title: Aml12_KD_rep2

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

description: Hi-C

data_processing:
Library strategy: HiC-Seq
Raw HiC data were processed through the HiC-Pro pipeline (PMID: 26619908) (including read mapping/binning/ICE correction).
To eliminate the bias from the different sequencing depth, We random sampled the contacts of each sample to 200M, and then convert the sampled contacts to contact matrix at different resolutions by Juicer Tools
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.

growth_protocol: The mouse hepatocyte cell line alpha mouse liver 12 (AML12)  cells were cultured in DMEM/F12 (HyClone) supplemented with 10% fetal bovine serum (FBS, Biowest), ITS Liquid Media Supplement (Sigma) and 0.1μM dexamethasone (Sigma) at 37 °C and 5% CO2.

extract_protocol:
Biotin-DNA was isolated with strepavidin-beads
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

value: SRRM2 KD


title: Aml12_KD_rep1

status: Public on Jun 30 2019

type: SRA

city: Shanghai

country: China

description: Hi-C

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: genotype/variation


title: E18.5-DMSO

city: Hangzhou

first: Bingjue

last: Li

address: Qingchun Road 79

institute: Zhejiang University

description: Sample 8

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adapter sequences at the two ends of raw reads were cleaned by Trimmomatic. Then, the cleaned reads were mapped to the mm10 by STAR.
Transcripts per million (TPM) were calculated using a protocol from Wagner GP et al.,Theory Biosci.,2012. In short, first divide the read counts by the length of each gene in kilobases and get the  reads per kilobase (RPK); second count up all the RPK values in a sample and divide this number by 1,000,000, this is the “per million” scaling factor; at last, divide the RPK values by the “per million” scaling factor and this is the TPM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: embryonic kidney

extract_protocol:
2 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

tag: tissue

value: embryonic kidney

tag: strain

value: ICR

tag: agent

value: DMSO


title: E16.5-DMSO

description: Sample 7


title: Aml12_Ctrl_rep1

description: Hi-C

value: control


title: GM-DC treated with mock, biological rep3

type: RNA

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

country: France

institute: INSERM

description: Gene expression data from GM-DC treated with mock during 24 hr

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Microarray data were background-corrected and normalized using the robust multi-array average (RMA) algorithm by using affy R package

label: biotin

source_name: GM-DC treated with mock during 24 hr

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: GM-DC were differentiated from bone marrow in DMEM containing 20 ng/ml mouse recombinant GM-CSF,  10% FCS, 2 mM L-glutamine, 4.5 g/L glucose, and 10 g/ml gentamycin during 10 days.

extract_protocol: RNeasy Micro Kit was used to extract total RNA according to the manufacturer's instructions

treatment_protocol: GM-DC were treated with 3 ug/ml IMQ with or without PA or OA conjugated with BSA (0.5 mM, molar ratio PA:BSA 6:1) during 24 hr in DMEM containing 10% FCS, 2 mM L-glutamine, 4.5 g/L glucose, and 10 ug/ml gentamycin

tag: gender

value: male

tag: genotype


title: GM-DC treated with mock, biological rep2


title: E16.5-CPF

description: Sample 3

value: CPF


title: E18.5-CPF

description: Sample 4


title: E12.5-CPF

description: Sample 1


title: PDD1 KO small RNAs @10 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

description: PDD1 KO 10h

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012; Noto et al. 2015). Briefly, following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed, and reads that perfectly match the MIC genome were used.
Genome_build: Tetrahymena thermophila MIC genome assembly released in 2016 was used for mapping. The positions of the predicted IESs were described in (Noto et al. 2015).
Supplementary_files_format_and_content: Sequenced 26 to 32 nt RNAs that map uniquely to the IES5, IES737, IES4092 and 3,293 compiled Type-B IESs are counted, and normalized numbers (reads per kb per million reads [RPKM]) are shown.

organism: Tetrahymena thermophila

source_name: total RNA

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight.

extract_protocol:
Total RNA was extracted with TRIzol reagent . 1 mL of Trizol reagent was used to lyse1x10e6 cells.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

treatment_protocol: To induce conjugation, exponentially growing cells (~3-5x 10e5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 10e5/ml) at 30°C.

value: PDD1 KO W3-3 x W39-1

tag: time

value: 10 hpm


title: E14.5-CPF

description: Sample 2


title: PDD1 KO small RNAs @12 hpm

description: PDD1 KO 12h

value: 12 hpm


title: TPB2 mutant cross2 small RNAs @3 hpm

description: TPB2 mut cross#2 3h

value: TPB2 mutant #41 x #44

value: 3 hpm


title: TPB2 mutant cross2 small RNAs @10 hpm

description: TPB2 mut cross#2 10h


title: E12.5-DMSO

description: Sample 5


title: TPB2 mutant cross1 small RNAs @12 hpm

description: TPB2 mut cross#1 12h

value: TPB2 mutant #6 x #38


title: TPB2 mutant cross1 small RNAs @10 hpm

description: TPB2 mut cross#1 10h


title: TPB2 mutant cross2 small RNAs @12 hpm

description: TPB2 mut cross#2 12h


title: TPB2 mutant cross1 small RNAs @3 hpm

description: TPB2 mut cross#1 3h


title: GM-DC treated with mock, biological rep1


title: E14.5-DMSO

description: Sample 6


title: DC from mice fed HFD and  treated with IMQ, biological rep2

description: Gene expression data from GM-DC treated with mock in the presence of PA during 24 hr

source_name: DC sorted from  inguinal lymph nodes

label_protocol: Biotinylated ssDNA were prepared using  5 ng RNA from sorted cDC, amplified and labeled with Ovation Pico WTA Systems V2.

growth_protocol: Animals were housed within the specific pathogen-free facility at the Institut Pasteur de Lille with ad libitum access to water and food. CD3−CD19−CD64−Ly6G−CD11c+MHCII+ DCs were sorted from mouse iLN using BD Influx Cell Sorter (BD Biosciences).

extract_protocol: Total RNA was isolated from sorted cDC with Arcturus Picopure RNA isolation Kit

treatment_protocol: Mice were treated with a daily topical dose (62.5 mg) of IMQ cream (Aldara 5%) on the shaved abdominal skin for 5 days and sacrificed 24 hr later.


title: wild-type small RNAs @12 hpm

description: WT 12h

value: wild-type B2086 x CU428


title: Aml12_Ctrl_rep2

description: Hi-C


title: wild-type small RNAs @10 hpm

description: WT 10h


title: wild-type small RNAs @8 hpm

description: WT 8h

value: 8 hpm


title: wild-type small RNAs @3 hpm


title: school age_severe asthma_007

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

country: United Kingdom

institute: GalxoSmithKline

description: school age severe asthma

hyb_protocol: Standard procedure for Affymetrix GeneTitan running Affymetrix GeneChip Command Console 2.0.

data_processing: Scans were imported into ArrayStudio V8.0 and pre-processed using the default RMA pipeline

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood sample collected at baseline

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation RNA amplification system V2 with OvationWB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: RNA was extracted from blood collected in PAXgene tubes using the PAXgene blood miRNA kit

tag: cohort

tag: disease

value: severe asthma

tag: age group

value: school age


title: wild-type small RNAs @6 hpm

description: WT 6h

value: 6 hpm


title: 1243C

type: genomic

city: Minneapolis

first: Aimee

last: Merino

state: MN

address: 420 Delaware Street SE

country: USA

institute: University of Minnesota

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium methylation EPIC BeadChips using standard Illumina protocol

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

data_processing: Genome Studio; Average Beta

label: cy3, cy5

source_name: pelleted Nk cells after culture with NKG2C antibody

label_protocol: Standard Illumina Protocol

growth_protocol: NK grown in B0 media with 10 ng/mL IL-15 for seven days after isolation with Miltenyi CD3 and CD19 depletion kits from PBMCs.

extract_protocol: genomic DNA was extracted and purified from pelleted NK cells using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: platebound antibodies (either control isotype, anti-NKG2C, or anti-NKG2C/A) anti NKG2C and anti NKG2C/A antibodies were supplied by R&D Biosystems

tag: cell type


title: 1243B

source_name: pelleted Nk cells after culture with NKG2C/A antibody


title: 1195A

source_name: pelleted Nk cells after culture with isotype antibody


title: 1195C

value: pelleted Nk cells after culture with NKG2C antibody


title: 1211B

value: pelleted Nk cells after culture with NKG2C/A antibody


title: 1215B


title: 1195B


title: MGhR

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description:
Sample 20
Experiment 1061-315F (FMI)

data_processing:
HCS 2.2.58 was used with default parameters for base calling.
bcl2fastq 1.8.4 (Illumina) was used to generate fastq files
Raw reads were preprocessed using the R(v3.3.0)/Bioconductor package QuasR(1.12.0): Reads with more than 2Ns were removed with the function preprocessReads(). The remaining reads were aligned to mm10 using the qAlign() with splicedAlignments=TRUE and the following parameters: Rbowtie v1.4.0 (parameters: -max_intron 400000 -min_intron 20000 -max_multi_hit 10 -selectSingleHit TRUE -seed_mismatch 1 -read_mismatch 2 -try_hard yes)
The QuasR function qCount() was used to extract a table with raw read counts per gene for all Entrez genes for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: table containig raw read counts per gene. First column: ENTREZ gene ID, subsequent columns: number of unique, non-masked bases for all exons of the gene for each sample

source_name: Mammary gland

growth_protocol: Ret-induced tumors were generated in Ret/MTB females by chronic induction (4-12 months) of the mouse system administrating doxycycline into the food (Dox-food). Ret-induced regressed tumors were generated by Dox-food withdrawal for 2 days. Hyperplastic glands were a results of 2 months of  chronic administration of Dox-food to the animals. Mammary tissue from single transgenic Ret/-, MTB/- females under Dox-food or bitransgenic Ret/MTB  females under Normal-food are used as a control in this study.

extract_protocol:
Tumor or mammary gland tissues were removed, flash frozen on dry ice, and RNA was harvested using Quiagen RNA extraction Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/N

value: Normal mammary gland

tag: protocol

value: on Dox-food

value: Ret/-


title: MGbRM

description:
Sample 21
Experiment 1061-315F (FMI)

value: on Normal-food

value: Ret/MTB


title: MGaRM

description:
Sample 23
Experiment 1061-315F (FMI)


title: MGcRM

description:
Sample 22
Experiment 1061-315F (FMI)


title: Neurons 24 hr ZFPA batch2 biological rep4

city: Richmond

first: Bryan

last: Zeitler

state: California

address: 501 Canal Blvd.

institute: Sangamo Therapeutics

description: Gene expression data from HD neurons treated with ZFPA for 24 hours

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Arrays. Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: PrimeView Human Gene Expression Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Robust Multi-array Average (RMA) was used to normalize the raw signal from each probe set.  Fold-change analysis was performed using Transcriptome Analysis Console 4.0 (Affymetrix) with “Analysis Type – Expression (Gene)” and “Summarization – RMA” options selected. Addtionally, batch correction was applied to combine the three batches into a single analysis.

source_name: HD neurons ZFPA 24 hours Batch2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for 3’ IVT PLUS kits.

growth_protocol: HD-ESCs were passaged with accutase and cultured on matrigel coated plates in E8 media (Thermo Fisher Scientific). Neural stem cells were derived using StemPro Neural Induction Medium (Thermo Fisher Scientific). StemPro NSC SFM medium (Life Technologies) was used to culture HD-NSCs. Neuronal differentiation from NSC was induced by changing to neural differentiation media (NDIFF) consisting of Neurobasal media with B-27 Serum-Free Supplement and GlutaMAX (ThermoFisher Scientific). Medium was changed every 3-4 days. See methods for more details.

extract_protocol: After 24 hrs, cells were washed 1X with PBS, then processed for total RNA extraction (High Pure, Roche).

treatment_protocol: 1500 ng in vitro-transcribed mRNA encoding the ZFP-TFs or GFP was transfected into 1.5e5 GENEA020 hESC-derived accutase-detached neurons using an Amaxa shuttle, setting CA-138, solution P4 (Lonza).

