title: RNAseq_KO_24h_rep1_TPM

status: Public on Mar 19 2024

city: Berlin

first: Maximilian

last: Stötzel

state: Berlin

address: Ihnestraße 65

department: Meissner

institute: Max-Planck-Institute for molecular genetics

data_processing:
RNAseq reads were pre-processed using cutadapt v2.4 to remove adapter and trim low quality bases.
Reads were subsequently aligned against the reference gnenome mm10 using STAR v2.7.3a (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie v2.0 was used for transcript quantification, e.g. calculation of strand-specific coverage, RPKMs and TPMs (reference: mm10 gencode gene annotation gtf). TPMs were normalized according to ERCC RNA Spike-In Mix (Thermo, 4456740) manufacturers information.
Assembly: mm10
Supplementary files format and content: tab delimited text file (.bed) <Reference> <Strand> <Start> <End> <Gene ID> <Gene Name> <TPM>

source_name: E14 TET1/2 DKO, 24 hours

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74004). Samples were spiked-in using ERCC RNA Spike-In Mix (Thermo, 4456740) and 500ng RNA was used as input for library preparacion. Library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (Roche, 8098131702) following manufacturer's instructions.

treatment_protocol: Cells were cultured without (0h) or in presence of the mTOR inhibitor Ink128 (24h, 72h, 144h)

value: embryonic stem cell

tag: cell line

value: E14 TET1/2 DKO

tag: treatment

value: mTORi


title: RNAseq_KO_N_rep2_TPM

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: E14 TET1/2 DKO, 0 hours

tag: tissue

value: control


title: RNAseq_KO_72h_rep2_TPM

source_name: E14 TET1/2 DKO, 72 hours


title: UKE_BCN_KGU #15

status: Public on Mar 20 2024

type: genomic

city: Hamburg

first: Richard

last: Drexler

address: Martinistraße 52

department: Neurosurgery

institute: Medical Center Hamburg-Eppendorf

description: SAMPLE 15

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
All idats corresponding to methylation array data were processed similarly using the minfi package in R (version 1.40.0).52 The data was processed using the preprocessIllumina function. Only probes with detection p-values <0.01 were kept for further analysis. Also, probes with <3 beads in at least 5% of samples, as well as all non-CpG probes, SNP-related probes, and probes located on X and Y chromosomes were discarded.
normalized data matrix contains: The CpG intensities were converted into beta values representing total methylation levels (between 0 and 1).
non-normalized data matrix contains: Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Glioblastoma

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted with the Maxwell® 16FFPE Plus LEV DNA Kit (Promega, Fitchburg, USA) and a Maxwell DNA extractor

value: Glioblastoma

tag: age at time of surgery (years)

tag: year of surgery

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]

tag: progression-free survival [months]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: RNAseq_KO_24h_rep2_TPM

tag: tissue

tag: cell line

tag: treatment


title: RNAseq_WT_72h_rep1_TPM

source_name: E14 wild-type, 72 hours

value: E14 wild-type


title: RNAseq_WT_72h_rep2_TPM


title: RNAseq_WT_24h_rep1_TPM

source_name: E14 wild-type, 24 hours


title: UKE_BCN_KGU #10

description: SAMPLE 10

tag: age at time of surgery (years)

tag: year of surgery

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)


title: WT_5d_3

status: Public on Jan 29 2024

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

data_processing:
Genome_build: genome of Arabidopsis thaliana TAIR10
genome mapping and counts of reads by gene locus are done with STAR/HTSeqcount; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts

organism: Arabidopsis thaliana

growth_protocol: Long day conditions: 16 h light from 6 am to 10 pm ½ MS solid media prepared with Murashige Skoog Basal Salts (Sigma M6899), 0.05% MES hydrate (Sigma M8250), pH adjusted to 5.70 with KOH (5 M), 0.5% agar type E (Sigma A4675). Autoclaved/ 60% hygrometry/ 23°C/ 180 µmol.m-².s-1

extract_protocol:
WT_5d_3(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: no treatment

tag: genotype

value: WT - mutant=knock-out,insertional mutagen,T-DNA-

tag: developmental stage

value: seedling,whole plant


title: WT_5d_2

extract_protocol:
WT_5d_2(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: RNAseq_WT_N_rep1_TPM

source_name: E14 wild-type, 0 hours


title: RNAseq_KO_N_rep1_TPM


title: RNAseq_WT_144h_rep2_TPM

source_name: E14 wild-type, 144 hours


title: UKE_BCN_KGU #5

description: SAMPLE 5

tag: frontal tumor location (0=no, 1=yes)

tag: parietal tumor location (0=no, 1=yes)

tag: temporal tumor location (0=no, 1=yes)

tag: occipital tumor location (0=no, 1=yes)

tag: hemisphere [1=left, 2=right, 3=both]

tag: extent of resection [1=gross total resection (100% ce removal), 2=near gross total resection (>90% ce removal), 3=partial resection or biopsy (<90% ce removal))


title: UKE_BCN_KGU #8

description: SAMPLE 8

tag: karnofsky performance status before starting chemo-radiotherapy [%]

tag: tumor progression [0=no, 1=yes, 2=n/a]

tag: progression-free survival [months]

tag: dead at last follow-up [0=no, 1=yes, 2=n/a]

tag: overall survival [months]

tag: neural-glioblastoma subgroup [0=low-neural, 1=high-neural]


title: WT_5d_1

extract_protocol:
WT_5d_1(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: tissue


title: WT_12d_2

growth_protocol: Long day conditions: 16 h light from 6 am to 10 pm (½ MS solid media prepared with Murashige Skoog Basal Salts (Sigma M6899), 0.05% MES hydrate (Sigma M8250), pH adjusted to 5.70 with KOH (5 M), 0.5% agar type E (Sigma A4675). Autoclaved 60% hygrometry 23°C 180 µmol.m-².s-1)

extract_protocol:
WT_12d_2(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

value: WT - mutant=knock-out,-


title: WT_12d_3

extract_protocol:
WT_12d_3(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT_12d_1

extract_protocol:
WT_12d_1(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: RNAseq_WT_24h_rep2_TPM

tag: cell line

tag: treatment


title: snap33_5d_3

extract_protocol:
snap33_5d_3(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: genotype

value: snap33 - mutant=knock-out,insertional mutagen,T-DNA-


title: RNAseq_WT_N_rep2_TPM


title: RNAseq_KO_72h_rep1_TPM


title: RNAseq_WT_144h_rep1_TPM


title: snap33_5d_1

extract_protocol:
snap33_5d_1(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: developmental stage


title: snap33_12d_3

extract_protocol:
snap33_12d_3(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: snap33_12d_2

extract_protocol:
snap33_12d_2(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: snap33_12d_1

extract_protocol:
snap33_12d_1(35ug)
rna_selection:selection polyA,single,3'seq, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: LO3_LN_RHIZO_ROOT_2

status: Public on Dec 13 2023

data_processing:
Genome_build: genome of Zeamays+Rhizophagus-irregularis(DAOM197198)
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

organism: Zea mays

growth_protocol: clay beads+peat Greenhouse

extract_protocol:
LO3_LN_RHIZO_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx

value: wild type (L03)

value: roots


title: LO3_LN_RHIZO_ROOT_3

extract_protocol:
LO3_LN_RHIZO_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_RHIZO_ROOT_1

extract_protocol:
LO3_LN_RHIZO_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_RHIZO_LEAF_3

extract_protocol:
LO3_LN_RHIZO_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx

value: leaf


title: LO3_LN_CTRL_ROOT_3

extract_protocol:
LO3_LN_CTRL_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_RHIZO_LEAF_2

extract_protocol:
LO3_LN_RHIZO_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_RHIZO_LEAF_1

extract_protocol:
LO3_LN_RHIZO_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_CTRL_ROOT_2

extract_protocol:
LO3_LN_CTRL_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_CTRL_LEAF_3

extract_protocol:
LO3_LN_CTRL_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_CTRL_LEAF_2

extract_protocol:
LO3_LN_CTRL_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_CTRL_LEAF_1

extract_protocol:
LO3_LN_CTRL_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_ROOT_3

extract_protocol:
LO3_HN_RHIZO_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_ROOT_1

extract_protocol:
LO3_HN_RHIZO_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_LN_CTRL_ROOT_1

extract_protocol:
LO3_LN_CTRL_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_LEAF_3

extract_protocol:
LO3_HN_RHIZO_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_ROOT_2

extract_protocol:
LO3_HN_RHIZO_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_LEAF_1

extract_protocol:
LO3_HN_RHIZO_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_RHIZO_LEAF_2

extract_protocol:
LO3_HN_RHIZO_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_CTRL_ROOT_2

extract_protocol:
LO3_HN_CTRL_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_CTRL_LEAF_3

extract_protocol:
LO3_HN_CTRL_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: snap33_5d_2

extract_protocol:
snap33_5d_2(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: LO3_HN_CTRL_ROOT_1

extract_protocol:
LO3_HN_CTRL_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_CTRL_LEAF_1

extract_protocol:
LO3_HN_CTRL_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_RHIZO_ROOT_3

growth_protocol: clay beads+peat greehouse

extract_protocol:
B73_LN_RHIZO_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx

value: wild type (B73)


title: LO3_HN_CTRL_LEAF_2

extract_protocol:
LO3_HN_CTRL_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_RHIZO_ROOT_1

extract_protocol:
B73_LN_RHIZO_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: LO3_HN_CTRL_ROOT_3

extract_protocol:
LO3_HN_CTRL_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_RHIZO_LEAF_3

extract_protocol:
B73_LN_RHIZO_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_RHIZO_ROOT_2

extract_protocol:
B73_LN_RHIZO_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_ROOT_3

extract_protocol:
B73_LN_CTRL_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_ROOT_2

extract_protocol:
B73_LN_CTRL_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_LEAF_2

