title: RNA-Seq bone marrow Progenitor Vav-Cre Pax5(fl/fl) _2

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438), and mm9 (samples 12521-15072).
ChIP-Seq and ATAC-Seq reads were aligned with Bowtie 1.0.0 (Langmead, B. et al. ,2009). Read coverages were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013].
RNA-Seq reads were aligned with STAR 2.4.2a [Dobin, 2013] in transcriptome guided alignment mode (samples 111733-111741, 181421-181438), and tophat 1.4.1 (samples 12521-15072). Transcripts per million (TPMs) were calculated as described previously.
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: bone marrow

extract_protocol:
NebNext UltraII RNA Library Prep Kit
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bone marrow

tag: cell type

value: Progenitor

tag: genotype

value: Vav-Cre Pax5(fl/fl)

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: chip antibody

tag: replicate number


title: RNA-Seq bone marrow Pro-B cell Pax5(+/+)_2

status: Public on Aug 24 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

value: Pro-B cell


title: BMI_VG_2.smallRNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

country: China

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.

molecule: total RNA

organism: Sus scrofa

source_name: vesicular 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)

value: vesicular gland


title: BMI_VG_3.smallRNAseq


title: BMI_PG_1.smallRNAseq

source_name: prostate gland

value: prostate gland


title: BMI_VG_1.smallRNAseq


title: RNA-Seq bone marrow Pro-B cell Pax5(+/+)_1


title: DSE_Epi_3.smallRNAseq

source_name: epididymis

value: epididymis


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1/DCRD1)_2


title: BLCA_Trp_99

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: induction + radiotherapy

tag: lundtax rna-subtype

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumU

tag: rm-lymphnode

value: no

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other

value: yes


title: COX354A439_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description:
ATAC_IL-12_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.

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-12

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).

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

tag: treatment

value: CD4+ T cells driven with IL-12

tag: timepoint

value: Day 2


title: DSE_Epi_2.smallRNAseq

tag: tissue


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1/DCRD1)_1

tag: strain

value: bone marrow

tag: cell type

tag: genotype

tag: cell preparation

tag: chip antibody

tag: replicate number


title: BLCA_Nac_103

description: Re-analysis of GSM5203512

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: neoadjuvant

tag: lundtax rna-subtype

value: BASQ

tag: lundtax ihc-subtype


title: COX354A531_IL-12_prdm1 fl/fl maf fl/fl_Day 3

description:
ATAC_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 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: DSE_Epi_1.smallRNAseq


title: RNA-Seq bone marrow Progenitor Vav-Cre Pax5(fl/fl) _1

value: Progenitor

value: Vav-Cre Pax5(fl/fl)

value: Ex-vivo FACS sorted from bone marrow


title: BLCA_Nac_98

description: Re-analysis of GSM5203508

value: GeneChip WT Pico kit

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: BLCA_Nac_97

description: Re-analysis of GSM5203507

value: UroB

value: LumP

tag: rm-other


title: COX354A475_IL-12_prdm1 fl/fl maf fl/fl_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: strain

tag: treatment

tag: timepoint


title: BMI_Epi_3.smallRNAseq

tag: tissue

value: epididymis


title: COX354A271_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.


title: COX354A283_IL-12_prdm1 fl/fl maf fl/fl_Day 3


title: BMI_Epi_2.smallRNAseq


title: RNA-Seq bone marrow Pro-B cell Pax5(+/+)_5

tag: cell type

value: Pro-B cell

tag: genotype

tag: cell preparation

tag: chip antibody

tag: replicate number


title: RNA-Seq thymus DN3a Rag2(-/-)_2 [15072]

source_name: thymus

value: thymus

value: Ex-vivo FACS sorted from thymus


title: COX354A487_IL-12_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

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

value: CD4+ T cells driven with IL-12


title: BLCA_Nac_85

description: Re-analysis of GSM5203495

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: UroC

tag: lundtax ihc-subtype

value: Uro

value: no

value: yes


title: BLCA_Nac_88

description: Re-analysis of GSM5203498

value: induction

value: GU

tag: consensus classifier subtype

value: LumU

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: COX354A483_IL-12_prdm1 fl/fl maf fl/fl_Day 2

description:
ATAC_IL-12_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.

tag: strain

value: prdm1 fl/fl maf fl/fl

tag: treatment

tag: timepoint

value: Day 2


title: BLCA_Nac_80

description: Re-analysis of GSM5203493

value: GeneChip WT Pico kit

value: neoadjuvant

value: BASQ

tag: rm-other


title: BMI_Epi_1.smallRNAseq

tag: tissue

value: epididymis


title: COX354A435_IL-12_prdm1 fl/fl maf fl/fl_Day 2


title: RNA-Seq thymus DN3a Rag2(-/-)_1 [15069]

value: thymus

tag: cell type

tag: genotype

tag: cell preparation

tag: chip antibody

tag: replicate number


title: BLCA_Nac_76

description: Re-analysis of GSM5203491

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

value: StromaRich


title: DSE_Tes_3.smallRNAseq

source_name: testis

value: testis


title: RNA-Seq thymus DN2b wild type_2 [14597]

value: wild type

value: Ex-vivo FACS sorted from thymus


title: DSE_Tes_2.smallRNAseq


title: RNA-Seq thymus Dn2a wild type_1 [14596]


title: BLCA_Nac_55

description: Re-analysis of GSM5203485

value: Uro

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone


title: BLCA_Nac_52

description: Re-analysis of GSM5203482

value: ScNE

value: no

tag: rm-other


title: COX354A239_IL-12_prdm1 fl/fl CD4-Cre_Day 3

description:
ATAC_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 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

value: CD4+ T cells driven with IL-12

tag: timepoint

value: Day 3


title: COX354A7_IL-12_prdm1 fl/fl CD4-Cre_Day 2

description:
ATAC_IL-12_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: BMI_Tes_3.smallRNAseq

tag: tissue


title: BLCA_Nac_47

description: Re-analysis of GSM5203478

tag: labeling kit

value: yes


title: RNA-Seq thymus DN2a wild type_2 [14594]

