1

value: pT3a PN0 pMx


title: DCLPB,Stress_OS,Slevel_LOW,T24,REPLICATE_2


title: ATAC, Brain, FA


title: DCLPB,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_2


title: Bisufite, WhiteMuscle, FB

description: Methyl-MiniSeq

source_name: Rainbow trout White muscle

value: Rainbow trout White muscle


title: Bisufite, WhiteMuscle, FA

description: Methyl-MiniSeq


title: Bisufite, Spleen, FB

description: Methyl-MiniSeq


title: Bisufite, Liver, FB

description: Methyl-MiniSeq


title: DCLPB,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_2

value: DCLPB RB-TN Library


title: Patient Brazil 16

value: intermediate Capra-S

value: pT2c pN0


title: DCLPB,Stress_HS,Slevel_HIGH,T24,REPLICATE_2

value: transposon mutagenesis library

value: DCLPB


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_2


title: DCLPB,Stress_HS,Slevel_LOW,T24,REPLICATE_2


title: Bisufite, Spleen, FA

description: Methyl-MiniSeq

value: Rainbow trout Spleen


title: Bisufite, Liver, FA

description: Methyl-MiniSeq

value: Rainbow trout Liver


title: Bisufite, Intestine, FB

description: Methyl-MiniSeq

source_name: Rainbow trout Intestine

value: Rainbow trout Intestine


title: Bisufite, Kidney, FB

description: Methyl-MiniSeq

source_name: Rainbow trout Kidney

value: Rainbow trout Kidney


title: DCLPB,Stress_CAN,Slevel_LOW,T24,REPLICATE_1


title: DCLPB,Stress_OS,Slevel_HIGH,T24,REPLICATE_1


title: Input, WhiteMuscle, FA

source_name: White muscle

value: White muscle

tag: chip antibody


title: Input, WhiteMuscle, FB


title: Bisufite, Intestine, FA

description: Methyl-MiniSeq


title: DCLPB,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_1


title: DCLPB,Stress_HS,Slevel_LOW,T24,REPLICATE_1


title: Input, Spleen, FB

source_name: Spleen

value: Spleen


title: DCLPB,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_1


title: Bisufite, Brain, FA

description: Methyl-MiniSeq

value: Rainbow trout Brain


title: Bisufite, Brain, FB

description: Methyl-MiniSeq


title: DCLPB,Stress_OS,Slevel_LOW,T24,REPLICATE_1


title: DCLPB,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_1


title: DCLPB,Stress_HS,Slevel_HIGH,T24,REPLICATE_1


title: DCLPB,Stress_OS,Slevel_HIGH,T24,REPLICATE_2


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_1


title: Input, Liver, FB

source_name: Liver

value: Liver


title: Input, Spleen, FA


title: Input, Liver, FA


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_3


title: Input, Kidney, FB

source_name: Kidney

value: Kidney


title: Bisufite, Kidney, FA

description: Methyl-MiniSeq


title: DCLPB,Stress_CAN,Slevel_HIGH,T24,REPLICATE_1

source_name: DCLPB RB-TN Library


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_1


title: DNAK-NI,Stress_CAN,Slevel_LOW,T24,REPLICATE_3

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: Input, Brain, FB

source_name: Brain

value: Brain


title: Input, Brain, FA


title: DNAK-NI,Stress_CAN,Slevel_HIGH,T24,REPLICATE_3


title: DNAK-NI,Stress_OS,Slevel_LOW,T24,REPLICATE_3


title: DNAK-NI,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_3


title: DNAK-NI,Stress_OS,Slevel_HIGH,T24,REPLICATE_3


title: Input, Intestine, FB

source_name: Intestine

value: Intestine


title: H3K4me3, WhiteMuscle, FA


title: DNAK-NI,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_3

source_name: DNAK-NI RB-TN Library


title: H3K4me3, Spleen, FB


title: H3K4me3, Spleen, FA


title: H3K4me3, WhiteMuscle, FB


title: DNAK-NI,Stress_HS,Slevel_HIGH,T24,REPLICATE_3


title: DNAK-NI,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_3


