title: MesAur_Brain_day2_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG05_d2low_brain


title: MesAur_Brain_day2_CoV2_100pfu_3

status: Public on Nov 11 2020

type: SRA

city: New York

first: Rasmus

last: Moeller

state: NY

address: 1 Gustave L. Levy Place

department: Microbiology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
HAG_brain_count_matrix.csv
HAG06_d2low_brain

library_source: transcriptomic

data_processing:
automated base-calling performed with bcl2fastq (Illumina)
fastq files were aligned using RNA-Seq Alignment application (Basespace, Illumina).
total counts were extracted and comiled in .csv files for each tissue
Genome_build: Ensembl MesAur1.0
Supplementary_files_format_and_content: All processed data files are .csv files containining total counts of each gene after alignment. Each file contains counts from one tissue.

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: brain without olfactory bulb

extract_protocol:
Tissues were homogenized in 1ml TRIzol reagent (invitrogen) and RNA total RNA was extracted my phenol/chloroform extraction following manufacturer's protocol.
All libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Starting material: 1µg total RNA

treatment_protocol: Syrian golden hamsters were infected with SARS-CoV-2 or IAV intranasally with 100µl of inoculum (virus in PBS) under anaesthesia with ketamine/xylazine at doses indicated and organs were collected at the times indicated. All hamsters were perfused before the collection of organs.

tag: age

value: 3-5 weks old

tag: Sex

value: male

tag: tissue

value: brain

tag: virus

value: SARS-CoV-2, USA-WA1/2020 strain

tag: dosage

value: 100 pfu

tag: time point

value: 2 days


title: MesAur_Brain_day2_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG04_d2low_brain


title: MesAur_Brain_day1_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG02_day1low_brain

value: 1 day


title: MesAur_Brain_day1_CoV2_100pfu_3

description:
HAG_brain_count_matrix.csv
HAG03_d1low_brain_r


title: MesAur_Brain_mock_5

description:
HAG_brain_count_matrix.csv
HAB18_day7_PBS_brain


title: MesAur_Brain_day1_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG01_day1low_brain


title: MesAur_Brain_mock_2

description:
HAG_brain_count_matrix.csv
HAB17_day7_PBS_brain


title: MesAur_Brain_mock_4

description:
HAG_brain_count_matrix.csv
HAJ03_brain


title: MesAur_Brain_mock_1

description:
HAG_brain_count_matrix.csv
HAB16_day7_PBS_brain


title: MesAur_Trachea_day14_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAG36_day14high_trachea

source_name: trachea

value: trachea

value: 14 days


title: MesAur_Brain_mock_3

description:
HAG_brain_count_matrix.csv
HAJ02_mock_brain


title: MesAur_Trachea_day14_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAG35_day14high_trachea


title: MesAur_Trachea_day14_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAG34_day14high_trachea


title: MesAur_Trachea_day8_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAG33_day8high_trachea_F04

value: 8 days


title: MesAur_Trachea_day8_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAG32_day8high_trachea_F02


title: MesAur_Trachea_day6_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAG29_d6high_trachea

value: 6 days


title: MesAur_Trachea_day6_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAG30_d6high_trachea


title: MesAur_Trachea_day6_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAG28_d6high_trachea


title: MesAur_Trachea_day8_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAG31_day8high_trachea_E04


title: MesAur_Trachea_day4_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAG26_d4high_trachea

value: 4 days


title: MesAur_Trachea_day2_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAG23_trachea


title: MesAur_Trachea_day4_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAG25_d4high_trachea


title: MesAur_Trachea_day2_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAG24_d2high_trachea


title: MesAur_Trachea_day1_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAB03_day1_CoV2_trachea


title: MesAur_Trachea_day2_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAG22_d2high_trachea


title: MesAur_Trachea_day1_CoV2_10000pfu_2

description:
HAG_trachea_count_matrix.csv
HAB02_day1_CoV2_trachea


title: MesAur_Trachea_day1_CoV2_10000pfu_1

description:
HAG_trachea_count_matrix.csv
HAB01_day1_CoV2_trachea


title: MesAur_Trachea_day14_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAG17_d14low_trachea_r