tag: cell type

tag: genotype

tag: cell preparation

tag: chip antibody

tag: replicate number


title: BLCA_Nac_46

description: Re-analysis of GSM5203477

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

tag: consensus classifier subtype


title: BMI_Tes_2.smallRNAseq


title: COX354A215_IL-12_prdm1 fl/fl CD4-Cre_Day 2

value: Day 2


title: RNA-Seq thymus DN1 wild type_1 [14593]


title: COX354A35_IL-12_prdm1 fl/fl_Day 3

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl


title: COX354A63_IL-12_prdm1 fl/fl CD4-Cre_Day 3


title: RNA-Seq bone marrow LMPP wild type_2 [14592]

value: bone marrow

value: LMPP

value: Ex-vivo FACS sorted from bone marrow


title: BMI_Tes_1.smallRNAseq


title: RNA-Seq thymus DN1 wild type_2 [14591]

value: thymus


title: COX354A3_IL-12_prdm1 fl/fl_Day 2

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: COX354A251_IL-12_prdm1 fl/fl_Day 3


title: RNA-Seq thymus DN2b wild type_2 [14590]


title: RNA-Seq thymus DN2b wild type_1 [14595]


title: BLCA_Nac_42

description: Re-analysis of GSM5203473

value: GeneChip WT Pico kit

value: neoadjuvant

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: DSE_Tes_1.smallRNAseq

tag: tissue

value: testis


title: COX354A211_IL-12_prdm1 fl/fl_Day 2

tag: strain

tag: treatment

tag: timepoint


title: BLCA_Trp_36

tag: labeling kit

value: GU

value: LumU


title: 200nM_R3

first: Gantas

last: Perez Mockus

address: 1 Brill Place

institute: Francis Crick Institute

description: replicate 3

data_processing:
RNASeq - sequenced reads were aligned to the genome using hisat2 (v. 2.1.0)
RNASeq - The bam file was indexed and sorted using samtools (v.1.13)
RNASeq - subread (v2.0.1) was used to count reads mapping to genes
RNASeq - Differentially expressed genes were identified using DESeq2 (v1.32.0)
RNASeq - Normalized counts were generated using DESeq2 (v1.32.0) processed data files format and content: comma delimited table that contains DESeq2 results for each comparison for each gene
Assembly: DGBP6 annotation ensemble release 84
Supplementary files format and content: processed data files format and content: comma delimited table that contains normalized counts for all genes in each sample

organism: Drosophila melanogaster

source_name: Wing imaginal Disc

growth_protocol: Animals were raised at 25C. Animals where selected at the L2-L3 transition.

extract_protocol:
RNA was extracted with an RNeasy Mini Kit (Qiagen, 74104).
1.2-2.1 μg were used as a template to generate a sequencing library with the NEBNext Ultra II Directional PolyA mRNA (NEB, E7760S)

treatment_protocol: Wing discs were dissected 24h AL2-L3, and incubated for 2.5 in Dye media supplemented with different concentrations of 20E.

value: Wing imaginal Disc

tag: genotype

value: wildtype (w1118)


title: BLCA_Nac_41

description: Re-analysis of GSM5203472

tag: labeling batch

tag: clinical tnm staging

value: ScNE

value: no


title: BLCA_Nac_33

description: Re-analysis of GSM5203467

tag: chemotherapy type

tag: lundtax rna-subtype

value: UroA

value: LumP


title: COX354A183_IL-12_maf fl/fl CD4-Cre_Day 3

description:
ATAC_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 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

value: CD4+ T cells driven with IL-12

value: Day 3


title: RNA-Seq thymus DN2a wild type_1 [14589]

tag: cell type

value: wild type

tag: cell preparation

value: Ex-vivo FACS sorted from thymus

tag: chip antibody

tag: replicate number


title: RNA-Seq thymus DN1 wild type_2 [14588]

value: thymus


title: 2000nM_R2

description: replicate 2


title: COX354A127_IL-12_maf fl/fl CD4-Cre_Day 3


title: 200nM_R2

description: replicate 2


title: 2000nM_R3

description: replicate 3


title: BLCA_Nac_22

description: Re-analysis of GSM5203457

value: GeneChip WT Pico kit

value: BASQ

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: yes

tag: rm-local

tag: rm-lung

tag: rm-liver


title: RNA-Seq bone marrow LMPP wild type_1 [14587]

tag: strain

tag: tissue

value: bone marrow

value: LMPP

value: Ex-vivo FACS sorted from bone marrow


title: BLCA_Nac_45

description: Re-analysis of GSM5203476

tag: labeling kit

value: neoadjuvant

tag: rm-bone

tag: rm-other


title: COX354A159_IL-12_maf fl/fl CD4-Cre_Day 2

description:
ATAC_IL-12_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: treatment

tag: timepoint

value: Day 2


title: RNA-Seq thymus DN3b wild type_2 [13330]

tag: cell type

tag: genotype


title: 0nM_R3

description: replicate 3

value: Wing imaginal Disc

value: wildtype (w1118)


title: COX354A95_IL-12_maf fl/fl CD4-Cre_Day 2


title: BLCA_Trp_20

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: curative radiochemotherapy

tag: lundtax rna-subtype

value: Uro

value: StromaRich

value: no


title: 20nM_R2

description: replicate 2


title: RNA-Seq thymus DN3b wild type_1 [13324]

value: wild type

tag: cell preparation

tag: chip antibody

tag: replicate number


title: BLCA_Nac_19

description: Re-analysis of GSM5203456

value: UroA

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver


title: 0nM_R2

description: replicate 2

tag: tissue

tag: treatment


title: COX354A187_IL-12_maf fl/fl_Day 3

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: strain

value: maf fl/fl

value: CD4+ T cells driven with IL-12

tag: timepoint

value: Day 3


title: COX354A123_IL-12_maf fl/fl_Day 3


title: RNA-Seq thymus DN3a wild type_2 [12522]

value: thymus

tag: cell type

tag: genotype

value: Ex-vivo FACS sorted from thymus


title: RNA-Seq thymus DN3a wild type_1 [12521]


title: 200nM_R1

description: replicate 1


title: COX354A75_IL-12_maf fl/fl_Day 2

description:
ATAC_IL-12_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: ATAC-Seq bone marrow Pro-B cell Pax5(+/+)_2