tag: cell line

value: GENEA020 neurons

tag: dose

value: 1500 ng mRNA

tag: treatment

value: ZFPA for 24 hours


title: 1211C


title: Neurons 24 hr ZFPB batch3 biological rep2

description: Gene expression data from HD neurons treated with ZFPB for 24 hours

source_name: HD neurons ZFPB 24 hours Batch3

value: ZFPB for 24 hours


title: Neurons 24 hr ZFPB batch3 biological rep3


title: Neurons 24 hr GFP batch2 biological rep1

description: Gene expression data from HD neurons treated with GFP for 24 hours

source_name: HD neurons GFP 24 hours Batch2

value: GFP for 24 hours


title: Neurons 24 hr GFP batch3 biological rep1

source_name: HD neurons GFP 24 hours Batch3


title: Neurons 24 hr GFP batch3 biological rep4


title: Neurons 24 hr ZFPB batch3 biological rep4


title: Neurons 24 hr ZFPA batch2 biological rep1


title: Neurons 24 hr ZFPB batch3 biological rep1


title: Neurons 24 hr GFP batch2 biological rep3


title: Neurons 24 hr ZFPA batch2 biological rep2


title: Neurons 24 hr GFP batch2 biological rep2


title: Neurons 24 hr GFP batch2 biological rep4


title: Neurons 24 hr GFP batch3 biological rep3


title: Neurons 24 hr GFP batch3 biological rep2


title: Neurons 24 hr ZFPA batch2 biological rep3


title: MGdR

description:
Sample 19
Experiment 1061-315F (FMI)


title: 1215C


title: NA10858_batch 2 (control nucleic acid)

source_name: control

value: control


title: MGcR

description:
Sample 18
Experiment 1061-315F (FMI)


title: 1233C


title: T13OUT

description:
Sample 17
Experiment 1061-315F (FMI)

source_name: Mammary tumor

value: Mammary tumor

value: regressed after  Dox-food withdrawal


title: 1243A

value: pelleted Nk cells after culture with isotype antibody


title: 1211A


title: Neurons 24 hr GFP batch1 biological rep4

source_name: HD neurons GFP 24 hours Batch1


title: T12

description:
Sample 14
Experiment 1061-315F (FMI)

value: growing under Dox-food


title: T10OUT

description:
Sample 16
Experiment 1061-315F (FMI)


title: T11

description:
Sample 13
Experiment 1061-315F (FMI)


title: Neurons 24 hr GFP batch1 biological rep3


title: 1233A


title: Uninvolved epidermis from AD skin, sample 7, set 2

description: Gene expression in human epidermis

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies) according to manufacturer's protocol

scan_protocol: Slides were scanned with the Agilent G2505B scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1). Data were background-corrected with 'normexp' option and quantile normalized using limma R package

source_name: Human uninvolved epidermis from AD skin, sample 7 (laser capture microdissection)

label_protocol: 10 ng RNA were amplified with ExpressArt Kit and labeled (Cy3) with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) according to manufacturer's protocol

extract_protocol: RNA was isolated with Arcturus Picopure RNA isolation Kit according to manufacturer's protocol

treatment_protocol: Epidermis and dermis were obtained from human skin biopsies by laser capture microdissection using Arcturus XT (MDS Analytical Technologies) system

value: epidermis

value: atopic dermatitis


title: Neurons 24 hr GFP batch1 biological rep1


title: Neurons 24 hr ZFPC batch1 biological rep4

description: Gene expression data from HD neurons treated with ZFPC for 24 hours

source_name: HD neurons ZFPC 24 hours Batch1

value: ZFPC for 24 hours


title: 1233B

value: pelleted Nk cells after culture with NKG2C/A antibody


title: 1215A


title: T1

description:
Sample 12
Experiment 1061-315F (FMI)

value: FVB/N


title: Neurons 24 hr GFP batch1 biological rep2


title: NA10858_batch 1 (control nucleic acid)


title: Neurons 24 hr ZFPC batch1 biological rep3


title: Neurons 24 hr ZFPC batch1 biological rep2


title: T18

description:
Sample 11
Experiment 723R (FMI)


title: Neurons 24 hr ZFPC batch1 biological rep1


title: T15

description:
Sample 9
Experiment 723R (FMI)


title: T9OUT

description:
Sample 15
Experiment 1061-315F (FMI)


title: 1089C


title: 959B


title: 961C

value: pelleted Nk cells after culture with NKG2C antibody


title: 953C


title: TG5 RM4

description:
Sample 8
Experiment 723R (FMI)

value: Hyperplastic mammary gland

value: on Dox-food

value: Ret/MTB


title: TG5 RM1

description:
Sample 5
Experiment 723R (FMI)


title: TG5 R4

description:
Sample 4
Experiment 723R (FMI)

value: Normal mammary gland

value: Ret/-


title: TG5 RM3

description:
Sample 7
Experiment 723R (FMI)


title: 1089A


title: TG5 R3

description:
Sample 3
Experiment 723R (FMI)


title: TG5 R2

description:
Sample 2
Experiment 723R (FMI)


title: 961B


title: 953A


title: 1089B


title: TG5 R1

description:
Sample 1
Experiment 723R (FMI)


title: 1027B


title: 959C


title: 953B


title: 959A


title: T16

description:
Sample 10
Experiment 723R (FMI)


title: 1027A


title: TG5 RM2

description:
Sample 6
Experiment 723R (FMI)


title: BEAS-2B_Vector

city: Guangzhou

first: junchao

last: Cai

address: zhongshan er road

institute: Sun-yat sen university

description: normal lung epithelial cells duplicate a passage every 3-4 days

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

source_name: BEAS-2B cells with retroviral vector stably transduced

growth_protocol: Both the BEAS-2B_Vector and BEAS-2B_HRasV12 cells were cultured in LHC-9 medium as instructed by the providers..

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: pBabe-HRasV12-neo or empty vector was co-transfected with the pIK packaging plasmid in 293FT cells by using standard calcium phosphate transfection method. Thirty-six hours after the co-transfection, supernatants were collected and incubated with cells to be infected for 24 hours in the presence of polybrene (2.5 μg/mL).  Following infection, neomycin (1.5μg/mL) was used to select stably transduced cells for 10 days.

value: human bronchial epithelial cell line

tag: phenotype

value: normal lung epithelial cells without cellular senescence


title: 961A


title: 1027C


title: Mouse Brain-Tumor-4

city: San Francisco

first: Anders

middle: I

last: Persson

state: CA

address: 675 Nelson Rising Lane

department: Neurology

institute: University of California San Francisco

hyb_protocol: See manufacturer's protocol (www.nanostring.com)

data_processing: Data was processed and normalized log2 values were calculated using nSolver 4.0 software

label: oligonucleotide probe

source_name: Tumor tissue postnatal day 134

growth_protocol: Wild-type CD1 mice and transgenic hGFAP-HaV12-Ras mice (CD1 strain) were aged.

extract_protocol: Mouse brain and tumor tissue were dissected and flash-frozen for isolation of RNA using the miRVana miRNA isolation kit (Invitrogen)

tag: developmental stage

value: adult

tag: Sex

value: male

value: transgenic hGFAP-HaV12-Ra

value: tumor

tag: age

value: postnatal day 134


title: Mouse Brain-Tumor-1

scan_protocol: See manufacturer's protocol (www.nanostring.com)

source_name: Tumor tissue postnatal day 65

tag: strain

tag: tissue

value: postnatal day 65


title: Mouse Brain-Tumor-2

source_name: Tumor tissue postnatal day 104

label_protocol: See manufacturer's protocol (www.nanostring.com)

value: female

value: postnatal day 104


title: BEAS-2B_HRasV12

description: premature cell cycle arrest followed by cell death in approximatelynearly 7 days

scan_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

source_name: BEAS-2B cells with retroviral HRasV12 stably transduced

value: present cellular senescence


title: 13-DKO-TFH1

status: Public on Jun 29 2019

city: Indianapolis

first: Alexander

last: Dent

state: IN

address: 950 W. Walnut St. R2 302, Walther Oncology Center

institute: Alexander Dent

description: RNA from TFH cells

data_processing:
The sequencing data were first assessed using FastQC for quality control.
All sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils (from ngsutils).
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10”.
Quality control of sequencing and mapping results was summarized using MultiQC.
Genes with read count per million (CPM) > 0.5 in more than 4 of the samples were kept. The data was normalized using TMM (trimmed mean of M values) method.
Differentially expressed genes (fold change³1.8 and FDR£5% ) were identified by linear modeling in  edgeR R package.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: An excel file including gene expression ( raw counts and RPKM in log scale with base 2) and statistics from differential expression analysis.

source_name: BCL6-BLIMP1-FC mouse

extract_protocol:
RNA was extracted and prepared by Qiagen RNAeasy Plus Micro Kit.
KAPA mRNA Hyperprep Kit (KK8581). Dual Index. .

treatment_protocol: mice were immunized with peanut protein + cholera toxin 2x i.g.

value: TFH cells


title: 12-BLIMP1-TFH4

description: RNA from TFH cells

source_name: BLIMP1FC mouse


title: 11-BLIMP1-TFH3

description: RNA from TFH cells


title: 14-DKO-TFH2

description: RNA from TFH cells


title: 15-DKO-TFH3

description: RNA from TFH cells


title: 10-BLIMP1-TFH2

description: RNA from TFH cells


title: 6-BCL6-TFH2

description: RNA from TFH cells

source_name: BCL6FC mouse


title: 7-BCL6-TFH3

description: RNA from TFH cells


title: 4-WT-TFH4

description: RNA from TFH cells

source_name: WT mouse


title: 5-BCL6-TFH1

description: RNA from TFH cells


title: 3-WT-TFH3

description: RNA from TFH cells


title: 2-WT-TFH2

description: RNA from TFH cells


title: Mouse Brain-Tumor-3

source_name: Tumor tissue postnatal day 125

value: postnatal day 125


title: Monocytes with anti-TLR2 and stimulated with Bb12

city: Hermosillo

first: Marina

last: Arenas-Padilla

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas 46

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo A. C.

description:
Swine monocytes stimulated with Bb12, previous anti-TLR2 treatment.
Bb12Ant

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1. Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; 2. Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 40°C for 16 hours. After RNA hybridization, tag-conjugating Cy3 dye was circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193).

organism: Sus scrofa

source_name: Swine monocytes with anti-TLR2 and stimulated with Bb12

label_protocol: Microarray assay was performed using a service provider (LC Sciences). A strand-labeling reaction was carried out with total RNA (1 ug), control oligo-nucleotides, App-Cap3 (5’-adenylated and 3’-dideoxy oligo-adaptor) and T4 RNA ligase (Rnl2tr-K227Q, New England BioLabs) in T4 RNA ligase buffer with PEG 8000 and RNase inhibitor (Promega).  The reaction mixture was incubated at 16ºC for 16 hours and stopped by adding equal volume of hybridization buffer. The adapter sequence contains a tag segment for capturing fluorescent dye during a later dye staining process.

growth_protocol: Peripheral blood was collected in tubes with 1.5 mg/mL ethylenediaminetetraacetic acid (EDTA) as an anticoagulant. Peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation using Ficoll-Paque Plus (GE Healthcare Bio-Sciences, Sweden). PBMCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen Co., USA) supplemented with 5000 IU/mL penicillin, 5 µg/mL streptomycin (Sigma-Aldrich) and 10% fetal bovine serum (FBS, Gibco, USA). Cells (5 x 107) were placed in a T75 flask (Corning Inc., USA) and incubated at 37 °C and 5% CO2 for 90 min to allow monocytes to adhere.

