title: No47.W.CM.MSN08-13R.Alone.PAZ Rep 3

city: New York

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-PAZ-R3_S47

data_processing:
The data processing pipeline consists of the following three steps:
First of all, use the script Build-Genome-Index.GEO.sh to generate a set of index files with a read length of 100 bp for the UCSC human genome reference library (version hg38) used by the STAR alignment program.
Secondly, launch the script Align-RNAseq-Reads.GEO.sh that uses the STAR aligner to align the 100-bp sequence reads contained in the FASTQ-format sequence data files (obtained from high-throughput random-primed mRNA-sequencing assays) to the reference library and generate the BAM-format alignment result files that contain the sequence reads tagged with alignment information, one alignment file for each sample.
Lastly, run the script Count-RNAseq-Reads.GEO.sh that uses the featureCounts program from the Subread software to assign the tagged sequence reads contained in the alignment files to corresponding genes annotated in the reference library and then create a read counts table that contains the number of sequence reads uniquely mapped to each reference gene in rows and for every sequenced sample in columns.
Assembly: UCSC human genome referece library (version hg38)
Supplementary files format and content: Gene-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence reads for 48 cardiomyocyte samples
Supplementary files format and content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.

molecule: nuclear RNA

source_name: cardiomyocyte differentiation

growth_protocol: Differentiated Cardiomyocytes were produced from human iPSC-derived skin fibroblasts.

extract_protocol:
Cardiomyocytes were lysed with Trizol, and followed by mRNA purification.
Illumina TruSeq Random primed

treatment_protocol: Cardiomyocytes and HCAEC were co-cultured for 48hrs in Cardiomyocte media, and followed by drug treatment or DMSO control for additional 48hrs. We also have control Cardiomyocytes that were not co-cultured with HCAEC cells but underwent the same drug treatments.

value: MSN08 13R

value: human iPSC derived cardiomyocytes

tag: time

value: 48 hours

tag: biological replicate


title: No46.V.CM.MSN08-13R.Alone.PAZ Rep 2

status: Public on Jan 22 2024

type: SRA

state: NY

country: USA

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-PAZ-R2_S46

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: UC026

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

country: Germany

institute: Christian-Albrechts Universität zu Kiel

description: 3'-biased mRNA

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Pipeline rnaseq v1.3 https://zenodo.org/record/2610144
Alignment with STAR v2.6.1d
Feature counting with FeatureCounts from the subread package v1.6.4
for more details, see pipeline documentation
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma-separated values of raw feature counts results

molecule: total RNA

source_name: Whole Blood

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in all samples. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

tag: disease

value: UC

tag: age

tag: sequencing plate number (used for batch correction)


title: GL78_270_WN-S2-P2_I14_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S264

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

library_source: transcriptomic single cell

data_processing:
Raw data was aligned to the reference mouse genome using STAR aligner tool (v2.7.3)
Gene counts were extracted from BAM files using HTSeq software (v0.9.1)
Python (v3.7.3) and scanpy (v1.4.4) for data pre-processing
As QC, cells with less than 2,500 expressed genes and less than 50,000 counts were discarded, and no more than 5% mitochondrial gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value file: scRNAseq_Cell_annotation.txt: cell sample metadata table. For each cell (row, 860 in total): cell full name, corresponding plate/well, embryo developmental stage, cell population, batch name, FACS index data for (in this order) DLL4, NOTCH2, CKIT, GFI1, CD41, NOTCH1, CD31, JAG1 and CD45. Additionally, for those cells passing the QC, UMAP coordinates and annotated cluster (Louvain method, see publication for details) are included.
Supplementary files format and content: Tab-separated value file: scRNAseq_Raw_counts.txt: full-length RNAseq (SMART-Seq2).Raw expression levels for each gene (46,170 rows) in each single cell (860 columns) as calculated using HTseq. This data is prior to conducting any QC.
Supplementary files format and content: Tab-separated value file: scRNAseq_Norm_counts_filtered.txt. Normalized expression levels after QC. Matrix comprises 30,362 rows (genes) per 775 columns (cells). Counts were normalized per cell with pp.normalize_total function from scanpy (target sum of 1e4) and values logarithmize with pp.log1p scanpy function.

organism: Mus musculus

source_name: AGM

growth_protocol: E10.5 and E11.5 AGMs were prepared for flow sorting

extract_protocol:
Single cells were sorted into well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol. Briefly, cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher).
Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems).

treatment_protocol: no treatments, only FACS staining

value: Hematopoietic cells

tag: tissue

value: AGM

tag: strain

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old

tag: developmental stage

tag: population

tag: batch


title: No45.U.CM.MSN08-13R.Alone.PAZ Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-PAZ-R1_S45


title: GL78_269_WN-S2-P2_K14_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S263


title: Bovine Bone Marrow Mesenchymal Stromal Cells

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation using cellranger v6.1.1
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab separated values and matrices

organism: Bos taurus

source_name: bone marrow

growth_protocol: DMEM (low glucose) supplemented with 30% FBS, 1X P/S and 1X L-glutamine

extract_protocol:
Tissue was collected from one healthy first-lactation Holstein-Frisian cow and cultured until MSC colonies were visible.
According to manufacturer instructions, single cell 3' v3.1 protocol (10X Genomics)

value: bone marrow

value: BM-MSC

value: MSC


title: UC025

description: 3'-biased mRNA


title: GL78_268_WN-S2-P2_L14_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S262


title: GL53_116_Plate3_l16_Gfi1_neg_IAHC_S308

description:
SMART-Seq2
Not included in final analysis


title: No48.X.CM.MSN08-13R.Alone.PAZ Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-PAZ-R4_S48


title: UC023

description: 3'-biased mRNA


title: GL78_267_WN-S2-P2_M14_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S261


title: UC022

description: 3'-biased mRNA


title: No43.S.CM.MSN08-13R.Alone.DMSO Rep 3

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DMSO-R3_S43


title: No42.L.CM.MSN08-13R.WithHCAEC.PAZ Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-PAZ-R4_S42


title: GL53_117_Plate3_m16_Gfi1_neg_IAHC_S309


title: UC030

description: 3'-biased mRNA


title: GL53_119_Plate3_o16_Gfi1_neg_IAHC_S311


title: GL78_266_WN-S2-P2_O14_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S260


title: No41.K.CM.MSN08-13R.WithHCAEC.PAZ Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-PAZ-R3_S41


title: GL78_265_WN-S2-P2_C15_AGM_E11-5_SP_48-49_Gfi1_HE__S259

value: Hemogenic endothelium cells


title: UC021

description: 3'-biased mRNA


title: GL53_115_Plate3_k16_Gfi1_pos_IAHC_S307


title: No44.T.CM.MSN08-13R.Alone.DMSO Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DMSO-R4_S44


title: GL53_113_Plate3_i16_Gfi1_pos_IAHC_S305


title: No40.J.CM.MSN08-13R.WithHCAEC.PAZ Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-PAZ-R2_S40


title: GL53_114_Plate3_j16_Gfi1_pos_IAHC_S306


title: GL53_118_Plate3_n16_Gfi1_neg_IAHC_S310


title: GL53_112_Plate3_h16_Gfi1_pos_IAHC_S304


title: GL78_264_WN-S2-P2_G15_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S258


title: UC019

description: 3'-biased mRNA


title: No39.I.CM.MSN08-13R.WithHCAEC.PAZ Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-PAZ-R1_S39


title: UC024

description: 3'-biased mRNA


title: GL53_111_Plate3_g16_Gfi1_pos_IAHC_S303


title: GL78_263_WN-S2-P2_H15_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S257


title: UC018

description: 3'-biased mRNA


title: No38.H.CM.MSN08-13R.WithHCAEC.DMSO Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DMSO-R4_S38


title: GL53_110_Plate3_f16_Gfi1_pos_IAHC_S302


title: No37.G.CM.MSN08-13R.WithHCAEC.DMSO Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DMSO-R3_S37


title: OB127C

type: RNA

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Sample name = 57

data_processing:
Non-normalized data: Background filtered Cq-values.
Normalized data: All data was normalised to the average of assays detected in all samples (dCq = global mean Cq – assay Cq (sample)).
Fold-change data: 2^dCq

label: SYBR green

source_name: skeletal muscle, OB, 4 months post-surgery

label_protocol: 30 ng RNA was reverse transcribed in 30 μl reactions using the miRCURY LNA Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 100x and assayed in 10 ul PCR reactions according to the protocol; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Human Panel I using ExiLENT SYBR® Green master mix. Negative controls excluding template from the reverse transcription reaction was performed and profiled like the samples. The amplification was performed in a LightCycler® 480 Real-Time PCR System (Roche) in 384-well plates.

growth_protocol: 16 severely obese patients without type 2 diabetes mellitus (OB) and nine severely obese patients with type 2 diabetes mellitus (T2DM) were elected for Roux-en-Y gastric bypass surgery. We examined the participants after a diet-induced weight loss (B) and approximately 4 months post-surgery (C).

extract_protocol: Total RNA was extracted from approximately 20 mg of muscle tissue using Trizol (Invitrogen).

treatment_protocol: We sampled skeletal muscle biopsies from vastus lateralis with a Bergstrom needle using suction and local anaesthesia (1% lidocaine) at both visits (B and C). Biopsies were snap-frozen in liquid nitrogen and stored at -80°C subsequently.

tag: phenotype

value: obese

tag: disease status

value: without type 2 diabetes mellitus

value: skeletal muscle (vastus lateralis)

value: Roux-en-Y gastric bypass surgery

tag: timepoint

value: 4 months post-surgery

tag: individual identifier


title: GL78_262_WN-S2-P2_I15_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S256


title: UC017

description: 3'-biased mRNA


title: No36.R.CM.MSN08-13R.Alone.DMSO Rep 2

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DMSO-R2_S36

value: MSN08 13R

value: human iPSC derived cardiomyocytes

tag: time

tag: biological replicate


title: GL53_109_Plate3_e16_Gfi1_HE_S301

tag: cell type


title: UC016

description: 3'-biased mRNA


title: No35.Q.CM.MSN08-13R.Alone.DMSO Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DMSO-R1_S35

tag: cell line

tag: genotype

value: WT

value: 48 hours


title: GL78_259_WN-S2-P2_L15_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S253

value: Hematopoietic cells


title: UC020

description: 3'-biased mRNA

tag: disease

value: UC


title: GL78_260_WN-S2-P2_K15_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S254