value: bone marrow

value: Pro-B cell


title: 20nM_R1

description: replicate 1


title: BLCA_Nac_11

description: Re-analysis of GSM5203448

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: neoadjuvant

value: ScNE

value: GU

tag: rm-bone

value: yes

tag: rm-other


title: BLCA_Nac_13

description: Re-analysis of GSM5203450

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

value: Uro

tag: consensus classifier subtype

value: LumP


title: COX354A147_IL-12_maf fl/fl_Day 2

value: Day 2


title: BLCA_Nac_10

description: Re-analysis of GSM5203447

value: UroC

value: LumNS

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

value: no


title: 20nM_R3

description: replicate 3

tag: tissue

value: Wing imaginal Disc

value: wildtype (w1118)

tag: treatment


title: BLCA_Nac_7

description: Re-analysis of GSM5203444

value: BASQ

tag: rm-liver


title: ATAC-Seq bone marrow Pro-B cell Pax5(+/+)_1

tag: strain

tag: cell type

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: replicate number


title: 0nM_R1

description: replicate 1

tag: genotype


title: COX354A541_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

description:
ATAC_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 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: Medium

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

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 3


title: ATAC-Seq bone marrow Progenitor Vav-Cre Pax5(fl/fl) _2

value: bone marrow

value: Progenitor

value: Vav-Cre Pax5(fl/fl)


title: COX354A477_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: HH20 limb bud explant, SU5402, 48h, rep 3

city: Sheffield

first: Sofia

last: Sedas Perez

address: Western Bank

institute: The University of Sheffield

data_processing:
Raw sequencing reads were cleaned by removing reads containing adapter, reads containing poly-N and low quality reads.
Reads were mapped to the reference genome using Hisat2 v2.0.5 with default parameters.
featureCounts v1.5.0-p3 was used to quatify reads mapped to each gene. FPKM was then calculated to noramlize values for sequencing depth and gene length.
Differential expression analyisis between DMSO and SU5402 samples was performed using DESEq2 v1.20.0.
Genes with an adjusted P-value <=0.05 and |log2(FoldChange)| >=1 were assigned as differentially expressed.
Assembly: ensembl_gallus_gallus_grcg6a_gca_000002315_5
Supplementary files format and content: sample_FPKM.txt are tab-delimited text files that include FPKM values of each sample per gene and features of the gene.
Supplementary files format and content: sample_DESeq.txt are tab-delimited text files that include normalized count of sample, normalized count of replicate group, log2FoldChange, p-value and p-adjusted value (padj) per gene for each sample.

organism: Gallus gallus

source_name: HH20 limb bud explant

growth_protocol: HH20 limb bud explants embedded in GFR matrigel were maintained in CMRL supplemented with 10% fetal bovine serum (FBS), 1% PenStrep and 1% L-Glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from samples using Trizol-chloroform extractions and concentrated through the Zymo RNA Clean and Concentrator Kit as per manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. First strand cDNA was synthesised using random hexamers, followed by second strand cDNA synthesis using either dUTP or dTTP for directional and non directional library, respectively.
Followed by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion (for directional library only), amplification and purification.

treatment_protocol: Explants were treated with either DMSO or SU5402 5µM in the culture media at 0h. Explants were cultured for 48h before collection.

value: HH20 limb bud explant

value: Mesenchyme

value: WT

value: SU5402 in explant culture


title: ATAC-Seq bone marrow Progenitor Vav-Cre Pax5(fl/fl) _1


title: HH20 limb bud explant, SU5402, 48h, rep 2


title: BLCA_Nac_6

description: Re-analysis of GSM5203443

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: induction

value: UroB

value: Uro

value: LumP

value: yes

tag: rm-bone


title: COX354A285_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: BLCA_Nac_2

description: Re-analysis of GSM5203439

tag: lundtax rna-subtype

value: BASQ

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: no

tag: rm-other


title: BLCA_Nac_3

description: Re-analysis of GSM5203440

value: neoadjuvant

value: GU

value: LumU

tag: rm-local

tag: rm-lung

tag: rm-liver


title: 2000nM_R1

description: replicate 1

tag: tissue

value: Wing imaginal Disc

value: wildtype (w1118)

tag: treatment


title: COX354A485_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

description:
ATAC_Medium_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.

tag: strain

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

value: CD4+ T cells driven with Medium

value: Day 2


title: Cntl2_ROI_12_well_G01

city: Limoges

first: Simon

last: Parreau

state: Haute-Vienne

address: 16 rue Bernard Descottes

country: France

institute: Dupuytren hospital

description:
DSP-1012340003501-F-G01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
*library strategy: GeoMx Seq
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
The freshly cut sections were stained with fluorescently labeled imaging reagents and mRNA markers. Briefly, sections were labeled with the cell markers, α-smooth muscle actin, CD3, and CD68, and the nuclear stain SYTO 13
The NanoString commercial Human Whole Transcriptome Atlas (GeoMx WTA) panel (18,000 protein-coding genes) was selected. Four slides (two with GCA patients and two with controls) were scanned on a GeoMx DSP instrument (NanoString Technologies Inc., Seattle, WA, USA) and individual regions of interest (ROIs) with a maximum diameter of 400 μm were created within each of the four arterial layers in GCA and controls. Once each ROI was compartmentalized, ultraviolet-cleaved indexing oligonucleotides were collected into a 96-well plate. Libraries were prepared according to the manufacturer’s instructions (protocol 01/2019). The library quality and quantity were assessed using Bioanalyzer DNA High Sensitivity Analysis. Samples were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) and reads were digitally quantified and normalized using GeoMx DSP Data Analysis software
The library quality and quantity were assessed using Bioanalyzer DNA High Sensitivity Analysis. Samples were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) and reads were digitally quantified and normalized using GeoMx DSP Data Analysis software
Data obtained from the NanoString GeoMx DSP platform were analyzed using dedicated software (GeoMx Analysis Suite 2.3). The quality control analysis showed that all ROIs had raw read counts above 1 million and good alignment rate and sequencing saturation. The local outliers were negative control probes and were removed from the ROIs.
ROIs with deduplicated probe counts Q3 (upper quartile) < 2 were excluded. Furthermore, ROIs were removed if < 1% of their genes had read counts higher than the limit of quantification (LOQ). LOQ was defined as geomean(NegProbe) × geoSD(NegProbe)² for each ROI. Target filtering was applied to retain gene targets with read counts above LOQ in at least 10% of ROIs. Q3 normalization was applied on the filtered ROIs and gene targets.

source_name: Heart

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

treatment_protocol: Temporal artery specimens were cross-sectioned serially. Tissues were fixed in 10% neutral buffered formalin for 24 h, followed by transfer to 70% ethanol before paraffin embedding. For each patient and control, segments were grouped into formalin-fixed paraffin-embedded (FFPE) temporal artery blocks using the tissue microarray method. Tissue microarrays were constructed from 2-mm-diameter cores punched from each FFPE tissue block. FFPE temporal artery blocks from GCA and control patients were sectioned to a thickness of 5 μm. The sections were mounted on an adhesive or positively charged slides (cat# S21.2113.A; Bond Plus slides; Leica Biosystems, Richmond, VA, USA).