extract_protocol:
B73_LN_CTRL_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_LEAF_3

extract_protocol:
B73_LN_CTRL_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_ROOT_1

extract_protocol:
B73_LN_CTRL_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_LN_CTRL_LEAF_1

extract_protocol:
B73_LN_CTRL_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_RHIZO_ROOT_2

extract_protocol:
B73_HN_RHIZO_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_RHIZO_ROOT_1

extract_protocol:
B73_HN_RHIZO_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_RHIZO_LEAF_3

extract_protocol:
B73_HN_RHIZO_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_RHIZO_LEAF_1

extract_protocol:
B73_HN_RHIZO_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_CTRL_ROOT_3

extract_protocol:
B73_HN_CTRL_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_RHIZO_LEAF_2

extract_protocol:
B73_HN_RHIZO_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_CTRL_ROOT_2

extract_protocol:
B73_HN_CTRL_ROOT_2(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: UKE_BCN_KGU #40

description: SAMPLE 40

extract_protocol: DNA was extracted with the Maxwell® 16FFPE Plus LEV DNA Kit (Promega, Fitchburg, USA) and a Maxwell DNA extractor

tag: age at time of surgery (years)

tag: year of surgery

tag: sex (0=male, 1=female)

tag: preoperative karnofsky performance status (%)

tag: frontal tumor location (0=no, 1=yes)

tag: mgmt promoter methylation status [0=non-methylated, 1=methylated]


title: B73_HN_CTRL_LEAF_1

extract_protocol:
B73_HN_CTRL_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_CTRL_LEAF_3

extract_protocol:
B73_HN_CTRL_LEAF_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: B73_HN_CTRL_LEAF_2

extract_protocol:
B73_HN_CTRL_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: N-sufficient_9

status: Public on Dec 01 2023

data_processing:
Genome_build: genome of TAIR 10
genome mapping and counts of reads by gene locus are done with STAR and featureCount; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,count_stranded

growth_protocol: Media=soil,Temperature=21°C DAY 19°C NIGHT, Light=15000LUX,soil water content 60%. After 3 days of stratification, the seeds were grown for 8 days in previous growth conditions, before the installation of the seedlings on the Phenoscope for 19 days. The water content was decreased to 60% over the first 4 days and then maintained to 60% for the rest of the experiment. In the Nitrogen-sufficient condition, the plants were watered with a solution containing 5mM of NO3.

extract_protocol:
N-sufficient_9(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf

treatment_protocol: NITROGEN_sufficient-environmental treatment-nitrogen concentration-nitrogenquantity 5mM time 19day

value: wild type (WT)

value: rosette


title: N-sufficient_7

data_processing:
Genome_build: genome of TAIR 10
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

extract_protocol:
N-sufficient_7(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-sufficient_8

extract_protocol:
N-sufficient_8(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: B73_LN_RHIZO_LEAF_1

extract_protocol:
B73_LN_RHIZO_LEAF_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: N-sufficient_6

extract_protocol:
N-sufficient_6(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: B73_LN_RHIZO_LEAF_2

extract_protocol:
B73_LN_RHIZO_LEAF_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: N-sufficient_5

extract_protocol:
N-sufficient_5(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-sufficient_4

extract_protocol:
N-sufficient_4(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-sufficient_2

extract_protocol:
N-sufficient_2(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-sufficient_1

extract_protocol:
N-sufficient_1(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-sufficient_3

extract_protocol:
N-sufficient_3(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_9

growth_protocol: Media=soil,Temperature=21°C DAY 19°C NIGHT, Light=15000LUX,soil water content 60%. After 3 days of stratification, the seeds were grown for 8 days in previous growth conditions, before the installation of the seedlings on the Phenoscope for 19 days. The water content was decreased to 60% over the first 4 days and then maintained to 60% for the rest of the experiment.

extract_protocol:
N-limiting_9(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf

treatment_protocol: NITROGEN_limited-environmental treatment-nitrogen concentration-nitrogenquantity 2.5mM time 19day  In the nitrogen-limiting conditions, the plants were watered with 0,8ml of a solution containing 2.5mM of NO3 and the complement (to 60% soil water content) was provided with a 0mM solution.


title: N-sufficient_10

extract_protocol:
N-sufficient_10(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: B73_HN_RHIZO_ROOT_3

extract_protocol:
B73_HN_RHIZO_ROOT_3(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: N-limiting_7

extract_protocol:
N-limiting_7(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_6

extract_protocol:
N-limiting_6(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_8

extract_protocol:
N-limiting_8(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_4

extract_protocol:
N-limiting_4(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_2

extract_protocol:
N-limiting_2(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_1

extract_protocol:
N-limiting_1(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: N-limiting_5

extract_protocol:
N-limiting_5(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: B73_HN_CTRL_ROOT_1

extract_protocol:
B73_HN_CTRL_ROOT_1(1ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:PT_Illumina_Stranded_mRNA_Ligation_Prep_Demi-volume_input250ng_B_17-11-2021.docx


title: 13B,rep2

status: Public on Nov 02 2023

city: La Jolla

first: Songpeng

last: Zu

state: CA

address: 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

country: USA

institute: University of California San Diego

library_source: genomic

data_processing:
Paired-end sequencing reads were demultiplexed and the cell index transferred to the read name. Sequencing reads were aligned to mm10 reference genome using bwa.
We combined the sequencing reads to fragments with the function make_fragment_file in SnapATAC2. , and for each fragment we followed the quality controls: 1) Keep only fragments with quality scores MAPQ > 30; 2) remove PCR duplicates. Reads were also sorted based on cell barcodes in read names, and shifted +4 bp for positive strand and -5 bp for negative strand to correct the 9-bp duplication induced from Tn5 transposase.
We used the function filter_cells in SnapATAC2 to calculate TSSenrichment (TSSe). Nuclei with >=1,000 uniquely mapped fragments and TSSe >= 10 were filtered for each of 234 samples by following the ENCODE ATAC-seq data standards and process pipeline(https://www.encodeproject.org/atac-seq/). We used the function filter_cells in SnapATAC2 to filter out cells.
We applied a modified version of Scrublet to remove potential doublets for every sample independently using SnapATAC2. Firstly, we used the function of add_tile_matrix to add the 500-bp genomic bin features, then used the function of select_features to filter out the features with the frequencies along the samples lower than 0.5% or higher than 99.5%. Then applied the function of scrublet in SnapATAC2 to get the doublet scores. The parameter expected_doublet_rate is set to 0.08, which is based on our previous experiment on the snATAC-seq pipeline. Barcodes with the scrublet scores larger than 0.5 will be treated as potential doublets, and then removed from our analysis.
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: SnapATAC2 HDF5 matrix files (cells with the raw fragments, 500bp bmat)

source_name: brain

extract_protocol:
Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56-63 day old mice and sectioned into 600 µm coronal sections along the anterior-posterior axis in ice-cold dissection media. Specific brain regions were dissected according to the Allen Brain Reference Atlas (Wang, Q. et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell (2020). https://doi.org:10.1016/j.cell.2020.04.007). For each region, dissected brain tissues were pooled from 2-31 male C57BL/6J mice  to obtain enough nuclei for single nucleus ATAC-seq for each biological replica, and two biological replicas were performed.
Brain nuclei were pelleted with a swinging bucket centrifuge (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT and cOmpleteTM, EDTA-free protease inhibitor cocktail (Roche) in PBS) and pelleted again (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei were resuspended in 500 μl high-salt tagmentation buffer (36.3 mM Tris-acetate (pH 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% dimethylformamide) and counted using a haemocytometer. Concentration was adjusted to 1,000–4,500 nuclei per 9 μl, and 1,000–4,500 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1 μl barcoded Tn5 transposomes26 were added using a BenchSmart 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μl of 40 mM EDTA was added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μl 2× sort buffer (2% BSA, 2 mM EDTA in PBS) were added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei were sorted per well into eight 96-well plates (total of 768 wells, 30,720 nuclei total, 15,360 nuclei per sample) containing 10.5 μl EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). If processing two samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together. Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After the addition of 1 μl 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). Then, 1 μl 12.5% Triton X-100 was added to each well to quench the SDS. Next, 12.5 μl NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added and samples were amplified by PCR (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72 °C 60 s) × 11 or 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life Technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries generated with indexing version 1 were sequenced on a HiSeq2500 sequencer (Illumina) using custom sequencing primers, 25% spike-in library and following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). Libraries generated with indexing version 2 were sequenced on a Libraries were sequenced on a HiSeq 4000 (Illumina) or a NovaSeq 6000 (Illumina) with these settings:  50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: brain

tag: tissue region

value: HPF

tag: strain

tag: number of_animals_pooled

tag: Sex

value: Male

tag: age

value: 8-9 weeks old

tag: library type

value: ATAC-seq


title: 7H,rep2

tag: tissue

value: AMY


title: N-limiting_10

extract_protocol:
N-limiting_10(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: 12E,rep2


title: 13D,rep2

value: MB


title: 14C,rep2

value: Pons


title: 13B,rep1


title: 14C,rep1


title: 13D,rep1


title: 9G,rep2


title: 12D,rep1


title: 9H,rep2


title: 9G,rep1


title: 8E,rep1


title: 9H,rep1


title: 8E,rep2


title: D5_UK_5

city: Rush

first: keith

last: nehrke

state: NY

address: 1514 Rush Scottsville Rd

department: Medicine

institute: University of Rochester Medical Center

description: At day 2, TGFb1was removed, replaced with new treatment as indicated, and cells were harvested three days later at day 5

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: Felis Catus 9.0, ensemble release 108
Supplementary files format and content: gene counts

molecule: polyA RNA

organism: Felis catus

source_name: cornea

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per manufacturers recommendations. RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NovaSeq6000 sequencer (Illumina, San Diego, CA) SP flow cell.