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

tag: age


title: GL53_108_Plate3_g15_Gfi1_pos_IAHC_S300

value: 6-8 weeks old


title: UC014

description: 3'-biased mRNA

tag: sequencing plate number (used for batch correction)


title: GL53_107_Plate3_f15_Gfi1_pos_IAHC_S299

tag: tissue


title: UC013

description: 3'-biased mRNA


title: UC012

description: 3'-biased mRNA


title: No33.O.CM.MSN08-13R.Alone.DAB Rep 3

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DAB-R3_S33

tag: treatment


title: No34.P.CM.MSN08-13R.Alone.DAB Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DAB-R4_S34


title: GL53_106_Plate3_e15_Gfi1_HE_S298

tag: strain

tag: developmental stage


title: GL53_105_Plate3_d15_Gfi1_HE_S297

tag: population

tag: batch


title: GL78_257_WN-S2-P2_N15_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S251


title: GL53_104_Plate3_c15_Gfi1_HE_S296


title: No31.M.CM.MSN08-13R.Alone.DAB Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DAB-R1_S31


title: GL78_258_WN-S2-P2_M15_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S252


title: GL78_261_WN-S2-P2_J15_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S255


title: UC011

description: 3'-biased mRNA


title: GL53_103_Plate3_b15_Gfi1_HE_S295


title: No30.F.CM.MSN08-13R.WithHCAEC.DMSO Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DMSO-R2_S30


title: GL78_256_WN-S2-P2_F16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S250


title: UC010

description: 3'-biased mRNA


title: UC015

description: 3'-biased mRNA


title: GL78_255_WN-S2-P2_G16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S249


title: GL78_254_WN-S2-P2_H16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S248


title: No29.E.CM.MSN08-13R.WithHCAEC.DMSO Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DMSO-R1_S29


title: GL78_252_WN-S2-P2_J16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S246


title: UC008

description: 3'-biased mRNA


title: No28.D.CM.MSN08-13R.WithHCAEC.DAB Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DAB-R4_S28


title: GL53_100_Plate3_o14_Gfi1_neg_IAHC_S292


title: GL53_102_Plate3_a15_Gfi1_HE_S294


title: UC009

description: 3'-biased mRNA


title: GL78_253_WN-S2-P2_I16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S247


title: No27.C.CM.MSN08-13R.WithHCAEC.DAB Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DAB-R3_S27


title: GL53_101_Plate3_p14_Gfi1_neg_IAHC_S293


title: GL78_251_WN-S2-P2_K16_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S245


title: UC007

description: 3'-biased mRNA


title: GL53_099_Plate3_n14_Gfi1_neg_IAHC_S291

description:
SMART-Seq2
Not included in final analysis


title: UC006

description: 3'-biased mRNA


title: GL53_098_Plate3_m14_Gfi1_neg_IAHC_S290


title: GL78_250_WN-S2-P2_L16_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S244


title: No26.B.CM.MSN08-13R.WithHCAEC.DAB Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DAB-R2_S26


title: No25.A.CM.MSN08-13R.WithHCAEC.DAB Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-WithHCAEC-DAB-R1_S25


title: GL53_097_Plate3_l14_Gfi1_neg_IAHC_S289


title: GL78_249_WN-S2-P2_M16_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S243


title: UC004

description: 3'-biased mRNA


title: UC005

description: 3'-biased mRNA


title: GL53_096_Plate3_l13_Gfi1_neg_IAHC_S96


title: No23.W.CM.MSN09-04R.Alone.PAZ Rep 3

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-PAZ-R3_S23

value: MSN09 04R


title: No24.X.CM.MSN09-04R.Alone.PAZ Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-PAZ-R4_S24


title: GL78_248_WN-S2-P2_O16_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S242


title: UC003

description: 3'-biased mRNA


title: GL53_095_Plate3_k13_Gfi1_pos_IAHC_S95


title: No22.V.CM.MSN09-04R.Alone.PAZ Rep 2

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-PAZ-R2_S22


title: GL53_094_Plate3_j13_Gfi1_pos_IAHC_S94


title: UC002

description: 3'-biased mRNA


title: No21.U.CM.MSN09-04R.Alone.PAZ Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-PAZ-R1_S21


title: GL53_093_Plate3_i13_Gfi1_pos_IAHC_S93


title: GL78_245_WN-S2-P2_E17_AGM_E11-5_SP_48-49_Gfi1_HE__S239


title: Control243

description: 3'-biased mRNA

value: Control


title: GL78_246_WN-S2-P2_B17_AGM_E11-5_SP_48-49_Gfi1_HE__S240

value: Hemogenic endothelium cells


title: No20.T.CM.MSN09-04R.Alone.DMSO Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DMSO-R4_S20


title: GL78_244_WN-S2-P2_F17_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S238


title: GL53_092_Plate3_h13_Gfi1_pos_IAHC_S92


title: No19.S.CM.MSN09-04R.Alone.DMSO Rep 3

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DMSO-R3_S19


title: GL53_091_Plate3_g13_Gfi1_pos_IAHC_S91


title: Control242

description: 3'-biased mRNA


title: Control241

description: 3'-biased mRNA


title: GL78_242_WN-S2-P2_J17_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S236


title: No17.K.CM.MSN09-04R.WithHCAEC.PAZ Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-PAZ-R3_S17


title: GL78_247_WN-S2-P2_P16_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S241


title: GL53_089_Plate3_e13_Gfi1_HE_S89


title: GL78_241_WN-S2-P2_L17_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S235


title: No16.J.CM.MSN09-04R.WithHCAEC.PAZ Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-PAZ-R2_S16


title: Control239

description: 3'-biased mRNA


title: GL78_240_WN-S2-P2_N17_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S234


title: GL53_088_Plate3_d13_Gfi1_HE_S88


title: No15.I.CM.MSN09-04R.WithHCAEC.PAZ Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-PAZ-R1_S15


title: Control238

description: 3'-biased mRNA


title: GL53_087_Plate3_c13_Gfi1_HE_S87


title: No14.H.CM.MSN09-04R.WithHCAEC.DMSO Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DMSO-R4_S14


title: GL78_238_WN-S2-P2_P17_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S232


title: GL78_239_WN-S2-P2_O17_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S233


title: Control237

description: 3'-biased mRNA


title: GL53_086_Plate3_b13_Gfi1_HE_S86


title: GL78_243_WN-S2-P2_H17_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S237


title: UC001

description: 3'-biased mRNA


title: No13.G.CM.MSN09-04R.WithHCAEC.DMSO Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DMSO-R3_S13


title: Control236

description: 3'-biased mRNA


title: No18.L.CM.MSN09-04R.WithHCAEC.PAZ Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 10uM pazopanib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-PAZ-R4_S18


title: No12.R.CM.MSN09-04R.Alone.DMSO Rep 2

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DMSO-R2_S12


title: Control240

description: 3'-biased mRNA


title: GL78_236_WN-S2-P2_G18_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S230


title: GL53_085_Plate3_a13_Gfi1_HE_S85


title: No11.Q.CM.MSN09-04R.Alone.DMSO Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DMSO-R1_S11


title: GL53_090_Plate3_f13_Gfi1_pos_IAHC_S90


title: Control234

description: 3'-biased mRNA


title: Control235

description: 3'-biased mRNA


title: GL53_084_Plate3_b12_Gfi1_HE_S84


title: GL53_083_Plate3_a12_Gfi1_HE_S83


title: Control233

description: 3'-biased mRNA


title: No10.P.CM.MSN09-04R.Alone.DAB Rep 4

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DAB-R4_S10


title: GL53_082_Plate3_p11_Gfi1_neg_IAHC_S82


title: GL78_234_WN-S2-P2_I18_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S228


title: No09.O.CM.MSN09-04R.Alone.DAB Rep 3

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DAB-R3_S9


title: GL78_235_WN-S2-P2_H18_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S229


title: Control232

description: 3'-biased mRNA


title: GL78_233_WN-S2-P2_J18_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S227


title: GL53_080_Plate3_n11_Gfi1_neg_IAHC_S80


title: Control231

description: 3'-biased mRNA


title: GL78_232_WN-S2-P2_K18_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S226


title: No08.N.CM.MSN09-04R.Alone.DAB Rep 2

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DAB-R2_S8


title: GL78_237_WN-S2-P2_B18_AGM_E11-5_SP_48-49_Gfi1_HE__S231


title: No07.M.CM.MSN09-04R.Alone.DAB Rep 1

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-Alone-DAB-R1_S7


title: GL53_081_Plate3_o11_Gfi1_neg_IAHC_S81


title: GL53_079_Plate3_m11_Gfi1_neg_IAHC_S79

description:
SMART-Seq2
Not included in final analysis


title: No06.F.CM.MSN09-04R.WithHCAEC.DMSO Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DMSO-R2_S6


title: Control229

description: 3'-biased mRNA


title: Control230

description: 3'-biased mRNA


title: GL78_230_WN-S2-P2_P18_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S224


title: No05.E.CM.MSN09-04R.WithHCAEC.DMSO Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DMSO-R1_S5


title: GL53_078_Plate3_k11_Gfi1_pos_IAHC_S78


title: Control228

description: 3'-biased mRNA


title: No04.D.CM.MSN09-04R.WithHCAEC.DAB Rep 4

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DAB-R4_S4


title: GL78_229_WN-S2-P2_A19_AGM_E11-5_SP_48-49_Gfi1_HE__S223


title: Control227

description: 3'-biased mRNA


title: GL53_077_Plate3_i11_Gfi1_pos_IAHC_S77


title: GL53_076_Plate3_h11_Gfi1_pos_IAHC_S76


title: GL78_228_WN-S2-P2_C19_AGM_E11-5_SP_48-49_Gfi1_HE__S222


title: Control226

description: 3'-biased mRNA


title: No03.C.CM.MSN09-04R.WithHCAEC.DAB Rep 3

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DAB-R3_S3


title: GL78_227_WN-S2-P2_F19_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S221


title: GL53_075_Plate3_g11_Gfi1_pos_IAHC_S75


title: No02.B.CM.MSN09-04R.WithHCAEC.DAB Rep 2

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DAB-R2_S2


title: Control225

description: 3'-biased mRNA


title: GL78_226_WN-S2-P2_G19_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S220


title: GL53_074_Plate3_f11_Gfi1_pos_IAHC_S74


title: GL78_231_WN-S2-P2_O18_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S225


title: GL78_225_WN-S2-P2_H19_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S219


title: No01.A.CM.MSN09-04R.WithHCAEC.DAB Rep 1

description:
cardiomyocytes cocultured with HACECs, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN09-04R-WithHCAEC-DAB-R1_S1


title: GL53_073_Plate3_e11_Gfi1_HE_S73


title: Control223

description: 3'-biased mRNA


title: GL78_224_WN-S2-P2_I19_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S218


title: GL53_072_Plate3_g10_Gfi1_pos_IAHC_S72


title: PC9, osimertinib 1w treat, p53 ChiP

city: Fukuoka

first: RITSU

last: IBUSUKI

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Respiratory Medicine

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using Bowtie2 (Version 2.3.4.2).
Peak calling with input was performed using the MACS2 (Version 2.1.2) callpeak command with parameters "--nomodel -q 0.01".
The raw read counts were normalized by Trimmed mean of M values (TMM) and differentially analysis was conducted with edgeR (Version 3.26.8).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: Cells were cultured (1 × 10^6 cells into a 6 well plate) for 24 hours before treatment on uncoated plastic in RPMI 1640 (Gibco, Carlsbad, CA, USA) supplemented with 10 % fetal bovine serum and 1 % penicillin–streptomycin (Gibco) .