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Cntl2_ROI_11_well_F12

description:
DSP-1012340003501-F-F12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: BLCA_Trp_1

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-bone

tag: rm-other


title: HH20 limb bud explant, SU5402, 48h, rep 1

tag: tissue

value: HH20 limb bud explant

tag: cell type

value: Mesenchyme

tag: genotype

value: WT

tag: treatment

value: SU5402 in explant culture


title: HH20 limb bud explant, DMSO, 48h, rep 3

value: DMSO in explant culture


title: COX354A421_Medium_prdm1 fl/fl maf fl/fl CD4-Cre_Day 2

tag: strain

tag: timepoint


title: COX354A529_Medium_prdm1 fl/fl maf fl/fl_Day 3

description:
ATAC_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 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: Cntl2_ROI_9_well_F10

description:
DSP-1012340003501-F-F10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: HH20 limb bud explant, DMSO, 48h, rep 2

tag: tissue

tag: cell type


title: COX354A473_Medium_prdm1 fl/fl maf fl/fl_Day 3

tag: treatment


title: HH20 limb bud explant, DMSO, 48h, rep 1

tag: genotype


title: Cntl2_ROI_8_well_F09

description:
DSP-1012340003501-F-F09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: BLCA_Cx_306

description: Re-analysis of GSM2213212

tag: labeling kit

value: SensationPlus FFPE Amplification and WT labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: adjuvant

tag: lundtax rna-subtype

value: UroA

tag: lundtax ihc-subtype

value: Uro

tag: consensus classifier subtype

value: LumP

tag: rm-lymphnode

value: yes

tag: rm-local

value: no

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Cx_305

description: Re-analysis of GSM2213211

value: neoadjuvant

value: UroB


title: Cntl2_ROI_7_well_F08

description:
DSP-1012340003501-F-F08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: COX354A481_Medium_prdm1 fl/fl maf fl/fl_Day 2

description:
ATAC_Medium_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.

tag: strain

tag: treatment

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 2


title: S8

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

country: USA

institute: University of Iowa

data_processing:
Raw files were processed with cellranger-atac-2.0.0.
Raw files were processed with split-pipe (v0.9.6p).
Outputs for each samples are provided in tar.gz files.
Assembly: mm10
Supplementary files format and content: cellranger-atac_outputs.tar.gz:
Supplementary files format and content: Compressed directory containing cellrange-atac outputs. filtered_feature_bc.matrix.h5 contains expression data. singlecell.csv contains the metadata. fragments.tsv.gz contains the fragments file. fragments.tsv.gz.tbi contains the fragments file index.
Supplementary files format and content: split-pipe_outputs.tar.gz:
Supplementary files format and content: Compressed directory containing split-pipe outputs. all_genes.csv contains the gene name, gene id, and genome for each column in DGE.mtx. cell_metadata.csv contains information about each cell including the cell barcode, species, sample, well in each round of barcoding, and number of transcript/genes detected. DGE.mtx is a sparse matrix with counts that depend on the experiment.

source_name: brain

extract_protocol:
snATAC-seq: Frozen hippocampal tissue was homogenized in pre-chilled lysis buffer using Dounce homogenizers. The homogenate was then transferred into pre-chilled Nuclei Isolation Columns, and the columns were centrifuged. The flowthrough was briefly vortexed, followed by centrifugation. The nuclear pellet was resuspended in Debris Removal Buffer and centrifuged. The nuclear pellet was then resuspended in Wash Buffer, centrifuged, and finally resuspended in Resuspension Buffer.
SPLIT-seq: Frozen hippocampal tissue was homogenized in homogenization buffer using Dounce homogenizers. The homogenate was filtered through strainer and centrifuged. The pellet was resuspended in PBS containing BSA and centrifuged. The pellet was resuspended in PBS and passed through a cell strainer.
The Single Cell ATAC-Seq protocol, comprising of the Transposition, GEM Generation, Barcoding, and Library Construction steps were carried out according to the manufacturer’s protocol (Chromium Next GEM Single Cell ATAC Kit, 10x Genomics). Libraries were sequenced in paired end in Illumina Novaseq.
RNA from the fixed nuclei were subjected to multiple rounds of reverse transcription barcoding and ligation barcoding in customized 96-well thermocycler plates that contain barcoded primers in each well. After the final round of thermocycling, nuclei were pooled together and distributed into 8 sublibraries. Barcoded DNA in each sublibrary was then amplified, following which Template Switching and SPRI Clean-Up steps were performed. Sublibraries were then subjected to Fragmentation, End Repair, and A-Tailing; followed by Post-Fragmentation Double sided SPRI selection, Adaptor Ligation, and Sublibrary Index PCR. Finally, Post-Amplification Double-sided size selection was performed before sequencing them on an Illumina Novaseq Sequencer.