value: cornea

tag: cell type

value: fibroblast

value: UK-5099 (30 uM) biological replicate 5


title: N-limiting_3

extract_protocol:
N-limiting_3(3ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: D5_UK_4

tag: treatment

value: UK-5099 (30 uM) biological replicate 4


title: D5_UK_3

value: UK-5099 (30 uM) biological replicate 3


title: D5_UK_2

value: UK-5099 (30 uM) biological replicate 2


title: D5_UK_1

value: UK-5099 (30 uM) biological replicate 1


title: 11F,rep1


title: 12E,rep1


title: 7H,rep1


title: D5_Trog_4

value: Troglitazone (7.5 uM) biological replicate 4


title: 12D,rep2


title: 11F,rep2


title: D5_Trog_2

value: Troglitazone (7.5 uM) biological replicate 2


title: 2A,rep2

value: brain

value: Isocortex


title: 8H,rep2

value: Male


title: 8H,rep1

value: 8-9 weeks old


title: D5_Trog_3

value: Troglitazone (7.5 uM) biological replicate 3


title: D5_T_G_5

value: Troglitazone (7.5 uM) & GW9662 (10 uM) biological replicate 5


title: D5_Trog_1

value: Troglitazone (7.5 uM) biological replicate 1


title: D5_T_G_3

value: Troglitazone (7.5 uM) & GW9662 (10 uM) biological replicate 3


title: D5_T_G_1

value: cornea

value: Troglitazone (7.5 uM) & GW9662 (10 uM) biological replicate 1


title: D5_T_G_2

value: fibroblast

value: Troglitazone (7.5 uM) & GW9662 (10 uM) biological replicate 2


title: 8J,rep2

value: HPF

value: ATAC-seq


title: 11E,rep1


title: 8J,rep1


title: D5_T_G_4

value: Troglitazone (7.5 uM) & GW9662 (10 uM) biological replicate 4


title: 11E,rep2


title: D2_TGFb_4

description: As above, following two days of treatment with TFGb1

value: TGFb1 (1ng/ml) biological replicate 4


title: D2_TGFb_3

value: TGFb1 (1ng/ml) biological replicate 3


title: D2_TGFb_5

value: TGFb1 (1ng/ml) biological replicate 5


title: D5_Trog_5

value: Troglitazone (7.5 uM) biological replicate 5


title: D2_TGFb_2

value: TGFb1 (1ng/ml) biological replicate 2


title: 9J,rep1

value: brain

value: Male

value: 8-9 weeks old


title: D2_TGFb_1

value: TGFb1 (1ng/ml) biological replicate 1


title: D0_FB_5

description: 1x10^5 cells/cm2 in collagen-coated 3.5 cm dishes, harvested on day 0 following quiescence

value: untreated control biological replicate 5


title: D0_FB_4

value: cornea

value: untreated control biological replicate 4


title: D0_FB_2

value: fibroblast

value: untreated control biological replicate 2


title: D0_FB_3

value: untreated control biological replicate 3


title: 6E,rep2

value: STR

value: ATAC-seq


title: 6E,rep1


title: D0_FB_1

value: untreated control biological replicate 1


title: 4E,rep1


title: 4E,rep2


title: mtran1-2-2-1_2

status: Public on Sep 03 2023

data_processing:
Genome_build: genome of Arabidopsis thaliana TAIR10
genome mapping and counts of reads by gene locus are done with STAR and featureCounts; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,featureCounts-results

growth_protocol: Media

extract_protocol:
mtran1-2-2-1_2(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf

tag: genotype

value: double mutant AT4G15640-AT3G21465

value: seedling


title: 3A,rep2

value: Isocortex


title: mtran1-2-2-1_1

extract_protocol:
mtran1-2-2-1_1(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf

tag: developmental stage


title: mtran1-2-2-1_3

extract_protocol:
mtran1-2-2-1_3(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: Mini glandB1

status: Public on Aug 20 2023

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

country: China

institute: Westlake University

library_source: transcriptomic single cell

data_processing:
Raw reads were trimmed by TrimGalore with paired end mode and default parameter. Quality control was done with fastqc . Then UMI-tools was used to get the count matrix. Briefly, top 100 barcode list were retained using whitelist tool in UMI-tools . Then barcode and UMI information which were extracted from read2 using extract tool in UMI-tools was added to read1. After that, read1 were aligned to the mm10 genome using STAR with default parameter except that the outFilterMultimapNmax was set to 1. Finally, we got the count matrix file, in which the number of UMIs represents transcript number of each gene within each individual cell, using featurecounts and count tools in UMI-tools.
Assembly: mm10
Supplementary files format and content: count expression profile; singlecell barcode sequence

source_name: mini gland basal cell

extract_protocol:
Single cell RNA-seq: single CD49fhiEpCAMmedLin- cell from different age mice or tumor was directly sorted into 96-well plate containing lysis buffer using FACS. Single cell was immediately lysed at 70 degree for 3min in the PCR system.
Single cell RNA libraries were prepared for sequencing using 3’ UTR Smartseq protocols. The sample was reverse transcribed to cDNA using SuperScriptIIreverse transcriptase (invitrogen, 18064-071) with a template switch oligo (TSO) primer and a sample-specific 25 nt oligo dT reverse transcription primer. Then the cDNA was amplified by 16 cycles of PCR with 3’P2 primer and IS primer using KAPA HiFi HotStart Ready Mix (Kapa Biosystem, KK2602). The barcoded DNAs were amplified using biotinylated pre-index primers. After purified by AMpure XP beads, cDNA was sonicated to approximately 300 bp fragments using Covaris ME220.  3’ terminal of the cDNA was enriched using Dynabeads® MyOne Streptavidin C1 beads (Invitrogen, 65001). The RNA-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystem, KK8504) according to the manufacturer’s instructions.

value: mini gland

value: FVB


title: Mini glandB2


title: 5E,rep1

value: brain

value: Male


title: Mini glandL1

source_name: mini gland luminal cell


title: FVBL

source_name: mammary gland luminal cell

value: mammary gland luminal cell


title: FVBB

source_name: mammary gland basal cell

value: mammary gland basal cell


title: 2A,rep1

value: 8-9 weeks old


title: 3F,rep2


title: 5E,rep2


title: 3F,rep1


title: 483ppm_3

status: Public on Jul 27 2023

data_processing:
Genome_build: transcriptome of Brachypodium distachyon V3.1
transcriptome mapping and counts of reads by gene locus are done with bowtie2; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,gene_length,counts_SEreads,counts_PEreads

organism: Brachypodium distachyon

growth_protocol: Media ground hygrometry 65% Temperature 20 Light 175

extract_protocol:
483ppm_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Ambiant-environmental treatment-abiotic stress-co2quantity 430 time 3week  from sowing

value: wild type (WT)

value: aerial


title: 3000ppm_3

extract_protocol:
3000ppm_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: High CO2-2-environmental treatment-abiotic stress-co2quantity 3000 time 3week  from sowing


title: 3A,rep1


title: 3000ppm_2

extract_protocol:
3000ppm_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: 483ppm_2

extract_protocol:
483ppm_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Mini glandL2


title: 483ppm_1

extract_protocol:
483ppm_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT 1

extract_protocol:
WT_1(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf

value: wild type (wt)


title: 9J,rep2

value: HPF


title: 3000ppm_1

extract_protocol:
3000ppm_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: 1000ppm_1

extract_protocol:
1000ppm_1(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: High CO2-1-environmental treatment-abiotic stress-co2quantity 3000 time 3week  from sowing


title: 1000ppm_2

extract_protocol:
1000ppm_2(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: WT 3

extract_protocol:
WT_3(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: WT 2

extract_protocol:
WT_2(1ug)
rna_selection:ribosomal depletion, single, stranded:yes, Protocol:truseq-stranded-total-rna-sample-prep-guide-15031048-E.pdf


title: total, +4sU, 60min galactose, rep2 [T8]

city: Charlottesville

first: David

last: Auble

state: VA

address: 1349 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia Health System

description:
T8
Total8

data_processing:
Sequence reads were aligned to S. cerevisiae genome (R64-1-1) with HISAT2 (2.0.4) with parameter --rna-strandness RF.
Sequence reads were aligned to S. pombe genome (ASM294v2) with HISAT2 (2.0.4) with parameter --rna-strandness RF. Total number of mapped reads were recorded for normalization purposes.
Count extraction over S. cerevisiae genes (R64-1-1) was done using Rsubread (2.4.3) featureCounts function with parameters GTF.featureType=”gene”, GTF.attrType=”gene_id”, countMultiMappingReads=TRUE, strandSpecific=2, isPairedEnd=TRUE.
Normalized counts were obtained by dividing raw counts by S. pombe normalization factor: the total number of reads mapped to S. pombe divided by 2,000,000.
Synthesis rates were estimated with DTA R package: DTA.estimate function with parameters: tnumber=Sc.tnumber, check=TRUE, ccl = 150, mRNAs=60000, condition="real_data", ratiomethod="bias", and time in the phenomat object was set to 6.
Assembly: sacCer3
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes S. pombe - normalized counts for each sample

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: diploid

growth_protocol: For nascent RNA labelling, W303 cells were grown as for competition ChIP and induced with galactose for 20 or 60 minutes. An 800 ml culture in YEP +2% raffinose was grown at 30 °C to an OD600 of 0.6, then 57ml of 30% galactose was added. Twenty minutes after galactose addition, 400 ml of the culture was divided into 200 ml aliquots and 500 ml of 2M 4-thiouracil (4-sU, Sigma-Aldrich Cat# 440736-1G) was added to one of the flasks with vigorous mixing and returned to the shaking incubator for 6 minutes. Cells with and without 4-sU were pelleted and washed with TBS. At the 60 minute time point the remaining 400 ml culture was split and treated as described for the 20 minute timepoint culture. Two biological replicates were obtained for each condition. S. pombe cells were used as a spike-in normalization control. 100 ml of S. pombe cells were grown in YE media (0.5% yeast extract+3% glucose) to an OD600 of 0.6 and labelled by adding 125 ml of 2M 4-sU for 6 minutes and collected by centrifugation.