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (Qiagen).

treatment_protocol: A total of 2 x 10^6 monocytes were added to 48-well plates and incubated with DMEM (negative control) or Bb12 (ratio 1:100 cell/bacteria) for 4 h. For TLR2 blocking experiments, 40 μg/mL of purified anti-mouse/human CD282 (TLR2) antibody (Biolegend, USA) was used 1 h prior to cell stimulation.

value: Peripheral blood monocytes


title: JS299 3 min

city: Bloomington

first: Jared

middle: Michael

last: Schrader

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
Reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
For each aligned read >=20 bases, the 5' nucleotide was used to measure fragment counts within each transcript.  For transcripts with >25 fragments at a given timepoint, the RPKM was calculated.
Genome_build: CP001340
Supplementary_files_format_and_content: Each line in the processed file is for a different transcript and contains many columns: Col 1: operon/locus ID. Col 2.-on: strain and indicated time point RPKM value.

organism: Caulobacter vibrioides NA1000

source_name: JS299 half-life profiling

growth_protocol: 5mL of JS299 cells were grown overnight in PYE medium supplied with 0.2% xylose, 0.5µg/mL gentamycin, and 5µg/mL kanamycin.  The overnight cultures were then washed 3 times with PYE growth media and used to inoculate 30 mL of PYE medium supplied with 500µM vanillate, 0.5µg/mL gentamycin, and 5µg/mL kanamycin.  The cells were grown for 8 hours and then before rif-treatment.

extract_protocol:
The cells were pelleted at (20,000xg) for 1 min and resuspended in 1mL of 65 °C hot TRizol Reagent (Ambion) and incubated 65 °C for 10 min in a heat block. 200µL of chloroform were added to the samples and the tubes were incubated at room temperature for 5 min before spinning at (20,000xg) for 10 min. RNA samples were chloroform extracted once and precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at −80 °C. The RNA samples were spun at 20,000 x g at 4 °C for 1 hour, pellets were washed with 80% ethanol for 10 min, air dried, and resuspended in 10 mM Tris-HCl (pH 7.0).  The RNA-Seq libraries were made using 5µg of total RNA samples, rRNA was removed by ribozero gram negative kit (illumina), and library construction was performed according to protocol (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].

treatment_protocol: The cells were innoculated with 200ug/mL rifampicin and placed immediately in RNAprotect bacterial reagent (qiagen) at the indicated timepoint.  0 min time-points were collected just prior to rifampicin addition.

tag: isolate

value: Strain JS299


title: Mouse Brain-2

source_name: Layer II-IV postnatal day 60

tag: genotype

value: Wild-type

value: brain, neocortex, layer II-IV

value: postnatal day 60


title: Mouse Brain-1


title: JS299 9 min


title: JS299 1 min


title: Monocytes stimulated with Bb12

description:
Swine monocytes stimulated with Bb12.
Bb12

source_name: Swine monocytes stimulated with Bb12


title: 16-DKO-TFH4

description: RNA from TFH cells


title: 1-WT-TFH1

description: RNA from TFH cells


title: Mouse Brain-3


title: Unstimulated monocytes

description:
Unstimulated swine monocytes.
SE

source_name: Swine monocytes_unstimulated


title: JS233 3 min

source_name: JS233 half-life profiling

value: Strain JS233


title: 8-BCL6-TFH4

description: RNA from TFH cells


title: JS233 9 min


title: JS233 1 min


title: JS221 9 min

source_name: JS221 half-life profiling

value: Strain JS221


title: JS221 0 min


title: JS221 3 min


title: JS221 1 min


title: JS38 9 min

source_name: JS38 half-life profiling

value: Strain JS38


title: JS38 1 min


title: JS38 3 min


title: BR-body enriched 1

data_processing:
Reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
For each aligned read >=20 bases, the 5' nucleotide was used to measure fragment counts within each transcript.  For transcripts with >25 fragments, RPKM was calculated for each sample, and the log2 ratio of the RPKM (enriched sample / lysate sample) was calcualted for each biological replicate.
Genome_build: CP001340
Supplementary_files_format_and_content: Each line in the processed file is for a different transcript and contains eight columns: Col 1: operon/locus ID. Col 2. Left coord.  Col 3. Right coord.  Col 4. Strand.  Col 5. Enriched replicate 1 RPKM.  Col 6. Enriched replicate 2 RPKM.  Col 7. whole cell lysate replicate 1 RPKM.  Col 8. whole cell lysate replicate 2 RPKM.

source_name: BR-bodies isolated from JS299

growth_protocol: 5mL of JS299 cells were grown overnight in PYE medium supplied with 0.2% xylose, 0.5µg/mL gentamycin, and 5µg/mL kanamycin.  The overnight cultures were then washed 3 times with PYE growth media and used to inoculate 30 mL of PYE medium supplied with 500µM vanillate, 0.5µg/mL gentamycin, and 5µg/mL kanamycin.  The cells were grown overnight and then pelleted at 11,000xg for 5 min.

extract_protocol:
Cell lysis was performed in a mixer-mill while frozen in liquid nitrogen.  After collecting a small scoop of the frozen lysate for the whole cell lysate sample, the cell lysate was spun at 2000xg for 5 min. to clear membranes.  The pellet was resuspended in 200 µL of lysis buffer and the samples were spun again at 10,000xg for 10 min.  The resulting pellet was resuspended again in 200 µL of lysis buffer and subjected to another spin at 20,000xg for 10 minutes. The BR-bodies enriched pellet was resuspended in 200 µL of lysis buffer and RNA was extracted from both whole cell lysate and BR-bodies enriched fractions.  RNA extraction was performed by adding 1mL of 65°C Trizol to the samples and incubating at 65°C for 10 min, then 200μL of chloroform was added and incubated for 5 min at room temperature.  The samples were then spun at max speed in a microcentrifuge for 10 min at room temperature and the aqueous layer was removed and incubated with 700μL of isopropanol.  The samples were then precipitated at −20°C for 1 hour, spun at 20,000 g for 1 hour at 4°C, and washed three times with 80% ethanol.  The pellet was air dried and resuspended in 10mM Tris pH 7.0.  RNA-seq library construction was performed as described in (Aretakis et al., 2018) using 1.0 µg of total RNA.
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].

treatment_protocol: The cell pellet was resuspended in 2.5 mL of lysis buffer (35mM NaCl, 20mM Tris-HCl-pH 7.4, 1mM β-mercaptoethanol, one tablet EDTA-free protease inhibitor (roche) per 25 mL of buffer, 1U/mL Superase IN, and 10U/ml RNase-free DNase I).  The cell suspension was flash frozen dropwise in liquid nitrogen.


title: whole cell lysate 2

source_name: whole cell lysate from JS299


title: whole cell lysate 1


title: BR-body enriched 2


title: JS233 0 min


title: JS299 0 min


title: JS38 0 min


title: 9-BLIMP1-TFH1

description: RNA from TFH cells


title: SMARCA2 test variant 5

status: Public on Jun 27 2019

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

country: Canada

institute: SickKids Research Institute

description: Genomic DNA extracted from blood had DNA methylation measured using the EPIC array (Illumina)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Using an Illumina HiScan

data_processing: Using an Illumina HiScan

label: Cy3 and Cy5

source_name: Blood

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications. Prior to extraction, red cells were lysed by exposure of the sample to 2x Lysis Buffer for 5 minutes in ice. The remaining cells were pelletted by centrifugation at 2300 RPM at 4 degrees celsius.

value: M

tag: age (years)


title: SMARCA2 test variant 6


title: SMARCA2 test variant 2


title: SMARCA2 test variant 4


title: NCBRS case 5


title: SMARCA2 test variant 9

value: F


title: Control sample 18


title: Control sample 25


title: Control sample 26


title: Control sample 22


title: Control sample 16


title: SMARCA2 test variant 8


title: Control sample 27


title: NCBRS case 6


title: NCBRS case 3


title: Control sample 15


title: SMARCA2 test variant 3


title: Control sample 20


title: Control sample 24


title: NCBRS case 7


title: SMARCA2 test variant 1


title: NCBRS case 8


title: NCBRS case 4


title: Control sample 23


title: Control sample 19


title: NCBRS case 2


title: SMARCA2 test variant 7


title: Control sample 17


title: WT5RNA

status: Public on Jun 25 2019

city: Montreal

first: Xiang-Jiao

last: Yang

state: Quebec

address: 1160 Pine Ave W

institute: McGill University

description:
WT5RNA_S40
cultured from E16.5 cerebrum in neural stem cell culture media till day 4
processed data file:
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_log2FC_DESeq2
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_FC_cufflinks

data_processing:
Method#1 Adaptors were trimmed by Trim Galore package
Method#1 The trimmed fastq files were then mapped to mm9 genome using STAR package
Method#1 Mapped reads were counted using featureCounts
Method#1 Infer_experiment package was used to determine our files are reverse stranded
Method#1 The count matrix were applied to DESeq2 package
Method#2 Trimming
Method#2 Alignment using bowtie package
Method#2 Get FPKM values using cufflinks package
Method#1 and #2 denotes two different ways for analyzing differential expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: excel files
Supplementary_files_format_and_content: Neurospheres_DEGs_GO_Biological_Process_2018_table.xlsx: GO analysis for the neurospheres RNA-seq with differential genes log2 fold change >0.8 or <-0.8
Supplementary_files_format_and_content: Cerebrum_DEGs_GO_Biological_Process_2018_table.xlsx: GO analysis for the cerebrum RNA-seq with differential genes log2 fold change >0.8 or <-0.8.

source_name: wild-type neurospheres cultured from E16.5 cerebrum

extract_protocol:
E16.5 cultured neurospheres or P0 cortices were collected into clean eppendorf tubes containing 0.7 ml QIAZOL (Qiagen) and made into single cells by passing though needles. Total RNA was isolated using miRNeasy Mini kit (Qiagen). The concentration and integrity were assessed by the sequencing facility (Omega Bioservices) using a RNA screentape. Once passed the sample quality control, the samples were used for oligo-dT primed RNA-Seq (Illumina TruSeq stranded mRNA) on HiSeq2500 sequencers (Illumina)
RNA library were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: wild-type

value: brain

value: neurospheres


title: WT6RNA

description:
WT6RNA_S41
cultured from E16.5 cerebrum in neural stem cell culture media till day 4
processed data file:
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_log2FC_DESeq2
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_FC_cufflinks


title: Hdac3-Emx1-KO2-RNA

description:
Hdac3-Emx1-KO2-RNA_S3
dissected out from P0 brains directly
processed data file:
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_log2FC_DESeq2
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_FC_cufflinks

source_name: Hdac3 KO cerebral cortex from P0 pups

value: Hdac3 KO

value: neural cells


title: KO7RNA

description:
KO7RNA_S42
cultured from E16.5 cerebrum in neural stem cell culture media till day 4
processed data file:
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_log2FC_DESeq2
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_FC_cufflinks

source_name: Hdac3 KO neurospheres cultured from E16.5 cerebrum


title: NCBRS case 1


title: MHV68_HE2.1 [deepCAGE]

city: Gainesville

first: Scott

last: Tibbetts

state: FL

department: Molecular Genetics & Microbiology

institute: University of Florida

data_processing:
Illumina 1.9 basecalling
Alignment to the MHV68.ORF73bla genome (MH636806) using STAR version 2.3.0.1 with default parameters
Generation of wig files using IGVTools
Genome_build: MHV68.ORF73bla (MH636806)
Supplementary_files_format_and_content: plus and minus strand wig files for the MHV68.ORF73bla genome

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-glutamine, 4.5g/L glucose and sodium pyruvate supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C and were passaged 1:15 every three days.

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared for sequencing using nAnT-iCAGE protocols

treatment_protocol: Cells were plated at a density of 2 x 10^5 cells/well in a flat-bottom 6-well TC-treated cell culture plate.  Reactivation of HE2.1 B cells was induced using 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment (20 ng/ml) for 18 hours prior to RNA extraction.

value: untreated

tag: virus strain

value: MHV68 HE2.1


title: MHV68_HE2_TPA [deepCAGE]

value: TPA


title: MHV68bla_3T12_18h_B [deepCAGE]

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-glutamine, 4.5g/L glucose and sodium pyruvate supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

treatment_protocol: Cells were plated at a density of 2 x 10^5 cells/well in a flat-bottom 6-well TC-treated cell culture plate. Twenty four hours later, cells were infected at MOI 5 with a floxed, BAC-derived wild-type MHV68 which carries a β-lactamase marker fused to ORF73 (MHV68.ORF73bla). RNA was harvested after 18 hours.

value: NIH 3T12

tag: hpi


title: Control sample 21


title: MHV68bla_3T12_6h [deepCAGE]


title: MHV68_3T12_12h [deepCAGE]

value: MHV68 WUMS


title: MHV68bla_3T12_18h_A [deepCAGE]


title: MHV68_HE2.1 [BGISEQ]

data_processing:
BGI basecalling
Alignment to the MHV68.ORF73bla genome using STAR version 2.3.0.1 with default parameters
Generation of wig files using IGVTools
Genome_build: MHV68.ORF73bla
Supplementary_files_format_and_content: plus and minus strand wig files for the MHV68.ORF73bla genome

extract_protocol:
Total RNA was extracted using TRIzol reagent
BGISEQ-500


title: MHV68bla_3T12_12h [BGISEQ]


title: Hdac3-Emx1-KO1-RNA

description:
Hdac3-Emx1-KO1-RNA_S2
dissected out from P0 brains directly
processed data file:
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_log2FC_DESeq2
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_FC_cufflinks

tag: cell type


title: Hdac3-WT2-RNA

description:
Hdac3-WT2-RNA_S1
dissected out from P0 brains directly
processed data file:
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_log2FC_DESeq2
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_FC_cufflinks

source_name: wild-type cerebral cortex from P0 pups


title: Hdac3-WT1-RNA

description:
Hdac3-WT1-RNA_S4
dissected out from P0 brains directly
processed data file:
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_log2FC_DESeq2
Wild_type_vs_P0_Hdac3_mutant_cerebrum_FPKM_FC_cufflinks


title: MHV68_3T12_12h [BGISEQ]

tag: cell line


title: KO8RNA

description:
KO8RNA_S43
cultured from E16.5 cerebrum in neural stem cell culture media till day 4
processed data file:
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_log2FC_DESeq2
Wild_type_vs_E16.5_Hdac3_mutant_neurosphere_FPKM_FC_cufflinks


title: Control sample 13


title: DE_IgG_(20180205_MM_HsSc_0122MPM153)

status: Public on Jun 24 2019

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&RUN for IgG in definitive endoderm cells using pA/MN with standard protocol, 3 min digestion