title: MesAur_Trachea_day14_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAG16_day14low_trachea


title: MesAur_Trachea_day8_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAG15_day8low_trachea_E02


title: MesAur_Trachea_day6_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAG12_d6low_trachea


title: MesAur_Trachea_day8_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAG14_day8low_trachea_D04


title: MesAur_Trachea_day8_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAG13_day8low_trachea_D02


title: MesAur_Trachea_day6_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAG11_d6low_trachea


title: MesAur_Trachea_day4_CoV2_10000pfu_3

description:
HAG_trachea_count_matrix.csv
HAG27_d4high_trachea


title: MesAur_Trachea_day4_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAG09_d4low_trachea


title: MesAur_Trachea_day4_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAG08_d4low_trachea


title: MesAur_Trachea_day4_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAG07_d4low_trachea


title: MesAur_Trachea_day2_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAG05_d2low_trachea


title: MesAur_Trachea_day1_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAP04_d1low_trachea


title: MesAur_Trachea_day1_CoV2_100pfu_2

description:
HAG_trachea_count_matrix.csv
HAP02_d1low_trachea


title: MesAur_Trachea_day2_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAG04_d2low_trachea


title: MesAur_Sm_int_day6_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG28_d6high_sm_int

source_name: proximal small intestine

value: small intestine


title: MesAur_Trachea_day1_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAP01_d1low_trachea


title: MesAur_Sm_int_day8_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG15_day8low_sm_int


title: MesAur_Trachea_mock_6

description:
HAG_trachea_count_matrix.csv
HAB18_day7_PBS_trachea


title: MesAur_Trachea_mock_1

description:
HAG_trachea_count_matrix.csv
HAB13_day1_PBS_trachea


title: MesAur_Trachea_mock_2

description:
HAG_trachea_count_matrix.csv
HAB14_day1_PBS_trachea


title: MesAur_Trachea_mock_3

description:
HAG_trachea_count_matrix.csv
HAB15_day1_PBS_trachea


title: MesAur_Trachea_day14_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAG18_day14low_trachea


title: MesAur_Trachea_mock_5

description:
HAG_trachea_count_matrix.csv
HAB17_day7_PBS_trachea


title: MesAur_Lung_day14_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAG36_day14high_lung

source_name: whole lung

value: lung


title: MesAur_Trachea_mock_4

description:
HAG_trachea_count_matrix.csv
HAB16_day7_PBS_trachea


title: MesAur_Lung_day14_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAG35_day14high_lung_rep


title: MesAur_Lung_day14_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAG34_day14high_lung_rep


title: MesAur_Lung_day8_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAG32_day8high_lung_F01


title: MesAur_Lung_day8_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAG31_day8high_lung_E03


title: MesAur_Trachea_day2_CoV2_100pfu_3

description:
HAG_trachea_count_matrix.csv
HAG06_trachea


title: MesAur_Lung_day6_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAG28_d6high_lung


title: MesAur_Lung_day6_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAG30_d8high_lung_r


title: MesAur_Lung_day6_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAG29_d6high_lung


title: MesAur_Lung_day4_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAG27_d4high_lung


title: MesAur_Lung_day4_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAG25_d4high_lung


title: MesAur_Lung_day2_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAG23_day2high_lung_rep


title: MesAur_Lung_day2_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAG24_d2high_lung


title: MesAur_Lung_day2_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAG22_d2high_lung


title: MesAur_Lung_day1_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAB03_day1_CoV2_lung


title: MesAur_Lung_day1_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAB02_day1_CoV2_lung


title: MesAur_Lung_day1_CoV2_10000pfu_1

description:
HAG_lung_count_matrix.csv
HAB01_day1_CoV2_lung


title: MesAur_Trachea_day6_CoV2_100pfu_1

description:
HAG_trachea_count_matrix.csv
HAG10_d6low_trachea


title: MesAur_Lung_day14_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAG16_day14low_lung_rep


title: MesAur_Lung_day14_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAG17_day14low_lung_rep


title: MesAur_Lung_day8_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAG15_day8low_lung_E01


title: MesAur_Lung_day8_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAG13_day8low_lung_D01