extract_protocol:
The S. cerevisiae W303 cells and S. pombe cells were mixed in an 8:1 ratio for each condition and RNA was isolated using the Ribopure Yeast Kit (Ambion Cat# AM1924). 40 mg of RNA was biotinylated with 4 mg of MTSEA Biotin XX (Biotium Cat# 90066). The biotinylated RNA was isolated by binding to 80 ml of a Dynabeads MyOne Streptavidin C1 bead suspension (Invitrogen Cat# 65001) by rotating the tube for 15 minutes, and the unbound supernatant was saved. The bound RNA was eluted in 50 ml of streptavidin elution buffer. The eluted RNA and the RNA in the flowthrough were purified and concentrated using RNeasy columns (Qiagen Cat# 74104).
Ribosomal RNA was depleted using the Ribo Minus Yeast module (Thermo Fisher Scientific Cat# 45-7013)  and libraries were constructed using the Ultra Directional RNA Library Prep Kit (NEBNext Cat# E74205) and Multiplex Oligos (NEBNext Cat# E73355).

value: diploid

tag: time in_galactose

value: 60 min

tag: 4su added

value: yes

tag: fraction

value: total

tag: biological replicate


title: total, +4sU, 60min galactose, rep1 [T6]

description:
T6
Total6


title: total, +4sU, 20min galactose, rep1 [T2]

description:
T2
Total2

value: 20 min


title: total, +4sU, 20min galactose, rep2 [T4]

description:
T4
Total4


title: total, -4sU, 60min galactose, rep2 [T7]

description:
T7
Total7

value: no


title: unlabeled, +4sU, 60min galactose, rep2 [U8]

description:
U8
Unlabeled8

value: unlabeled


title: total, -4sU, 60min galactose, rep1 [T5]

description:
T5
Total5


title: unlabeled, -4sU, 60min galactose, rep1 [U5]

description:
U5
Unlabeled5


title: unlabeled, +4sU, 20min galactose, rep2 [U4]

description:
U4
Unlabeled4


title: unlabeled, +4sU, 20min galactose, rep1 [U2]

description:
U2
Unlabeled2


title: total, -4sU, 20min galactose, rep2 [T3]

description:
T3
Total3


title: total, -4sU, 20min galactose, rep1 [T1]

description:
T1
Total1


title: unlabeled, +4sU, 60min galactose, rep1 [U6]

description:
U6
Unlabeled6


title: TFIIF-Myc, 60 min, ChIP [TF2FMyc60]

description:
MycTF2F60
myc_tfiif.txt

data_processing:
Reads were mapped to the sacSer3 reference genome using Bowtie2 (v2.2.6) with default settings.
Peaks of enrichment were identified using MACS2 (v2.1.0.20151222) applied to each of several early time point Myc datasets and using an input dataset as control and --nomodel --extsize 147.
Count tables were then generated by associating reads with the peak intervals using bedtools multicov.
Read counts were normalized in a three-step process. First, read counts in each peak and for each time point were normalized to the overall read depth. Next, read counts for the HA samples were normalized to the average relative levels of the factor of interest using the average values obtained from three independent western blots. Lastly, the normalized HA read count matrix was divided by the normalized Myc count matrix to yield the ratio count tables for mathematical modeling.
Assembly: sacCer3
Supplementary files format and content: tab delimited text files containing raw read counts

organism: Saccharomyces cerevisiae

extract_protocol:
The parental diploid strain W303 (Ralser et al., 2012) was used to generate all of the competition ChIP strains. For each GTF, one allele was N-terminally tagged with 3xHA and placed under the control of an inducible GAL1 promoter. The other allele was N-terminally tagged with 9xMyc and remained under the control of the endogenous promoter (Longtine et al., 1998). For construction of the GAL1-induced alleles, the plasmid pFA6-His3MX6-PGAL1-3HA (RRID:Addgene_41610, ref. (Longtine et al., 1998)) was used to obtain the HisMX6-PGAL1-3HA cassette by PCR amplification and was integrated into the genome using standard yeast molecular biology techniques. For the GTFs TFIIA, TFIIE, and TFIIF which consist of two subunits, one copy of each subunit was placed under GAL1 control to ensure balanced expression of the competitor isoform. Following integration of the HIS3-GAL1-3HA cassette at one gene subunit, the strain was transformed with the TRP1-GAL1 cassette from pFA6-TRP1-PGAL1 (RRID:Addgene_41606, ref. (Longtine et al., 1998)), placing the second subunit under GAL1 control but without an epitope tag. The 9xMyc tag was integrated into the genome of another isolate of W303 using the integration and Cre-recombinase knockout method and reagents developed by Gauss et al (Gauss et al., 2005). The 9xMyc tag and loxP-flanked KanMX6 marker were PCR amplified from pOM20 and integrated into the yeast genome using standard methods as above. The KanMX6 marker was then then deleted using the GAL-inducible Cre recombinase carried on the plasmid pSH47 (Güldener et al., 1996). The Myc-tagged strains were then transformed with pRS319 (RRID:Addgene_35459, ref. (Sikorski & Hieter, 1989)) to introduce a LEU3 marker for selection. In subsequent steps, diploid strains with HA- or Myc-tagged alleles were sporulated and haploid segregants were mated to yield the competition ChIP (CC) strains with different tags on each of the alleles for the GTF of interest. Proper integration and function of the targeted alleles were confirmed for all strains by PCR, Western blotting using anti-HA or anti-Myc antibodies, and targeted DNA sequencing of the modified loci. Each competition ChIP (CC) strain was inoculated in 100 ml YEP+2% raffinose at 30 °C and incubated overnight. These starter cultures were then used the next day to inoculate 2,250 ml cultures of YEP+2% raffinose at an initial OD600 of 0.05. When an OD of 0.6 was reached, for the 0 minute timepoint 250 ml of the culture was crosslinked by adding 6.75 ml formaldehyde (Thermo Fisher Scientific Cat# F79-500) to achieve a final concentration of 1% for 20 minutes. The reaching was then quenched by adding 15 ml of 2.5M glycine for 5 minutes and the cells were collected by centrifugation. To the rest of the 2,000 ml culture, 142.8 ml of 30% galactose was added to yield a final concentration of 2%. At 10, 20, 25, 30, 40, 60, 90, and 120 minute time points, 250 ml of the culture was collected, crosslinked, and quenched as for the 0 min time point. Cell pellets were washed 3 times with TBS buffer (40 mM Tris-HCl, pH 7.5 plus 300 mM NaCl) and ChIP was performed as described (Viswanathan et al., 2014). The HA and Myc antibodies used for ChIP were the same as those used for western blotting described above. Successful ChIP was confirmed by RT-PCR using primers to detect binding to the URA3 promoter (5’-AAGATGCCCATCACCAAAA-3’ and 5’-AAGAATACCGGTTCCCGATG-3’).
ChIP-seq libraries were prepared following the manufacturer’s instructions using the Illumina TruSeq ChIP library prep kit set A and B (Cat# IP-202-1012 and IP-202-1024). Successful amplification was confirmed by RT-PCR using the URA3 promoter primers. Library quality was assessed using an Agilent Bioanalyzer 2100 and the Agilent-1000 DNA kit (Agilent Cat# 5067-1504), and libraries were quantified using the Qubit dsDNA Quantitation, High Sensitivity kit (Cat# Q32851). A 5nM pool of each library was sequenced on by the UVA Genome Analysis and Technology Core (RRID:SCR_018883) using Illumina NextSeq500 and NextSeq2000 instruments.

tag: target

value: TFIIF

tag: tag

value: Myc

tag: promoter

value: constitutive

tag: time


title: TFIIF-Myc, 90 min, ChIP [TF2FMyc90]

description:
MycTF2F90
myc_tfiif.txt

tag: strain

value: 90 min


title: TFIIF-Myc, 120 min, ChIP [TF2FMyc120]

description:
MycTF2F120
myc_tfiif.txt

value: 120 min


title: unlabeled, -4sU, 20min galactose, rep2 [U3]

description:
U3
Unlabeled3


title: 1000ppm_3

extract_protocol:
1000ppm_3(3ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: labeled, +4sU, 60min galactose, rep2 [L8]

description:
L8
Labeled8

value: labeled


title: labeled, +4sU, 60min galactose, rep1 [L6]

description:
L6
Labeled6


title: unlabeled, -4sU, 20min galactose, rep1 [U1]

description:
U1
Unlabeled1


title: labeled, -4sU, 60min galactose, rep2 [L7]

description:
L7
Labeled7


title: labeled, +4sU, 20min galactose, rep1 [L2]

description:
L2
Labeled2


title: labeled, -4sU, 60min galactose, rep1 [L5]

description:
L5
Labeled5


title: TFIIF-Myc, 40 min, ChIP [TF2FMyc40]

description:
MycTF2F40
myc_tfiif.txt

value: 40 min


title: labeled, +4sU, 20min galactose, rep2 [L4]

description:
L4
Labeled4


title: labeled, -4sU, 20min galactose, rep2 [L3]

description:
L3
Labeled3


title: TFIIF-Myc, 30 min, ChIP [TF2FMyc30]

description:
MycTF2F30
myc_tfiif.txt

value: 30 min


title: labeled, -4sU, 20min galactose, rep1 [L1]

description:
L1
Labeled1


title: TFIIF-Myc, 20 min, ChIP [TF2FMyc20]

description:
MycTF2F20
myc_tfiif.txt


title: unlabeled, -4sU, 60min galactose, rep2 [U7]