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_3


title: DCLPA,Stress_CAN,Slevel_LOW,T24,REPLICATE_3

source_name: DCLPA RB-TN Library

value: DCLPA RB-TN Library

value: DCLPA


title: H3K4me3, Liver, FA


title: H3K4me3, Kidney, FB


title: DCLPB,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_2

value: DCLPB RB-TN Library

value: transposon mutagenesis library


title: Input, Kidney, FA


title: H3K4me3, Kidney, FA


title: H3K4me3, Intestine, FB


title: Input, Intestine, FA


title: DCLPA,Stress_CAN,Slevel_HIGH,T24,REPLICATE_3


title: DCLPA,Stress_OS,Slevel_LOW,T24,REPLICATE_3


title: DNAK-NI,Stress_HS,Slevel_LOW,T24,REPLICATE_3


title: H3K4me3, Intestine, FA


title: H3K4me3, Brain, FB


title: DCLPA,Stress_OS,Slevel_HIGH,T24,REPLICATE_3


title: DCLPA,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_3


title: H3K4me3, Brain, FA


title: DCLPA,Stress_HS,Slevel_LOW,T24,REPLICATE_3


title: H3K4me1, Spleen, FB


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_3


title: H3K4me1, Liver, FB


title: H3K4me1, Spleen, FA


title: DCLPA,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_3


title: DLON,Stress_CAN,Slevel_LOW,T24,REPLICATE_3

source_name: DLON RB-TN Library

value: DLON RB-TN Library

value: DLON


title: H3K4me3, Liver, FB


title: DLON,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_3


title: H3K4me1, Liver, FA


title: H3K4me1, Kidney, FB


title: DLON,Stress_CAN,Slevel_HIGH,T24,REPLICATE_3


title: DLON,Stress_OS,Slevel_LOW,T24,REPLICATE_3


title: DCLPA,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_3


title: H3K4me1, Kidney, FA


title: DLON,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_3


title: H3K4me1, Intestine, FB


title: H3K4me1, Intestine, FA


title: DLON,Stress_HS,Slevel_LOW,T24,REPLICATE_3


title: DLON,Stress_OS,Slevel_HIGH,T24,REPLICATE_3


title: H3K4me1, WhiteMuscle, FB


title: H3K4me1, WhiteMuscle, FA


title: DCLPA,Stress_HS,Slevel_HIGH,T24,REPLICATE_3


title: H3K4me1, Brain, FB


title: DLON,Stress_HS,Slevel_HIGH,T24,REPLICATE_3


title: DLON,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_3


title: DLON,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_3


title: DCLPA,Stress_HS,Slevel_LOW,T24,REPLICATE_1


title: WT,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_3

source_name: WT RB-TN Library

value: WT RB-TN Library

value: WT


title: WT,Stress_CAN,Slevel_HIGH,T24,REPLICATE_3


title: H3K27me3, WhiteMuscle, FA

value: White muscle


title: H3K27me3, WhiteMuscle, FB


title: WT,Stress_OS,Slevel_LOW,T24,REPLICATE_3


title: MC-CONTROL_2_re-analyzed

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with TAC 4.0

source_name: Human umbilical cord blood

label_protocol: 250 ng total RNA was used as input for amplification using Ambion WT expression sense kit (Life Technilogies, Grand Island, NY, USA), Poly A control was added as suggested by WT expression kit manual. cDNA amplification products were fragmented and labeled with biotin using Affymetrix GeneChip WT terminal labeling kit, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit, and then washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

growth_protocol: CD34+ cells were isolated from human umbilical cord blood and differentiated into mast cells using rhIL-6 and rh-SCF for 6-8 weeks.

extract_protocol: RNA samples were isolated from hCBMCs using the RNeasy Mini Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed (RIN > 7.0) on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: hCBMCs were treated with 10 and 20 ng/mL of IL-33 for the duration of 6 and 24 hours each.

