title: COX312A30_IL-27_prdm1 fl/fl_Day 3

description:
RNA_IL-27_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A26_IL-27_prdm1 fl/fl_Day 3

status: Public on Aug 24 2023

type: SRA

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

library_source: transcriptomic

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 genome and the GENCODE reference transcriptome version M22 with STAR software
Raw gene counts were retrieved using QoRTs software
Normalised read counts were retrieved using DeSeq2
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided  for RNA-seq data separated for both strands and normalised to RPKMs

molecule: total RNA

organism: Mus musculus

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 3

extract_protocol:
RNA was extracted using the QIAShredder and RNeasy Mini Kit, or RNeasy Micro kit, both with on-column DNase digestion, according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were made with total RNA equally pooled from the technical triplicate wells within an independent biological experiment, using the Illumina Stranded TruSeq Library preparation kit V2 and unique multiplexing indexes, according to the manufacturer’s instructions (Illumina).

treatment_protocol: Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.

tag: strain

value: prdm1 fl/fl

tag: treatment

value: CD4+ T cells driven with IL-27

tag: timepoint

value: Day 3


title: COX690A30_IL-27_prdm1 fl/fl CD4-Cre_Day 3

description:
RNA_IL-27_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl CD4-Cre


title: COX690A42_IL-27_prdm1 fl/fl_Day 3


title: COX312A14_IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A6_IL-27_prdm1 fl/fl_Day 2

description:
RNA_IL-27_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 2

value: Day 2


title: COX690A34_IL-27_prdm1 fl/fl_Day 3


title: COX312A10_IL-27_prdm1 fl/fl_Day 3


title: COX690A14_IL-27_maf fl/fl CD4-Cre_Day 3

description:
RNA_IL-27_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl CD4-Cre


title: COX312A2_IL-27_prdm1 fl/fl_Day 1

description:
RNA_IL-27_prdm1 fl/fl_Day 1
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 1

value: Day 1


title: COX312A26_IL-27_prdm1 fl/fl_Day 2


title: COX690A2_IL-27_maf fl/fl_Day 3

description:
RNA_IL-27_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl


title: COX690A10_IL-27_maf fl/fl_Day 3


title: COX690A18_IL-27_maf fl/fl_Day 3


title: COX690A22_IL-27_maf fl/fl CD4-Cre_Day 3


title: COX312A22_IL-27_prdm1 fl/fl_Day 1


title: COX312A65_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
RNA_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12+IL-27 at Day 3

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: CD4+ T cells driven with IL-12+IL-27


title: COX312A56_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3

description:
RNA_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl maf fl/fl


title: COX312A48_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: COX312A44_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: COX690A48_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3

description:
RNA_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt


title: COX312A16_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX690A32_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A36_IL-12+IL-27_prdm1 fl/fl_Day 4

description:
RNA_IL-12+IL-27_prdm1 fl/fl_Day 4
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12+IL-27 at Day 4

value: Day 4


title: COX312A20_IL-12+IL-27_prdm1 fl/fl_Day 4


title: COX312A40_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: COX690A6_IL-27_maf fl/fl CD4-Cre_Day 3


title: COX690A44_IL-12+IL-27_prdm1 fl/fl_Day 3

description:
RNA_IL-12+IL-27_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A36_IL-12+IL-27_prdm1 fl/fl_Day 3


title: COX690A40_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A12_IL-12+IL-27_prdm1 fl/fl_Day 3


title: COX312A28_IL-12+IL-27_prdm1 fl/fl_Day 2

description:
RNA_IL-12+IL-27_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12+IL-27 at Day 2


title: COX690A28_IL-12+IL-27_prdm1 fl/fl_Day 3


title: COX312A64_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: COX312A24_IL-12+IL-27_prdm1 fl/fl_Day 1

description:
RNA_IL-12+IL-27_prdm1 fl/fl_Day 1
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12+IL-27 at Day 1


title: COX690A24_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3

description:
RNA_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A20_IL-12+IL-27_maf fl/fl_Day 3

description:
RNA_IL-12+IL-27_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A12_IL-12+IL-27_maf fl/fl_Day 3


title: COX312A63_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
RNA_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12 at Day 3