description:
U7
Unlabeled7


title: TF2F-Myc, 0 min, ChIP [TF2FMyc0]

value: 0 min


title: TFIIF-Myc, 25 min, ChIP [TF2FMyc25]

description:
MycTF2F25
myc_tfiif.txt

value: 25 min


title: TFIIF-Input, 60 min [TF2FInput60]

value: diploid

value: none-input


title: TFIIF-HA, 120 min, ChIP [TF2FHA120]

description:
HATF2F120
ha_tfiif.txt

value: HA

value: inducible


title: TFIIF-Myc, 10 min, ChIP [TF2FMyc10]

description:
MycTF2F10
myc_tfiif.txt

value: 10 min


title: TFIIF-HA, 40 min, ChIP [TF2FHA40]

description:
HATF2F40
ha_tfiif.txt


title: TFIIF-HA, 30 min, ChIP [TF2FHA30]

description:
HATF2F30
ha_tfiif.txt


title: TFIIF-HA, 25 min, ChIP [TF2FHA25]

description:
HATF2F25
ha_tfiif.txt


title: TFIIF-HA, 90 min, ChIP [TF2FHA90]

description:
HATF2F90
ha_tfiif.txt


title: TFIIF-HA, 20 min, ChIP [TF2FHA20]

description:
HATF2F20
ha_tfiif.txt


title: TFIIF-HA, 60 min, ChIP [TF2FHA60]

description:
HATF2F60
ha_tfiif.txt

value: 60 min


title: TFIIB-Myc, 40 min, ChIP [TF2BMyc40]

description:
TF2BMyc40
myc_tfiib.txt

value: TFIIB


title: TFIIB-Myc, 90 min, ChIP [TF2BMyc90]

description:
TF2BMyc90
myc_tfiib.txt


title: TFIIB-Myc, 30 min, ChIP [TF2BMyc30]

description:
TF2BMyc30
myc_tfiib.txt


title: TFIIB-Myc, 120 min, ChIP [TF2BMyc120]

description:
TF2BMyc120
myc_tfiib.txt


title: TFIIB-Myc, 0 min, ChIP [TF2BMyc0]

description:
TF2BMyc0
myc_tfiib.txt


title: TFIIB-Myc, 10 min, ChIP [TF2BMyc10]

description:
TF2BMyc10
myc_tfiib.txt


title: TFIIB-Myc, 25 min, ChIP [TF2BMyc25]

description:
TF2BMyc25
myc_tfiib.txt


title: TFIIB-Input, 25 min [TF2BInput25]


title: TFIIB-HA, 120 min, ChIP [TF2BHA120]

description:
TF2BHA120
ha_tfiib.txt


title: TFIIB-HA, 90 min, ChIP [TF2BHA90]

description:
TF2BHA90
ha_tfiib.txt


title: TFIIB-HA, 60 min, ChIP [TF2BHA60]

description:
TF2BHA60
ha_tfiib.txt


title: TFIIB-Myc, 60 min, ChIP [TF2BMyc60]

description:
TF2BMyc60
myc_tfiib.txt


title: TFIIB-Myc, 20 min, ChIP [TF2BMyc20]

description:
TF2BMyc20
myc_tfiib.txt


title: TFIIB-HA, 25 min, ChIP [TF2BHA25]

description:
TF2BHA25
ha_tfiib.txt


title: TFIIB-HA, 30 min, ChIP [TF2BHA30]

description:
TF2BHA30
ha_tfiib.txt


title: TFIIB-HA, 40 min, ChIP [TF2BHA40]

description:
TF2BHA40
ha_tfiib.txt


title: TBP-Myc, 90 min, ChIP [TBPMyc90]

description:
TBPMyc90
myc_tbp.txt

value: TBP


title: TBP-Myc, 120 min, ChIP [TBPMyc120]

description:
TBPMyc120
myc_tbp.txt

value: Myc


title: TBP-Myc, 30 min, ChIP [TBPMyc30]

description:
TBPMyc30
myc_tbp.txt

value: constitutive


title: TBP-Myc, 40 min, ChIP [TBPMyc40]

description:
TBPMyc40
myc_tbp.txt


title: TBP-Myc, 20 min, ChIP [TBPMyc20]

description:
TBPMyc20
myc_tbp.txt


title: TBP-Myc, 25 min, ChIP [TBPMyc25]

description:
TBPMyc25
myc_tbp.txt


title: TBP-Myc, 0 min, ChIP [TBPMyc0]


title: TFIIB-Input, 60 min [TF2BInput60]


title: TBP-Input, 60 min [TBPInput60]


title: TBP-Myc, 10 min, ChIP [TBPMyc10]

description:
TBPMyc10
myc_tbp.txt


title: TBP-Input, 25 min [TBPInput25]


title: TBP-HA, 120 min, ChIP [TBPHA120]

description:
TBPHA120
ha_tbp.txt


title: TFIIF-Input, 25 min [TF2FInput25]


title: TFIIF-HA, 10 min, ChIP [TF2FHA10]

description:
HATF2F10
ha_tfiif.txt

value: TFIIF


title: TBP-HA, 40 min, ChIP [TBPHA40]

description:
TBPHA40
ha_tbp.txt


title: TBP-HA, 60 min, ChIP [TBPHA60]

description:
TBPHA60
ha_tbp.txt


title: TBP-HA, 90 min, ChIP [TBPHA90]

description:
TBPHA90
ha_tbp.txt

value: 90 min


title: TBP-HA, 20 min, ChIP [TBPHA20]

description:
TBPHA20
ha_tbp.txt


title: TBP-HA, 10 min, ChIP [TBPHA10]

description:
TBPHA10
ha_tbp.txt


title: TFIIB-HA, 20 min, ChIP [TF2BHA20]

description:
TF2BHA20
ha_tfiib.txt


title: TFIIE-Myc, 90 min, ChIP [TF2EMyc90]

description:
MycTF2E90
myc_tfiie.txt

value: TFIIE


title: TFIIB-HA, 10 min, ChIP [TF2BHA10]

description:
TF2BHA10
ha_tfiib.txt


title: TFIIE-Myc, 120 min, ChIP [TF2EMyc120]

description:
MycTF2E120
myc_tfiie.txt

value: 120 min


title: TBB-HA, 30 min, ChIP [TBPHA30]

description:
TBPHA30
ha_tbp.txt

value: 30 min


title: TBP-Myc, 60 min, ChIP [TBPMyc60]

description:
TBPMyc60
myc_tbp.txt


title: TFIIE-Myc, 20 min, ChIP [TF2EMyc20]

description:
MycTF2E20
myc_tfiie.txt


title: TFIIE-Myc, 25 min, ChIP [TF2EMyc25]

description:
MycTF2E25
myc_tfiie.txt


title: TFIIE-Input, 25 min [TF2EInput25]


title: TFIIE-Myc, 40 min, ChIP [TF2EMyc40]

description:
MycTF2E40
myc_tfiie.txt

value: 40 min


title: TFIIE-HA, 120 min, ChIP [TF2EHA120]

description:
HATF2E120
ha_tfiie.txt


title: TFIIE-Myc, 30 min, ChIP [TF2EMyc30]

description:
MycTF2E30
myc_tfiie.txt


title: TFIIE-Input, 60 min [TF2EInput60]


title: TFIIE-HA, 90 min, ChIP [TF2EHA90]

description:
HATF2E90
ha_tfiie.txt


title: TFIIE-Myc, 0 min, ChIP [TF2EMyc0]

value: 0 min


title: TFIIE-Myc, 10 min, ChIP [TF2EMyc10]

description:
MycTF2E10
myc_tfiie.txt

value: diploid


title: TFIIE-HA, 40 min, ChIP [TF2EHA40]

description:
HATF2E40
ha_tfiie.txt


title: TFIIE-HA, 60 min, ChIP [TF2EHA60]

description:
HATF2E60
ha_tfiie.txt


title: TFIIE-HA, 10 min, ChIP [TF2EHA10]

description:
HATF2E10
ha_tfiie.txt


title: TFIIE-HA, 30 min, ChIP [TF2EHA30]

description:
HATF2E30
ha_tfiie.txt


title: TBP-HA, 25 min, ChIP [TBPHA25]

description:
TBPHA25
ha_tbp.txt

value: 25 min


title: TFIIE-HA, 20 min, ChIP [TF2EHA20]

description:
HATF2E20
ha_tfiie.txt

value: HA


title: TFIIA-Myc, 120, ChIP [TF2AMyc120]

description:
TF2AMyc120
myc_tfiia.txt

value: TFIIA


title: TFIIA-Myc, 90 min, ChIP [TF2AMyc90]

description:
TF2AMyc90
myc_tfiia.txt


title: TFIIA-Myc, 60 min, ChIP [TF2AMyc60]

description:
TF2AMyc60
myc_tfiia.txt


title: TFIIA-Myc, 25 min, ChIP [TF2AMyc25]

description:
TF2AMyc25
myc_tfiia.txt


title: TFIIA-Myc, 40 min, ChIP [TF2AMyc40]

description:
TF2AMyc40
myc_tfiia.txt


title: TFIIA-Myc, 30 min, ChIP [TF2AMyc30]

description:
TF2AMyc30
myc_tfiia.txt


title: TFIIA-Myc, 10 min, ChIP [TF2AMyc10]

description:
TF2AMyc10
myc_tfiia.txt

value: 10 min


title: TFIIA-Myc, 20 min, ChIP [TF2AMyc20]

description:
TF2AMyc20
myc_tfiia.txt


title: TFIIE-Myc, 60 min, ChIP [TF2EMyc60]

description:
MycTF2E60
myc_tfiie.txt

value: 60 min


title: TFIIA-Myc, 0 min, ChIP [TF2AMyc0]


title: TFIIA-Input, 60 min [TF2AInput60]

value: none-input


title: TFIIA-HA, 40 min, ChIP [TF2AHA40]