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed).

source_name: CUT&RUN

tag: antibody

value: Rabbit IgG Abcam Ab172730

value: Definitive endoderm derived from H1 hESCs


title: MHV68bla_3T12_12h [deepCAGE]


title: MHV68_3T12_18h [deepCAGE]


title: MHV68_3T12_6h [deepCAGE]


title: RNA_JdAGO1

status: Public on Jun 22 2019

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

institute: University of Edinburgh

description: polyA RNA

data_processing:
Cut out sequencing library adapters (CTGTAGGCACC) with cutadapt.
Remove rRNA reads by hisat2 alignment to the rRNA index file
Align remaining reads to a hisat2 index file
Trim 5' mismatches from reads and remove reads with more than 2 mismatches via a call to trim5pmismatch.py
Make bedgraph files using bedtools genomecov
Genome_build: CNA3 (H99) or Cryne_JEC21_1 (JEC21)
Supplementary_files_format_and_content: Bedgraphs on plus and minus strand; text files with gene-by-gene summaries.
Supplementary_files_format_and_content: H99_RiboViz_ATG_table_tidy.txt: RNA/RPF counts on ORFs and ATGs for all samples from C.neoformans H99
Supplementary_files_format_and_content: JEC21_RiboViz_ATG_table_tidy.txt: RNA/RPF counts on ORFs and ATGs for all samples from C.neoformans JEC21
Supplementary_files_format_and_content: ribosum_H99.txt: Gene expression summary in TPM for C.neoformans H99
Supplementary_files_format_and_content: ribosum_JEC21.txt: Gene expression summary in TPM for C.deneoformans JEC21

organism: Cryptococcus deneoformans

source_name: exponential-phase yeast cells

growth_protocol: Cells were streaked out on yPAD plates for 2-3 days, one colony inoculated in 5mL liquid YPAD media and grown overnight, diluted to OD 0.002 in 800mL YPAD, then grown for 12-16hrs until mid-exponential phase (OD 0.6- 0.7), all at 30C with shaking of liquid media.

extract_protocol: Extract and library construction as described in Ingolia 2012: https://doi.org/10.1038/nprot.2012.086

treatment_protocol: Cycloheximide added to 100ug/mL for 2mins. For RNA-seq, 50mL culture removed, spun 3000rpm for 3mins at RT and flash-frozen. For ribosome-protected fragments, remaining 750mLculture spun 5000rpm for 3mins, resuspended in 3mL lysis buffer, flash-frozen in liquid nitrogen.

tag: strain/genotype

value: JEC21 delta AGO1 strain CM1489

tag: submission date


title: MHV68_HE2_TPA [BGISEQ]

tag: treatment


title: RPF_JdAGO1

description: other - ribosome-protected RNA


title: Control sample 8

tag: Sex


title: MHV68_3T12_6h [BGISEQ]


title: MHV68bla_3T12_18h_B [BGISEQ]


title: H1_IgG_(20180205_MM_HsSc_0122MPM145)

description: CUT&RUN for IgG in H1 hESCs using pA/MN with standard protocol, 3 min digestion

value: H1 hESC, human embryonic stem cells


title: Control sample 7


title: MHV68bla_3T12_6h [BGISEQ]


title: H1_Sox2_(20180205_MM_HsSc_0122MPM141)

description: CUT&RUN for Sox2 in H1 hESCs using pA/MN with standard protocol, 30 min digestion


title: Control sample 2


title: H1_FoxA2_(20180205_MM_HsSc_0122MPM143)

description: CUT&RUN for FoxA2 in H1 hESCs using pA/MN with standard protocol, 30 min digestion

value: FoxA2 Millipore Sigma 07-633


title: Sample_BF25 (MNT_MaxKO_Set2)

status: Public on Jun 20 2019

first: Haritha

last: Mathsyaraja

address: 1100 Fairview Ave N

institute: Fred Hutch

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
Alignment to mm10 with Bowtie 2, reads >700bp filtered out, samples library size normalized.
Peak calling employed a threshold peak calling script to differentiate signal to noise (Kasinathan et al. 2014 PMID: 24336359).
Peaks min. width 25bp min. separation between peaks 50bp.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: B220+ cells were isolated from spleens of  mice of each genotype.

extract_protocol:
CUT&RUN libraries were prepared for sequencing using custom protocols
CUT&RUN

treatment_protocol: Cells were bound to ConA beads and incubated with antibodies

value: mixed 129/ C57Bl6

value: Max KO

tag: age

value: 4-5 weeks

value: B220+ splenocytes


title: Control sample 10

value: F


title: Sample_BF9 (E2F1_MaxWT_Set2)

value: Max WT


title: Control sample 11

value: M


title: DE_Sox2_(20180205_MM_HsSc_0122MPM149)

description: CUT&RUN for Sox2 in definitive endoderm cells using pA/MN with standard protocol, 30 min digestion


title: Control sample 12


title: MHV68_3T12_18h [BGISEQ]


title: DE_FoxA2_(20180205_MM_HsSc_0122MPM151)

description: CUT&RUN for FoxA2 in definitive endoderm cells using pA/MN with standard protocol, 30 min digestion


title: Sample_BF4 (MAX_MaxWT_Set2)


title: Sample_BF2 (MYC_MaxWT_Set2)


title: Sample_DJ_MmSc_E2Fb_MN_0313 (E2f1_MaxKO_Set1)

value: 9 weeks


title: RPF_JEC21

description: other - ribosome-protected RNA

value: JEC21 wild-type strain CM1487


title: Control sample 4


title: Sample_BF22 (MYC_MaxKO_Set2)


title: Sample_BF21(IgG_MaxKO_Set2)


title: Sample_BF7 (MNT_MaxWT_Set2)


title: Sample_BF24 (MAX_MaxKO_Set2)


title: Sample_DJ_MmSc_IgG_WT_0313 (IgG_MaxWT_Set1)


title: Sample_DJ_MmSc_MYC1_WT_0313 (MYC_MaxWT_Set1)


title: Control sample 5


title: Control sample 14


title: Sample_BF1 (IgG_MaxWT_Set2)


title: Sample_DJ_MmSc_MNT_WT_0313 (MNT_MaxWT_Set1)


title: Sample_BF26 (E2F1_MaxKO_Set2)


title: G2_endo_01

status: Public on Jun 16 2019

city: Durham

first: Allison

last: Ashley-Koch

state: North Carolina

address: Duke Box 104775, 300 N Duke Street

department: Duke Molecular Physiology Institute

institute: Duke University Medical Center

data_processing:
Quality control analysis of each sequenced library was performed using fastQC version 0.11.7
Removal of primer adapters was performed with Trim Galore version 0.4.0
Trimmed sequencing reads were aligned and mapped using to the D. rerio (genome release GRCm38) using the STAR version 2.6.0c
reads were filtered, sorted and indexed with Samtools version 1.3
Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0
read counts were analyzed with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: .count files contain raw (unnormalized) read counts for input to DESeq2

organism: Danio rerio

source_name: zebrafish endothelium

growth_protocol: Zebrafish were injected immediately after fertilization (single cell stage) and enbryos were harvested 4 days post fertilization

extract_protocol:
RNA was extracted from purified cells using a Qiagen RNeasy micro kit
cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit (Clonetech)

treatment_protocol: Zebrafsih were injected with 1nL of either APOL1 mRNA (150pg/nL)  or phenol red

tag: line

value: human APOL1 G2 mRNA


title: G2_endo_03


title: G2_endo_02


title: Sample_DJ_MmSc_MNT_MN_0313 (MNT_MaxKO_Set1)


title: G0_endo_02

value: human APOL1 G0 mRNA


title: Sample_DJ_MmSc_IgG_MN_0313 (IgG_MaxKO_Set1)


title: Sample_DJ_MmSc_MAX_MN_0313 (MAX_MaxKO_Set1)


title: Control sample 9


title: G0_endo_03


title: control_endo_03

value: control


title: control_endo_02


title: G0_pod_03

source_name: zebrafish podocyte


title: G2_pod_01


title: G2_pod_03


title: Control sample 1


title: G2_pod_02


title: G0_pod_02


title: Control sample 6


title: Control sample 3


title: Sample_DJ_MmSc_MAX_WT_0313 (MAX_MaxWT_Set1)


title: control_pod_02


title: G0_pod_01


title: VUB014_5

status: Public on Jun 12 2019

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
mapping sequences:
STAR 2.5.3
STAR --runThreadN 8 --runMode alignReads \  --quantMode  TranscriptomeSAM \ --twopassMode Basic \  --outSAMtype BAM SortedByCoordinate
count tables:
RSEM 1.3.0
rsem-calculate-expression -p 8 \ --alignments Aligned.toTranscriptome.out.ba
RNA seq analysis:
edgeR and DESeq2
Genome_build: GRCh38.p10/hg19
Supplementary_files_format_and_content: expression.genes.results and expression.isoforms.results  for each sample containing: gene_id transcript_id(s) length effective_length expected_count TPM FPKM

growth_protocol: hESC cultured on Laminin-521 with Nutristem medium, refreshed every day. Passaged once a week in a 1:20 ratio

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit, following manufacturers instructions
Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen) according to manufacturer's protocol

value: hESC

tag: karyotype

value: wild type


title: G0_endo_01


title: control_endo_01


title: control_pod_01


title: VUB014_4


title: VUB014_3


title: VUB014_2


title: VUB02_2


title: VUB03_3


title: VUB03_2


title: VUB014_1


title: VUB03_1


title: VUB01_2


title: VUB02_1


title: VUB01_1


title: E13_5

status: Public on Jun 11 2019

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Zentrum Munich

data_processing:
The 10X Genomics core computational software Cellranger v.2.1 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.3.2, anndata v0.6.1 and scrublet v.0.1 were used. Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/pancreatic-endocrinogenesis
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format. The file contains the preprocessed, normalized and annotated count data of all four experiments (E12.5-15-5).

extract_protocol:
Embryonic pancreata from NVF homozygous mice were dissected and pooled together. The pancreata were then digested by Trypsin and the cell suspensions were applied to FACS for cell sorting.
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.
RNA Seq (10X Genomics)

value: Homozygous Neurogenin3 (Ngn3)-Venus fusion reporter line (NVF)

tag: source tissue

value: pancreatic epithelium

tag: developmental day

value: embryonic stage 13.5


title: E12_5

tag: genotype

value: embryonic stage 12.5


title: control_pod_03


title: E14_5

value: embryonic stage 14.5


title: RNA_JEC21

description: polyA RNA


title: VUB03_5


title: Sample_DJ_MmSc_MYC1_MN_0313 (MYC_MaxKO_Set1)

tag: strain background

value: mixed 129/ C57Bl6


title: VUB03_4


status: Public on May 13 2019

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Clone 2 AML246 cells untreated or Doxycline treated, and normal mouse peripheral blood neutrophils.

data_processing:
Sequenced reads were mapped using the align function in the Rsubread package (Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the sc_gene_counting function from the scPipe package with the ENSEMBL v86 mouse annotation.
Size factors used in normalization were calculated using the computeSumFactors function from scran (Lun et al. F1000Res 2016)
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Generalised linear models were fitted to summarise the count values using the glmFit function from the edgeR package.
Genome_build: NCBI Build 38 patch 7
Supplementary_files_format_and_content: gene_count.csv
Supplementary_files_format_and_content: Counts matrix with samples along the columns and genes along the rows

source_name: Clone 2 AML246 cells untreated and Doxycline treated 14 days

growth_protocol: AML246 cells were cultured in standard medium (10% FCS in IMDM) supplemented with IL-3

extract_protocol:
Single cells were indexed sorted into 384 well plate format directly into lysis buffer as adapted from Celseq2 protocol
CelSeq2 (adapted at WEHI)
single cell RNA-Seq

treatment_protocol: 0.1 ug/mL Doxycycline was administered at day 0, and withdrawn at day 12, resulting in shutdown of GFP-linked shRNA expression and restoration of endogenous PU.1 expression

tag: facs markers

value: GFP+ for untreated and GFP- Mac1+  for DOX treated

tag: umi coordinate

value: 1 to 6 in R1

tag: barcode coordinate

value: 7 to 14 in R1


title: RNA2_hNP_FOXP2KE_rep1

status: Public on May 07 2019

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Protocol 2
second_RNA_Seq_COUNTS.txt
second_RNA_seq_CPM.txt
second_RNA_seq_RPKM.txt

data_processing:
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
ATAC-seq paired end reads were aligned with bowtie version 0.12.7 using options "bowtie -p 12 -y -v 2 --best --strata -m 3 -k 1 -X 2000"
ATAC-seq peaks were colled using MACS2 version 2.1.1.20160226 callpeak was used to identify peaks with the following parameters:  "--nomodel --nolambda --keep-dup all"  (Zhang et al., 2008). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/).
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (hg38, Gencode v.24). HiSeq 2500 and NextSeq 500 counts per gene were further added into a final count to calculate RPKM values and downstream analysis.
RNA-seq RPKM and CPM values were then quantified using in-home scripts, providing gene definitions (hg38, Gencode v.24).
Gene-level RPKMs or CPM quantifications were used for all downstream processing.
Genome_build: Human hg38
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each Sample.
Supplementary_files_format_and_content: tab-delimited text file with CPM values for each Sample.
Supplementary_files_format_and_content: unfiltered narrowPeak files including coordinates of the detected peaks from ATAC-Seq.