extract_protocol:
Cells were first incubated with 4% formaldehyde for 10 min at 37°C to induce cross-linking, and were then subjected to ultrasonic treatment to shear cross-linked DNA into fragments of ~200 to 500 bp with a Bioruptor UCD-300 device (Cosmo Bio, Tokyo, Japan). DNA-protein complexes were immunoprecipitated with antibodies to p53 (#2527 Cell Signaling Technology). DNA was purified from the precipitates with the use of a QIAquick PCR Purification Kit (#28104, Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (ThruPLEX DNA-Seq 48D Kit). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: 600nM osimertinib or DMSO as a control for 24 hours or 1 week

value: Lung adenocarcinoma cells

tag: chip antibody

value: TP53 R248Q mutation

value: osimertinib 1week


title: GL78_223_WN-S2-P2_J19_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S217


title: PC9, osimertinib 1w treat, Input


title: GL53_071_Plate3_f10_Gfi1_pos_IAHC_S71


title: PC9, osimertinib 1d treat, p53 ChiP

value: osimertinib 1day


title: Control221

description: 3'-biased mRNA


title: Control220

description: 3'-biased mRNA


title: PC9, nontreat, p53 ChiP


title: GL53_070_Plate3_e10_Gfi1_HE_S70


title: PC9, osimertinib 1d treat, Input


title: Control219

description: 3'-biased mRNA


title: GL78_221_WN-S2-P2_L19_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S215


title: Control224

description: 3'-biased mRNA


title: GL53_068_Plate3_b10_Gfi1_HE_S68


title: Control218

description: 3'-biased mRNA


title: GL78_220_WN-S2-P2_N19_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S214


title: GL78_218_WN-S2-P2_B20_AGM_E11-5_SP_48-49_Gfi1_HE__S212


title: PC9, nontreat, Input


title: GL53_066_Plate3_p9_Gfi1_neg_IAHC_S66


title: GL78_219_WN-S2-P2_A20_AGM_E11-5_SP_48-49_Gfi1_HE__S213


title: Control217

description: 3'-biased mRNA


title: Control222

description: 3'-biased mRNA


title: GL78_217_WN-S2-P2_E20_AGM_E11-5_SP_48-49_Gfi1_HE__S211


title: Control216

description: 3'-biased mRNA


title: GL53_065_Plate3_o9_Gfi1_neg_IAHC_S65


title: K562,WT,PE7 mutant editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep4

city: Princeton

first: Brittany

last: Adamson

state: NJ

address: 144 Carl Icahn Laboratory, South Drive

department: Molecular Biology

institute: Princeton University

description: mRNAseq_Sample24_K562_ATCC_PJY331_miniprep1_PJY321_PRNP_6GtoT_rep4

data_processing:
For small RNA-seq analysis, sequencing reads were demultiplexed through HTSEQ (Princeton University High Throughput Sequencing Database). The reads were trimmed, aligned, and processed using a Snakemake workflow and R scripts available at https://github.com/Princeton-LSI-ResearchComputing/PE-small-RNA-seq-analysis.
For mRNA-seq analysis, sequencing reads were demultiplexed through HTSEQ (Princeton University High Throughput Sequencing Database). Alignment, quantification, and differential expression were performed using a Snakemake workflow (https://doi.org/10.5281/zenodo.4737358) and R scripts available on GitHub https://github.com/Princeton-LSI-ResearchComputing/PE-mRNA-seq-diffexp.
Assembly: GRCh38 (Ensembl release 107) for small RNA-seq, GRCh38 (Ensembl release 100) for mRNA-seq
Supplementary files format and content: Tab delimited files with human gene counts for each sample. Tab delimited file with the counts of expressed pegRNA or epegRNA by category for each small RNA-seq sample
Supplementary files format and content: A tab delimited file with counts for genes based on the alignment to GRCh38 (from Ensembl release 100) for each mRNA-seq sample

growth_protocol: K562 cells were cultured and passaged in RPMI medium 1640 (Gibco 22400089) supplemented with 10% (v/v) fetal bovine serum (Corning 35-010-CV) and 1x penicillin-streptomycin-glutamine (Gibco 10378016). For nucleofection, 1x penicillin-streptomycin-glutamine was replaced by 1x L-Glutamine at 292 μg mL-1 final concentration (Corning 25-005-CI). K562 cells were incubated, maintained, and cultured at 37 °C with 5% CO2.

extract_protocol:
For small RNA-seq, total RNA containing small RNA was harvested using the mirVana miRNA Isolation Kit with phenol (Invitrogen AM1560). For mRNA-seq, total RNA was harvested using the RNeasy Plus Mini Kit (Qiagen 74134) with on column DNase I treatment
The small RNA libraries were constructed with 1000 ng total RNA as the input using NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) (New England Biolabs E7300S) and NEBNext Multiplex Oligos for Illumina Index Primers Set 3 (New England Biolabs E7710S) and Set 4 (New England Biolabs E7730S) according to the manufacturer’s protocol. The 3′ mRNA SMART-seq libraries were prepared using total RNA as input on an Apollo NGS library prep system (Takara 640078) following the manufacturer’s protocol.

treatment_protocol: For small RNA-seq, 5E6 K562 PEmax parental (WT) and La-knockout (clone 4, P1E10) cells were nucleofected with 5000 ng mDNMT1 6GtoC pegRNA/epegRNA or 2500 ng (e)pegRNA plasmid mastermix 1/2 and the cells were collected day 1 and day 2 post nucleofection. For mRNA-seq, 1E6 K562 cells were nucleofected with 750 ng PEmax, PE7 or PE7 mutant editor plasmid and 250 ng pegRNA plasmid encoding HEK3 1TtoA or PRNP 6GtoT and the cells were collected day 3 post nucleofection.

value: lymphoblast

value: Day 3


title: K562,WT,PE7 mutant editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample23_K562_ATCC_PJY331_miniprep1_PJY321_PRNP_6GtoT_rep3


title: GL53_067_Plate3_a10_Gfi1_HE_S67


title: GL78_222_WN-S2-P2_K19_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S216


title: K562,WT,PE7 mutant editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample22_K562_ATCC_PJY331_miniprep1_PJY321_PRNP_6GtoT_rep2


title: GL53_064_Plate3_n9_Gfi1_neg_IAHC_S64


title: GL78_216_WN-S2-P2_F20_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S210


title: GL53_069_Plate3_d10_Gfi1_HE_S69


title: K562,WT,PE7 mutant editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample21_K562_ATCC_PJY331_miniprep1_PJY321_PRNP_6GtoT_rep1


title: Control214

description: 3'-biased mRNA


title: No32.N.CM.MSN08-13R.Alone.DAB Rep 2

description:
cardiomyocytes cultured in isolation, treated for 48 hrs with 2.5uM dabrafenib in DMSO, 100bp single-end random-primed RNAseq
MSN08-13R-Alone-DAB-R2_S32

value: MSN08 13R

value: human iPSC derived cardiomyocytes


title: GL78_215_WN-S2-P2_G20_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S209


title: Control215

description: 3'-biased mRNA


title: GL53_063_Plate3_m9_Gfi1_neg_IAHC_S63


title: GL78_214_WN-S2-P2_K20_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S208


title: K562,WT,PE7 editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep4

description: mRNAseq_Sample20_K562_ATCC_old_PJY251_6_1_mini_PJY321_PRNP_6GtoT_rep4

value: WT


title: GL53_062_Plate3_l9_Gfi1_neg_IAHC_S62

value: Hematopoietic cells


title: Control212

description: 3'-biased mRNA


title: K562,WT,PE7 editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample19_K562_ATCC_old_PJY251_6_1_mini_PJY321_PRNP_6GtoT_rep3


title: GL53_060_Plate3_l8_Gfi1_neg_IAHC_S60


title: K562,WT,PE7 editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample18_K562_ATCC_old_PJY251_6_1_mini_PJY321_PRNP_6GtoT_rep2


title: K562,WT,PE7 editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample17_K562_ATCC_old_PJY251_6_1_mini_PJY321_PRNP_6GtoT_rep1


title: GL53_061_Plate3_k9_Gfi1_pos_IAHC_S61


title: GL78_213_WN-S2-P2_N20_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S207


title: Control211

description: 3'-biased mRNA


title: GL53_059_Plate3_k8_Gfi1_pos_IAHC_S59


title: Control210

description: 3'-biased mRNA


title: Control209

description: 3'-biased mRNA


title: GL53_058_Plate3_j8_Gfi1_pos_IAHC_S58


title: Control208

description: 3'-biased mRNA


title: GL78_210_WN-S2-P2_B21_AGM_E11-5_SP_48-49_Gfi1_HE__S204


title: Control213

description: 3'-biased mRNA


title: K562,WT,PEmax editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep4

description: mRNAseq_Sample16_K562_ATCC_pCMV_PEmax9_4_mini_PJY321_PRNP_6GtoT_rep4


title: GL53_057_Plate3_i8_Gfi1_pos_IAHC_S57


title: Control207

description: 3'-biased mRNA


title: K562,WT,PEmax editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample15_K562_ATCC_pCMV_PEmax9_4_mini_PJY321_PRNP_6GtoT_rep3


title: K562,WT,PEmax editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample14_K562_ATCC_pCMV_PEmax9_4_mini_PJY321_PRNP_6GtoT_rep2


title: GL78_208_WN-S2-P2_G21_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S202


title: GL78_211_WN-S2-P2_P20_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S205


title: GL78_207_WN-S2-P2_H21_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S201


title: GL78_209_WN-S2-P2_D21_AGM_E11-5_SP_48-49_Gfi1_HE__S203


title: GL78_212_WN-S2-P2_O20_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S206


title: GL53_055_Plate3_g8_Gfi1_pos_IAHC_S55


title: K562,WT,PE7 mutant editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep4

description: mRNAseq_Sample12_K562_ATCC_PJY331_miniprep1_PJY181_HEK3_1TtoA_rep4


title: GL78_206_WN-S2-P2_J21_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S200


title: Control205

description: 3'-biased mRNA


title: K562,WT,PE7 mutant editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample11_K562_ATCC_PJY331_miniprep1_PJY181_HEK3_1TtoA_rep3


title: Control204

description: 3'-biased mRNA


title: GL53_053_Plate3_e8_Gfi1_HE_S53


title: GL78_205_WN-S2-P2_F22_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S199


title: K562,WT,PE7 mutant editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample10_K562_ATCC_PJY331_miniprep1_PJY181_HEK3_1TtoA_rep2


title: Control203

description: 3'-biased mRNA


title: GL53_052_Plate3_d8_Gfi1_HE_S52


title: Control202

description: 3'-biased mRNA


title: K562,WT,PE7 mutant editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample09_K562_ATCC_PJY331_miniprep1_PJY181_HEK3_1TtoA_rep1


title: GL53_051_Plate3_c8_Gfi1_HE_S51


title: K562,WT,PEmax editor and PRNP 6GtoT pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample13_K562_ATCC_pCMV_PEmax9_4_mini_PJY321_PRNP_6GtoT_rep1


title: K562,WT,PE7 editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep4

description: mRNAseq_Sample08_K562_ATCC_old_PJY251_6_1_mini_PJY181_HEK3_1TtoA_rep4