value: brain

tag: Sex

value: male

tag: condition

value: home cage + spatial object recognition training


title: Cntl2_ROI_6_well_F07

description:
DSP-1012340003501-F-F07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: slide id


title: S6


title: BLCA_Cx_285

description: Re-analysis of GSM2213191

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: induction

tag: lundtax rna-subtype

value: BASQ

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: S7

tag: strain

tag: Sex


title: COX354A425_Medium_prdm1 fl/fl maf fl/fl_Day 2

value: prdm1 fl/fl maf fl/fl

tag: treatment

tag: timepoint


title: BLCA_Cx_258

description: Re-analysis of GSM2213164

tag: labeling kit

value: SensationPlus FFPE Amplification and WT labeling kit

value: UroA

value: StromaRich


title: Cntl2_ROI_10_well_F11

description:
DSP-1012340003501-F-F11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Cntl2_ROI_5_well_F06

description:
DSP-1012340003501-F-F06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: COX354A61_Medium_prdm1 fl/fl CD4-Cre_Day 3

description:
ATAC_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 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

value: Day 3


title: COX354A229_Medium_prdm1 fl/fl CD4-Cre_Day 3

tag: treatment


title: COX354A281_Medium_prdm1 fl/fl maf fl/fl_Day 3

tag: timepoint


title: COX354A5_Medium_prdm1 fl/fl CD4-Cre_Day 2

description:
ATAC_Medium_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: Cntl2_ROI_3_well_F04

description:
DSP-1012340003501-F-F04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: BLCA_Cx_235

description: Re-analysis of GSM2213141

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: palliative

tag: lundtax rna-subtype

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: no

tag: rm-local

tag: rm-lung

tag: rm-liver

value: yes

tag: rm-bone

tag: rm-other


title: Cntl2_ROI_2_well_F03

description:
DSP-1012340003501-F-F03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: COX354A213_Medium_prdm1 fl/fl CD4-Cre_Day 2

tag: strain

tag: treatment

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 2


title: S5

value: brain

tag: Sex

value: male

tag: condition

value: home cage + spatial object recognition training


title: S3

tag: tissue


title: Cntl2_ROI_1_well_F02

description:
DSP-1012340003501-F-F02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number


title: S2


title: BLCA_Cx_244

description: Re-analysis of GSM2213150

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: neoadjuvant

tag: lundtax rna-subtype

value: UroB

tag: lundtax ihc-subtype

value: BASQ

tag: consensus classifier subtype

value: LumP

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Cx_241

description: Re-analysis of GSM2213147

value: SensationPlus FFPE Amplification and WT labeling kit

value: induction

value: UroA

value: Uro


title: Cntl2_ROI_4_well_F05

description:
DSP-1012340003501-F-F05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: S4

tag: tissue

tag: strain

tag: Sex

tag: condition


title: S1


title: COX354A33_Medium_prdm1 fl/fl_Day 3

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

value: prdm1 fl/fl

tag: treatment

tag: timepoint

value: Day 3


title: BLCA_Cx_298

description: Re-analysis of GSM2213204

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: palliative

tag: lundtax rna-subtype

value: ScNE

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: no

tag: rm-local

tag: rm-lung

value: yes

tag: rm-liver

tag: rm-bone

tag: rm-other


title: SOR-2

tag: tissue

value: brain

tag: strain

tag: Sex

value: spatial object recognition training


title: COX354A209_Medium_prdm1 fl/fl_Day 2

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.

tag: treatment

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 2


title: BLCA_Cx_204

description: Re-analysis of GSM2213110

tag: labeling kit

tag: labeling batch

value: GU

value: StromaRich


title: COX354A249_Medium_prdm1 fl/fl_Day 3


title: SOR-1

value: male

tag: condition


title: GCA2_ROI_16_well_F01

description:
DSP-1012340003501-F-F01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: GCA2_ROI_15_well_E12

description:
DSP-1012340003501-F-E12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue


title: BLCA_Cx_229

description: Re-analysis of GSM2213135

value: SensationPlus FFPE Amplification and WT labeling kit

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: UroB

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: BASQ

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Cx_234

description: Re-analysis of GSM2213140

tag: labeling kit

tag: labeling batch

value: neoadjuvant


title: COX354A1_Medium_prdm1 fl/fl_Day 2

tag: strain

value: prdm1 fl/fl

tag: treatment

tag: timepoint


title: GCA2_ROI_14_well_E11

description:
DSP-1012340003501-F-E11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: BLCA_Cx_198

description: Re-analysis of GSM2213104

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumP

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: GCA2_ROI_13_well_E10

description:
DSP-1012340003501-F-E10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: BLCA_Cx_197

description: Re-analysis of GSM2213103

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: ScNE

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: no


title: HC-1

tag: tissue

value: brain

tag: strain

tag: Sex

tag: condition

value: home cage


title: COX354A173_Medium_maf fl/fl CD4-Cre_Day 3

description:
ATAC_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 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

tag: treatment

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 3


title: BLCA_Cx_188

description: Re-analysis of GSM2213094

value: palliative

value: GU

value: Uro

value: LumU

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

value: yes

tag: rm-liver

tag: rm-bone

tag: rm-other


title: COX354A125_Medium_maf fl/fl CD4-Cre_Day 3


title: BLCA_Cx_178

description: Re-analysis of GSM2213078

tag: labeling kit

value: SensationPlus FFPE Amplification and WT labeling kit

tag: labeling batch

tag: clinical tnm staging

value: UroA


title: COX354A77_Medium_maf fl/fl CD4-Cre_Day 2

description:
ATAC_Medium_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: GCA2_ROI_11_well_E08

description:
DSP-1012340003501-F-E08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: COX354A157_Medium_maf fl/fl CD4-Cre_Day 2

tag: strain

tag: treatment

tag: timepoint


title: GCA2_ROI_9_well_E06

description:
DSP-1012340003501-F-E06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue


title: COX354A65_Medium_maf fl/fl_Day 2

description:
ATAC_Medium_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: maf fl/fl


title: HC-2

tag: Sex

value: male

tag: condition


title: COX354A121_Medium_maf fl/fl_Day 3

description:
ATAC_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 either Day 2 or Day 3 with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf.