value: CD4+ T cells driven with IL-12


title: COX690A4_IL-12+IL-27_maf fl/fl_Day 3


title: COX690A8_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3


title: COX312A59_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: COX312A43_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: COX312A47_IL-12_prdm1 fl/fl maf fl/fl_Day 3

description:
RNA_IL-12_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A39_IL-12_prdm1 fl/fl CD4-Cre_Day 3

description:
RNA_IL-12_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt


title: COX312A55_IL-12_prdm1 fl/fl maf fl/fl_Day 3


title: COX312A39_IL-12_prdm1 fl/fl maf fl/fl_Day 3


title: COX690A47_IL-12_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A32_IL-12+IL-27_prdm1 fl/fl_Day 3


title: COX312A15_IL-12_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A8_IL-12+IL-27_prdm1 fl/fl_Day 2


title: COX690A43_IL-12_prdm1 fl/fl_Day 3

description:
RNA_IL-12_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt


title: COX690A31_IL-12_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A19_IL-12_prdm1 fl/fl_Day 4

description:
RNA_IL-12_prdm1 fl/fl_Day 4
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12 at Day 4


title: COX690A35_IL-12_prdm1 fl/fl_Day 3


title: COX690A27_IL-12_prdm1 fl/fl_Day 3


title: COX312A4_IL-12+IL-27_prdm1 fl/fl_Day 1


title: COX312A31_IL-12_prdm1 fl/fl_Day 3


title: COX312A11_IL-12_prdm1 fl/fl_Day 3


title: COX690A16_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3


title: COX312A7_IL-12_prdm1 fl/fl_Day 2

description:
RNA_IL-12_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12 at Day 2


title: COX312A3_IL-12_prdm1 fl/fl_Day 1

description:
RNA_IL-12_prdm1 fl/fl_Day 1
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12 at Day 1


title: BLCA_Trp_287

type: RNA

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45° at 60rpm Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
probe group file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
meta-probeset file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1

label: biotin

organism: Homo sapiens

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit or GeneChip WT Pico kit.

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: adjuvant

tag: lundtax rna-subtype

value: UroC

tag: lundtax ihc-subtype

value: GU

tag: consensus classifier subtype

value: LumNS

tag: rm-lymphnode

value: yes

tag: rm-local

value: no

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: COX312A34_IL-27_prdm1 fl/fl_Day 4

description:
RNA_IL-27_prdm1 fl/fl_Day 4
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 4

value: prdm1 fl/fl

value: CD4+ T cells driven with IL-27


title: COX690A7_IL-12_maf fl/fl CD4-Cre_Day 3

description:
RNA_IL-12_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl CD4-Cre

value: Day 3


title: COX312A23_IL-12_prdm1 fl/fl_Day 1

value: Day 1


title: COX690A15_IL-12_maf fl/fl CD4-Cre_Day 3


title: COX690A23_IL-12_maf fl/fl CD4-Cre_Day 3


title: COX690A3_IL-12_maf fl/fl_Day 3

description:
RNA_IL-12_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl


title: COX690A19_IL-12_maf fl/fl_Day 3


title: COX312A61_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
RNA_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: Medium at Day 3

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: CD4+ T cells driven with Medium


title: COX312A57_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: COX690A11_IL-12_maf fl/fl_Day 3


title: BLCA_Nac_269

description: Re-analysis of GSM5203554

value: neoadjuvant

value: UroB

value: StromaRich


title: COX312A41_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: BLCA_Trp_241

value: GeneChip WT Pico kit

value: palliative

value: BASQ


title: BLCA_Trp_276

value: adjuvant

value: GU

value: LumU


title: COX312A45_Medium_prdm1 fl/fl maf fl/fl_Day 3

description:
RNA_Medium_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl maf fl/fl


title: COX312A53_Medium_prdm1 fl/fl maf fl/fl_Day 3


title: COX690A37_Medium_prdm1 fl/fl CD4-Cre_Day 3

description:
RNA_Medium_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl CD4-Cre


title: COX312A37_Medium_prdm1 fl/fl maf fl/fl_Day 3


title: COX690A45_Medium_prdm1 fl/fl CD4-Cre_Day 3


title: COX690A29_Medium_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A33_Medium_prdm1 fl/fl_Day 4