title: GL53_050_Plate3_b8_Gfi1_HE_S50

description:
SMART-Seq2
Not included in final analysis


title: Control206

description: 3'-biased mRNA


title: Control201

description: 3'-biased mRNA


title: GL78_202_WN-S2-P2_J22_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S196


title: GL78_203_WN-S2-P2_I22_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S197


title: GL78_204_WN-S2-P2_H22_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S198


title: GL53_054_Plate3_f8_Gfi1_HE_S54


title: GL78_201_WN-S2-P2_L22_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S195


title: GL53_048_Plate3_a7_Gfi1_HE_S48


title: GL78_200_WN-S2-P2_N22_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S194


title: GL53_049_Plate3_a8_Gfi1_HE_S49


title: K562,WT,PE7 editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample06_K562_ATCC_old_PJY251_6_1_mini_PJY181_HEK3_1TtoA_rep2


title: Control199

description: 3'-biased mRNA


title: GL53_056_Plate3_h8_Gfi1_pos_IAHC_S56


title: Control198

description: 3'-biased mRNA


title: GL78_199_WN-S2-P2_O22_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S193


title: GL53_047_Plate3_p6_Gfi1_neg_IAHC_S47


title: K562,WT,PEmax editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep4

description: mRNAseq_Sample04_K562_ATCC_pCMV_PEmax9_4_mini_PJY181_HEK3_1TtoA_rep4


title: GL53_046_Plate3_n6_Gfi1_neg_IAHC_S46


title: GL78_198_WN-S2-P2_A23_AGM_E11-5_SP_48-49_Gfi1_HE__S192


title: GL53_045_Plate3_m6_Gfi1_neg_IAHC_S45


title: Control200

description: 3'-biased mRNA


title: GL78_197_WN-S2-P2_F23_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S191


title: GL53_044_Plate3_l6_Gfi1_neg_IAHC_S44


title: Control195

description: 3'-biased mRNA


title: K562,WT,PE7 editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample07_K562_ATCC_old_PJY251_6_1_mini_PJY181_HEK3_1TtoA_rep3


title: GL78_195_WN-S2-P2_H23_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S189


title: K562,WT,PEmax editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample01_K562_ATCC_pCMV_PEmax9_4_mini_PJY181_HEK3_1TtoA_rep1


title: K562,WT,PEmax editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep2

description: mRNAseq_Sample02_K562_ATCC_pCMV_PEmax9_4_mini_PJY181_HEK3_1TtoA_rep2


title: GL53_043_Plate3_k6_Gfi1_pos_IAHC_S43


title: Control194

description: 3'-biased mRNA


title: GL78_196_WN-S2-P2_G23_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S190


title: K562,WT,PE7 editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep1

description: mRNAseq_Sample05_K562_ATCC_old_PJY251_6_1_mini_PJY181_HEK3_1TtoA_rep1


title: GL53_042_Plate3_j6_Gfi1_pos_IAHC_S42


title: GL78_193_WN-S2-P2_L23_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S187


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep3

value: PEmax knockin,WT

value: Day 2


title: Control193

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep2


title: GL53_041_Plate3_i6_Gfi1_pos_IAHC_S41

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: GL53_040_Plate3_h6_Gfi1_pos_IAHC_S40

value: 6-8 weeks old


title: GL78_192_WN-S2-P2_M23_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S186


title: GL78_194_WN-S2-P2_I23_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S188


title: Control192

description: 3'-biased mRNA

value: Control


title: Control197

description: 3'-biased mRNA


title: K562,WT,PEmax editor and HEK3 1TtoA pegRNA plasmids transfection,Day 3,rep3

description: mRNAseq_Sample03_K562_ATCC_pCMV_PEmax9_4_mini_PJY181_HEK3_1TtoA_rep3


title: Control196

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep1


title: GL78_191_WN-S2-P2_N23_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S185


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep3

value: Day 1


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep2


title: Control189

description: 3'-biased mRNA


title: GL53_039_Plate3_g6_Gfi1_pos_IAHC_S39


title: Control190

description: 3'-biased mRNA


title: Control188

description: 3'-biased mRNA


title: GL78_190_WN-S2-P2_P23_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S184


title: GL53_037_Plate3_e6_Gfi1_HE_S37

value: Hemogenic endothelium cells


title: GL53_038_Plate3_f6_Gfi1_HE_S38


title: Control187

description: 3'-biased mRNA


title: GL78_183_WN-S2-P1_J23_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S183


title: GL53_036_Plate3_e5_Gfi1_HE_S36


title: GL78_182_WN-S2-P1_H23_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S182


title: Control186

description: 3'-biased mRNA


title: Control191

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep3


title: Control185

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep1


title: Control184

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep2


title: GL53_034_Plate3_c5_Gfi1_HE_S34


title: GL78_179_WN-S2-P1_D23_AGM_E10-5_SP_32-33_Gfi1_HE__S179


title: Control183

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep1


title: GL53_032_Plate3_a5_Gfi1_HE_S32


title: GL53_033_Plate3_b5_Gfi1_HE_S33


title: GL78_178_WN-S2-P1_C23_AGM_E10-5_SP_32-33_Gfi1_HE__S178


title: GL78_177_WN-S2-P1_B23_AGM_E10-5_SP_32-33_Gfi1_HE__S177


title: Control182

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep1


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep3

value: PEmax knockin,La knockout


title: Control181

description: 3'-biased mRNA


title: GL78_176_WN-S2-P1_A23_AGM_E10-5_SP_32-33_Gfi1_HE__S176


title: GL53_031_Plate3_p4_Gfi1_neg_IAHC_S31


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep2


title: GL53_030_Plate3_n4_Gfi1_neg_IAHC_S30


title: GL78_181_WN-S2-P1_G23_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S181


title: GL78_175_WN-S2-P1_J22_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S175


title: GL53_035_Plate3_d5_Gfi1_HE_S35


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 2,rep1


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep3


title: GL53_029_Plate3_m4_Gfi1_neg_IAHC_S29


title: GL53_028_Plate3_l4_Gfi1_neg_IAHC_S28


title: Control178

description: 3'-biased mRNA


title: GL78_180_WN-S2-P1_E23_AGM_E10-5_SP_32-33_Gfi1_HE__S180


title: GL53_027_Plate3_k4_Gfi1_pos_IAHC_S27


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep3


title: GL78_173_WN-S2-P1_H22_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S173


title: K562,PEmax knockin,WT,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep2


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep2


title: GL53_026_Plate3_j4_Gfi1_pos_IAHC_S26


title: Control177

description: 3'-biased mRNA


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix2 transfection,Day 1,rep1


title: GL78_171_WN-S2-P1_F22_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S171


title: Control180

description: 3'-biased mRNA


title: GL53_025_Plate3_i4_Gfi1_pos_IAHC_S25


title: GL53_024_Plate3_j3_Gfi1_pos_IAHC_S24


title: Control176

description: 3'-biased mRNA


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep3


title: GL78_170_WN-S2-P1_E22_AGM_E10-5_SP_32-33_Gfi1_HE__S170


title: Control175

description: 3'-biased mRNA


title: Control174

description: 3'-biased mRNA


title: GL78_169_WN-S2-P1_D22_AGM_E10-5_SP_32-33_Gfi1_HE__S169


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep2


title: GL53_023_Plate3_i3_Gfi1_pos_IAHC_S23


title: GL78_174_WN-S2-P1_I22_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S174


title: Control173

description: 3'-biased mRNA


title: GL78_168_WN-S2-P1_C22_AGM_E10-5_SP_32-33_Gfi1_HE__S168


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 2,rep1


title: GL53_022_Plate3_h3_Gfi1_pos_IAHC_S22


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep3


title: Control179

description: 3'-biased mRNA


title: Control172

description: 3'-biased mRNA


title: GL78_167_WN-S2-P1_B22_AGM_E10-5_SP_32-33_Gfi1_HE__S167


title: Control171

description: 3'-biased mRNA


title: GL53_021_Plate3_g3_Gfi1_pos_IAHC_S21


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep2


title: GL78_166_WN-S2-P1_J21_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S166


title: GL53_020_Plate3_f3_Gfi1_HE_S20


title: K562,PEmax knockin,La knockout,(e)pegRNA plasmid mastermix1 transfection,Day 1,rep1


title: GL78_165_WN-S2-P1_I21_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S165


title: Control170

description: 3'-biased mRNA


title: GL53_019_Plate3_e3_Gfi1_HE_S19


title: GL78_164_WN-S2-P1_G21_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S164


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep4


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep3


title: GL53_018_Plate3_d3_Gfi1_HE_S18


title: GL53_017_Plate3_b3_Gfi1_HE_S17


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep2


title: GL78_162_WN-S2-P1_D21_AGM_E10-5_SP_32-33_Gfi1_HE__S162


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep1


title: GL53_016_Plate3_a3_Gfi1_HE_S16


title: GL78_163_WN-S2-P1_F21_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S163


title: Control168

description: 3'-biased mRNA


title: Control167

description: 3'-biased mRNA


title: Control166

description: 3'-biased mRNA


title: GL53_015_Plate3_n2_Gfi1_neg_IAHC_S15


title: GL53_014_Plate3_m2_Gfi1_neg_IAHC_S14


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep4


title: Control165

description: 3'-biased mRNA


title: Control164

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep3


title: GL53_013_Plate3_l2_Gfi1_neg_IAHC_S13


title: GL78_160_WN-S2-P1_A21_AGM_E10-5_SP_32-33_Gfi1_HE__S160


title: GL78_159_WN-S2-P1_J20_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S159


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep2


title: GL78_161_WN-S2-P1_C21_AGM_E10-5_SP_32-33_Gfi1_HE__S161


title: GL53_012_Plate3_m1_Gfi1_neg_IAHC_S12


title: K562,PEmax knockin,WT,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep1


title: Control163

description: 3'-biased mRNA


title: GL78_157_WN-S2-P1_H20_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S157


title: Control162

description: 3'-biased mRNA


title: GL53_011_Plate3_k1_Gfi1_pos_IAHC_S11


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep1


title: GL78_156_WN-S2-P1_G20_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S156


title: GL53_010_Plate3_j1_Gfi1_pos_IAHC_S10


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep4


title: Control160

description: 3'-biased mRNA


title: Control159

description: 3'-biased mRNA


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep3


title: GL53_009_Plate3_i1_Gfi1_pos_IAHC_S9


title: GL53_008_Plate3_h1_Gfi1_pos_IAHC_S8


title: GL78_154_WN-S2-P1_E20_AGM_E10-5_SP_32-33_Gfi1_HE__S154


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep2


title: GL78_153_WN-S2-P1_D20_AGM_E10-5_SP_32-33_Gfi1_HE__S153


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep4


title: GL53_007_Plate3_g1_Gfi1_pos_IAHC_S7


title: Control169

description: 3'-biased mRNA


title: GL53_006_Plate3_f1_Gfi1_HE_S6


title: GL78_158_WN-S2-P1_I20_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S158