source_name: Proliferating neural progenitor cells (hNP)

growth_protocol: Proliferating and differentiated human neural progenitor cell lines were used.

extract_protocol:
Total RNA was extracted using Qiagen’s miRNeasy kit according to the manufacturer’s instructions. All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep as per the manufacturer’s instructions by UTSW McDermott Next Generation Sequencing Core

treatment_protocol: Tissue culture was performed as previously described (PMID: 21647150). Lentivirus was delivered via pLUGIP (ATCC 10326372) .

tag: cell type

value: Neural progenitor cells

tag: strain

tag: genotype/variation

value: Female


title: RNA2_hNP_CTRL_rep3

value: CTRL


title: RNA2_hNP_FOXP2KE_rep2


title: RNA2_hDN_FOXP2WT_rep1

source_name: Differentiated neural progenitor cells (hDN)


title: RNA2_hNP_CTRL_rep2


title: RNA2_hNP_CTRL_rep1


title: RNA2_hNP_FOXP2KE_rep3


title: RNA2_hDN_FOXP2KE_rep1


title: RNA2_hDN_FOXP2KE_rep2


title: RNA2_hDN_CTRL_rep2


title: RNA2_hDN_FOXP2WT_rep3


title: RNA2_hNP_FOXP2WT_rep1


title: RNA2_hNP_FOXP2WT_rep2


title: RNA2_hDN_FOXP2WT_rep2


title: RNA2_hDN_CTRL_rep3


title: RNA2_hDN_CTRL_rep1


title: RNA2_hDN_FOXP2KE_rep3


title: ATAC_hNP_FOXP2WT_rep3

description: Protocol 3

extract_protocol:
DNA was purified using Qiagen Qiaquick PCR purification kit and quantified using a Qubit Fluorometer according to the manufacturer’s instructions.
Libraries were prepared using previously published protocols (PMID: 25559105)

treatment_protocol: ATAC prococol was started 4 days or 28 days after lentiviral infection.


title: ATAC_hNP_FOXP2WT_rep2

description: Protocol 3


title: ATAC_hNP_FOXP2WT_rep4

description: Protocol 3


title: ATAC_hNP_FOXP2KE_rep3

description: Protocol 3


title: RNA2_hNP_FOXP2WT_rep3


title: ATAC_hNP_FOXP2KE_rep4

description: Protocol 3


title: E15_5

value: embryonic stage 15.5


title: ATAC_hNP_FOXP2WT_rep1

description: Protocol 3


title: ATAC_hNP_FOXP2KE_rep2

description: Protocol 3


title: ATAC_hNP_FOXP2KE_rep1

description: Protocol 3


title: ATAC_hNP_CTRL_rep4

description: Protocol 3


title: ATAC_hNP_CTRL_rep2

description: Protocol 3


title: ATAC_hNP_CTRL_rep1

description: Protocol 3


title: ATAC_hDN_FOXP2KE_rep4

description: Protocol 3


title: ATAC_hDN_FOXP2WT_rep4

description: Protocol 3


title: ATAC_hDN_FOXP2WT_rep1

description: Protocol 3


title: ATAC_hDN_CTRL_rep3

description: Protocol 3


title: ATAC_hDN_FOXP2WT_rep2

description: Protocol 3


title: ATAC_hDN_FOXP2KE_rep1

description: Protocol 3


title: ATAC_hDN_CTRL_rep1

description: Protocol 3


title: ATAC_hDN_CTRL_rep2

description: Protocol 3


title: ATAC_hDN_CTRL_rep4

description: Protocol 3


title: ATAC_hDN_FOXP2KE_rep2

description: Protocol 3


title: B04_Dual_RNA_c88

status: Public on May 02 2019

city: New York

first: Federico

last: Gaiti

state: NY

address: 413 East 69th St.

institute: Weill Cornell Medicine

data_processing:
Each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. Read pairs with a read shorter than 36bp after trimming were discarded. We aligned trimmed reads in single-end mode to the hg19 human genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For downstream analyses, a site was considered methylated or unmethylated only if there was 90% agreement of the methylation state for all reads mapped to the site.
The sequenced paired-end read fragments were mapped against the hg19 human genome assembly using the 2pass default mode of STAR98 (version 2.5.2a) with the annotation of GENCODE99 (version 19). The number of read counts overlapping with annotated genes were quantified applying the ‘GeneCounts’ option in the STAR alignment.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include the number of read counts overlapping with annotated genes for all cells. Comma-separated values files contain the list of cell barcodes used in MscRRBS library construction and the sequencing summary statistics for each cell.

source_name: Healthy donor 4 Dual Protocol scRNAseq

extract_protocol:
Single cell experiments were performed by sorting DAPI negative cells in 96-well plates in 3 µL of 0.1X CutSmart buffer (New England Biolabs) per well using a BD Influx sorter (Becton Dickinson, Franklin Lakes, NJ). Normal B cells for sample B04, B05, and B06 were further index-sorted using a BD Influx sorter using the following sorting strategy: NBC (CD27-, IgM+, IgD+++), loMBC (CD27-, IgM+, IgD+), intMBC (CD27+, IgM+, IgD++) and hiMBC (CD27+, IgG+). The antibodies used were: FITC Mouse Anti-Human IgD (Clone IA6-2, BD Pharmingen), APC Mouse Anti-Human IgG (#562025, BD Biosciences), APC/Cy7 anti-human IgM Antibody (Clone MHM-88, BioLegend) and PE/Cy7 anti-human CD27 Antibody (clone O323, Bio Legend). Plates were then stored at -80C until further processing. The day of the experiment, cells were lysed for 2 hours at 50C in 1X CutSmart buffer supplemented with Proteinase K (0.2U, NEB) and Triton X-100 (0.3%, Sigma Aldrich) for a final volume of 5 µL. Proteinase K was heat-inactivated for 30 min at 75C. DNA was incubated with 10 units of the restriction enzyme Msp1 (Fermentas) in 6.5 µL final volume reaction during 90 min at 37C. Heat-inactivation was performed for 10 min at 70C. Digested DNA was filled-in and A-tailed at the 3’ sticky ends in 8.5 µL final volume of 1X CutSmart with 2.5 units of Klenow fragment (Exo-, Fermentas). Reaction was supplemented with 1 mM dATP and 0.1 mM dCTP and 0.1 mM dGTP (NEB) and performed as follows in a thermocycler: 30C for 25 min, 37C for 25 min and heat-inactivation at 70C for 10 min. Custom barcoded methylated adaptors (0.1 µM) were then ligated overnight at 16C with the dA-tailed DNA fragments in the presence of 800 units of T4 DNA ligase (NEB) and 1 mM ATP (Roche) in a final volume of 11.5 µL of 1X CutSmart buffer. T4 DNA ligase heat-inactivation was performed at 70C for 15 min the next day. Genomic DNA from 24 individual cells were pooled together according to their barcodes, giving, for a 96-well plate, 4 pools of 24 cells. Pooled genomic DNA was cleaned-up and concentrated using 1.8X SPRI beads (Agencourt AMPure XP - Beckman Coulter). Each pool was then sodium bisulfite converted (Fast Epitect Bisulfite, Qiagen) following manufacture recommendations. To ensure full bisulfite conversion, two cycles of conversion were performed. The double-stranded DNA was first denatured 10 min at 98°C and then incubated for 20 min at 60°C. 100 ng of dephosphorylated and sheared bacterial DNA was added as carrier to every pool prior to conversion.
Converted DNA was then amplified using primers containing Illumina i7 and i5 index. Following Illumina pooling guidelines, a different i7 index was used for every 24-cell pool, allowing multiplexing of 96 cells for sequencing on one Illumina HiSeq lane. Library enrichment was done using KAPA HiFi Uracil+ master mix (Kapa Biosystems) and the following PCR condition was used: 98°C for 45 secs; 6 cycles of: 98°C for 20 secs, 58°C for 30 secs, 72°C for 1 min; followed by 12 cycles of: 98°C for 20 secs, 65°C for 30 secs, 72°C for 1 min. PCR was terminated by an incubation at 72°C for 5 min. Enriched libraries were cleaned-up and concentrated using 1.3X SPRI beads. DNA fragments between 200 bp and 1 Kb were size-selected and recovered after resolving on a 3% NuSieve 3:1 agarose gel. Libraries molarity concentration calculation was obtained by measuring concentration of double stranded DNA (Qubit) and quantifying the average library size (bp) using an Agilent Bioanalyzer. Every 24-cells pool was mixed with the others pool in an equimolar ratio. All cells from a 96-well plate were sequenced as paired-end on HiSeq 2500 with 10% PhiX spike-in. Negative controls were used to control for non-specific amplification of the libraries.
Single cells are sorted by flow cytometry into 2.5 uL of RLT Plus buffer (Qiagen) supplemented with 1 U/uL of RNase Inhibitor (Lucigen). Sorted cells were immediately store at -80°C. Genomic DNA and mRNA have been separated manually as previously described. Single-cell complementary DNA was amplified from the tubes containing the captured mRNA according to the Smart2-seq protocol. After amplification and purification using 0.8X SPRI beads, 0.5ng cDNA was used for Nextera Tagmentation and library construction. Library quality and quantity were assessed using Agilent Bioanalyzer 2100 and Qubit, respectively.

value: CD19+ B cells

tag: patient donor

value: donor 4


title: B04_Dual_RNA_c92


title: B04_Dual_RNA_c93


title: B04_Dual_RNA_c91


title: B06

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: Healthy donor 6 stand-alone MscRRBS

value: donor 6


title: B04_Dual_RNA_c87


title: B04_Dual_RNA_c90


title: B04_Dual_RNA_c95


title: B04_Dual_RNA_c86


title: B04_Dual_RNA_c85


title: ATAC_hDN_FOXP2WT_rep3

description: Protocol 3


title: B04_Dual_RNA_c84


title: B05

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: Healthy donor 5 stand-alone MscRRBS

value: donor 5


title: B04_Dual_RNA_c89


title: ATAC_hDN_FOXP2KE_rep3

description: Protocol 3


title: B04_Dual_RNA_c74


title: B04_Dual_RNA_c83


title: B04_Dual_RNA_c73


title: B04_Dual_RNA_c82


title: B04_Dual_RNA_c80


title: B04_Dual_RNA_c81


title: B04_Dual_RNA_c71


title: B04_Dual_RNA_c79


title: B04_Dual_RNA_c75


title: B04_Dual_RNA_c76


title: B04_Dual_RNA_c78


title: B04_Dual_RNA_c66


title: B04_Dual_RNA_c70


title: B04_Dual_RNA_c68


title: B04_Dual_RNA_c65


title: B04_Dual_RNA_c72


title: B04_Dual_RNA_c64


title: B04_Dual_RNA_c62


title: B04_Dual_RNA_c63


title: B04_Dual_RNA_c58


title: B04_Dual_RNA_c69


title: B04_Dual_RNA_c67


title: B04_Dual_RNA_c59


title: B04_Dual_RNA_c61


title: B04_Dual_RNA_c60


title: B04_Dual_RNA_c77


title: B04_Dual_RNA_c56


title: B04_Dual_RNA_c55


title: ATAC_hNP_CTRL_rep3

description: Protocol 3


title: B04_Dual_RNA_c51


title: B04_Dual_RNA_c54


title: B04_Dual_RNA_c50


title: B04_Dual_RNA_c53


title: B04_Dual_RNA_c52


title: B04_Dual_RNA_c57


title: B04_Dual_RNA_c46


title: B04_Dual_RNA_c48


title: B04_Dual_RNA_c47


title: Sample_DJ_MmSc_E2Fb_WT_0313 (E2f1_MaxWT_Set1)