description:
TF2AHA40
ha_tfiia.txt

value: inducible


title: TFIIA-Input, 25 min [TF2AInput25]


title: TFIIA-HA, 10 min, ChIP [TF2AHA10]

description:
TF2AHA10
ha_tfiia.txt


title: TFIIA-HA, 25 min, ChIP [TF2AHA25]

description:
TF2AHA25
ha_tfiia.txt


title: TFIIA-HA, 30 min, ChIP [TF2AHA30]

description:
TF2AHA30
ha_tfiia.txt


title: TFIIA-HA, 60 min, ChIP [TF2AHA60]

description:
TF2AHA60
ha_tfiia.txt


title: TFIIA-HA, 20 min, ChIP [TF2AHA20]

description:
TF2AHA20
ha_tfiia.txt


title: TFIIE-HA, 25 min, ChIP [TF2EHA25]

description:
HATF2E25
ha_tfiie.txt


title: S-2P- B cell v2M6 Rep2 - VDJ

status: Public on Jul 07 2023

city: Bethesda

first: Susan

last: Moir

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: 10x Genomics

data_processing:
The GEX and ADT libraries were mapped to the GRCh38 human reference genome using CellRanger version 6.0.1. Data were further processed using Seurat version 4.1.0 running in R v4.1.0.
B cell receptor V(D)J data processing, B cell receptor (BCR) V(D)J repertoire data processing and analysis were carried out using tools in the Immcantation framework (www.immcantation.org). V(D)J genes were re-assigned from CellRanger output using IgBLAST v.1.15.0. Cells with multiple IGH V(D)J sequences were assigned to the most abundant IGH V(D)J sequence by UMI count. Following V(D)J gene annotation, non-functional sequences were removed from further analysis, and functional V(D)J sequences were assigned into clonal groups using Change-O v.1.0.0. Then, the immune repertoire information was added into Seurat object as meta data integrated to the transcriptome information at a per-cell level.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, antibody feature reference csv files

extract_protocol:
B cells of three vaccinees were isolated from thawed cryopreserved peripheral blood mononuclear cells (PBMC) by negative magnetic bead-based selection using a B cell enrichment cocktail (StemCell Technologies). The isolated B cells were stained with PE-Cy7-conjugated anti-human CD19 (ThermoFisher, cat# 25-0198-42) and APC-H7-conjugated anti-human CD20 (BD Biosciences, cat# 560734). SARS-CoV-2-specific B cells were identified using biotinylated spike protein (S-2P) tetramerized with PE-Cy5.5-labeled streptavidin (SA) (ThermoFisher, cat# SA1018) at a molar ratio of 4:1. Three B cell populations were sorted, (1) CD20+S-2P+ B cell, (2) CD20+S-2P-  B cell, and (3) CD20- B cell (plasmablast) populations, using a BD FACSAria Fusion instrument (BD Biosciences).
Isolated B cells from different donors were pooled evenly before cell sorting. Cells from each donor were demultiplexed in silico using donor-specific single nucleotide polymorphism (SNP) information collected during data analysis. Multiple cell pools were prepared, such that cells from the same donors but different time points were in different pools. After cell sorting, cell pools from v2D28 and v2M6 timepoints were Fc blocked (Human TruStain FcX, BioLegend), CITE-seq and hashtag stained with custom TotalSeq-C cocktail antibodies, (including RBD and S1 oligo-tagged tetramers, and washed 3x with staining buffer (2% BSA in PBS). Due to the lower frequency of S-2P+ B cells at earlier time points, pools from v1D14 to v2D14 timepoints were CITE-seq and hashtag (HTO) stained before cell sorting to avoid cell loss during washes. No RBD and S1 oligo-tagged tetramers could be added due to technical reasons. Final cell pools were suspended in 0.04% BSA in PBS and then counted before being immediately processed by the single cell partitioning step. Cell pools were mixed with a reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using the 10x Chromium Single Cell Immune Profiling Next GEM v2 Chemistry Kit (10x Genomics, Pleasanton, CA). The RT step was conducted using a C1000 touch Thermo Cycler (BioRad, Hercules, CA). Single-cell gene expression (GEX), cell surface protein (ADT) and B cell receptor (BCR) libraries were prepared as instructed by 10x Genomics Single Cell Immune Profiling kit v.2 user guide. A total of 84 libraries were quality control tested using a TapeStation 4200 (Agilent, Santa Clara, CA) and quantified using the KAPA Library Quantification kit (Roche, Wilmington, MA). These libraries were then pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics user guide. The minimum sequencing depths were 50,000 read pairs/cell for the GEX library, 5,000 read pairs/cell for the BCR library, and 5,000 read pairs/cell for the ADT library. Sequencing saturation of the libraries was 80% for the GEX and 10% for the BCR and ADT libraries.

value: S-2P- B cell

tag: timepoint


title: Plasmablast v1D14 Rep1 - VDJ

description: 10x Genomics

value: Plasmablast


title: Plasmablast v1D14 Rep2 - VDJ

description: 10x Genomics


title: S-2P+ B cell v1D14 - VDJ

description: 10x Genomics

value: S-2P+ B cell


title: Plasmablast v2D6 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2M6 Rep1 - VDJ

description: 10x Genomics


title: TFIIA-HA, 120 min, ChIP [TF2AHA120]

description:
TF2AHA120
ha_tfiia.txt


title: S-2P+ B cell v2M6 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v1D14 Rep2 - VDJ

description: 10x Genomics


title: Plasmablast v2D6 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2M6 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v1D14 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D6 Rep1 - VDJ

description: 10x Genomics


title: TFIIA-HA, 90 min, ChIP [TF2AHA90]

description:
TF2AHA90
ha_tfiia.txt

value: 90 min


title: S-2P+ B cell v2D9 Rep2 - VDJ

description: 10x Genomics


title: Plasmablast v2D9 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D9 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D9 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D14 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D14 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D28 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep2 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep1 - VDJ

description: 10x Genomics


title: ID21, CTL,

status: Public on May 26 2023

city: Manhasset

first: Ona

last: Bloom

state: New York

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institute

data_processing:
Partek Genomics Flow software
trimmed reads aligned to hg38 genome assembly using STAR
filtered for expression >50
normalized using the Trimmed Mean of M-values (TMM) method using the edgeR package
log2 transformed
Assembly: hg38

source_name: Whole blood

extract_protocol:
Total RNA was isolated using the PAXgene total RNA kit and the Qiagen QIAcube, acccording to manufacturer's protocol
RNA seq libraries were prepared using Illumina TruSeq Stranded Total RNA according to manufacturer's instructions.

value: Whole blood

tag: group

value: CTL


title: S-2P+ B cell v2D14 Rep2 - VDJ

description: 10x Genomics


title: ID14, CTL,


title: S-2P- B cell v2D6 Rep2 - VDJ

description: 10x Genomics


title: ID13, CTL,


title: ID19, CTL,


title: ID9v0, SCI,  Acute

value: SCI

value: Acute


title: ID7v0, SCI,  Acute


title: ID18, CTL,


title: ID17, CTL,


title: ID16, CTL,


title: ID2v0, SCI, Acute


title: ID15, CTL,


title: D30, DDX5 iKO SPL P14 CD8+ T cells ADT

status: Public on May 23 2023

city: San Diego

first: John

last: Chang

address: UCSD

institute: UC San Diego

description:
D30_SPL_KO_barcodes.tsv.gz
D30_SPL_KO_features.tsv.gz
D30_SPL_KO_matrix.mtx.gz

library_source: other

data_processing:
Cell Ranger (v6.0.1) was used to process sequencing information and single cell barcodes.
Gene and cell filtering, clustering, differential and average expression using Seurat (v4.1.1)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Spleen

extract_protocol:
Control and Ddx5cKO CD8+ T cells were harvested from the spleen at days 4, 7, and 30 post-infection, FACS isolated, and prepared for single-cell libraries.
Single-cell RNA libraries were prepared according to the 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) User Guide and sequenced on a HiSeq 4000 (Illumina)

value: Spleen

value: CD8+ T cells

tag: library type

value: ADT

value: DDX5 iKO, CD8+

tag: antibodies/tags


title: D30, Control SPL P14 CD8+ T cells ADT

description:
D30_SPL_WT_barcodes.tsv.gz
D30_SPL_WT_features.tsv.gz
D30_SPL_WT_matrix.mtx.gz

tag: tissue

tag: cell type

value: Control


title: ID1v0, SCI, Acute

tag: treatment


title: ID20, CTL,


title: S-2P+ B cell v2D6 Rep1 - VDJ

description: 10x Genomics


title: ID10v0, SCI, Acute


title: S-2P+ B cell v2D6 Rep2 - VDJ

description: 10x Genomics


title: D30, Control SPL P14 CD8+ T cells RNA

value: RNA

tag: genotype


title: D4, DDX5 iKO SPL P14 CD8+ T cells RNA

description:
D4_SPL_KO_barcodes.tsv.gz
D4_SPL_KO_features.tsv.gz
D4_SPL_KO_matrix.mtx.gz


title: D4, DDX5 iKO SPL P14 CD8+ T cells ADT


title: ID5v0, SCI,  Acute


title: ID4v0, SCI, Acute


title: D4, Control SPL P14 CD8+ T cells RNA

description:
D4_SPL_WT_barcodes.tsv.gz
D4_SPL_WT_features.tsv.gz
D4_SPL_WT_matrix.mtx.gz


title: ID8v0, SCI, Acute


title: ID6v0, SCI, Acute


title: D30, DDX5 iKO SPL P14 CD8+ T cells RNA


title: D7, Control SPL P14 CD8+ T cells ADT

description:
D7_SPL_WT_barcodes.tsv.gz
D7_SPL_WT_features.tsv.gz
D7_SPL_WT_matrix.mtx.gz