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep3


title: Control157

description: 3'-biased mRNA


title: GL53_005_Plate3_e1_Gfi1_HE_S5


title: GL78_172_WN-S2-P1_G22_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S172


title: Control156

description: 3'-biased mRNA


title: GL78_151_WN-S2-P1_A20_AGM_E10-5_SP_32-33_Gfi1_HE__S151


title: GL78_152_WN-S2-P1_C20_AGM_E10-5_SP_32-33_Gfi1_HE__S152


title: GL78_150_WN-S2-P1_J19_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S150


title: GL78_155_WN-S2-P1_F20_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S155


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep2


title: Control161

description: 3'-biased mRNA


title: Control155

description: 3'-biased mRNA


title: Control154

description: 3'-biased mRNA


title: GL78_149_WN-S2-P1_I19_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S149


title: GL53_003_Plate3_c1_Gfi1_HE_S3


title: K562,PEmax knockin,WT,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep1


title: Control158

description: 3'-biased mRNA


title: GL78_148_WN-S2-P1_H19_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S148


title: Control153

description: 3'-biased mRNA


title: GL53_002_Plate3_b1_Gfi1_HE_S2


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep4

description: P1E10_sorted_PJY300_epegRNA_day2_K32_rep4


title: Control152

description: 3'-biased mRNA


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep3

description: P1E10_sorted_PJY300_epegRNA_day2_K31_rep3


title: GL78_147_WN-S2-P1_G19_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S147


title: GL53_001_Plate3_a1_Gfi1_HE_S1


title: Control151

description: 3'-biased mRNA


title: GL78_146_WN-S2-P1_F19_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S146


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep1

description: P1E10_sorted_PJY300_epegRNA_day2_K29_rep1


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 2,rep2

description: P1E10_sorted_PJY300_epegRNA_day2_K30_rep2


title: GL78_144_WN-S2-P1_C19_AGM_E10-5_SP_32-33_Gfi1_HE__S144


title: Control149

description: 3'-biased mRNA


title: GL78_145_WN-S2-P1_D19_AGM_E10-5_SP_32-33_Gfi1_HE__S145


title: Control150

description: 3'-biased mRNA


title: GL53_004_Plate3_d1_Gfi1_HE_S4


title: 7_week

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Demultiplexing was performed using the mkfastq function in Cell Ranger (version 1.3.1) (10x Genomics)
Alignment and generation of gene-barcode matrix was performed using the count function in Cell Ranger (version 1.3.1) (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx: filtered gene-barcode matrix in MEX format

molecule: polyA RNA

extract_protocol:
CD45.1+ cells from the pancreas of 7 or 12 week old female NOD mice were sorted by flow cytometry, then single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.
CD45.1+ cells from the pancreas of 7 or 12 week old female NOD mice were sorted by flow cytometry, then single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.

tag: strain background

value: NOD/ShiLtJ

tag: time point

value: 7 week old

value: immune cells

tag: cell subset

value: CD45.1+ cells


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep4

description: P1E10_sorted_PJY300_epegRNA_day1_K24_rep4

value: lymphoblast

tag: time


title: 12_week

value: 12 week old

tag: cell type


title: Control148

description: 3'-biased mRNA


title: NOD_CD8_islet_2

data_processing:
Reads were aligned to the mouse reference genome (mm9) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm9
Supplementary_files_format_and_content: genes.read_group_tracking_RNA_spleen_islet contains the FPKM values for each gene in each replicate

extract_protocol:
IGRP206-214-specific CD8 T cells from the spleen and pancreatic islets of 11-week-old female NOD mice were sorted directly into lysis buffer (Picelli et al., Nature Protocols 2014). Spleen samples were sorted from individual mice, while pancreatic islet samples were pooled from two or more mice each.
Libraries were prepared using the SMART-seq protocol (Picelli et al., 2013; Picelli et al., 2014)

value: 11 week old

value: CD8 T cell

value: CD45.1+ CD8+ CD4- CD19- CD11c- CD44+ IGRP-tetramer+


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep3

description: P1E10_sorted_PJY300_epegRNA_day1_K23_rep3

tag: cell line


title: GL78_143_WN-S2-P1_B19_AGM_E10-5_SP_32-33_Gfi1_HE__S143


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep2

description: P1E10_sorted_PJY300_epegRNA_day1_K22_rep2

tag: genotype


title: GL78_142_WN-S2-P1_A19_AGM_E10-5_SP_32-33_Gfi1_HE__S142


title: NOD_CD8_islet_1


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC epegRNA plasmid transfection,Day 1,rep1

description: P1E10_sorted_PJY300_epegRNA_day1_K21_rep1


title: GL78_141_WN-S2-P1_J18_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S141

value: Hematopoietic cells


title: Control146

description: 3'-biased mRNA

tag: disease


title: Control147

description: 3'-biased mRNA

tag: age


title: NOD_CD8_spleen_4


title: Control145

description: 3'-biased mRNA

tag: sequencing plate number (used for batch correction)


title: GL78_140_WN-S2-P1_H18_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S140

tag: tissue

value: AGM


title: NOD_CD8_spleen_3


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep4

description: P1E10_sorted_PJY103_pegRNA_day2_K16_rep4

tag: treatment

value: Day 2


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep3

description: P1E10_sorted_PJY103_pegRNA_day2_K15_rep3


title: NOD_CD8_spleen_2


title: GL78_138_WN-S2-P1_F18_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S138

tag: strain

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: NOD_CD8_islet_3


title: Control143

description: 3'-biased mRNA

value: Control


title: NOD_CD8_spleen_1


title: GL78_137_WN-S2-P1_E18_AGM_E10-5_SP_32-33_Gfi1_HE__S137

value: Hemogenic endothelium cells

tag: developmental stage


title: Control142

description: 3'-biased mRNA


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep1

description: P1E10_sorted_PJY103_pegRNA_day2_K13_rep1

value: PEmax knockin,La knockout


title: Control141

description: 3'-biased mRNA


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep4

value: Day 1


title: BATF_2

data_processing:
Reads were aligned to the mouse reference genome (mm9) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm9
Supplementary_files_format_and_content: genes.read_group_tracking_rna_batf_oe contains the FPKM values for each gene in each replicate

source_name: BATF

growth_protocol: P14 cells were activated for one day with 100 ng/ml gp33. Cells were then spin transduced with 1 ml of either MSCV-IRES-GFP (MIG) or MIG-BATF retrovirus, 8 ug/ml polybrene, 10 ng/ml IL-2, and 10 mM HEPES Buffer (Corning) for 90 minutes at 32 ºC at 2,500 rpm. Retrovirus-containing media was then removed and replaced with the original media, followed by an additional one day of activation. P14 cells were then washed with PBS and cultured in 10 ng/ml IL-2 for two days for expansion. CD8+ GFP+ cells were then sorted and cultured in 1 ng/ml IL-2 for an additional two days and then prepared for RNA-seq.

extract_protocol:
Total RNA from P14 cells transduced with MIG or MIG-BATF was purified from sorted cells using RNeasy Plus Mini Kit (QIAGEN).
mRNA isolation and library preparation were completed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

value: P14 CD8 T cell

value: CD8+ MIG+


title: BATF_1


title: GL78_139_WN-S2-P1_G18_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S139

tag: population


title: Control139

description: 3'-biased mRNA


title: Control140

description: 3'-biased mRNA


title: MIG_2

source_name: MIG


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep3


title: GL78_135_WN-S2-P1_C18_AGM_E10-5_SP_32-33_Gfi1_HE__S135

tag: batch


title: MIG_1


title: Control144

description: 3'-biased mRNA


title: Control138

description: 3'-biased mRNA


title: GL78_134_WN-S2-P1_B18_AGM_E10-5_SP_32-33_Gfi1_HE__S134


title: GL78_133_WN-S2-P1_A18_AGM_E10-5_SP_32-33_Gfi1_HE__S133


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 2,rep2

description: P1E10_sorted_PJY103_pegRNA_day2_K14_rep2


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep2


title: Control136

description: 3'-biased mRNA


title: GL78_131_WN-S2-P1_J17_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S131


title: GL78_136_WN-S2-P1_D18_AGM_E10-5_SP_32-33_Gfi1_HE__S136


title: GL78_132_WN-S2-P1_K17_AGM_E10-5_SP_32-33_Gfi1_neg_IAHC__S132


title: Control137

description: 3'-biased mRNA


title: Control135

description: 3'-biased mRNA


title: scATAC-seq, Neural organoid, Line 409b2, Day 90 Veh-Veh, Replicate 1

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

department: Department Genes and Environment

institute: Max Planck Institute of Psychiatry

description:
Single-cell ATAC sequencing (10xGenomics Chromium)
Veh-Veh_R1

data_processing:
Count matrices, fragment files and associated metadata were produced from fastq files using 10x Genomics Cell Ranger ATAC v2.0.0 with the reference GRCh38 (Ensembl release 94).
Aggregated count matrices, fragment files and associated metadata over all samples were geneated using the "cellranger-atac aggr" command with the reference "homo_sapiens_GRCh38_ensrel94_cr2_0_0".
Assembly: hg38
Supplementary files format and content: filtered_peak_bc_matrix.h5: CellRanger output HDF5 file containing the filtered barcodes x peaks count matrix.
Supplementary files format and content: fragments.tsv.gz: CellRanger output compressed tab-delimited text file containing one line per unique observed ATAC-seq fragment.
Supplementary files format and content: fragments.tsv.gz.tbi: CellRanger output tabix index file for the fragments.tsv.gz file.
Supplementary files format and content: singlecell.csv: CellRanger output comma-separated text file containing per-barcode metadata.