title: GCA2_ROI_8_well_E05

description:
DSP-1012340003501-F-E05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number


title: GCA2_ROI_7_well_E04

description:
DSP-1012340003501-F-E04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

tag: area


title: GCA2_ROI_12_well_E09

description:
DSP-1012340003501-F-E09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi x coordinate

tag: roi y coordinate


title: GCA2_ROI_6_well_E03

description:
DSP-1012340003501-F-E03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: rawreads

tag: alignedreads


title: BLCA_Cx_130

description: Re-analysis of GSM2213030

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: neoadjuvant

tag: lundtax rna-subtype

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumNS

tag: rm-lymphnode

tag: rm-local

value: no

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: COX354A153_Medium_maf fl/fl_Day 2

tag: strain

tag: treatment

value: CD4+ T cells driven with Medium

tag: timepoint


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1,2/-)_2

tag: tissue

value: bone marrow

tag: cell type

value: Pro-B cell

tag: genotype

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: chip antibody

tag: replicate number


title: GCA2_ROI_5_well_E02

description:
DSP-1012340003501-F-E02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: BLCA_Cx_118

description: Re-analysis of GSM2213018

tag: labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

tag: lundtax rna-subtype

value: UroB

tag: lundtax ihc-subtype

value: Uro

tag: consensus classifier subtype

value: BASQ

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Cx_134

description: Re-analysis of GSM2213034

value: SensationPlus FFPE Amplification and WT labeling kit

value: induction

value: GU

value: StromaRich

value: yes


title: BLCA_Cx_82

description: Re-analysis of GSM2212982

value: adjuvant


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep3

city: San Francisco

first: Yizhu

last: Lin

state: CA

address: 513 Parnassus

department: Cell and Tissue Biology

institute: University of California, San Francisco

description: HEK293T cell with dox-inducible expression of PUM1-rABE and PUM2-APOBEC1, 1000 ng/ul doxcycline, 48h

data_processing:
Sequencing reads were processed with CCS and demultiplexed with lima
Reads were aligned and calibrated with Iso-seq 3 pipeline
Custom script for calling isoform specific PUM1 binding events: github.com/linyz/remora
Assembly: GRCh38
Supplementary files format and content: all_exon_alt_u_v2_all.csv (Isoform specific PUM1 binding events in csv table)

source_name: kidney

growth_protocol: HEK 293T cells were cultured in DMEM with 4.5 g / L glucose, L-glutamine & sodium pyruvate (Corning #10-0130CV) and 10% FBS (Avantor #97068-085) at 37 ˚C, 5% CO2.

extract_protocol:
Cellular RNA extraction was performed with Direct-zol RNA miniprep Kit (Zymo Research #R2053) following manufacturer’s protocol
We used PacBio Iso-seq Express Template Preparation Kit  (PN 101-763-800, v2)
PacBio IsoSeq

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: PUM1-rABE PUM2-APOBEC1

tag: treatment

value: 1000 ng/ml dox


title: BLCA_Cx_167

description: Re-analysis of GSM2213067

tag: labeling kit

tag: labeling batch

value: palliative

value: UroA

value: LumP

value: no


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep2


title: GCA2_ROI_10_well_E07

description:
DSP-1012340003501-F-E07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: ChIP-seq of H3K27ac of M121224 cells treated with TAL + LGX818 rep2

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: ChIP-seq single end (SE)

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
Assembly: hg38
Supplementary files format and content: bigwig, bed

extract_protocol:
Chromatin Immunoprecipitation experiments were carried out in M121224 cell lines using Active Motif ChIP-IT High sensitivity kit as per manufacturer's instructions. for H3K27Ac 10ug of chromatin and 3ug of H3K27ac (ab4729, Abcam) antibodies were used. Immunoprecipitation was carried out overnight at 4C with rotation.
Libraries were prepared using the NEBNext® Ultra DNA Library Prep for Illumina® kit (ref. E7370) according to the manufacturer's protocol. Briefly, input and ChIP enriched DNA were subjected to end repair and addition of “A” bases to 3′ ends, ligation of adapters and USER excision. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Library amplification was performed by PCR using NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1, ref. E7335), (Index Primers Set 2, ref. E7500), (Index Primers Set 3, ref. E7710) and (Index Primers Set 4, ref. E7730). Final libraries were analyzed using Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (ref. 5067-4626 or ref. DNF-474) to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot

tag: cell line

tag: cell type

value: Cancer metastatic

value: WT

value: TAL + LGX818


title: BLCA_Cx_73

description: Re-analysis of GSM2212973

value: SensationPlus FFPE Amplification and WT labeling kit

tag: clinical tnm staging

tag: chemotherapy type

value: neoadjuvant

tag: lundtax rna-subtype

value: GU

tag: lundtax ihc-subtype

tag: consensus classifier subtype

value: LumU

tag: rm-lymphnode

tag: rm-local

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Cx_64

description: Re-analysis of GSM2212964

tag: labeling kit

tag: labeling batch

value: UroC

value: Uro

value: LumNS

value: yes


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1,2/DCRD1,2)_2

tag: strain

tag: tissue

value: bone marrow

value: Pro-B cell

tag: genotype

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: chip antibody

tag: replicate number


title: GCA2_ROI_4_well_E01

description:
DSP-1012340003501-F-E01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep1

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: Human embryonic kidney

value: PUM1-rABE PUM2-APOBEC1

tag: treatment

value: 1000 ng/ml dox


title: COX354A169_Medium_maf fl/fl_Day 3

tag: strain

value: maf fl/fl

value: CD4+ T cells driven with Medium

tag: timepoint

value: Day 3


title: PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep2

description: HEK293T cell with dox-inducible expression of PUM1-APOBEC1 and PUM2-rABE, 1000 ng/ul doxcycline, 48h

tag: genotype

value: PUM1-APOBEC1 PUM2-rABE


title: GCA2_ROI_2_well_D11

description:
DSP-1012340003501-F-D11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA


title: ChIP-seq of H3K27ac of M121224 cells treated with TAL + LGX818 rep1

description: ChIP-seq single end (SE)

tag: chip antibody

value: ab4729, Abcam

value: Cancer metastatic

value: WT

value: TAL + LGX818


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1,2/DCRD1,2)_1

value: bone marrow

tag: cell preparation

tag: replicate number


title: GCA2_ROI_3_well_D12

description:
DSP-1012340003501-F-D12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD2/-)_2

tag: tissue

tag: cell type

value: Pro-B cell


title: GCA2_ROI_1_well_D10

description:
DSP-1012340003501-F-D10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: BLCA_Cx_283

description: Re-analysis of GSM2213189

tag: labeling kit

value: SensationPlus FFPE Amplification and WT labeling kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: adjuvant

tag: lundtax rna-subtype

value: UroC

tag: lundtax ihc-subtype

value: Uro

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: PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep1