description:
RNA_Medium_prdm1 fl/fl_Day 4
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: Medium at Day 4

value: prdm1 fl/fl

value: Day 4


title: COX312A17_Medium_prdm1 fl/fl_Day 4


title: COX312A13_Medium_prdm1 fl/fl CD4-Cre_Day 3

value: Day 3


title: COX312A27_IL-12_prdm1 fl/fl_Day 2

value: CD4+ T cells driven with IL-12

value: Day 2


title: BLCA_Trp_236

value: induction

value: UroA

value: Uro

value: LumP

value: yes

value: no


title: COX690A41_Medium_prdm1 fl/fl_Day 3

description:
RNA_Medium_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt

value: CD4+ T cells driven with Medium


title: COX690A33_Medium_prdm1 fl/fl_Day 3


title: COX312A9_Medium_prdm1 fl/fl_Day 3


title: COX312A29_Medium_prdm1 fl/fl_Day 3


title: COX312A25_Medium_prdm1 fl/fl_Day 2

description:
RNA_Medium_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: Medium at Day 2


title: COX312A5_Medium_prdm1 fl/fl_Day 2


title: COX312A21_Medium_prdm1 fl/fl_Day 1

description:
RNA_Medium_prdm1 fl/fl_Day 1
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: Medium at Day 1

value: Day 1


title: AsPC-1, HMOX1si1, rep2

city: Shenzhen

first: Qianying

last: Hu

state: State...

address: 3025 Shennanzhong Road,Shenzhen

country: China

institute: Sun Yat-sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: AsPC-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: HMOX1 specific siRNA and negative control siRNA were transfected into cells using jetPRIME transfection reagent (Polyplus Transfection, Illkirch, France) following the guideline.

tag: cell line

tag: cell type

value: tumor cells

tag: genotype

value: HMOX1 knockdown


title: AsPC-1, HMOX1si2, rep2


title: AsPC-1, HMOX1si2, rep1


title: COX312A1_Medium_prdm1 fl/fl_Day 1

tag: strain

tag: treatment

tag: timepoint


title: BLCA_Trp_212

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

value: palliative

value: UroC

value: LumU


title: COX690A21_Medium_maf fl/fl CD4-Cre_Day 3

description:
RNA_Medium_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl CD4-Cre

value: Day 3


title: AsPC-1, siControl, rep2

value: Control


title: COX312A35_IL-12_prdm1 fl/fl_Day 4

value: prdm1 fl/fl

value: CD4+ T cells driven with IL-12

value: Day 4


title: AsPC-1, siControl, rep1


title: COX690A9_Medium_maf fl/fl_Day 3

description:
RNA_Medium_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_MafKONormCounts_invitro_GEO_11Feb2022.txt

value: maf fl/fl


title: AsPC-1, HMOX1si1, rep1


title: COX690A13_Medium_maf fl/fl CD4-Cre_Day 3


title: COX690A17_Medium_maf fl/fl_Day 3


title: COX690A25_Medium_prdm1 fl/fl_Day 3


title: BLCA_Nac_206

description: Re-analysis of GSM5203553

tag: chemotherapy type

value: neoadjuvant

tag: lundtax rna-subtype

value: GU

tag: lundtax ihc-subtype

value: yes


title: BLCA_Trp_205

value: adjuvant

value: UroA

value: Uro

tag: consensus classifier subtype

value: LumP

tag: rm-lymphnode

tag: rm-local

value: no


title: BLCA_Trp_200

value: GeneChip WT Pico kit

value: LumNS

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: COX690A5_Medium_maf fl/fl CD4-Cre_Day 3