source_name: Unguided neural organoid

growth_protocol: Two primary human induced pluripotent stem cell (hiPSC) lines were used in this study. The first cell line was reprogrammed using hiPSCs from skin fibroblasts (HPS0076:409b2, RIKEN BRC cell bank, female) and is referred to as “Line 409b2” here. The second cell line was reprogrammed using a plasmid-based protocol for integration-free hiPSCs from peripheral blood mononuclear cells from a female donor through the BeCOME study and is referred to as “Line FOK4”here. MTA approvals were obtained for the use of both hiPSC lines. hiPSCs were cultured in Matrigel-coated (1:100 diluted in DMEM-F12 (Gibco™, 31330-038), Corning Incorporated, 354277) Costar® 6-well cell culture plates (Corning Incorporated, 3516) in mTESR1 Basal Medium (STEMCELL Technologies, 85851) supplemented with 1× mTESR1 Supplement (STEMCELL Technologies, 85852) at 37°C with 5 % CO2. Passaging was performed with Gentle Cell Dissociation Reagent (STEMCELL Technologies, 07174). RevitaCell Supplement (1:100 diluted, Gibco™, A2644501) was added for 24 hours after passaging to promote cell survival. Human neural organoids were created as described by Lancaster et al. with some modifications. Briefly, hiPSCs were dissociated in StemPro Accutase Cell Dissociation Reagent (Life Technologies, A1110501). Single cells (n=9000) were dispensed into each well of an Ultra-low attachment 96-well plate with round bottom wells (Corning Incorporated, 7007) in human embryonic stem cell medium (hESC, DMEM/F12-GlutaMAX (Gibco™, 31331-028) with 20 % Knockout Serum Replacement (Gibco™, 10828-028), 3 % FBS (Fetal Bovine Serum, Gibco™, 16141-061), 1 % non-essential amino acids (Gibco™, 11140-035), 0.1 mM 2-mercaptoethanol (Gibco™, 31350-010)) supplemented with 4 ng/ml human recombinant FGF (Fibroblast Growth Factor, Peprotech, 100-18B) and 50 µM Rock inhibitor Y27632 (Millipore, SCM075) for 4 days and in hESC medium without bFGF and Rock inhibitor for an additional 2 days to form embryoid bodies (EBs). On day 6, the medium was changed to neural induction medium (NIM, DMEM/F12 GlutaMAX supplemented with 1:100 N2 supplement (Gibco™, 15502-048), 1 % Non-essential amino acids and 1 µg/ml Heparin (Sigma, H3149)) and cultured for an additional 6 days. On day 12, the EBs were embedded in Matrigel (Corning Incorporated, 354234) drops and transferred to 10-cm cell culture plates (TPP, 93100) in neural differentiation medium without vitamin-A (NDM-A, DMEM/F12GlutaMAX and Neurobasal (Gibco™, 21103-049) in a 1:1 ration, additionally supplemented with 1:100 N2 supplement 1:100 B27 without Vitamin A (Gibco™, 12587-010), 0.5 % non-essential amino acids, insulin 2.5 µg/ml (Gibco™, 19278), 1:100 Antibiotic-Antimycotic (Gibco™, 15240-062) and 50 µM 2-mercaptoethanol) for 4 days. On day 16, Organoids were transferred onto an orbital shaker in NDM+A medium (same composition as NDM-A with the addition of B27 with Vitamin A (Gibco™, 17504-044) in the place of B27 without Vitamin A) and were grown in these conditions at 37°C with 5 % CO2. NDM+A medium was changed twice per week until the organoids were collected for cryopreservation or single-cell dissociation or fixation in paraformaldehyde.

extract_protocol:
Single cells were dissociated using StemPro Accutase Cell Dissociation Reagent (Life Technologies), filtered through 30uM and 20uM filters (Miltenyi Biotec) and cleaned of debris using a Percoll (Sigma, P1644) gradient. Single cells were resuspended in ice-cold Phosphate-Buffered Saline (PBS) supplemented with 0.04 % Bovine Serum Albumin and prepared for single-cell separation.
Subsequent nuclei preparation and scATACseq library generation was performed using the Chromium Single Cell ATAC Library & Gel Bead Kit (16 rxns PN-1000110) according to the manufacturer’s recommendations without any modifications (10x Genomics). Sequencing of the 10x Genomics single-cell ATAC-seq libraries was performed on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) at by the sequencing core facility at the Max Planck Institute for Molecular Genetics (Berlin, Germany).

treatment_protocol: Organoids were treated with glucocorticoids by dissolving Dexamethasone (Dex) in DMSO (dimethyl sulfoxide) and subsequently in the NDM+A culture medium. To achieve the final concentration of 100nM, Dex was first diluted in DMSO in a concentration of 100μM and subsequently diluted in NDM+A culture medium to a final concentration of 100nM. Vehicle control (Veh) organoids received equal amounts of DMSO. Chronic exposures (days 60-70 in culture) were performed by replacing supplemented media every two days. Organoids were either chronically treated (Dexamethasone 100nM, Chr-Veh condition) or vehicle-exposed (DMSO, Veh-Veh condition) for 10 days (day 60 - 70) and collected at day 90 following a 20-day washout period in unsupplemented media and an additional 12 hour acute exposure to the treatment vehicle DMSO immediately before collection.

value: Unguided neural organoid

tag: age (days)

tag: biological replicate_number

value: DMSO for 10 days (day 60 to day 70) + DMSO for 12 hours before collection at D90


title: scATAC-seq, Neural organoid, Line 409b2, Day 90 Veh-Veh, Replicate 2

description:
Single-cell ATAC sequencing (10xGenomics Chromium)
Veh-Veh_R2


title: scATAC-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 2

description:
Single-cell ATAC sequencing (10xGenomics Chromium)
Chr-Veh_R2

value: 100nM Dexamethasone in DMSO for 10 days (day 60 to day 70) + DMSO for 12 hours before collection at D90


title: GL78_130_WN-S2-P1_I17_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S130


title: Control134

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Veh-V1

data_processing:
Filtered count bc matrices were produced from fastq files using 10x Genomics Cell Ranger v3.0.2 with the transcriptome hg38_ensrel94.
Assembly: hg38
Supplementary files format and content: barcodes.tsv: CellRanger output tab-delimited text file listing the barcodes appearing in the matrix.mtx filtered barcodes x features count matrix.
Supplementary files format and content: features.tsv: CellRanger output tab-delimited text file listing the features appearing in the matrix.mtx filtered barcodes x features count matrix.
Supplementary files format and content: matrix.mtx: CellRanger output matrix market file containing the filtered barcodes x features count matrix.

extract_protocol:
Single cells were dissociated using StemPro Accutase Cell Dissociation Reagent (Life Technologies), filtered through 30uM and 20uM filters (Miltenyi Biotec) and cleaned of debris using a Percoll (Sigma, P1644) gradient. Single cells were resuspended in ice-cold Phosphate-Buffered Saline (PBS) supplemented with 0.04 % Bovine Serum Albumin and prepared for single-cell separation.
Experiments were performed in a paired case-control design with 2 or 4 conditions at day 70 and day 90 respectively run in parallel. Single cells were run through the Chromium controller to form gel emulsion beads containing barcoded single cells and prepared into single-cell libraries using the Chromium Single Cell 3’ Reagent Kits v2 according to the manufacturer’s recommendations without any modifications (10x Genomics). To reach an optimal target cell number, 10,000 cells per sample were loaded onto a channel of the 10x chip. All libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent) and KAPA Library Quantification kit for Illumina (KAPA Biosystems). Sequencing of the 10x Genomics single-cell RNA-seq libraries was performed on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) at the sequencing core facility of the Max Planck Institute for Molecular Genetics (Berlin, Germany).

treatment_protocol: Organoids were treated with glucocorticoids by dissolving Dexamethasone (Dex) in DMSO (dimethyl sulfoxide) and subsequently in the NDM+A culture medium. To achieve the final concentration of 100nM, Dex was first diluted in DMSO in a concentration of 100μM and subsequently diluted in NDM+A culture medium to a final concentration of 100nM. Vehicle control (Veh) organoids received equal amounts of DMSO. Chronic exposures (days 60-70 in culture) were performed by replacing supplemented media every two days. Some organoids were collected at day 70 following 10 days of exposure. Other organoids from the same batch were subsequently cultured in normal unsupplemented media for a 20-day wash-out period followed by an acute exposure (day 90 in culture) with 100nM Dex or DMSO for 12 hours.


title: K562,PEmax knockin,La knockout,mDNMT1 6GtoC pegRNA plasmid transfection,Day 1,rep1

value: lymphoblast


title: GL78_127_WN-S2-P1_E17_AGM_E10-5_SP_32-33_Gfi1_HE__S127


title: scATAC-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 1

description:
Single-cell ATAC sequencing (10xGenomics Chromium)
Chr-Veh_R1


title: Control131

description: 3'-biased mRNA


title: GL78_128_WN-S2-P1_G17_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S128


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Veh-V2


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Veh-C2


title: Control133

description: 3'-biased mRNA


title: Control130

description: 3'-biased mRNA


title: Control132

description: 3'-biased mRNA


title: GL78_125_WN-S2-P1_B17_AGM_E10-5_SP_32-33_Gfi1_HE__S125


title: GL78_129_WN-S2-P1_H17_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S129


title: GL78_126_WN-S2-P1_C17_AGM_E10-5_SP_32-33_Gfi1_HE__S126


title: Control129

description: 3'-biased mRNA


title: GL78_124_WN-S2-P1_A17_AGM_E10-5_SP_32-33_Gfi1_HE__S124


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Acu, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Acu-V1

value: 100nM Dexamethasone in DMSO for 10 days (day 60 to day 70) + 100nM Dexamethasone in DMSO for 12 hours before collection at D90


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Veh-C1


title: Control128

description: 3'-biased mRNA


title: GL78_123_WN-S2-P1_I16_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S123


title: GL78_122_WN-S2-P1_H16_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S122


title: Control127

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Acu, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Acu-C1


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Veh, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Veh-V2

value: DMSO (treatment vehicle) for 10 days (day 60 to day 70)


title: Kouiki_K_150114_G15

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Gene Expression Custom 8×60K Array (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner G4900DA using one color scan setting for 8x60k array slides (AgilentG3_HiSen_GX_1Color).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (Protocol: GE1_1105_Oct12 and Grid: 069025_D_F_20140811) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Cryptomeria japonica

source_name: Kumamoto, Jan-15,  replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from  200 ng total RNA using the One-Color Low Input Quick Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cuttings of Japanese cedar were planted in three regions (Yamagata, Ibaraki and Kumamoto, Japan) in 2013.

extract_protocol: The total RNA was extracted from 500 mg samples as Gehrig et al. (2000) reported using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), and a DNase digestion was performed on-column using an RNase-free DNase Set (Qiagen).

treatment_protocol: All samples were immediately frozen in liquid nitrogen and stored at -80 °C until use.

value: shoot

tag: day of sampling

tag: geographical location

value: Kumamoto


title: GL78_120_WN-S2-P1_F16_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S120

value: Hematopoietic cells

value: AGM


title: Kouiki_K_141208_G03

source_name: Kumamoto, Dec-14,  replicate 1


title: Kouiki_K_150210_G25

source_name: Kumamoto, Feb-15,  replicate 2


title: Kouiki_K_141208_G18

source_name: Kumamoto, Dec-14,  replicate 2


title: Kouiki_K_141112_G10

source_name: Kumamoto, Nov-14,  replicate 2


title: Kouiki_K_141112_G09

source_name: Kumamoto, Nov-14,  replicate 1


title: Kouiki_K_150210_G10

source_name: Kumamoto, Feb-15,  replicate 1


title: GL78_121_WN-S2-P1_G16_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S121

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: Kouiki_K_140916_G18

source_name: Kumamoto, Sep-14,  replicate 2


title: Kouiki_K_141011_G25

source_name: Kumamoto, Oct-14,  replicate 2


title: Control124

description: 3'-biased mRNA

value: Control


title: Control125

description: 3'-biased mRNA


title: Kouiki_K_150114_G05

source_name: Kumamoto, Jan-15,  replicate 1


title: Kouiki_K_141011_G15

source_name: Kumamoto, Oct-14,  replicate 1


title: Kouiki_K_140916_G05

source_name: Kumamoto, Sep-14,  replicate 1


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Acu, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Acu-V2


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Veh, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Veh-C2