value: CD34+ cells differentiated into mast cells

tag: batch

value: sample re-analyzed from GSE201473

tag: condition

value: Normal


title: H3K27me3, Spleen, FB

value: Spleen


title: WT,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_3


title: MC-CONTROL_1_re-analyzed


title: WT,Stress_OS,Slevel_HIGH,T24,REPLICATE_3


title: WT,Stress_HS,Slevel_LOW,T24,REPLICATE_3


title: H3K27me3, Spleen, FA


title: WT,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_3


title: MAST3-20_24

value: IL33 20 ng/ml 24 hours


title: WT,Stress_HS,Slevel_HIGH,T24,REPLICATE_3


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_3

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: MAST2-20_6

value: IL33 20 ng/ml 6 hours


title: H3K27me3, Liver, FA

value: Liver


title: H3K27me3, Liver, FB


title: WT,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_3


title: WT,Stress_CAN,Slevel_LOW,T24,REPLICATE_3


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_3

value: DCLPA RB-TN Library

value: DCLPA


title: H3K4me1, Brain, FA

value: Brain


title: MAST3-10_24

value: IL33 10 ng/ml 24 hours


title: MAST2-10_6

value: IL33 10 ng/ml 6 hours


title: DLON,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_3

value: DLON RB-TN Library

value: transposon mutagenesis library

value: DLON


title: H3K27me3, Kidney, FB

value: Kidney


title: WT,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_3

value: WT RB-TN Library

value: WT


title: DNAK-NI,Stress_CAN,Slevel_LOW,T24,REPLICATE_2


title: H3K27me3, Kidney, FA


title: DNAK-NI,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_2


title: IL33-10-24

value: CD34+ cells differentiated into mast cells

value: Normal


title: DNAK-NI,Stress_CAN,Slevel_HIGH,T24,REPLICATE_2

value: DNAK-NI RB-TN Library


title: IL33-20-6


title: IL33-20-24

value: IL33 20 ng/ml 24 hours


title: H3K27me3, Intestine, FB

value: Intestine


title: DNAK-NI,Stress_OS,Slevel_LOW,T24,REPLICATE_2

value: DNAK-NI


title: DNAK-NI,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_2


title: IL33-10-6


title: evoCDA, replicate 3, CD19 negative, pooled, endogenous

city: Boston

first: Eric

last: Che

address: 531 Newbury St

institute: Harvard Medical School

description: pooled, endogenous

data_processing:
After sequencing, the sequencing core facility performed the primary demultiplexing based on the P7 index. Subsequently, our laboratory conducted a secondary demultiplexing step using the P5 index, which is located internally within the read.
For each demultiplexed FASTQ, “raw” guide mapping was performed using CRISPR-SURF Count in base-editing mode. To identify significant regions based on the mapped guide RNA counts, we ran CRISPR-SURF Deconvolution on both the ABE8e and evoCDA datasets.
The paired-end FASTQs were also quality controlled with FastQC and MultiQC to ensure sufficient sequencing quality of our samples. Next, the paired-end FASTQs were passed into CRISPResso2 for read merging, alignment, and quantification of the edited alleles. The CRISPResso2 allele frequency tables were encoded into a feature indicator matrix containing columns for all possible REF>ALT variants across the amplicon and rows for all unique alleles. The matrices are then modeled by Millipede, a PyTorch-based Bayesian variable selection model, to generate beta coefficients and posterior inclusion probabilities for each feature (per-nucleotide).
The encoding matrix from CRISPR-Millipede, along with a design matrix describing the conditions of each sample (replicate and sorting population), was also passed into into pyDESeq2, a statistical package used to calculate differential expression of alleles between the CD19 positive and CD19 negative populations. The log fold change and adjusted p-value were plotted for the alleles observed across the cellular populations.
Assembly: N/A
Supplementary files format and content: "encoding" tsv file, produced by encoding the CRISPresso2 allele frequency tables into a feature indicator matrix, fed into CRISPR-Millipede
Supplementary files format and content: "hit_table" csv file, table of scores for hits modeled by CRISPR-Millipede

growth_protocol: NALM6 cells (CVCL_0092) were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% Fetal Bovine Serum, 100U/mL Penicillin-Streptomycin and 2mM L-Glutamine (referred to as RPMI complete) at 37°C, 5% CO2.

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen).
For sgRNA count, the sgRNA cassette was PCR amplified from genomic DNA using primers carrying partial Illumina adaptor. PCR products were then re-amplified using primers carrying sample-specific barcode combinations. The endogenous CD19 enhancer sequence was PCR-amplified and barcoded using a similar strategy.
Distributions of edits within a 346 bp fragment of the CD19 enhancer were obtained by targeted amplicon sequencing using MiSeq at PE250 and PE300 configuration. Guide RNAs were enumerated by NGS as previously reported (Seruggia et al. Mol Cell 2019).

treatment_protocol: ABE8e-SpRY and evoCDA expressing NALM-6 cell lines were produced through lentiviral transduction and and selected with 10 ug/mL Blasticidin for five days. Expression of base editors was confirmed by Western Blot using a Cas9 antibody.

value: B cell precursor leukemia

value: CD19 enhancer pertubation

value: CD19 negative

value: Cytosine base editing


title: evoCDA, unedited, pooled, endogenous

description: pooled, endogenous

value: CD19 enhancer unedited

value: unedited