value: maf fl/fl CD4-Cre

value: CD4+ T cells driven with Medium


title: gfp_enriched_rep3

city: Edinburgh

first: Hannah

last: Long

address: Crewe Rd South

department: MRC Human Genetics Unit

institute: University of Edinburgh

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v6.1.2) was used to perform alignment, filtering, barcode counting, and UMI counting. A custom reference genome was created for alignment using cellranger mkref, combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells (Lun et al., 2019). Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size, detected genes, and mitochondrial reads (McCarthy et al., 2017). Cells with detected genes ≥ 500, library size ≥ 800, and mitochondrial reads ≤ 10% were retained. Within the processed dataset, mean reads per cell = 11239, and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single-cell transcriptome atlas (Aran et al., 2019; Farnsworth et al., 2019). Expression matrix and cell annotation data were downloaded from the UCSC cell browser (http://zebrafish-dev.cells.ucsc.edu); only the 2 dpf data were used for mapping. Erroneously sorted cells of non-retinal identity (for example pigmented cell types such as melanocytes with high autofluorescence) were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat (v4) was used for clustering and further analysis for a total of 6,288 cells (Butler et al., 2018). SCTransform was used to perform log-normalisation, scaling, and highly variable gene (HVG) detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used, with regression of mitochondrial expression and cell-cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis (PCA) on the normalized counts matrix restricted to HVGs, using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples, we then used Harmony to generate PCs corrected for batch effects between libraries (Korsunsky et al., 2019). The Harmony PCs were then used to perform K-nearest neighbour analysis (k=20) and Louvain clustering using Seurat (15 dimensions and resolution 0.6). Clusters were annotated as retinal cell types based on the highest expressed marker genes, and other known genes for each cell type, using information from the literature and ZFIN (Sprague et al., 2008). Cell cycle scoring was performed using the Seurat CellCycleScoring function, using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat.
Assembly: GRCz11
Supplementary files format and content: Tab separated values files, matrix files, Seurat object RDS file

molecule: polyA RNA

organism: Danio rerio

source_name: Eye

extract_protocol:
NRE-eGFP/HS5-mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf, embryos were anaesthetised with Tricaine (20–30 mg/l) and placed into Danieau's solution. Eyes were dissected from ~100-150 embryos using fine forceps (Dumont #5SF), and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C, then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution, and once with FACSmax (Amsbio). In a final 500 µl FACSmax, the samples were passed through a 35 µm cell strainer to obtain single cell suspension (on ice). Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II (BD) or CytoFLEX SRT (Beckman Coulter) machine. Forward and side scatter sorting was used to select single cells from clumps and debris, and DAPI staining was used to exclude dead cells.
Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology (v3.1).

tag: tissue

value: Eye

tag: developmental stage

value: 48 hpf


title: mcherry_enriched_rep2

tag: genotype


title: mcherry_enriched_rep3


title: gfp_enriched_rep2


title: mcherry_enriched_rep1


title: COX354A518_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
ATAC_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

library_source: genomic

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 with BWA-MEM
Duplicates were removed using Picard
alignment QC, discarded alignments with a mapQ below 30 using SAMtools 1.3.1
Discarded alignemnts done to mitochondrial DNA, shifted Reads to represent the Tn5 insertion, and remove fragments spanning nucleosomes (size >99 bp) using awk and BEDTools 2.4.2. Fragments spanning nucleosomes were not removed for the one untreated sample
MACS2 2.1.1 (parameters --keep-dup all, --nomodel, --shift -100, --extsize 200) was used to call peaks (q-value < 0.01)
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided fro ATAC-seq data normalised to RPKMs (fragments spanning nucleosomes excluded), for peaks called bed files are provided

molecule: genomic DNA

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27

extract_protocol:
50,000 cells were lysed with cold ATAC-seq lysis buffer containing 10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet™ P40 substitute (all Sigma) and the nuclei incubated for 2 hours at 37°C with 50μl of TDE1/TD transposase reaction mix (Illumina).
Tagmented DNA was purified using the MinElute kit (Qiagen) and amplified under standard ATAC PCR conditions: 72°C for 5 min; 98°C for 30s and thermocycling at 98°C for 10s, 63 °C for 30s and 72°C for 1 min for 12 cycles. Following amplification, ATAC-seq libraries were cleaned up using 90μl of AMPure XP beads (Beckman Coulter) and two 80% Ethanol washes whilst being placed on a magnetic plate stand, before being eluted in 1mM (0.1x) Tris-EDTA buffer, pH8 (Sigma) diluted with DEPC-treated water (Ambion).