value: Max KO

value: 9 weeks

value: B220+ splenocytes


title: B04_Dual_RNA_c42


title: B04_Dual_RNA_c37


title: B04_Dual_RNA_c38


title: B04_Dual_RNA_c36


title: B04_Dual_RNA_c33


title: B04_Dual_RNA_c31


title: B04_Dual_RNA_c43


title: B04_Dual_RNA_c45


title: B04_Dual_RNA_c34


title: B04_Dual_RNA_c32


title: B04_Dual_RNA_c40


title: B04_Dual_RNA_c30


title: B04_Dual_RNA_c49


title: B04_Dual_RNA_c44


title: B04_Dual_RNA_c39


title: B04_Dual_RNA_c35


title: B04_Dual_RNA_c29


title: B04_Dual_RNA_c41


title: B04_Dual_RNA_c26


title: B04_Dual_RNA_c28


title: B04_Dual_RNA_c27


title: B04_Dual_RNA_c23


title: B04_Dual_RNA_c25


title: B04_Dual_RNA_c22


title: B04_Dual_RNA_c24


title: B04_Dual_RNA_c21


title: B04_Dual_RNA_c15


title: B04_Dual_RNA_c16


title: B04_Dual_RNA_c17


title: B04_Dual_RNA_c18


title: B04_Dual_RNA_c14


title: B04_Dual_RNA_c9


title: B04_Dual_RNA_c10


title: B04_Dual_RNA_c12


title: B04_Dual_RNA_c7


title: B04_Dual_RNA_c11


title: B04_Dual_RNA_c13


title: B04_Dual_RNA_c20


title: B04_Dual_RNA_c19


title: B04_Dual_RNA_c5


title: B04_Dual_RNA_c4


title: B04_Dual_RNA_c3


title: B04_Dual_RNA_c2


title: CLL12_Dual_RNA_c96

source_name: CLL patient 12 Dual Protocol scRNAseq

value: primary human chronic lymphocytic leukemia (CLL) cells

value: patient 12


title: CLL12_Dual_RNA_c95


title: B04 Dual MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: Healthy donor 4 Dual Protocol MscRRBS


title: B04_Dual_RNA_c1


title: CLL12_Dual_RNA_c94


title: CLL12_Dual_RNA_c91


title: CLL12_Dual_RNA_c92


title: CLL12_Dual_RNA_c88


title: CLL12_Dual_RNA_c89


title: B04_Dual_RNA_c8


title: CLL12_Dual_RNA_c90


title: CLL12_Dual_RNA_c85


title: CLL12_Dual_RNA_c86


title: CLL12_Dual_RNA_c87


title: CLL12_Dual_RNA_c84


title: CLL12_Dual_RNA_c83


title: CLL12_Dual_RNA_c80


title: CLL12_Dual_RNA_c82


title: CLL12_Dual_RNA_c79


title: B04

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: Healthy donor 4 stand-alone MscRRBS


title: CLL12_Dual_RNA_c78


title: CLL12_Dual_RNA_c93


title: CLL12_Dual_RNA_c77


title: CLL12_Dual_RNA_c76


title: CLL12_Dual_RNA_c74


title: CLL12_Dual_RNA_c75


title: CLL12_Dual_RNA_c73


title: CLL12_Dual_RNA_c72


title: CLL12_Dual_RNA_c70


title: CLL12_Dual_RNA_c65


title: CLL12_Dual_RNA_c67


title: CLL12_Dual_RNA_c69


title: CLL12_Dual_RNA_c68


title: CLL12_Dual_RNA_c81


title: CLL12_Dual_RNA_c66


title: B04_Dual_RNA_c6


title: CLL12_Dual_RNA_c63


title: CLL12_Dual_RNA_c64


title: CLL12_Dual_RNA_c60


title: CLL12_Dual_RNA_c57


title: CLL12_Dual_RNA_c59


title: CLL12_Dual_RNA_c54


title: CLL12_Dual_RNA_c56


title: CLL12_Dual_RNA_c55


title: CLL12_Dual_RNA_c53


title: CLL12_Dual_RNA_c52


title: CLL12_Dual_RNA_c71


title: CLL12_Dual_RNA_c51


title: CLL12_Dual_RNA_c49


title: CLL12_Dual_RNA_c48


title: CLL12_Dual_RNA_c50


title: CLL12_Dual_RNA_c47


title: CLL12_Dual_RNA_c62


title: CLL12_Dual_RNA_c61


title: CLL12_Dual_RNA_c45


title: CLL12_Dual_RNA_c46


title: CLL12_Dual_RNA_c58


title: CLL12_Dual_RNA_c44


title: CLL12_Dual_RNA_c42


title: CLL12_Dual_RNA_c38


title: CLL12_Dual_RNA_c41


title: CLL12_Dual_RNA_c36


title: B04_Dual_RNA_c94


title: CLL12_Dual_RNA_c34


title: CLL12_Dual_RNA_c35


title: CLL12_Dual_RNA_c31


title: CLL12_Dual_RNA_c39


title: CLL12_Dual_RNA_c37


title: CLL12_Dual_RNA_c32


title: CLL12_Dual_RNA_c33


title: CLL12_Dual_RNA_c30


title: CLL12_Dual_RNA_c29


title: CLL12_Dual_RNA_c28


title: CLL12_Dual_RNA_c43


title: CLL12_Dual_RNA_c40


title: CLL12_Dual_RNA_c11


title: CLL12_Dual_RNA_c19


title: CLL12_Dual_RNA_c12


title: CLL12_Dual_RNA_c26


title: CLL12_Dual_RNA_c15


title: CLL12_Dual_RNA_c13


title: CLL12_Dual_RNA_c23


title: CLL12_Dual_RNA_c20


title: CLL12_Dual_RNA_c24


title: CLL12_Dual_RNA_c10


title: CLL12_Dual_RNA_c21


title: CLL12_Dual_RNA_c17


title: CLL12_Dual_RNA_c14


title: CLL12_Dual_RNA_c16


title: CLL12_Dual_RNA_c22


title: CLL12_Dual_RNA_c25


title: CLL12_Dual_RNA_c18


title: CLL12_Dual_RNA_c6


title: CLL12_Dual_RNA_c27


title: CLL12_Dual_RNA_c4


title: CLL12_Dual_RNA_c8


title: CLL12_Dual_RNA_c2


title: CLL12_Dual_RNA_c5


title: CLL12_Dual_RNA_c3


title: CLL12_Dual_RNA_c1


title: CLL12 Dual MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 12 Dual Protocol MscRRBS