title: MesAur_Lung_day14_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAG18_day14low_lung_rep


title: MesAur_Lung_day8_CoV2_10000pfu_3

description:
HAG_lung_count_matrix.csv
HAG33_day8high_lung_F03


title: MesAur_Lung_day6_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAG12_d6low_lung


title: MesAur_Lung_day6_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAG10_day6low_lung_rep


title: MesAur_Lung_day4_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAG09_d4low_lung


title: MesAur_Lung_day6_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAG11_d6low_lung


title: MesAur_Lung_day4_CoV2_10000pfu_2

description:
HAG_lung_count_matrix.csv
HAG26_d4high_lung


title: MesAur_Lung_day2_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAG05_lung


title: MesAur_Lung_day4_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAG07_d4low_lung


title: MesAur_Lung_day2_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAG04_d2low_lung


title: MesAur_Lung_day1_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAP02_d1low_lung


title: MesAur_Lung_mock_6

description:
HAG_lung_count_matrix.csv
HAJ03_mock_lung_rep


title: MesAur_Lung_mock_4

description:
HAG_lung_count_matrix.csv
HAJ01_mock_lung_rep


title: MesAur_Lung_mock_3

description:
HAG_lung_count_matrix.csv
HAB18_day7_PBS_lung


title: MesAur_Lung_day8_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAG14_day8low_lung_D03


title: MesAur_Lung_mock_1

description:
HAG_lung_count_matrix.csv
HAB16_day7_PBS_lung


title: MesAur_Lung_mock_2

description:
HAG_lung_count_matrix.csv
HAB17_day7_PBS_lung


title: MesAur_Lung_day4_CoV2_100pfu_2

description:
HAG_lung_count_matrix.csv
HAG08_d4low_lung


title: MesAur_Lung_day2_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAG06_d2low_lung


title: MesAur_Lung_day1_CoV2_100pfu_3

description:
HAG_lung_count_matrix.csv
HAP04_d1low_lung


title: MesAur_Lung_day1_CoV2_100pfu_1

description:
HAG_lung_count_matrix.csv
HAP01_d1low_lung


title: MesAur_Lung_mock_5

description:
HAG_lung_count_matrix.csv
HAJ02_mock_lung_rep


title: L. infantum PABP1-HA rep1

city: Jaboatão dos Guararapes

first: LUDMILA

middle: A

last: ASSIS

state: PE

address: Rua Coronel Dário Ferraz De Sá, 5357, Casa 1

department: Microbiologia

country: Brazil

institute: Instituto Aggeu Magalhães

description: mRNAs co-immunprecipitated with HA-tagged PABP1, replicate 1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using Trimmomatic version 0.36 with default parameters
The reads were then mapped to Leishmania infantum JPCM5 whole genome using STAR software, version  2.7.0a with --quantMode GeneCounts option to obtain the raw counts files
Genome_build: L. infantum JPCM5, version 2018-07-13
Supplementary_files_format_and_content: raw counts text files for every gene and every sample

organism: Leishmania infantum

source_name: L. infantum cytoplasmic extract

growth_protocol: Late exponentially growth L. infantum promastigotes were harvested to a concentration of 1 to 2x109 cells/ml. The cells were lysis using nitrogen cavitation method.

extract_protocol:
Imunoprecipitation triplicates were carried out with cytoplasmic extracts derived from wild-type L. infantum and transfected cells expressing HA-RBP23, HA-DRBD2 and the three HA-tagged PABPs. RNA were extracted according with the QIAGEN RNAeasy Mini Kit protocol.
RNA Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: untreated

tag: strain

tag: genotype

value: Expressing recombinant HA-tagged

tag: ip antibody

value: Anti-HA Magnetic Beads (Thermo Scientific, 88836)