title: ID3v0, SCI,  Acute


title: D7, DDX5 iKO SPL P14 CD8+ T cells ADT

description:
D7_SPL_KO_barcodes.tsv.gz
D7_SPL_KO_features.tsv.gz
D7_SPL_KO_matrix.mtx.gz


title: 9721367027_R01C01

status: Public on Mar 31 2023

city: Buffalo

first: Yao

last: Song

address: Carlton House - A349, Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing:
The raw intensity IDATfiles were extracted using GenomeStudio,and processed by the minfi R package
Processed data file contains: Average Beta

label: Cy5 and Cy386

source_name: FFPE breast tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

value: breast tumor

tag: Sex

value: Female


title: 9721367006_R06C02

description: Tumor

label: Cy5 and Cy385


title: 9721367027_R01C02

description: Tumor

label: Cy5 and Cy387


title: D7, DDX5 iKO SPL P14 CD8+ T cells RNA


title: 9721367006_R04C02

description: Tumor

label: Cy5 and Cy381


title: D4, Control SPL P14 CD8+ T cells ADT


title: D7, Control SPL P14 CD8+ T cells RNA


title: 9721367027_R02C02

description: Tumor

label: Cy5 and Cy389


title: 9721367006_R04C01

description: Tumor

label: Cy5 and Cy380


title: 9721367027_R02C01

description: Tumor

label: Cy5 and Cy388


title: 9721367006_R03C02

description: Tumor

label: Cy5 and Cy379


title: 9721367006_R05C02

description: Tumor

label: Cy5 and Cy383


title: 9721367006_R05C01

description: Tumor

label: Cy5 and Cy382


title: 9721367006_R03C01

description: Tumor

label: Cy5 and Cy378


title: 9721367027_R03C02

description: Tumor

label: Cy5 and Cy391


title: 9721367006_R02C01

description: Tumor

label: Cy5 and Cy377


title: 9721366156_R06C02

description: Tumor

label: Cy5 and Cy374


title: 9721367006_R01C01

description: Tumor

label: Cy5 and Cy375


title: 9721366156_R04C02

description: Tumor

label: Cy5 and Cy371


title: 9721367006_R01C02

description: Tumor

label: Cy5 and Cy376


title: 9721366156_R03C01

description: Tumor

label: Cy5 and Cy368


title: 9721366156_R06C01

description: Tumor

label: Cy5 and Cy373


title: 9721366156_R05C01

description: Tumor

label: Cy5 and Cy372


title: 9721366156_R02C02

description: Tumor

label: Cy5 and Cy367


title: 9721366156_R02C01

description: Tumor

label: Cy5 and Cy366


title: 9721366156_R01C02

description: Tumor

label: Cy5 and Cy365


title: 9721366156_R04C01

description: Tumor

label: Cy5 and Cy370


title: 9721366155_R05C01

description: Tumor

label: Cy5 and Cy361


title: 9721366156_R01C01

description: Tumor

label: Cy5 and Cy364


title: 9721366155_R06C02

description: Tumor

label: Cy5 and Cy363


title: 9721366155_R03C01

description: Tumor

label: Cy5 and Cy357


title: 9721366155_R03C02

description: Tumor

label: Cy5 and Cy358


title: 9721366156_R03C02

description: Tumor

label: Cy5 and Cy369


title: 9721366155_R04C01

description: Tumor

label: Cy5 and Cy359


title: 9721366155_R01C02

description: Tumor

label: Cy5 and Cy354


title: 9721366141_R02C02

description: Tumor

label: Cy5 and Cy348


title: 9721366141_R03C02

description: Tumor

label: Cy5 and Cy350


title: 9721366141_R01C01

description: Tumor

label: Cy5 and Cy345


title: 9721366140_R06C02

description: Tumor

label: Cy5 and Cy344


title: 9721366155_R06C01

description: Tumor

label: Cy5 and Cy362


title: 9721366155_R04C02

description: Tumor

label: Cy5 and Cy360


title: 9721366155_R02C01

description: Tumor

label: Cy5 and Cy355


title: 9721366155_R02C02

description: Tumor

label: Cy5 and Cy356


title: 9721366140_R05C01

description: Tumor

label: Cy5 and Cy341


title: 9721366140_R05C02

description: Tumor

label: Cy5 and Cy342


title: 9721366155_R01C01

description: Tumor

label: Cy5 and Cy353


title: 9721366141_R05C01

description: Tumor

label: Cy5 and Cy352


title: 9721366140_R04C02

description: Tumor

label: Cy5 and Cy340


title: 9721366141_R04C02

description: Tumor

label: Cy5 and Cy351


title: 9721366140_R03C01

description: Tumor

label: Cy5 and Cy337


title: 9721366140_R03C02

description: Tumor

label: Cy5 and Cy338


title: 9721366140_R02C02

description: Tumor

label: Cy5 and Cy336


title: 9721366141_R03C01

description: Tumor

label: Cy5 and Cy349


title: 9721366122_R06C02

description: Tumor

label: Cy5 and Cy333


title: 9721366140_R02C01

description: Tumor

label: Cy5 and Cy335


title: 9721366122_R05C02

description: Tumor

label: Cy5 and Cy332


title: 9721366141_R02C01

description: Tumor

label: Cy5 and Cy347


title: 9721366141_R01C02

description: Tumor

label: Cy5 and Cy346


title: 9721366122_R04C02

description: Tumor

label: Cy5 and Cy330


title: 9721366140_R06C01

description: Tumor

label: Cy5 and Cy343


title: 9721366140_R01C02

description: Tumor

label: Cy5 and Cy334


title: 9721366140_R04C01

description: Tumor

label: Cy5 and Cy339


title: 9721366122_R04C01

description: Tumor

label: Cy5 and Cy329


title: 9721366122_R03C02

description: Tumor

label: Cy5 and Cy328


title: 9721366122_R03C01

description: Tumor

label: Cy5 and Cy327


title: 9721366122_R02C02

description: Tumor

label: Cy5 and Cy326


title: 9721366118_R04C02

description: Tumor

label: Cy5 and Cy320


title: 9721366118_R03C02

description: Tumor

label: Cy5 and Cy319


title: 9721366118_R05C01

description: Tumor

label: Cy5 and Cy321


title: 9721366118_R06C02

description: Tumor

label: Cy5 and Cy322


title: 9721366122_R02C01

description: Tumor

label: Cy5 and Cy325


title: 9721366118_R03C01

description: Tumor

label: Cy5 and Cy318


title: 9721366118_R01C02

description: Tumor

label: Cy5 and Cy315


title: 9721366118_R01C01

description: Tumor

label: Cy5 and Cy314


title: 9721366122_R05C01

description: Tumor

label: Cy5 and Cy331


title: 9721366114_R06C02

description: Tumor

label: Cy5 and Cy313


title: 9721366114_R04C02

description: Tumor

label: Cy5 and Cy309


title: 9721366114_R05C02

description: Tumor

label: Cy5 and Cy311


title: 9721366118_R02C02

description: Tumor

label: Cy5 and Cy317


title: 9721366114_R04C01

description: Tumor

label: Cy5 and Cy308


title: 9721366114_R03C02

description: Tumor

label: Cy5 and Cy307


title: 9721366114_R02C01

description: Tumor

label: Cy5 and Cy304


title: 9721366114_R03C01

description: Tumor

label: Cy5 and Cy306


title: 9721366114_R01C02

description: Tumor

label: Cy5 and Cy303


title: 9721366114_R02C02

description: Tumor

label: Cy5 and Cy305


title: 9721366122_R01C01

description: Tumor

label: Cy5 and Cy323


title: 9721366122_R01C02

description: Tumor

label: Cy5 and Cy324


title: 9721366113_R06C02

description: Tumor

label: Cy5 and Cy302


title: 9721366113_R06C01

description: Tumor

label: Cy5 and Cy301


title: 9721366113_R05C01

description: Tumor

label: Cy5 and Cy299


title: 9721366113_R05C02

description: Tumor

label: Cy5 and Cy300


title: 9721366113_R03C01

description: Tumor

label: Cy5 and Cy296


title: 9721366113_R04C01

description: Tumor

label: Cy5 and Cy297


title: 9721366113_R04C02

description: Tumor

label: Cy5 and Cy298


title: 9721366118_R02C01

description: Tumor

label: Cy5 and Cy316


title: 9721366113_R02C02

description: Tumor

label: Cy5 and Cy295


title: 9721366114_R05C01

description: Tumor

label: Cy5 and Cy310


title: 9721366113_R01C01

description: Tumor

label: Cy5 and Cy293


title: 9721366093_R06C02

description: Tumor

label: Cy5 and Cy292


title: 9721366093_R06C01

description: Tumor

label: Cy5 and Cy291


title: 9721366114_R06C01

description: Tumor

label: Cy5 and Cy312


title: 9721366093_R04C01

description: Tumor

label: Cy5 and Cy287


title: 9721366093_R02C02

description: Tumor

label: Cy5 and Cy284


title: 9721366093_R04C02

description: Tumor

label: Cy5 and Cy288


title: 9721366093_R03C02

description: Tumor

label: Cy5 and Cy286


title: 9721366093_R05C01

description: Tumor

label: Cy5 and Cy289


title: 9721366093_R03C01

description: Tumor

label: Cy5 and Cy285


title: 9721366093_R05C02

description: Tumor

label: Cy5 and Cy290


title: 9721366092_R06C02

description: Tumor

label: Cy5 and Cy281


title: 9721366093_R02C01

description: Tumor

label: Cy5 and Cy283


title: 9721366092_R06C01

description: Tumor

label: Cy5 and Cy280


title: 9721366093_R01C01

description: Tumor

label: Cy5 and Cy282


title: 9721366092_R05C02

description: Tumor

label: Cy5 and Cy279


title: 9721366092_R05C01

description: Tumor