title: CLL12_Dual_RNA_c7


title: CLL12_Dual_RNA_c9


title: CLL09

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 9 stand-alone MscRRBS

value: patient 9


title: CLL10

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 10 stand-alone MscRRBS

value: patient 10


title: CLL07

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 7 stand-alone MscRRBS

value: patient 7


title: CLL08

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 8 stand-alone MscRRBS

value: patient 8


title: CLL05_T1_Dual_RNA_c94

source_name: CLL patient 5 time-point 2 Dual Protocol scRNAseq

value: patient 5

tag: time point

value: time-point 2


title: CLL05_T1_Dual_RNA_c79


title: CLL05_T1_Dual_RNA_c95


title: CLL05_T1_Dual_RNA_c77


title: CLL06

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 6 stand-alone MscRRBS

value: patient 6


title: CLL05_T1_Dual_RNA_c80


title: CLL05_T1_Dual_RNA_c76


title: CLL05_T1_Dual_RNA_c86


title: CLL05_T1_Dual_RNA_c84


title: CLL05_T1_Dual_RNA_c91


title: CLL05_T1_Dual_RNA_c90


title: CLL05_T1_Dual_RNA_c89


title: CLL05_T1_Dual_RNA_c85


title: CLL05_T1_Dual_RNA_c81


title: CLL05_T1_Dual_RNA_c88


title: CLL05_T1_Dual_RNA_c82


title: CLL05_T1_Dual_RNA_c83


title: CLL05_T1_Dual_RNA_c93


title: CLL05_T1_Dual_RNA_c92


title: CLL05_T1_Dual_RNA_c74


title: CLL05_T1_Dual_RNA_c73


title: CLL05_T1_Dual_RNA_c72


title: CLL05_T1_Dual_RNA_c71


title: CLL05_T1_Dual_RNA_c70


title: CLL05_T1_Dual_RNA_c96


title: CLL05_T1_Dual_RNA_c75


title: CLL05_T1_Dual_RNA_c68


title: CLL05_T1_Dual_RNA_c69


title: CLL05_T1_Dual_RNA_c87


title: CLL05_T1_Dual_RNA_c78


title: CLL05_T1_Dual_RNA_c67


title: CLL05_T1_Dual_RNA_c65


title: CLL05_T1_Dual_RNA_c64


title: CLL05_T1_Dual_RNA_c48


title: CLL05_T1_Dual_RNA_c47


title: CLL05_T1_Dual_RNA_c62


title: CLL05_T1_Dual_RNA_c46


title: CLL05_T1_Dual_RNA_c60


title: CLL05_T1_Dual_RNA_c58


title: CLL05_T1_Dual_RNA_c43


title: CLL05_T1_Dual_RNA_c45


title: CLL05_T1_Dual_RNA_c53


title: CLL05_T1_Dual_RNA_c44


title: CLL05_T1_Dual_RNA_c52


title: CLL05_T1_Dual_RNA_c56


title: CLL05_T1_Dual_RNA_c54


title: CLL05_T1_Dual_RNA_c51


title: CLL05_T1_Dual_RNA_c57


title: CLL05_T1_Dual_RNA_c59


title: CLL05_T1_Dual_RNA_c55


title: CLL05_T1_Dual_RNA_c42


title: CLL05_T1_Dual_RNA_c40


title: CLL05_T1_Dual_RNA_c50


title: CLL05_T1_Dual_RNA_c41


title: CLL05_T1_Dual_RNA_c37


title: CLL05_T1_Dual_RNA_c38


title: CLL05_T1_Dual_RNA_c66


title: CLL05_T1_Dual_RNA_c63


title: CLL05_T1_Dual_RNA_c61


title: CLL05_T1_Dual_RNA_c36


title: CLL05_T1_Dual_RNA_c34


title: CLL05_T1_Dual_RNA_c31


title: CLL05_T1_Dual_RNA_c33


title: CLL05_T1_Dual_RNA_c30


title: CLL05_T1_Dual_RNA_c26


title: CLL05_T1_Dual_RNA_c39


title: CLL05_T1_Dual_RNA_c24


title: CLL05_T1_Dual_RNA_c28


title: CLL05_T1_Dual_RNA_c23


title: CLL05_T1_Dual_RNA_c49


title: CLL05_T1_Dual_RNA_c22


title: CLL05_T1_Dual_RNA_c25


title: CLL05_T1_Dual_RNA_c29


title: CLL05_T1_Dual_RNA_c19


title: CLL05_T1_Dual_RNA_c18


title: CLL05_T1_Dual_RNA_c21


title: CLL05_T1_Dual_RNA_c27


title: CLL05_T1_Dual_RNA_c12


title: CLL05_T1_Dual_RNA_c11


title: CLL05_T1_Dual_RNA_c13


title: CLL05_T1_Dual_RNA_c14


title: CLL05_T1_Dual_RNA_c10


title: CLL05_T1_Dual_RNA_c17


title: CLL05_T1_Dual_RNA_c8


title: CLL05_T1_Dual_RNA_c9


title: CLL05_T1_Dual_RNA_c32


title: CLL05_T1_Dual_RNA_c15


title: CLL05_T1_Dual_RNA_c16


title: CLL05_T1_Dual_RNA_c35


title: CLL05_T1_Dual_RNA_c7


title: CLL05_T1_Dual_RNA_c6


title: CLL05_T1_Dual_RNA_c20


title: CLL05_T1_Dual_RNA_c3


title: CLL05_T1_Dual_RNA_c4


title: CLL05_T1_Dual_RNA_c2


title: CLL05_T0_Dual_RNA_c96

source_name: CLL patient 5 time-point 1 Dual Protocol scRNAseq

value: time-point 1


title: CLL05_T0_Dual_RNA_c95


title: CLL05_T1_Dual_RNA_c1


title: CLL05_T0_Dual_RNA_c94


title: CLL05_T0_Dual_RNA_c93


title: CLL05_T0_Dual_RNA_c92


title: CLL05_T0_Dual_RNA_c89


title: CLL05_T0_Dual_RNA_c91


title: CLL05_T0_Dual_RNA_c90


title: CLL05_T0_Dual_RNA_c82


title: CLL05_T0_Dual_RNA_c84


title: CLL05_T0_Dual_RNA_c81


title: CLL05_T0_Dual_RNA_c85


title: CLL05_T0_Dual_RNA_c87


title: CLL05_T0_Dual_RNA_c83


title: CLL05_T0_Dual_RNA_c75


title: CLL05_T0_Dual_RNA_c77


title: CLL05_T0_Dual_RNA_c74


title: CLL05_T0_Dual_RNA_c86


title: CLL05_T0_Dual_RNA_c76


title: CLL05_T0_Dual_RNA_c80


title: CLL05_T1_Dual_RNA_c5


title: CLL05_T0_Dual_RNA_c78


title: CLL05_T0_Dual_RNA_c79


title: CLL05_T0_Dual_RNA_c72


title: CLL05_T0_Dual_RNA_c73


title: CLL05_T0_Dual_RNA_c71


title: CLL05_T0_Dual_RNA_c70


title: CLL05_T0_Dual_RNA_c69


title: CLL05_T0_Dual_RNA_c88


title: CLL05_T0_Dual_RNA_c68


title: CLL05_T0_Dual_RNA_c66


title: CLL05_T0_Dual_RNA_c67


title: CLL05_T0_Dual_RNA_c65


title: CLL05_T0_Dual_RNA_c62


title: CLL05_T0_Dual_RNA_c63


title: CLL05_T0_Dual_RNA_c64


title: CLL05_T0_Dual_RNA_c61


title: CLL05_T0_Dual_RNA_c60


title: CLL05_T0_Dual_RNA_c59


title: CLL05_T0_Dual_RNA_c54


title: CLL05_T0_Dual_RNA_c56


title: CLL05_T0_Dual_RNA_c51


title: CLL05_T0_Dual_RNA_c53


title: CLL05_T0_Dual_RNA_c49


title: CLL05_T0_Dual_RNA_c50


title: CLL05_T0_Dual_RNA_c52


title: CLL05_T0_Dual_RNA_c47


title: CLL05_T0_Dual_RNA_c46


title: CLL05_T0_Dual_RNA_c45


title: CLL05_T0_Dual_RNA_c48


title: CLL05_T0_Dual_RNA_c55


title: CLL05_T0_Dual_RNA_c43


title: CLL05_T0_Dual_RNA_c42


title: CLL05_T0_Dual_RNA_c40


title: CLL05_T0_Dual_RNA_c37


title: CLL05_T0_Dual_RNA_c39


title: CLL05_T0_Dual_RNA_c41


title: CLL05_T0_Dual_RNA_c38


title: CLL05_T0_Dual_RNA_c36


title: CLL05_T0_Dual_RNA_c44


title: CLL05_T0_Dual_RNA_c58


title: CLL05_T0_Dual_RNA_c35


title: CLL05_T0_Dual_RNA_c57


title: CLL05_T0_Dual_RNA_c33


title: CLL05_T0_Dual_RNA_c34


title: CLL05_T0_Dual_RNA_c32


title: CLL05_T0_Dual_RNA_c30


title: CLL05_T0_Dual_RNA_c29


title: CLL05_T0_Dual_RNA_c31


title: CLL05_T0_Dual_RNA_c27


title: CLL05_T0_Dual_RNA_c25


title: CLL05_T0_Dual_RNA_c24


title: CLL05_T0_Dual_RNA_c23


title: CLL05_T0_Dual_RNA_c26


title: CLL05_T0_Dual_RNA_c28


title: CLL05_T0_Dual_RNA_c19


title: CLL05_T0_Dual_RNA_c17


title: CLL05_T0_Dual_RNA_c16


title: CLL05_T0_Dual_RNA_c22


title: CLL05_T0_Dual_RNA_c20


title: CLL05_T0_Dual_RNA_c21


title: CLL05_T0_Dual_RNA_c14


title: CLL05_T0_Dual_RNA_c12


title: CLL05_T0_Dual_RNA_c13


title: CLL05_T0_Dual_RNA_c11


title: CLL05_T0_Dual_RNA_c10


title: CLL05_T0_Dual_RNA_c8


title: CLL05_T0_Dual_RNA_c5


title: CLL05_T0_Dual_RNA_c7


title: CLL05_T0_Dual_RNA_c6


title: CLL05_T0_Dual_RNA_c3


title: CLL05_T0_Dual_RNA_c4


title: CLL05_T0_Dual_RNA_c2


title: CLL05_T1_Dual_MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 5 time-point 2 Dual Protocol MscRRBS


title: CLL05_T0_Dual_RNA_c18


title: CLL05_T0_Dual_RNA_c1


title: CLL05_T0_Dual_RNA_c15


title: CLL05

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 5 time-point 1 stand-alone MscRRBS


title: CLL04_T1_Dual_RNA_c91

source_name: CLL patient 4 time-point 2 Dual Protocol scRNAseq

value: patient 4


title: CLL04_T1_Dual_RNA_c94


title: CLL04_T1_Dual_RNA_c95


title: CLL04_T1_Dual_RNA_c96


title: CLL04_T1_Dual_RNA_c90


title: CLL04_T1_Dual_RNA_c89


title: CLL04_T1_Dual_RNA_c87


title: CLL04_T1_Dual_RNA_c86


title: CLL04_T1_Dual_RNA_c81


title: CLL04_T1_Dual_RNA_c84


title: CLL04_T1_Dual_RNA_c83


title: CLL04_T1_Dual_RNA_c82


title: CLL04_T1_Dual_RNA_c85


title: CLL04_T1_Dual_RNA_c80


title: CLL04_T1_Dual_RNA_c75


title: CLL04_T1_Dual_RNA_c79


title: CLL04_T1_Dual_RNA_c77


title: CLL04_T1_Dual_RNA_c78


title: CLL04_T1_Dual_RNA_c73


title: CLL04_T1_Dual_RNA_c72


title: CLL04_T1_Dual_RNA_c92


title: CLL05_T0_Dual_RNA_c9


title: CLL05_T0_Dual_MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 5 time-point 1 Dual Protocol MscRRBS