tag: strain

value: prdm1 fl/fl maf fl/fl CD4-Cre

tag: treatment

value: CD4+ T cells driven with IL-27

value: Day 3


title: gfp_enriched_rep1


title: Patient_271_FFPE

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

hyb_protocol: The samples were prepared for nCounter gene expression profiling (metabolic pathway panel) according to the manufacturer’s recommendations (NanoString Technologies, USA). Briefly, 300 ng RNA samples were prepared by an overnight hybridization (65 °C) to nCounter Reporter and Capture probes. Subsequently, samples were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the average geometric mean of the top 100 probes detected. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

label: oligonucleotide probe

source_name: FFPE

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (Nanostring Technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from 3 consecutive 8 μm thick formalin-fixed, paraffin-embedded (FFPE) sections. Tumor-rich regions of interest were identified and marked on the hematoxylin&eosin stained slides and confirmed by a pathologist to decrease the risk of false negative results. The tissue fragments were deparaffinized by incubation with deparaffinization solution (Qiagen, Hilden, Germany). For gene expression analysis (Nanostring platform), total RNA was extracted from deparaffinized tissue by proteinase K digestion and column chromatography using the RNeasy FFPE extraction kit (Qiagen) in accordance with the manufacturer's protocol. The RNA concentration was assessed by Qubit (Invitrogen, Carlsbad, USA).

treatment_protocol: not applicable

tag: tisue

value: endometrial cancer

tag: age

tag: body weight

tag: Stage

tag: grade


title: Patient_272_FFPE

value: IA


title: Patient_263_FFPE


title: COX354A478_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

treatment_protocol: Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: timepoint


title: COX354A270_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: Patient_215_FFPE

value: IB


title: Patient_212_FFPE

value: IIIC


title: Patient_28_FFPE


title: COX690A1_Medium_maf fl/fl_Day 3

value: maf fl/fl


title: COX354A486_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

description:
ATAC_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: Day 2


title: Patient_251_FFPE

value: IIIB


title: Patient_92_FFPE


title: Patient_71_FFPE


title: Patient_5_FFPE

value: IIIA


title: Patient_254_FFPE

value: IVA


title: Patient_242_FFPE


title: COX354A438_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2


title: COX354A474_IL-27_prdm1 fl/fl maf fl/fl_Day 3

description:
ATAC_IL-27_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl maf fl/fl


title: COX354A282_IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: COX354A418_IL-27_prdm1 fl/fl maf fl/fl_Day 2

description:
ATAC_IL-27_prdm1 fl/fl maf fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: Patient_239_FFPE


title: COX354A482_IL-27_prdm1 fl/fl maf fl/fl_Day 2


title: Patient_229_FFPE


title: Patient_113_FFPE


title: Patient_211_FFPE


title: Patient_250_FFPE


title: Patient_194_FFPE


title: Patient_258_FFPE


title: Patient_191_FFPE


title: Patient_252_FFPE

value: II


title: COX354A38_IL-27_prdm1 fl/fl CD4-Cre_Day 3

description:
ATAC_IL-27_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl CD4-Cre


title: Patient_188_FFPE


title: COX354A538_IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: Patient_179_FFPE


title: COX354A254_IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX354A206_IL-27_prdm1 fl/fl CD4-Cre_Day 2

description:
ATAC_IL-27_prdm1 fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: COX354A6_IL-27_prdm1 fl/fl CD4-Cre_Day 2


title: COX354A58_IL-27_prdm1 fl/fl_Day 3

description:
ATAC_IL-27_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl


title: Patient_164_FFPE


title: Patient_230_FFPE


title: Patient_150_FFPE


title: Patient_158_FFPE


title: Patient_160_FFPE


title: Patient_146_FFPE


title: Patient_141_FFPE


title: COX354A226_IL-27_prdm1 fl/fl_Day 3


title: Patient_136_FFPE


title: COX354A194_IL-27_prdm1 fl/fl_Day 2

description:
ATAC_IL-27_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: COX354A2_IL-27_prdm1 fl/fl_Day 2


title: COX354A174_IL-27_maf fl/fl CD4-Cre_Day 3

description:
ATAC_IL-27_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: maf fl/fl CD4-Cre