title: L. infantum WT 2 rep3

description: Negative control for samples 13-21, replicate 3

value: Wild-type


title: L. infantum PABP2-HA rep3

description: mRNAs co-immunprecipitated with HA-tagged PABP2, replicate 3


title: L. infantum DRBD2-HA rep2

description: mRNAs co-immunprecipitated with HA-tagged DRBD2, replicate 2


title: L. infantum PABP2-HA rep2

description: mRNAs co-immunprecipitated with HA-tagged PABP2, replicate 2


title: L. infantum PABP1-HA rep2

description: mRNAs co-immunprecipitated with HA-tagged PABP1, replicate 2


title: L. infantum RBP23-HA rep3

description: mRNAs co-immunprecipitated with HA-tagged RBP23, replicate 3


title: L. infantum PABP3-HA rep2

description: mRNAs co-immunprecipitated with HA-tagged PABP3, replicate 2


title: L. infantum DRBD2-HA rep1

description: mRNAs co-immunprecipitated with HA-tagged DRBD2, replicate 1


title: L. infantum PABP3-HA rep3

description: mRNAs co-immunprecipitated with HA-tagged PABP3, replicate 3


title: L. infantum PABP2-HA rep1

description: mRNAs co-immunprecipitated with HA-tagged PABP2, replicate 1


title: L. infantum WT 2 rep1

description: Negative control for samples 13-21, replicate 1


title: MesAur_Olf_bulb_day6_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG30_day6high_olf_bulb

source_name: olfactory bulb

value: 3-5 weks old

value: olfactory bulb


title: L. infantum WT rep2

description: Negative control for samples 4-9, replicate 2


title: L. infantum RBP23-HA rep2

description: mRNAs co-immunprecipitated with HA-tagged RBP23, replicate 2


title: L. infantum DRBD2-HA rep3

description: mRNAs co-immunprecipitated with HA-tagged DRBD2, replicate 3


title: L. infantum RBP23-HA rep1

description: mRNAs co-immunprecipitated with HA-tagged RBP23, replicate 1


title: L. infantum PABP1-HA rep3

description: mRNAs co-immunprecipitated with HA-tagged PABP1, replicate 3


title: L. infantum WT rep1

description: Negative control for samples 4-9, replicate 1


title: L. infantum PABP3-HA rep1

description: mRNAs co-immunprecipitated with HA-tagged PABP3, replicate 1


title: MesAur_Olf_bulb_day6_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG29_d6high_olf_bulb

value: male


title: L. infantum WT 2 rep2

description: Negative control for samples 13-21, replicate 2


title: NAI, in vivo (SARS-CoV-2), replicate #2

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
SARS-CoV-2 RNA, NAI treated in living infected host cells
SHAPE_invivo.wig

data_processing:
Library strategy: SHAPE-MaP
Analysis of SHAPE-MaP data has been conducted using RNA Framework v2.6.9 (https://github.com/dincarnato/RNAFramework). Reads pre-processing and mapping was performed using the rf-map module (parameters: -ctn -cmn 0 -cqo -cq5 20 -b2 -mp "--very-sensitive-local"). Reads were trimmed of terminal Ns and low-quality bases (Phred < 20). Reads with internal Ns were discarded. Mapping was performed using the “very-sensitive-local” preset of Bowtie2. The mutational signal was then derived using the rf-count module (parameters: -m -rd), enabling the right re-alignment of deletions. When processing SARS-CoV-2 data, a mask file containing the sequences of primer pairing regions was passed along (through the -mf parameter). Generated RC files from both the even and odd sets, containing per base mutation counts and coverage, were then combined in a single RC file using the rf-rctools module (mode: merge). Data normalization was performed using the rf-norm module (parameters: -sm 3 -nm 3 -n 1000 -mm 1), by setting the minimum base coverage to 1,000X and the maximum mutation frequency to 1, and by using the Siegfried et al., 2014 scoring scheme and box-plot normalization of SHAPE reactivities.
Supplementary_files_format_and_content: Additional data files (RC/XML files for analysis with RNA Framework [http://www.rnaframework.com]) are available at: http://www.incarnatolab.com/datasets/SARS_Manfredonia_2020.php