title: CLL04_T1_Dual_RNA_c70


title: CLL04_T1_Dual_RNA_c71


title: CLL04_T1_Dual_RNA_c88


title: CLL04_T1_Dual_RNA_c69


title: CLL04_T1_Dual_RNA_c66


title: CLL04_T1_Dual_RNA_c65


title: CLL04_T1_Dual_RNA_c68


title: CLL04_T1_Dual_RNA_c67


title: CLL04_T1_Dual_RNA_c63


title: CLL04_T1_Dual_RNA_c93


title: CLL04_T1_Dual_RNA_c64


title: CLL04_T1_Dual_RNA_c61


title: CLL04_T1_Dual_RNA_c74


title: CLL04_T1_Dual_RNA_c62


title: CLL04_T1_Dual_RNA_c59


title: CLL04_T1_Dual_RNA_c60


title: CLL04_T1_Dual_RNA_c55


title: CLL04_T1_Dual_RNA_c56


title: CLL04_T1_Dual_RNA_c76


title: CLL04_T1_Dual_RNA_c53


title: CLL04_T1_Dual_RNA_c51


title: CLL04_T1_Dual_RNA_c54


title: CLL04_T1_Dual_RNA_c57


title: CLL04_T1_Dual_RNA_c49


title: CLL04_T1_Dual_RNA_c52


title: CLL04_T1_Dual_RNA_c50


title: CLL04_T1_Dual_RNA_c48


title: CLL04_T1_Dual_RNA_c46


title: CLL04_T1_Dual_RNA_c47


title: CLL04_T1_Dual_RNA_c45


title: CLL04_T1_Dual_RNA_c42


title: CLL04_T1_Dual_RNA_c37


title: CLL04_T1_Dual_RNA_c40


title: CLL04_T1_Dual_RNA_c38


title: CLL04_T1_Dual_RNA_c58


title: CLL04_T1_Dual_RNA_c39


title: CLL04_T1_Dual_RNA_c35


title: CLL04_T1_Dual_RNA_c36


title: CLL04_T1_Dual_RNA_c34


title: CLL04_T1_Dual_RNA_c33


title: CLL04_T1_Dual_RNA_c31


title: CLL04_T1_Dual_RNA_c32


title: CLL04_T1_Dual_RNA_c28


title: CLL04_T1_Dual_RNA_c26


title: CLL04_T1_Dual_RNA_c44


title: CLL04_T1_Dual_RNA_c27


title: CLL04_T1_Dual_RNA_c29


title: CLL04_T1_Dual_RNA_c21


title: CLL04_T1_Dual_RNA_c19


title: CLL04_T1_Dual_RNA_c20


title: CLL04_T1_Dual_RNA_c41


title: CLL04_T1_Dual_RNA_c18


title: CLL04_T1_Dual_RNA_c17


title: CLL04_T1_Dual_RNA_c16


title: CLL04_T1_Dual_RNA_c43


title: CLL04_T1_Dual_RNA_c22


title: CLL04_T1_Dual_RNA_c25


title: CLL04_T1_Dual_RNA_c15


title: CLL04_T1_Dual_RNA_c13


title: CLL04_T1_Dual_RNA_c10


title: CLL04_T1_Dual_RNA_c12


title: CLL04_T1_Dual_RNA_c11


title: CLL04_T1_Dual_RNA_c30


title: CLL04_T1_Dual_RNA_c7


title: CLL04_T1_Dual_RNA_c8


title: CLL04_T1_Dual_RNA_c23


title: CLL04_T1_Dual_RNA_c24


title: CLL04_T1_Dual_RNA_c4


title: CLL04_T1_Dual_RNA_c3


title: CLL04_T1_Dual_RNA_c6


title: CLL04_T1_Dual_RNA_c2


title: CLL04_T1_Dual_RNA_c5


title: CLL04_T0_Dual_RNA_c95

source_name: CLL patient 4 time-point 1 Dual Protocol scRNAseq


title: CLL04_T1_Dual_RNA_c1


title: CLL04_T0_Dual_RNA_c92


title: CLL04_T0_Dual_RNA_c96


title: CLL04_T0_Dual_RNA_c93


title: CLL04_T0_Dual_RNA_c91


title: CLL04_T1_Dual_RNA_c9


title: CLL04_T0_Dual_RNA_c90


title: CLL04_T0_Dual_RNA_c85


title: CLL04_T0_Dual_RNA_c88


title: CLL04_T0_Dual_RNA_c87


title: CLL04_T0_Dual_RNA_c89


title: CLL04_T0_Dual_RNA_c86


title: CLL04_T1_Dual_RNA_c14


title: CLL04_T0_Dual_RNA_c80


title: CLL04_T0_Dual_RNA_c81


title: CLL04_T0_Dual_RNA_c83


title: CLL04_T0_Dual_RNA_c84


title: CLL04_T0_Dual_RNA_c82


title: CLL04_T0_Dual_RNA_c78


title: CLL04_T0_Dual_RNA_c77


title: CLL04_T0_Dual_RNA_c76


title: CLL04_T0_Dual_RNA_c75


title: CLL04_T0_Dual_RNA_c73


title: CLL04_T0_Dual_RNA_c94


title: CLL04_T0_Dual_RNA_c79


title: CLL04_T0_Dual_RNA_c71


title: CLL04_T0_Dual_RNA_c68


title: CLL04_T0_Dual_RNA_c74


title: CLL04_T0_Dual_RNA_c72


title: CLL04_T0_Dual_RNA_c67


title: CLL04_T0_Dual_RNA_c65


title: CLL04_T0_Dual_RNA_c66


title: CLL04_T0_Dual_RNA_c61


title: CLL04_T0_Dual_RNA_c63


title: CLL04_T0_Dual_RNA_c60


title: CLL04_T0_Dual_RNA_c69


title: CLL04_T0_Dual_RNA_c59


title: CLL04_T0_Dual_RNA_c58


title: CLL04_T0_Dual_RNA_c64


title: CLL04_T0_Dual_RNA_c62


title: CLL04_T0_Dual_RNA_c56


title: CLL04_T0_Dual_RNA_c57


title: CLL04_T0_Dual_RNA_c55


title: CLL04_T0_Dual_RNA_c53


title: CLL04_T0_Dual_RNA_c51


title: CLL04_T0_Dual_RNA_c49


title: CLL04_T0_Dual_RNA_c50


title: CLL04_T0_Dual_RNA_c47


title: CLL04_T0_Dual_RNA_c48


title: CLL04_T0_Dual_RNA_c46


title: CLL04_T0_Dual_RNA_c45


title: CLL04_T0_Dual_RNA_c43


title: CLL04_T0_Dual_RNA_c52


title: CLL04_T0_Dual_RNA_c42


title: CLL04_T0_Dual_RNA_c40


title: CLL04_T0_Dual_RNA_c44


title: CLL04_T0_Dual_RNA_c41


title: CLL04_T0_Dual_RNA_c38


title: CLL04_T0_Dual_RNA_c37


title: CLL04_T0_Dual_RNA_c54


title: CLL04_T0_Dual_RNA_c35


title: CLL04_T0_Dual_RNA_c36


title: CLL04_T0_Dual_RNA_c34


title: CLL04_T0_Dual_RNA_c33


title: CLL04_T0_Dual_RNA_c30


title: CLL04_T0_Dual_RNA_c31


title: CLL04_T0_Dual_RNA_c32


title: CLL04_T0_Dual_RNA_c70


title: CLL04_T0_Dual_RNA_c22


title: CLL04_T0_Dual_RNA_c23


title: CLL04_T0_Dual_RNA_c21


title: CLL04_T0_Dual_RNA_c20


title: CLL04_T0_Dual_RNA_c26


title: CLL04_T0_Dual_RNA_c28


title: CLL04_T0_Dual_RNA_c29


title: CLL04_T0_Dual_RNA_c39


title: CLL04_T0_Dual_RNA_c27


title: CLL04_T0_Dual_RNA_c25


title: CLL04_T0_Dual_RNA_c15


title: CLL04_T0_Dual_RNA_c14


title: CLL04_T0_Dual_RNA_c18


title: CLL04_T0_Dual_RNA_c17


title: CLL04_T0_Dual_RNA_c13


title: CLL04_T0_Dual_RNA_c12


title: CLL04_T0_Dual_RNA_c10


title: CLL04_T0_Dual_RNA_c11


title: CLL04_T0_Dual_RNA_c24


title: CLL04_T0_Dual_RNA_c8


title: CLL04_T0_Dual_RNA_c7


title: CLL04_T0_Dual_RNA_c6


title: CLL04_T0_Dual_RNA_c16


title: CLL04_T0_Dual_RNA_c2


title: CLL04_T0_Dual_RNA_c4


title: CLL04_T0_Dual_RNA_c5


title: CLL04_T0_Dual_RNA_c3


title: CLL03_T1_Dual_RNA_c95

source_name: CLL patient 3 time-point 2 Dual Protocol scRNAseq

value: patient 3


title: CLL04_T0_Dual_MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 4 time-point 1 Dual Protocol MscRRBS


title: CLL04

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 4 time-point 1 stand-alone MscRRBS


title: CLL03_T1_Dual_RNA_c93


title: CLL03_T1_Dual_RNA_c94


title: CLL03_T1_Dual_RNA_c86


title: CLL03_T1_Dual_RNA_c87


title: CLL04_T1_Dual_MscRRBS

description:
Barcodes.xlsx
Cell_statistics.csv

source_name: CLL patient 4 time-point 2 Dual Protocol MscRRBS


title: CLL03_T1_Dual_RNA_c89


title: CLL03_T1_Dual_RNA_c91


title: CLL03_T1_Dual_RNA_c82


title: CLL03_T1_Dual_RNA_c92


title: CLL04_T0_Dual_RNA_c1


title: CLL03_T1_Dual_RNA_c81


title: CLL03_T1_Dual_RNA_c83


title: CLL04_T0_Dual_RNA_c9


title: CLL03_T1_Dual_RNA_c80


title: CLL03_T1_Dual_RNA_c96


title: CLL03_T1_Dual_RNA_c85


title: CLL03_T1_Dual_RNA_c78


title: CLL03_T1_Dual_RNA_c88


title: CLL04_T0_Dual_RNA_c19


title: CLL03_T1_Dual_RNA_c90


title: CLL03_T1_Dual_RNA_c77


title: CLL03_T1_Dual_RNA_c75


title: CLL03_T1_Dual_RNA_c73


title: CLL03_T1_Dual_RNA_c84


title: CLL03_T1_Dual_RNA_c71


title: CLL03_T1_Dual_RNA_c70


title: CLL03_T1_Dual_RNA_c69


title: CLL03_T1_Dual_RNA_c63


title: CLL03_T1_Dual_RNA_c67


title: CLL03_T1_Dual_RNA_c62


title: CLL03_T1_Dual_RNA_c61


title: CLL03_T1_Dual_RNA_c64


title: CLL03_T1_Dual_RNA_c57


title: CLL03_T1_Dual_RNA_c66


title: CLL03_T1_Dual_RNA_c58


title: CLL03_T1_Dual_RNA_c59


title: CLL03_T1_Dual_RNA_c56


title: CLL03_T1_Dual_RNA_c68


title: CLL03_T1_Dual_RNA_c53


title: CLL03_T1_Dual_RNA_c54


title: CLL03_T1_Dual_RNA_c74


title: CLL03_T1_Dual_RNA_c51


title: CLL03_T1_Dual_RNA_c52


title: CLL03_T1_Dual_RNA_c50


title: CLL03_T1_Dual_RNA_c48


title: CLL03_T1_Dual_RNA_c60


title: CLL03_T1_Dual_RNA_c47


title: CLL03_T1_Dual_RNA_c65


title: CLL03_T1_Dual_RNA_c46


title: CLL03_T1_Dual_RNA_c76


title: CLL03_T1_Dual_RNA_c79


title: CLL03_T1_Dual_RNA_c55


title: CLL03_T1_Dual_RNA_c44


title: CLL03_T1_Dual_RNA_c43


title: CLL03_T1_Dual_RNA_c42


title: CLL03_T1_Dual_RNA_c40


title: CLL03_T1_Dual_RNA_c45


title: CLL03_T1_Dual_RNA_c49


title: CLL03_T1_Dual_RNA_c38


title: CLL03_T1_Dual_RNA_c36


title: CLL03_T1_Dual_RNA_c37


title: CLL03_T1_Dual_RNA_c33


title: CLL03_T1_Dual_RNA_c35


title: CLL03_T1_Dual_RNA_c34


title: CLL03_T1_Dual_RNA_c39


title: CLL03_T1_Dual_RNA_c30


title: CLL03_T1_Dual_RNA_c31


title: CLL03_T1_Dual_RNA_c28


title: CLL03_T1_Dual_RNA_c32


title: CLL03_T1_Dual_RNA_c29


title: CLL03_T1_Dual_RNA_c27


title: CLL03_T1_Dual_RNA_c26


title: CLL03_T1_Dual_RNA_c25


title: CLL03_T1_Dual_RNA_c22


title: CLL03_T1_Dual_RNA_c23


title: CLL03_T1_Dual_RNA_c19


title: CLL03_T1_Dual_RNA_c24


title: CLL03_T1_Dual_RNA_c21


title: CLL03_T1_Dual_RNA_c17


title: CLL03_T1_Dual_RNA_c20


title: CLL03_T1_Dual_RNA_c18


title: CLL03_T1_Dual_RNA_c41


title: CLL03_T1_Dual_RNA_c16


title: CLL03_T1_Dual_RNA_c13


title: CLL03_T1_Dual_RNA_c15


title: CLL03_T1_Dual_RNA_c14


title: CLL03_T1_Dual_RNA_c12


title: CLL03_T1_Dual_RNA_c10


title: CLL03_T1_Dual_RNA_c8


title: CLL03_T1_Dual_RNA_c9


title: CLL03_T1_Dual_RNA_c6


title: CLL03_T1_Dual_RNA_c11


title: CLL03_T1_Dual_RNA_c7


title: CLL03_T1_Dual_RNA_c4


title: CLL03_T1_Dual_RNA_c2


title: CLL03_T1_Dual_RNA_c5


title: CLL03_T1_Dual_RNA_c1


title: CLL03_T0_Dual_RNA_c96

source_name: CLL patient 3 time-point 1 Dual Protocol scRNAseq


title: CLL03_T0_Dual_RNA_c93


title: CLL03_T0_Dual_RNA_c95


title: CLL03_T0_Dual_RNA_c91


title: CLL03_T0_Dual_RNA_c94


title: CLL03_T0_Dual_RNA_c83


title: CLL03_T0_Dual_RNA_c86


title: CLL03_T0_Dual_RNA_c85


title: CLL03_T0_Dual_RNA_c88


title: CLL03_T0_Dual_RNA_c79


title: CLL03_T0_Dual_RNA_c87


title: CLL03_T1_Dual_RNA_c3


title: CLL03_T0_Dual_RNA_c77


title: CLL03_T0_Dual_RNA_c84


title: CLL03_T0_Dual_RNA_c75


title: CLL03_T0_Dual_RNA_c76


title: CLL03_T0_Dual_RNA_c73


title: CLL03_T0_Dual_RNA_c78


title: CLL03_T0_Dual_RNA_c74


title: CLL03_T0_Dual_RNA_c69


title: CLL03_T0_Dual_RNA_c71


title: CLL03_T0_Dual_RNA_c89


title: CLL03_T0_Dual_RNA_c66


title: CLL03_T0_Dual_RNA_c72


title: CLL03_T1_Dual_RNA_c72


title: CLL03_T0_Dual_RNA_c80


title: CLL03_T0_Dual_RNA_c68


title: CLL03_T0_Dual_RNA_c67


title: CLL03_T0_Dual_RNA_c90


title: CLL03_T0_Dual_RNA_c60


title: CLL03_T0_Dual_RNA_c58


title: CLL03_T0_Dual_RNA_c64


title: CLL03_T0_Dual_RNA_c57


title: CLL03_T0_Dual_RNA_c81


title: CLL03_T0_Dual_RNA_c55


title: CLL03_T0_Dual_RNA_c59


title: CLL03_T0_Dual_RNA_c56


title: CLL03_T0_Dual_RNA_c70


title: CLL03_T0_Dual_RNA_c62


title: CLL03_T0_Dual_RNA_c53


title: CLL03_T0_Dual_RNA_c54


title: CLL03_T0_Dual_RNA_c51


title: CLL03_T0_Dual_RNA_c50


title: CLL03_T0_Dual_RNA_c61


title: CLL03_T0_Dual_RNA_c49


title: CLL03_T0_Dual_RNA_c48


title: CLL03_T0_Dual_RNA_c47


title: CLL03_T0_Dual_RNA_c65


title: CLL03_T0_Dual_RNA_c43


title: CLL03_T0_Dual_RNA_c42


title: CLL03_T0_Dual_RNA_c44


title: CLL03_T0_Dual_RNA_c82


title: CLL03_T0_Dual_RNA_c41


title: CLL03_T0_Dual_RNA_c63


title: CLL03_T0_Dual_RNA_c45


title: CLL03_T0_Dual_RNA_c38


title: CLL03_T0_Dual_RNA_c37


title: CLL03_T0_Dual_RNA_c36


title: CLL03_T0_Dual_RNA_c52


title: CLL03_T0_Dual_RNA_c35


title: CLL03_T0_Dual_RNA_c34


title: CLL03_T0_Dual_RNA_c32


title: CLL03_T0_Dual_RNA_c30


title: CLL03_T0_Dual_RNA_c25


title: CLL03_T0_Dual_RNA_c40


title: CLL03_T0_Dual_RNA_c29


title: CLL03_T0_Dual_RNA_c27


title: CLL03_T0_Dual_RNA_c28


title: CLL03_T0_Dual_RNA_c33


title: CLL03_T0_Dual_RNA_c46


title: CLL03_T0_Dual_RNA_c23


title: CLL03_T0_Dual_RNA_c24


title: CLL03_T0_Dual_RNA_c22


title: CLL03_T0_Dual_RNA_c31


title: CLL03_T0_Dual_RNA_c20


title: CLL03_T0_Dual_RNA_c21


title: CLL03_T0_Dual_RNA_c19


title: CLL03_T0_Dual_RNA_c14


title: CLL03_T0_Dual_RNA_c15


title: CLL03_T0_Dual_RNA_c18


title: CLL03_T0_Dual_RNA_c12


title: CLL03_T0_Dual_RNA_c9


title: CLL03_T0_Dual_RNA_c10


title: CLL03_T0_Dual_RNA_c26


title: CLL03_T0_Dual_RNA_c11


title: CLL03_T0_Dual_RNA_c8


title: CLL03_T0_Dual_RNA_c17


title: CLL03_T0_Dual_RNA_c16


title: CLL03_T0_Dual_RNA_c4


title: CLL03_T0_Dual_RNA_c39


title: CLL03_T0_Dual_RNA_c3


title: CLL03_T0_Dual_RNA_c5