title: Patient_128_FFPE


title: Patient_108_FFPE


title: Patient_119_FFPE


title: Patient_117_FFPE


title: Patient_102_FFPE


title: Patient_262_FFPE


title: Patient_174_FFPE


title: COX354A110_IL-27_maf fl/fl CD4-Cre_Day 3


title: Patient_257_FFPE


title: BLCA_Trp_173

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: adjuvant

tag: lundtax rna-subtype

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: StromaRich

value: yes

value: no

tag: rm-other


title: BLCA_Trp_169

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: Patient_134_FFPE

tag: tisue

value: endometrial cancer

tag: age

tag: body weight

value: IB


title: COX354A86_IL-27_maf fl/fl CD4-Cre_Day 2

description:
ATAC_IL-27_maf fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: strain

tag: treatment

value: CD4+ T cells driven with IL-27

tag: timepoint

value: Day 2


title: COX354A178_IL-27_maf fl/fl_Day 3

description:
ATAC_IL-27_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: maf fl/fl

value: Day 3


title: Patient_241_FFPE

tag: Stage

value: IA

tag: grade


title: Patient_253_FFPE


title: Patient_214_FFPE


title: Patient_240_FFPE


title: Patient_225_FFPE


title: Patient_223_FFPE


title: Patient_267_FFPE


title: Patient_235_FFPE


title: Patient_152_FFPE

value: II


title: Patient_207_FFPE


title: COX354A122_IL-27_maf fl/fl_Day 3


title: Patient_156_FFPE


title: Patient_145_FFPE


title: COX354A154_IL-27_maf fl/fl_Day 2

description:
ATAC_IL-27_maf fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: BLCA_Trp_162

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: Uro


title: Patient_210_FFPE

value: IIIB


title: COX354A134_IL-27_maf fl/fl CD4-Cre_Day 2

value: maf fl/fl CD4-Cre


title: Patient_124_FFPE


title: BLCA_Trp_168

value: GeneChip WT Pico kit

value: BASQ

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-other


title: Patient_126_FFPE

tag: tisue

tag: age


title: BLCA_Trp_160

value: adjuvant

value: GU

value: LumU

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: Patient_125_FFPE

tag: body weight

tag: Stage


title: COX354A456_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
ATAC_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12+IL-27

tag: strain

value: prdm1 fl/fl maf fl/fl CD4-Cre

tag: treatment

value: CD4+ T cells driven with IL-12+IL-27

tag: timepoint


title: Patient_111_FFPE

value: endometrial cancer

tag: grade


title: COX354A90_IL-27_maf fl/fl_Day 2

value: CD4+ T cells driven with IL-27


title: COX354A272_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: Patient_247_FFPE

value: endometrium


title: COX354A504_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

description:
ATAC_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: Day 2


title: Patient_245_FFPE


title: COX354A424_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2


title: BLCA_Trp_157

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: curative radiochemotherapy

tag: lundtax rna-subtype

value: UroA

value: LumP

value: no

value: yes


title: Patient_236_FFPE


title: COX354A540_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3

description:
ATAC_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl maf fl/fl

value: Day 3


title: Patient_233_FFPE


title: Patient_244_FFPE


title: Synechocystis, low-to-high nitrogen 4 h, rep2

city: Shanghai

first: Weimin

last: Ma

address: No.100 Guilin Rd

department: College of Life Sciences

institute: Shanghai Normal University

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences;
In order to get high-quality reads that could be used for later analysis, raw reads need to be filtered by quality;
Trimmomatic software was first used for quality control and linker removal;
and then low-quality bases and N-bases or low-quality reads were filtered out;
Finally, we got high-quality clean reads.
Assembly: NC_000911.1
Supplementary files format and content: A txt file includes expression data of all gene of Experimental groups (low-to-high nitrogen for 4h) and control groups (continuous low nitrogen)

organism: Synechocystis sp. PCC 6803

source_name: Prokaryote

growth_protocol: Synechocystis sp. strain PCC 6803 were cultured at 30°C in BG-11 medium