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

tag: treatment

value: 1000 ng/ml dox


title: PUM2-APOBEC1, 1000 ng/ml dox, rep2

description: HEK293T cell with dox-inducible expression of PUM2-APOBEC1, 1000 ng/ul doxcycline, 48h


title: GCA1_ROI_23_well_D08

description:
DSP-1012340003501-F-D08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1,2/-)_1

tag: strain

tag: tissue

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow

tag: chip antibody

tag: replicate number


title: GCA1_ROI_24_well_D09

description:
DSP-1012340003501-F-D09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD2/DCRD2)_1

tag: cell type

tag: genotype


title: PUM2-APOBEC1, 1000 ng/ml dox, rep1

tag: cell line

tag: treatment


title: ChIP-seq of H3K27ac of M121224 cells rep2

description: ChIP-seq single end (SE)

value: Cancer metastatic

value: WT


title: GCA1_ROI_22_well_D07

description:
DSP-1012340003501-F-D07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD2/-)_1

value: bone marrow


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1/-)_2

value: Pro-B cell


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD2/DCRD2)_2


title: PUM2-rABE, 1000 ng/ml dox, rep3

description: HEK293T cell with dox-inducible expression of PUM2-rABE, 1000 ng/ul doxcycline, 48h


title: GCA1_ROI_21_well_D06

description:
DSP-1012340003501-F-D06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: RNA-Seq bone marrow Pro-B cell Pax5(DCRD1/-)_1

tag: strain

tag: tissue

tag: cell preparation

tag: chip antibody


title: PUM2-rABE, 1000 ng/ml dox, rep2

tag: cell type

tag: genotype


title: ChIP-seq of H3K27ac of M121224 cells rep1

description: ChIP-seq single end (SE)

tag: cell line

value: ab4729, Abcam

tag: treatment


title: SAM611128

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

hyb_protocol: Samples were hybridized to GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Inc.).  Arrays were washed and stained in the Affymetrix Fluidics station and scanned on a GeneChip® scanner 3000.

scan_protocol: GeneChip® scanner 3000

data_processing: Expression signals were obtained using the Affymetrix GeneChip® operating system and analysis software. The data was normalized using RMA and probesets that failed to meet the affymetrix A-classification were removed.

source_name: joint tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

tag: disease

value: Control


title: SAM612809

value: OA


title: PUM2-APOBEC1, 1000 ng/ml dox, rep3


title: SAM612838


title: SAM612810


title: PUM2-rABE, 1000 ng/ml dox, rep1


title: SAM612823


title: GCA1_ROI_20_well_D05

description:
DSP-1012340003501-F-D05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: sequencingsaturation


title: GCA1_ROI_19_well_D04

description:
DSP-1012340003501-F-D04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: RNA-Seq bone marrow Pro-B cell Pax5(DOP,HD/DOP,HD)_1

tag: strain

tag: tissue

tag: cell preparation

tag: replicate number


title: SAM625204

value: RA


title: PUM1-APOBEC1, 1000 ng/ml dox, rep3

description: HEK293T cell with dox-inducible expression of PUM1-APOBEC1, 1000 ng/ul doxcycline, 48h

tag: cell line

tag: cell type

tag: genotype


title: GCA1_ROI_18_well_D03

description:
DSP-1012340003501-F-D03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: trimmedreads

tag: stitchedreads


title: RNA-Seq bone marrow Pro-B cell Pax5(DOP/DOP)_2

tag: chip antibody


title: PUM1-APOBEC1, 1000 ng/ml dox, rep2

tag: treatment


title: RNA-Seq bone marrow Pro-B cell Pax5(DHD/DHD)_2


title: PUM1-rABE, 1000 ng/ml dox, rep3

description: HEK293T cell with dox-inducible expression of PUM1-rABE, 1000 ng/ul doxcycline, 48h


title: RNA-Seq bone marrow Pro-B cell Pax5(DOP/DOP)_1


title: GCA1_ROI_16_well_D01

description:
DSP-1012340003501-F-D01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: sequencingsaturation


title: GCA1_ROI_15_well_C12

description:
DSP-1012340003501-F-C12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: PUM1-APOBEC1, 1000 ng/ml dox, rep1

tag: tissue

tag: cell line


title: RNA-Seq bone marrow Pro-B cell Pax5(DHD/DHD)_1

tag: strain

tag: cell type

tag: genotype

tag: cell preparation

tag: replicate number


title: RNA-Seq bone marrow Pro-B cell Pax5(DOP,HD/DOP,HD)_2

tag: chip antibody


title: PUM1-rABE, 1000 ng/ml dox, rep2

tag: treatment


title: RNA-Seq bone marrow Pro-B cell Pax5(+/+)_4


title: GCA1_ROI_17_well_D02

description:
DSP-1012340003501-F-D02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: segment type

tag: trimmedreads

tag: stitchedreads


title: GCA1_ROI_14_well_C11

description:
DSP-1012340003501-F-C11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: PUM1-rABE, 1000 ng/ml dox, rep1

tag: tissue

tag: cell line


title: RNA-Seq bone marrow Pro-B cell Pax5(+/+)_3

tag: strain

tag: cell type

tag: genotype


title: APOBEC1, 1000 ng/ml dox, rep3

description: HEK293T cell with dox-inducible expression of APOBEC1, 1000 ng/ul doxcycline, 48h


title: GCA1_ROI_13_well_C10

description:
DSP-1012340003501-F-C10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: alignedreads

tag: deduplicatedreads


title: SAM612875

tag: disease


title: GCA1_ROI_12_well_C09

description:
DSP-1012340003501-F-C09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number


title: APOBEC1, 1000 ng/ml dox, rep2

tag: treatment


title: GCA1_ROI_11_well_C08

description:
DSP-1012340003501-F-C08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

tag: trimmedreads

tag: stitchedreads


title: SAM612796


title: RNA-seq denervation gastrocnemius 3 [DENV3]

city: Houston

first: Zhaoyong

last: Hu

state: Texas

address: One Baylor Plaza

department: Nephrology

institute: Baylor college of medicine

data_processing:
Paired-end reads were mapped to the mouse genome using Bowtie2 v2.2.9. The abundance  was estimated using RSEM v1.3.0 and the differential expression analysis was done  using EdgeR v3.12.1 in the Bioconductor package.
Assembly: NCBIM37
Supplementary files format and content: read coverage files in bigWig format
Supplementary files format and content: gene and sample matrix

source_name: Gastrocnemius muscle

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle

extract_protocol:
Total RNA from whole gastrocnemius muscle of normal control mice (n=3) and mice with denervation (n=3) were extracted using Qiazol and precipitated in isopropanol.
RNA samples, which passed quality-control examination, were submitted to LC Sciences LLC (Houston, TX. lcsciences.com) for library preparation and paired-end 50 bp sequencing using the standard Illumina mRNA-seq protocol.