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Veh, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Veh-V1


title: GL78_119_WN-S2-P1_D16_AGM_E10-5_SP_32-33_Gfi1_HE__S119

source_name: AGM

value: Hemogenic endothelium cells


title: Control123

description: 3'-biased mRNA

source_name: Whole Blood


title: Control126

description: 3'-biased mRNA


title: GL78_118_WN-S2-P1_B16_AGM_E10-5_SP_32-33_Gfi1_HE__S118


title: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Acu, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D90-Chr-Acu-C2


title: Control122

description: 3'-biased mRNA


title: GL78_117_WN-S2-P1_A16_AGM_E10-5_SP_32-33_Gfi1_HE__S117


title: Control121

description: 3'-biased mRNA


title: Kouiki_K_140811_G03

source_name: Kumamoto, Aug-14,  replicate 1


title: Kouiki_K_140811_G10

source_name: Kumamoto, Aug-14,  replicate 2


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Chr, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Chr-V2

source_name: Unguided neural organoid

value: 100nM Dexamethasone in DMSO for 10 days (day 60 to day 70)


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Chr, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Chr-V1


title: Control120

description: 3'-biased mRNA


title: Kouiki_K_140711_G15

source_name: Kumamoto, Jul-14,  replicate 2


title: GL78_115_WN-S2-P1_I15_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S115


title: Control119

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Chr, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Chr-C1


title: GL78_114_WN-S2-P1_H15_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S114


title: GL78_113_WN-S2-P1_G15_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S113


title: Control118

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Veh, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Veh-C1


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Veh, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Veh-V2


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Veh, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Veh-V1


title: GL78_116_WN-S2-P1_J15_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S116


title: Control117

description: 3'-biased mRNA


title: Control116

description: 3'-biased mRNA


title: Kouiki_K_140610_G18

source_name: Kumamoto, Jun-14,  replicate 1


title: Kouiki_K_140711_G09

source_name: Kumamoto, Jul-14,  replicate 1


title: Kouiki_K_140513_G05

source_name: Kumamoto, May-14,  replicate 1


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Veh, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Veh-C2


title: Kouiki_K_140513_G10

source_name: Kumamoto, May-14,  replicate 2


title: Control115

description: 3'-biased mRNA


title: Kouiki_K_140610_G25

source_name: Kumamoto, Jun-14,  replicate 2


title: GL78_110_WN-S2-P1_B15_AGM_E10-5_SP_32-33_Gfi1_HE__S110


title: Kouiki_K_140409_G15

source_name: Kumamoto, Apl-14,  replicate 2


title: Control113

description: 3'-biased mRNA


title: GL78_108_WN-S2-P1_K14_AGM_E10-5_SP_32-33_Gfi1_neg_IAHC__S108


title: scRNA-seq, Neural organoid, Line 409b2, Day 70 Chr, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
HSP0076-D70-Chr-C2


title: Control112

description: 3'-biased mRNA


title: Kouiki_K_140409_G03

source_name: Kumamoto, Apl-14,  replicate 1


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Acu, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Acu-V1


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Acu, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Acu-V2


title: GL78_107_WN-S2-P1_I14_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S107


title: GL78_112_WN-S2-P1_F15_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S112


title: GL78_106_WN-S2-P1_H14_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S106


title: Control111

description: 3'-biased mRNA


title: Kouiki_K_140310_G09

source_name: Kumamoto, Mar-14,  replicate 1


title: GL78_109_WN-S2-P1_A15_AGM_E10-5_SP_32-33_Gfi1_HE__S109


title: GL78_104_WN-S2-P1_D14_AGM_E10-5_SP_32-33_Gfi1_HE__S104


title: Control109

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Acu, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Acu-C2


title: GL78_111_WN-S2-P1_D15_AGM_E10-5_SP_32-33_Gfi1_HE__S111


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Veh, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Veh-V2


title: scRNA-seq, Neural organoid, Line FOK4, Day 90 Chr-Acu, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D90-Chr-Acu-C1


title: GL78_103_WN-S2-P1_C14_AGM_E10-5_SP_32-33_Gfi1_HE__S103


title: Kouiki_K_140219_G15

source_name: Kumamoto, Feb-14,  replicate 1


title: Kouiki_K_140219_G25

source_name: Kumamoto, Feb-14,  replicate 2


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Veh, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Veh-V1


title: Kouiki_I_150107_G07

source_name: Ibaraki, Jan-15,  replicate 2

value: Ibaraki


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Veh, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Veh-C2


title: GL78_105_WN-S2-P1_F14_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S105

source_name: AGM


title: Control107

description: 3'-biased mRNA

source_name: Whole Blood


title: Control106

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Veh, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Veh-C1


title: Kouiki_K_140310_G10

source_name: Kumamoto, Mar-14,  replicate 2


title: Kouiki_I_150209_G05

source_name: Ibaraki, Feb-15,  replicate 2


title: Control114

description: 3'-biased mRNA


title: Kouiki_I_150107_G03

source_name: Ibaraki, Jan-15,  replicate 1


title: Kouiki_I_141210_G04

source_name: Ibaraki, Dec-14,  replicate 2


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Chr, Replicate 3

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Chr-V3

source_name: Unguided neural organoid


title: Kouiki_I_150209_G03

source_name: Ibaraki, Feb-15,  replicate 1


title: Control105

description: 3'-biased mRNA


title: Control104

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Chr, Replicate 4

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Chr-V2


title: Control108

description: 3'-biased mRNA


title: GL78_100_WN-S2-P1_J13_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S100


title: GL78_102_WN-S2-P1_B14_AGM_E10-5_SP_32-33_Gfi1_HE__S102


title: Kouiki_I_141210_G03

source_name: Ibaraki, Dec-14,  replicate 1


title: GL78_098_WN-S2-P1_G13_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S98


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Chr, Replicate 1

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Chr-C3


title: GL78_101_WN-S2-P1_A14_AGM_E10-5_SP_32-33_Gfi1_HE__S101


title: Kouiki_I_141111_G05

source_name: Ibaraki, Nov-14,  replicate 1


title: Kouiki_I_141015_G05

source_name: Ibaraki, Oct-14,  replicate 2


title: Kouiki_I_141111_G07

source_name: Ibaraki, Nov-14,  replicate 2


title: Control102

description: 3'-biased mRNA


title: scRNA-seq, Neural organoid, Line FOK4, Day 70 Chr, Replicate 2

description:
Single-cell RNA sequencing (10xGenomics Chromium)
FOK4-D70-Chr-C2


title: XAUT1-POOL-SCG10

city: San Francisco

first: Michael

middle: George

last: Kattah

state: CA

address: 513 Parnassus Ave

department: Medicine-Gastroenterology

institute: UCSF

description:
XAUT1-POOL-SCG10_pool2: XAUT1-HS1-CLL1 XAUT1-HS2-CLR1 XAUT1-HS3-CLL1 XAUT1-HS4-CLR1 XAUT1-HS5-CLL1 XAUT1-HS6-CLR1 XAUT1-HS7-CLL1 XAUT1-HS9-CLL1 XAUT1-HS10-CLR1 XAUT1-HS11-CLL1 XAUT1-HS12-CLR1
biopsy_ADT.h5ad
biopsy_RNA_ADT_joint.h5ad

data_processing:
Briefly, sequencer obtained bcl files were demultiplexed into individual library fastq trios using the mkfastq program from the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com). Feature-barcode matrices were obtained for each sample by aligning the raw fastqs to GRCh38 reference genome (annotated with Ensembl v85) using the Cellranger count. Raw feature-barcode matrices were loaded into Seurat 3.1.5 and low-quality cells (with fewer than 100 features), and features in 3 or fewer cells were dropped from the dataset. The remaining events were assessed for inter-sample doublet detection (generated due to libraries containing samples pooled prior to loading) using Freemuxlet (https://github.com/statgen/popscle), the genotype-free version of Demuxlet.
Clusters of cells belonging to the same patient were identified via SNP concordance to a “truth set” generated by bulk RNASeq.
Clusters of cells belonging to a unique sample were mapped to patients using their individual Freemuxlet-generated genotype, and ground truth genotypes per patient identified via bulk RNA-seq. The pairwise discordance between inferred and ground-truth genotypes was assessed using the bcftools gtcheck command.
ADT counts were centered log-ratio (CLR) normalized. The resulting Harmony components were used to generate batch corrected UMAP visualizations and cell clustering
Assembly: GRCh38
Supplementary files format and content: Freemuxlet format: clust1.samples.gz
Supplementary files format and content: Seurat object (.rds) and anndata (.h5ad)
Library strategy: CITE-seq

source_name: colon biopsy

extract_protocol:
Colon biopsies were obtained with standard cold endoscopic biopsy forceps from two different regions of the colon (R=right/proximal and L=left/distal). Six biopsies were collected in a conical tube with Basal Media (Advanced DMEM/F12 with NEAA and Sodium Pyruvate, Thermo cat. No. 12634-010; 2mM Glutamax, Thermo cat. No. 35050061; 10 mM HEPES (Corning); Penicillin-Streptomycin-Neomycin (PSN) Antibiotic Mixture, Thermo cat. No. 15640055; Normocin 100 μg/mL, Invivogen cat. No. ant-nr-2; 1 mM N-acetylcysteine, Sigma-Aldrich, A9165) with 10 μM Y-27632 (MedChem Express) at 4°C. Biopsies were transferred into cryovials containing freezing media (90% (v/v) FCS, 10% (v/v) DMSO and 10 μM Y-27632). Colon biopsies were thawed for 2min with gentle agitation in a 37 C water bath, transferred to a gentleMACS Tube (Miltenyi Biotec), washed twice with basal media containing 10 μM Y-27632, and then incubated in 2 mL digestion buffer (basal media, 10 μM Y-27632, 600 U/mL Collagenase IV (Worthington cat. No.LS004189), 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513) and digested for 20 min at 37°C in a shaking incubator set at 225 rpm. Subsequently, samples were placed in the gentleMACS Dissociator, processed with the gentleMACS program m_intestine_01, followed by 15 min incubation at 37°C in a shaking incubator set at 225 rpm. The suspension was then strained through a 100 μm strainer (Miltenyi) and centrifuged at 450g for 5 min at RT. Two additional washes were performed in Hanks’ Balanced Salt Solution (HBSS) (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513). Dead cells were removed with the Dead Cell Removal Kit (Miltenyi) according to the manufacturer’s instructions. Cell suspensions were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). Live cell enriched colon single-cell suspensions were used for tissue scRNA-seq and CITE-seq, with a final pooled viability >75%. Colon single-cell suspensions from each patient were pooled with equivalent number of live cells. Samples from unique individuals were pooled, and samples from the proximal (Right,R) or distal (Left,L) colon of the same individual were placed in separate pools, so each sample could later be uniquely identified using demuxlet.
1x10^6 cells of both single-cell colon suspension pools were stained with a custom TotalSeq-A panel, (BioLegend) according to the manufacturer’s instructions and loaded into two wells. cDNA library generation using the Chromium Single Cell 3′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.