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

treatment_protocol: The nitrate (final concentration of 17.6 mM) was added to nitrogen-starved cultures (low-to-high nitrogen)or not (conyinuous low nitrogen)

tag: cell type

value: Prokaryote

tag: genotype

value: WT

value: Low-to-high nitrate


title: Patient_232_FFPE

tag: tisue

tag: age


title: Synechocystis, continuous low nitrogen, rep3

value: Continuous low nitrogen


title: Synechocystis, low-to-high nitrogen 4 h, rep1


title: Synechocystis, low-to-high nitrogen 4 h, rep3


title: Patient_226_FFPE


title: Synechocystis, continuous low nitrogen, rep1


title: Synechocystis, continuous low nitrogen, rep2


title: COX354A544_IL-12+IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

value: prdm1 fl/fl maf fl/fl CD4-Cre


title: Patient_237_FFPE


title: COX354A484_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 2

description:
ATAC_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: CD4+ T cells driven with IL-12+IL-27


title: BLCA_Nac_147

description: Re-analysis of GSM5203548

value: GeneChip WT Pico kit

value: neoadjuvant

value: UroB

tag: lundtax ihc-subtype

value: Uro

tag: consensus classifier subtype

value: StromaRich

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-other


title: COX354A284_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3

tag: strain

tag: treatment

tag: timepoint


title: Patient_222_FFPE

value: endometrium

tag: body weight

tag: Stage

tag: grade


title: BLCA_Nac_145

description: Re-analysis of GSM5203546

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: BASQ

tag: rm-bone


title: COX354A476_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: COX354A444_IL-12+IL-27_prdm1 fl/fl maf fl/fl_Day 2

value: Day 2


title: Patient_221_FFPE

tag: tisue

tag: age


title: BLCA_Nac_144

description: Re-analysis of GSM5203545

value: induction

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: yes

tag: rm-local

value: no

tag: rm-lung


title: COX354A64_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3

description:
ATAC_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: strain

value: prdm1 fl/fl CD4-Cre

tag: treatment

tag: timepoint

value: Day 3


title: BLCA_Nac_143

description: Re-analysis of GSM5203544

tag: rm-liver

tag: rm-other


title: Patient_217_FFPE

tag: body weight

tag: Stage

tag: grade


title: COX354A232_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: Patient_201_FFPE


title: Patient_208_FFPE


title: BLCA_Nac_138

description: Re-analysis of GSM5203539

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: UroA

value: LumP


title: COX354A200_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 2

description:
ATAC_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: CD4+ T cells driven with IL-12+IL-27


title: Patient_192_FFPE

tag: tisue

tag: age


title: COX354A8_IL-12+IL-27_prdm1 fl/fl CD4-Cre_Day 2


title: Patient_175_FFPE


title: COX354A36_IL-12+IL-27_prdm1 fl/fl_Day 3

description:
ATAC_IL-12+IL-27_prdm1 fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl


title: Patient_170_FFPE


title: Patient_171_FFPE


title: Patient_162_FFPE


title: Patient_153_FFPE


title: COX354A252_IL-12+IL-27_prdm1 fl/fl_Day 3


title: Patient_149_FFPE


title: COX354A4_IL-12+IL-27_prdm1 fl/fl_Day 2

description:
ATAC_IL-12+IL-27_prdm1 fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: BLCA_Trp_132

value: GeneChip WT Pico kit

value: neoadjuvant

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumU

tag: rm-lymphnode

tag: rm-local

tag: rm-bone


title: BLCA_Nac_127

description: Re-analysis of GSM5203534

tag: rm-lung

tag: rm-liver


title: Patient_138_FFPE

tag: body weight


title: Patient_130_FFPE

tag: Stage


title: Patient_143_FFPE

tag: grade


title: Patient_177_FFPE


title: Patient_122_FFPE


title: Patient_167_FFPE


title: BLCA_Nac_126

description: Re-analysis of GSM5203533

tag: labeling kit

value: UroC

value: Uro

tag: rm-other


title: COX354A196_IL-12+IL-27_prdm1 fl/fl_Day 2

tag: strain

tag: treatment

tag: timepoint


title: Patient_120_FFPE

tag: tisue

value: endometrium


title: BLCA_Nac_125

description: Re-analysis of GSM5203532

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype


title: COX354A168_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3

description:
ATAC_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: maf fl/fl CD4-Cre