label: Cy5 and Cy278


title: 9721366113_R01C02

description: Tumor

label: Cy5 and Cy294


title: 9721366092_R01C01

description: Tumor

label: Cy5 and Cy272


title: 9721366088_R06C02

description: Tumor

label: Cy5 and Cy271


title: 9721366092_R04C01

description: Tumor

label: Cy5 and Cy277


title: 9721366092_R03C01

description: Tumor

label: Cy5 and Cy276


title: 9721366092_R01C02

description: Tumor

label: Cy5 and Cy273


title: 9721366092_R02C02

description: Tumor

label: Cy5 and Cy275


title: 9721366088_R06C01

description: Tumor

label: Cy5 and Cy270


title: 9721366088_R05C02

description: Tumor

label: Cy5 and Cy269


title: 9721366088_R05C01

description: Tumor

label: Cy5 and Cy268


title: 9721366064_R06C02

description: Tumor

label: Cy5 and Cy260


title: 9721366088_R04C01

description: Tumor

label: Cy5 and Cy266


title: 9721366064_R06C01

description: Tumor

label: Cy5 and Cy259


title: 9721366064_R05C01

description: Tumor

label: Cy5 and Cy258


title: 9721366088_R02C02

description: Tumor

label: Cy5 and Cy264


title: 9721366064_R03C02

description: Tumor

label: Cy5 and Cy255


title: 9721366088_R01C02

description: Tumor

label: Cy5 and Cy262


title: 9721366088_R01C01

description: Tumor

label: Cy5 and Cy261


title: 9721366092_R02C01

description: Tumor

label: Cy5 and Cy274


title: 9721366064_R02C01

description: Tumor

label: Cy5 and Cy252


title: 9721366064_R02C02

description: Tumor

label: Cy5 and Cy253


title: 9721366064_R01C02

description: Tumor

label: Cy5 and Cy251


title: 9721366064_R04C02

description: Tumor

label: Cy5 and Cy257


title: 9721366088_R03C02

description: Tumor

label: Cy5 and Cy265


title: 9721366064_R04C01

description: Tumor

label: Cy5 and Cy256


title: 9721366088_R02C01

description: Tumor

label: Cy5 and Cy263


title: 9721366088_R04C02

description: Tumor

label: Cy5 and Cy267


title: 9721366053_R04C02

description: Tumor

label: Cy5 and Cy245


title: 9721366053_R05C01

description: Tumor

label: Cy5 and Cy246


title: 9721366053_R04C01

description: Tumor

label: Cy5 and Cy244


title: 9721366053_R06C01

description: Tumor

label: Cy5 and Cy248


title: 9721366064_R01C01

description: Tumor

label: Cy5 and Cy250


title: 9721366053_R06C02

description: Tumor

label: Cy5 and Cy249


title: 9721366053_R05C02

description: Tumor

label: Cy5 and Cy247


title: 9721366053_R03C01

description: Tumor

label: Cy5 and Cy243


title: 9721366048_R04C01

description: Tumor

label: Cy5 and Cy233


title: 9721366048_R04C02

description: Tumor

label: Cy5 and Cy234


title: 9721366064_R03C01

description: Tumor

label: Cy5 and Cy254


title: 9721366048_R03C01

description: Tumor

label: Cy5 and Cy231


title: 9721366048_R03C02

description: Tumor

label: Cy5 and Cy232


title: 9721366048_R02C02

description: Tumor

label: Cy5 and Cy230


title: 9721366053_R02C02

description: Tumor

label: Cy5 and Cy242


title: 9721366040_R05C01

description: Tumor

label: Cy5 and Cy224


title: 9721366053_R01C02

description: Tumor

label: Cy5 and Cy240


title: 9721366040_R02C02

description: Tumor

label: Cy5 and Cy220


title: 9721366040_R03C01

description: Tumor

label: Cy5 and Cy221


title: 9721367027_R03C01

description: Tumor

label: Cy5 and Cy390


title: 9721367006_R06C01

description: Tumor

label: Cy5 and Cy384


title: 9721366053_R01C01

description: Tumor

label: Cy5 and Cy239


title: 9721366048_R06C02

description: Tumor

label: Cy5 and Cy238


title: S-2P+ B cell v2D14 Rep1 - VDJ

description: 10x Genomics


title: 9721366048_R05C02

description: Tumor

label: Cy5 and Cy236


title: 9721366034_R02C01

description: Tumor

label: Cy5 and Cy208


title: 9721366048_R02C01

description: Tumor

label: Cy5 and Cy229


title: 9721366034_R02C02

description: Tumor

label: Cy5 and Cy209


title: 9721366048_R06C01

description: Tumor

label: Cy5 and Cy237


title: 9721366048_R05C01

description: Tumor

label: Cy5 and Cy235


title: 9721366048_R01C02

description: Tumor

label: Cy5 and Cy228


title: 9721366031_R06C01

description: Tumor

label: Cy5 and Cy204


title: 9721366031_R06C02

description: Tumor

label: Cy5 and Cy205


title: 9721366040_R05C02

description: Tumor

label: Cy5 and Cy225


title: 9721366040_R06C01

description: Tumor

label: Cy5 and Cy226


title: 9721366040_R06C02

description: Tumor

label: Cy5 and Cy227


title: 9721366040_R04C01

description: Tumor

label: Cy5 and Cy223


title: 9721366040_R03C02

description: Tumor

label: Cy5 and Cy222


title: 9721366040_R01C02

description: Tumor

label: Cy5 and Cy218


title: 9721366040_R02C01

description: Tumor

label: Cy5 and Cy219


title: 9721366053_R02C01

description: Tumor

label: Cy5 and Cy241


title: 9721366034_R06C02

description: Tumor

label: Cy5 and Cy216


title: 9721366034_R06C01

description: Tumor

label: Cy5 and Cy215


title: 9721366040_R01C01

description: Tumor

label: Cy5 and Cy217


title: 9721366029_R05C02

description: Tumor

label: Cy5 and Cy196


title: 9721366034_R05C02

description: Tumor

label: Cy5 and Cy214


title: 9721366031_R05C02

description: Tumor

label: Cy5 and Cy203


title: 9721366029_R02C02

description: Tumor

label: Cy5 and Cy190


title: 9721366029_R03C02

description: Tumor

label: Cy5 and Cy192


title: 9721366029_R02C01

description: Tumor

label: Cy5 and Cy189


title: 9721366034_R04C02

description: Tumor

label: Cy5 and Cy212


title: 9721366034_R04C01

description: Tumor

label: Cy5 and Cy211


title: 9721366034_R05C01

description: Tumor

label: Cy5 and Cy213


title: 9721366034_R03C02

description: Tumor

label: Cy5 and Cy210


title: 9721366029_R01C02

description: Tumor

label: Cy5 and Cy188


title: 9721366034_R01C02

description: Tumor

label: Cy5 and Cy207


title: 9721366029_R01C01

description: Tumor

label: Cy5 and Cy187


title: 9721366029_R05C01

description: Tumor

label: Cy5 and Cy195


title: 9721366026_R04C02

description: Tumor

label: Cy5 and Cy184


title: 9721366031_R05C01

description: Tumor

label: Cy5 and Cy202


title: 9721366026_R03C02

description: Tumor

label: Cy5 and Cy182


title: 9721366031_R02C01

description: Tumor

label: Cy5 and Cy199


title: 9721366031_R04C02

description: Tumor

label: Cy5 and Cy201


title: 9721366031_R02C02

description: Tumor

label: Cy5 and Cy200


title: 9721366031_R01C01

description: Tumor

label: Cy5 and Cy198


title: 9721366034_R01C01

description: Tumor

label: Cy5 and Cy206


title: 9721366029_R06C02

description: Tumor

label: Cy5 and Cy197


title: 9721366026_R02C01

description: Tumor

label: Cy5 and Cy179


title: 9721366017_R04C01

description: Tumor

label: Cy5 and Cy172


title: 9721366017_R06C01

description: Tumor

label: Cy5 and Cy175


title: 9721366017_R06C02

description: Tumor

label: Cy5 and Cy176


title: 9721366017_R03C02

description: Tumor

label: Cy5 and Cy171


title: 9721366017_R04C02

description: Tumor

label: Cy5 and Cy173


title: 9721366029_R04C01

description: Tumor

label: Cy5 and Cy193


title: 9721366029_R03C01

description: Tumor

label: Cy5 and Cy191


title: 9721366029_R04C02

description: Tumor

label: Cy5 and Cy194


title: 9721366015_R06C02

description: Tumor

label: Cy5 and Cy169


title: 9721366015_R06C01

description: Tumor

label: Cy5 and Cy168


title: 9721366026_R05C01

description: Tumor

label: Cy5 and Cy185


title: 9721366015_R05C01

description: Tumor

label: Cy5 and Cy166


title: 9721366026_R04C01

description: Tumor

label: Cy5 and Cy183


title: 9721366026_R03C01

description: Tumor

label: Cy5 and Cy181


title: 9721366015_R03C01

description: Tumor

label: Cy5 and Cy163


title: 9721366015_R01C01

description: Tumor

label: Cy5 and Cy159


title: 9721366015_R02C02

description: Tumor

label: Cy5 and Cy162


title: 9721366017_R05C02

description: Tumor

label: Cy5 and Cy174


title: 9704031162_R04C02

description: Tumor

label: Cy5 and Cy154


title: 9721366026_R02C02

description: Tumor

label: Cy5 and Cy180


title: 9721366026_R01C02

description: Tumor

label: Cy5 and Cy178


title: 9721366026_R01C01

description: Tumor

label: Cy5 and Cy177


title: 9704031162_R02C01

description: Tumor

label: Cy5 and Cy150


title: 9704031146_R05C02

description: Tumor

label: Cy5 and Cy145


title: 9721366017_R02C01

description: Tumor

label: Cy5 and Cy170


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