value: colon biopsy

tag: adt

value: custom TotalSeq-A panel, (BioLegend)


title: GL78_097_WN-S2-P1_F13_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S97

tag: cell type


title: XAUT1-POOL-SCG9

description:
XAUT1-POOL-SCG9_pool1: XAUT1-HS1-CLR1 XAUT1-HS2-CLL1 XAUT1-HS3-CLR1 XAUT1-HS4-CLL1 XAUT1-HS5-CLR1 XAUT1-HS6-CLL1 XAUT1-HS7-CLR1 XAUT1-HS8-CLL1 XAUT1-HS9-CLR1 XAUT1-HS11-CLR1
biopsy_ADT.h5ad
biopsy_RNA_ADT_joint.h5ad


title: Control100

description: 3'-biased mRNA


title: GL78_099_WN-S2-P1_H13_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S99


title: Control101

description: 3'-biased mRNA


title: Control103

description: 3'-biased mRNA


title: GL78_096_WN-S2-P1_C13_AGM_E10-5_SP_32-33_Gfi1_HE__S96


title: Control099

description: 3'-biased mRNA


title: XAUT1-POOL-SCG14

description:
XAUT1-POOL-SCG14 :XAUT1-HS1-BLD1 XAUT1-HS2-BLD1 XAUT1-HS3-BLD1 XAUT1-HS4-BLD1 XAUT1-HS6-BLD1 XAUT1-HS7-BLD1 XAUT1-HS8-BLD1 XAUT1-HS9-BLD1 XAUT1-HS10-BLD1 XAUT1-HS11-BLD1 XAUT1-HS12-BLD1
blood_RNA.rds
blood_RNA.h5ad

data_processing:
Briefly, sequencer obtained bcl files were demultiplexed into individual library fastq trios using the mkfastq program from the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com). Feature-barcode matrices were obtained for each sample by aligning the raw fastqs to GRCh38 reference genome (annotated with Ensembl v85) using the Cellranger count. Raw feature-barcode matrices were loaded into Seurat 3.1.5 and low-quality cells (with fewer than 100 features), and features in 3 or fewer cells were dropped from the dataset. The remaining events were assessed for inter-sample doublet detection (generated due to libraries containing samples pooled prior to loading) using Freemuxlet (https://github.com/statgen/popscle), the genotype-free version of Demuxlet.
Clusters of cells belonging to the same patient were identified via SNP concordance to a “truth set” generated by bulk RNASeq.
Clusters of cells belonging to a unique sample were mapped to patients using their individual Freemuxlet-generated genotype, and ground truth genotypes per patient identified via bulk RNA-seq. The pairwise discordance between inferred and ground-truth genotypes was assessed using the bcftools gtcheck command.
Assembly: GRCh38
Supplementary files format and content: Freemuxlet format: clust1.samples.gz
Supplementary files format and content: Seurat object (.rds) and anndata (.h5ad)

source_name: peripheral blood

extract_protocol:
peripheral blood leukocyte (PBL) isolation, peripheral blood was collected into EDTA tubes (BD, 366643). 2 mL aliquots of peripheral blood were treated with 30mL of RBC lysis buffer (Roche) for 5-8 minutes at room temperature with gentle mixing. Cells were resuspended in CryoStor CS10 (at 4°C) freezing medium. PBLs were thawed for 2min with gentle agitation in a 37 degree Celsius in water bath and then washed twice with complete DMEM (Thermo Fisher) supplemented with nonessential amino acids (Thermo Fisher Scientific), sodium pyruvate (Thermo Fisher Scientific), HEPES (10 mM; Corning), Glutamax (2 mM; Thermo Fisher Scientific), Normocin (100 μg/mL; Invivogen, ant-nr-2), penicillin-streptomycin (Thermo Fisher Scientific) and 10% Fetal Bovine Serum (VWR). Cells were incubated with ACK lysis buffer (Quality Biological) for 5min at room-temperature, washed twice with complete DMEM, treated with HBSS (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513)for 5 min, and then strained through a 20um pre-separation filter (Miltenyi). Cells were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). PBLs from each donor were pooled with equivelent number of cells for each patient and used for scRNA-seq with a final pooled viability of >85%. 60,000 cells were loaded per well and processed for single-cell encapsulation.
cDNA library generation using the Chromium Single Cell 3′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.

value: peripheral blood

value: peripheral leukocytes


title: GL78_095_WN-S2-P1_B13_AGM_E10-5_SP_32-33_Gfi1_HE__S95


title: XAUT1-POOL-SCG13

description:
XAUT1-POOL-SCG13 :XAUT1-HS1-BLD1 XAUT1-HS2-BLD1 XAUT1-HS3-BLD1 XAUT1-HS4-BLD1 XAUT1-HS6-BLD1 XAUT1-HS7-BLD1 XAUT1-HS8-BLD1 XAUT1-HS9-BLD1 XAUT1-HS10-BLD1 XAUT1-HS11-BLD1 XAUT1-HS12-BLD1
blood_RNA.rds
blood_RNA.h5ad


title: GL78_094_WN-S2-P1_A13_AGM_E10-5_SP_32-33_Gfi1_HE__S94


title: Control098

description: 3'-biased mRNA


title: GL78_093_WN-S2-P1_K12_AGM_E10-5_SP_32-33_Gfi1_neg_IAHC__S93


title: XAUT1-POOL-SCG12

description:
XAUT1-POOL-SCG12 :XAUT1-HS1-BLD1 XAUT1-HS2-BLD1 XAUT1-HS3-BLD1 XAUT1-HS4-BLD1 XAUT1-HS6-BLD1 XAUT1-HS7-BLD1 XAUT1-HS8-BLD1 XAUT1-HS9-BLD1 XAUT1-HS10-BLD1 XAUT1-HS11-BLD1 XAUT1-HS12-BLD1
blood_RNA.rds
blood_RNA.h5ad


title: Control097

description: 3'-biased mRNA


title: GL78_092_WN-S2-P1_H12_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S92


title: XAUT1-POOL-SCG11

description:
XAUT1-POOL-SCG11 :XAUT1-HS1-BLD1 XAUT1-HS2-BLD1 XAUT1-HS3-BLD1 XAUT1-HS4-BLD1 XAUT1-HS6-BLD1 XAUT1-HS7-BLD1 XAUT1-HS8-BLD1 XAUT1-HS9-BLD1 XAUT1-HS10-BLD1 XAUT1-HS11-BLD1 XAUT1-HS12-BLD1
blood_RNA.rds
blood_RNA.h5ad


title: GL78_091_WN-S2-P1_G12_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S91


title: Control096

description: 3'-biased mRNA


title: Kouiki_I_141015_G03

source_name: Ibaraki, Oct-14,  replicate 1


title: XAUT1-POOL-SCG8

description:
XAUT1-POOL-SCG8_pool2: XAUT1-HS1-CLL1 XAUT1-HS2-CLR1 XAUT1-HS3-CLL1 XAUT1-HS4-CLR1 XAUT1-HS5-CLL1 XAUT1-HS6-CLR1 XAUT1-HS7-CLL1 XAUT1-HS9-CLL1 XAUT1-HS10-CLR1 XAUT1-HS11-CLL1 XAUT1-HS12-CLR1
biopsy_RNA.rds
biopsy_RNA.h5ad

extract_protocol:
Colon biopsies were obtained with standard cold endoscopic biopsy forceps from two different regions of the colon (R=right/proximal and L=left/distal). Six biopsies were collected in a conical tube with Basal Media (Advanced DMEM/F12 with NEAA and Sodium Pyruvate, Thermo cat. No. 12634-010; 2mM Glutamax, Thermo cat. No. 35050061; 10 mM HEPES (Corning); Penicillin-Streptomycin-Neomycin (PSN) Antibiotic Mixture, Thermo cat. No. 15640055; Normocin 100 μg/mL, Invivogen cat. No. ant-nr-2; 1 mM N-acetylcysteine, Sigma-Aldrich, A9165) with 10 μM Y-27632 (MedChem Express) at 4°C. Biopsies were transferred into cryovials containing freezing media (90% (v/v) FCS, 10% (v/v) DMSO and 10 μM Y-27632). Colon biopsies were thawed for 2min with gentle agitation in a 37 C water bath, transferred to a gentleMACS Tube (Miltenyi Biotec), washed twice with basal media containing 10 μM Y-27632, and then incubated in 2 mL digestion buffer (basal media, 10 μM Y-27632, 600 U/mL Collagenase IV (Worthington cat. No.LS004189), 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513) and digested for 20 min at 37°C in a shaking incubator set at 225 rpm. Subsequently, samples were placed in the gentleMACS Dissociator, processed with the gentleMACS program m_intestine_01, followed by 15 min incubation at 37°C in a shaking incubator set at 225 rpm. The suspension was then strained through a 100 μm strainer (Miltenyi) and centrifuged at 450g for 5 min at RT. Two additional washes were performed in Hanks’ Balanced Salt Solution (HBSS) (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513). Dead cells were removed with the Dead Cell Removal Kit (Miltenyi) according to the manufacturer’s instructions. Cell suspensions were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). Live cell enriched colon single-cell suspensions were used for tissue scRNA-seq and CITE-seq, with a final pooled viability >75%. Colon single-cell suspensions from each patient were pooled with equivalent number of live cells. Samples from unique individuals were pooled, and samples from the proximal (Right,R) or distal (Left,L) colon of the same individual were placed in separate pools, so each sample could later be uniquely identified using demuxlet.
cDNA library generation using the Chromium Single Cell 3′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.


title: Control095

description: 3'-biased mRNA


title: Kouiki_I_140909_G08

source_name: Ibaraki, Sep-14,  replicate 2


title: XAUT1-POOL-SCG7

description:
XAUT1-POOL-SCG7_pool2: XAUT1-HS1-CLL1 XAUT1-HS2-CLR1 XAUT1-HS3-CLL1 XAUT1-HS4-CLR1 XAUT1-HS5-CLL1 XAUT1-HS6-CLR1 XAUT1-HS7-CLL1 XAUT1-HS9-CLL1 XAUT1-HS10-CLR1 XAUT1-HS11-CLL1 XAUT1-HS12-CLR1
biopsy_RNA.rds
biopsy_RNA.h5ad


title: Kouiki_I_140712_G07

source_name: Ibaraki, Jul-14,  replicate 2


title: Control094

description: 3'-biased mRNA


title: GL78_090_WN-S2-P1_F12_AGM_E10-5_SP_32-33_Gfi1_pos_IAHC__S90

source_name: AGM


title: XAUT1-POOL-SCG6

description:
XAUT1-POOL-SCG6_pool2: XAUT1-HS1-CLL1 XAUT1-HS2-CLR1 XAUT1-HS3-CLL1 XAUT1-HS4-CLR1 XAUT1-HS5-CLL1 XAUT1-HS6-CLR1 XAUT1-HS7-CLL1 XAUT1-HS9-CLL1 XAUT1-HS10-CLR1 XAUT1-HS11-CLL1 XAUT1-HS12-CLR1
biopsy_RNA.rds
biopsy_RNA.h5ad


title: Kouiki_I_140909_G07

source_name: Ibaraki, Sep-14,  replicate 1


title: Kouiki_I_140811_G03

source_name: Ibaraki, Aug-14,  replicate 1


title: GL78_089_WN-S2-P1_E12_AGM_E10-5_SP_32-33_Gfi1_HE__S89


title: GL78_088_WN-S2-P1_D12_AGM_E10-5_SP_32-33_Gfi1_HE__S88