title: Patient_114_FFPE

tag: age


title: BLCA_Nac_123

description: Re-analysis of GSM5203530

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumNS

tag: rm-lymphnode

tag: rm-local

tag: rm-bone


title: DSE_BG_3.smallRNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

data_processing:
smrtlink (version 9.0, parameters) was used to perform primer removal, polyA tail removal, chimeric reads removal, and reads clustering on the long reads (LRs).
The clustered LRs were aligned to the susScr11 reference genome using GMAP (version 2018-07-04, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: Long reads numbers mapped to each transcript have been summarized into Summary_PacBio.txt. Transcript TPM values were summarized into RNAseq_expression.tpm.txt. MiRNA RPM values were summarized into miRNAseq_expression.rpm.txt
Supplementary files format and content: PacBio's assembly file was tab-delimited.

organism: Sus scrofa

source_name: bulbourethral gland

growth_protocol: All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA)

tag: tissue

value: bulbourethral gland


title: DSE_BG_2.smallRNAseq


title: DSE_BG_1.smallRNAseq


title: COX354A80_IL-12+IL-27_maf fl/fl CD4-Cre_Day 2

description:
ATAC_IL-12+IL-27_maf fl/fl CD4-Cre_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: Day 2


title: BLCA_Nac_122

description: Re-analysis of GSM5203529

tag: labeling kit

value: ScNE

value: Mes

value: no

value: yes

tag: rm-lung

tag: rm-liver


title: Patient_103_FFPE

tag: body weight

tag: Stage

tag: grade


title: BMI_BG_3.smallRNAseq


title: BLCA_Nac_120

description: Re-analysis of GSM5203527

tag: labeling batch

value: LumP

tag: rm-other


title: BMI_BG_2.smallRNAseq


title: BMI_BG_1.smallRNAseq


title: COX354A136_IL-12+IL-27_maf fl/fl CD4-Cre_Day 2

tag: strain

tag: treatment

value: CD4+ T cells driven with IL-12+IL-27

tag: timepoint


title: BLCA_Nac_121

description: Re-analysis of GSM5203528

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: lundtax ihc-subtype


title: DSE_PG_3.smallRNAseq

source_name: prostate gland

value: prostate gland


title: BMI_PG_3.smallRNAseq


title: DSE_PG_1.smallRNAseq


title: COX354A180_IL-12+IL-27_maf fl/fl_Day 3

description:
ATAC_IL-12+IL-27_maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: maf fl/fl

value: Day 3


title: DSE_PG_2.smallRNAseq


title: COX354A116_IL-12+IL-27_maf fl/fl_Day 3


title: BLCA_Nac_116

description: Re-analysis of GSM5203523

value: GeneChip WT Pico kit

value: neoadjuvant

value: BASQ

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-bone


title: BMI_PG_2.smallRNAseq

tag: tissue


title: COX354A104_IL-12+IL-27_maf fl/fl CD4-Cre_Day 3


title: Patient_115_FFPE

tag: tisue

value: endometrium

tag: age

tag: body weight


title: BLCA_Nac_111

description: Re-analysis of GSM5203518

tag: labeling kit

tag: labeling batch

value: UroA

value: Uro

tag: rm-lung

tag: rm-liver


title: COX354A156_IL-12+IL-27_maf fl/fl_Day 2

description:
ATAC_IL-12+IL-27_maf fl/fl_Day 2
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: strain

tag: treatment

tag: timepoint


title: DSE_VG_3.smallRNAseq

source_name: vesicular gland

value: vesicular gland


title: BLCA_Nac_110

description: Re-analysis of GSM5203517

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: rm-other


title: DSE_VG_2.smallRNAseq


title: DSE_VG_1.smallRNAseq


title: COX354A535_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
ATAC_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-12

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: CD4+ T cells driven with IL-12


title: BLCA_Nac_108

description: Re-analysis of GSM5203515

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local


title: BLCA_Nac_109

description: Re-analysis of GSM5203516

value: no

tag: rm-bone


title: COX354A76_IL-12+IL-27_maf fl/fl_Day 2

value: Day 2


title: BLCA_Trp_106

value: UroC

value: LumNS

value: yes


title: COX354A455_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3