treatment_protocol: Mice were anesthetized and the left sciatic nerve was removed for a 2-mm piece. Gastrocnemius (Gas) muscles were harvested 2 weeks after denervation. Gas muscles from left hind limb of normal mice served as controls.

value: Gastrocnemius muscle

tag: Sex

value: male

tag: age

value: sciatic denervation


title: SAM612790


title: SAM612827


title: SAM612865


title: SAM613143


title: SAM612805


title: GCA1_ROI_10_well_C07

description:
DSP-1012340003501-F-C07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: RNA-seq denervation gastrocnemius 2 [DENV2]

tag: tissue

tag: strain


title: SAM612881


title: RNA-seq denervation gastrocnemius 1 [DENV1]


title: rABE, 1000 ng/ml dox, rep3

description: HEK293T cell with dox-inducible expression of rABE, 1000 ng/ul doxcycline, 48h

value: kidney

tag: cell line

tag: cell type

tag: genotype

value: rABE


title: RNA-seq normal gastrocnemius 3 [CTL3]

value: normal


title: SAM612889

tag: disease


title: GCA1_ROI_9_well_C06

description:
DSP-1012340003501-F-C06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Heart

tag: slide id

tag: roi number

tag: alignedreads

tag: deduplicatedreads


title: rABE, 1000 ng/ml dox, rep2

value: Human embryonic kidney

tag: treatment

value: 1000 ng/ml dox


title: RNA-seq normal gastrocnemius 2 [CTL2]

tag: Sex

tag: age


title: GCA1_ROI_8_well_C05

description:
DSP-1012340003501-F-C05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

value: DNA

tag: area

tag: roi x coordinate

tag: trimmedreads

tag: stitchedreads


title: APOBEC1, 1000 ng/ml dox, rep1

tag: tissue


title: GCA1_ROI_7_well_C04

description:
DSP-1012340003501-F-C04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: roi y coordinate

tag: rawreads

tag: sequencingsaturation


title: GCA1_ROI_6_well_C03

description:
DSP-1012340003501-F-C03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: RNA-seq normal gastrocnemius 1 [CTL1]

tag: strain


title: Hexb-CreER/CreER, oil 34_HEB88

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Hexb-CreER/CreER, oil
Hexb-CreER/CreER, oil

data_processing:
Aligned to mouse genome (mm10) using STAR spliced read aligner
Quantify the reads with htseq-count
Normalization and differential expression analysis using Bioconductor packages
Assembly: mm10
Supplementary files format and content: xlsx file with counts for each sample

source_name: Microglia

extract_protocol:
RNA was harvested using a phenol:chloroform extraction. RNA integrity was assessed on an Agilent 2100 Bioanalyzer and samples with RIN < 7 were excluded.
Libraries were prepared from the remaining samples using SMART-Seq v4 + Nextera XT and then sequenced on NovaSeq 6000 (Illumina) with PE 100X2.

treatment_protocol:
To induce CreER activity in adults, animals were injected once daily i.p. with 100 mg/kg tamoxifen Sigma T5648) dissolved 20 mg/mL in corn oil (Sigma C8267) on postnatal days 28, 29, 30, and 31.
10,000-50,000 microglia (DAPI- CD11b+ CD45Mid) were sorted per sample on a SONY MA800 or SONY MA900 into 1.5mL tubes containing 300µL Trizol LS reagent (Invitrogen)

value: Male

tag: cell type

value: Microglia

tag: genotype

value: Hexb(CreER/CreER)

value: Oil


title: rABE, 1000 ng/ml dox, rep1

tag: cell line


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Pax5(∆CRD1/-)_2

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438, 223632-223637,227407-227408,231740-42,231896-231899), and mm9 (samples 12521-15072).
ChIP-Seq and ATAC-Seq reads were aligned with Bowtie 1.0.0 (Langmead, B. et al. ,2009). Read coverages were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013].
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: bone marrow

extract_protocol:
NebNext UltraII RNA Library Prep Kit
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: In vitro pro-B cell


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Pax5(+/+)_2


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Pax5(∆CRD1/-)_1


title: GCA1_ROI_5_well_C02

description:
DSP-1012340003501-F-C02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number

tag: alignedreads

tag: deduplicatedreads


title: GCA1_ROI_4_well_C01

description:
DSP-1012340003501-F-C01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type


title: GCA1_ROI_3_well_B12

description:
DSP-1012340003501-F-B12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: area


title: SAM612852

tag: disease

value: OA


title: SAM612816


title: SAM613151

value: RA


title: Hexb-CreER/CreER, tamoxifen 33_HEB87

description:
Hexb-CreER/CreER, tamoxifen
Hexb-CreER/CreER, tamoxifen

tag: Sex

tag: treatment

value: Tamoxifen

tag: age


title: SAM618870


title: GCA1_ROI_2_well_B11

description:
DSP-1012340003501-F-B11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

tag: roi x coordinate

tag: roi y coordinate

tag: trimmedreads

tag: stitchedreads


title: SAM612819


title: Hexb-CreER/CreER, tamoxifen 32_HEB86

tag: cell type

tag: genotype


title: Hexb-CreER/CreER, tamoxifen 31_HEB83


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Input Pax5(∆CRD1,2/-)_1

tag: strain

value: Input Pax5({delta}CRD1,2/-)


title: Brg1 Ab ChIP-Seq bone marrow In vitro pro-B cell Input Pax5(∆CRD1/-)_1

value: Input Pax5({delta}CRD1/-)