molecule: total RNA

organism: Chlorocebus sabaeus

source_name: NAI, in vivo (SARS-CoV-2), replicate #2

extract_protocol:
200 µl of chloroform were added, followed by vigorous vortexing for 15 sec. Samples were then incubated at room temperature for 2 min, after which they were centrifuged at 12,500 x g for 15 min (4°C). After centrifugation, the upper aqueous phase was transferred to a clean 2 mL tube, and mixed with 2 volumes of 100% ethanol by vigorous vortexing. The entire volume was then transferred to an RNA Clean & Concentrator™-5 column and RNA was purified as per manufacturer instructions. RNA integrity was ensured by gel electrophoresis on a denaturing 2% agarose gel. Before proceeding to library preparation, traces of genomic DNA were removed by treatment with 2 U TURBO™ DNase at 37°C for 20 min.
Total RNA from infected and probed Vero E6 cells was first depleted of ribosomal RNAs using the RiboMinus™ Eukaryote System v2 (ThermoFisher Scientific, cat. A15026), following manufacturer instructions. RNA was then fragmented to a median size of 150 nt by incubation at 94°C for 8 min in RNA Fragmentation Buffer [65 mM Tris–HCl pH 8.0; 95 mM KCl; 4 mM MgCl2], then purified with NucleoMag NGS Clean-up and Size Select beads (Macherey Nagel, cat. 744970), supplemented with 10 U SUPERase•In™ RNase Inhibitor, and eluted in 8 μl NF H2O. Eluted RNA was supplemented with 1 μl 50 μM random hexamers and 1 μl dNTPs (10 mM each), then incubated at 70°C for 5 min and immediately transferred to ice for 1 min. Reverse transcription reactions were conducted in a final volume of 20 μl. Reactions were supplemented with 4 μl 5X RT Buffer [250 mM Tris–HCl pH 8.3; 375 mM KCl], 2 μl DTT 0.1 M, 1 μl MnCl2 120 mM, 20 U SUPERase•In™ RNase Inhibitor and 200 U SuperScript II RT. Reactions were incubated at 25°C for 10 min to allow partial primer extension, followed by 2 h at 42°C. SSII was heat-inactivated by incubating at 75°C for 15 min. 6 mM final EDTA was added to chelate Mn2+ ions, followed by 5 min incubation at room temperature and addition of 6 mM final MgCl2. Reverse transcription reactions were then used as input for the NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module (New England Biolabs, cat. E6111L). Second strand synthesis was performed by incubating 1 h at 16°C, as per manufacturer instructions. DsDNA was purified using NucleoMag NGS Clean-up and Size Select beads, and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, following manufacturer instructions.

treatment_protocol: Infected Vero E6 cells were resuspended in 1× PBS, and NAI from a 1 M stock (in DMSO) was added at a final concentration of 100 mM. A corresponding amount of DMSO was added to the control sample. Samples were then incubated at 37°C with constant shaking for 15 min, followed by quenching of NAI through the addition of DTT at a final concentration of 0.5 M. Following centrifugation at 10 000 × g for 1 min, the supernatant was discarded and cell pellets were resuspended in 2 mL ice-cold TriPure Isolation Reagent (Sigma Aldrich, cat. 11667157001), then stored at −80°C until further use.

tag: cell line

value: Vero E6

tag: sample type

value: SARS-CoV-2 RNA

tag: treatment


title: NAI, in vivo (SARS-CoV-2), replicate #1

source_name: NAI, in vivo (SARS-CoV-2), replicate #1

value: NAI treated in living infected host cells


title: L. infantum WT rep3

description: Negative control for samples 4-9, replicate 3


title: BackgroundPool23_T0_Rep1

city: San Francisco

first: David

last: Simpson

state: California

address: 1550 4th Street

institute: UCSF

description: BackgroundPoolCounts.txt

library_source: genomic

data_processing:
Library strategy: shRNAseq
Original fastq files for each GAIIx run were composed of 30-60 multiplexed samples. Each fastq was split by a barcode identifier using the FASTX-toolkit barcode_splitter.pl script
Count files were created in R (v. 3.1.1) using the edgeR package (v. 3.6.8) processHairpinReads function with no mismatches or shifting allowed, shRNAs with no counts were filtered out and all shRNAs were given an extra count to avoid dividing by zero counts
Analysis of shRNA abundance was performed in edgeR using a time-course design and generalized linear models to compare the initial (T0) and final (T1) timepoints (using the glmFit function) and perform a likelihood ratio test (using the glmLRT function) to report log2 fold change scores and significance.
Genome_build: no alignment necessary
Supplementary_files_format_and_content: tab delimited text files containing either counts for each shRNA (*.Counts.txt) or log2 fold change and likelihood ratio scores for each shRNA (*Analysis.txt)

molecule: genomic DNA

organism: Mus musculus

source_name: primary murine lung tumor organoids

growth_protocol: Primary lung tumor cells isolated from the KRAS/P53/YFP GEMM were depleted for CD45, CD31, and TER119, and 2x10^6 cells were spinfected with lentiviral shRNA libraries (100-150 shRNA/pool at an MOI <0.5) and seeded in equal parts Matrigel and 2x SCM (DMEM;F12, 10% FBS, and supplemented with N2 supplement, BPE, 10 ng/mL EGF, 10ng/mL FGF, and antibiotic/antimycotic) and overlayed with 1x SCM to grow into primary tumor spheres.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue kit
Lentiviral pLKO shRNA vectors were amplified using PCR with ExTaq, and each sample was given direct barcodes for multiplexing and Illumina compatible adapters using a secondary PCR step

treatment_protocol: Primary tumor spheres were selected with 1ug/mL Puromycin from 24h-72 hours in culture. After 7 days in culture, the first timepoint was collected as genomic DNA from 50% of cells, and the remaining 50% of cells were re-seeeded to form secondary spheres which were collected as genomic DNA after day 7 as secondary spheres.

tag: timepoint

tag: replicate


title: BackgroundPool21_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool21_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool23_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool21_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool22_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool22_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool22_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool21_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool22_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool23_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool23_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool23_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool22_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool24_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool25_T0_Rep2

description: BackgroundPoolCounts.txt


title: DMSO, in vivo (SARS-CoV-2)

description:
SARS-CoV-2 RNA, DMSO treated in living infected host cells
SHAPE_invivo.wig

source_name: DMSO, in vivo (SARS-CoV-2)


title: BackgroundPool22_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool21_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool23_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool21_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool20_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool18_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool19_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool17_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool16_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool15_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool12_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool11_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool13_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool09_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool14_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool06_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool07_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool08_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool06_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool06_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool06_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool10_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool06_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool04_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool01_T1_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T0_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool05_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T1_Rep3

description: BackgroundPoolCounts.txt


title: BackgroundPool02_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool03_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool01_T1_Rep3

description: BackgroundPoolCounts.txt


title: OncoSigPoolB_T1_Rep5

description: OncoSigPoolCounts.txt


title: BackgroundPool01_T1_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool01_T0_Rep2

description: BackgroundPoolCounts.txt


title: BackgroundPool01_T0_Rep1

description: BackgroundPoolCounts.txt


title: BackgroundPool01_T0_Rep3

description: BackgroundPoolCounts.txt


title: OncoSigPoolB_T1_Rep6

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T1_Rep4

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T1_Rep3

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T1_Rep2

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep6

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep4

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep5

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep2

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep3

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep3

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep5

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T0_Rep1

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep6

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep2

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep1

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T1_Rep4

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep5

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep1

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep3

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep6

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep2

description: OncoSigPoolCounts.txt


title: OncoSigPoolB_T1_Rep1

description: OncoSigPoolCounts.txt


title: OncoSigPoolA_T0_Rep4

description: OncoSigPoolCounts.txt


title: Kras biological replicate 1

type: RNA

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

country: United Kingdom

institute: CRUK Beatson Institute

hyb_protocol: Samples were hybridised according to the Affymetrix protocol

scan_protocol: Scanner was provided by the Paterson Institute, Manchester, UK

data_processing: CEL files were loaded into R, then background correction, quantile normalisation and probe summarization were performed using the RMA algorithm in the package affy. Differential expression was performed using the limma package, then probe Ids were annotated using the packages mouse4302.db and annotate.

label: biotin

source_name: Whole tissue from small intestine

label_protocol: Samples were labelled according to the Affymetrix protocol

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit according to the manufacturer’s protocol

tag: genetic background

value: villinCreER KrasG12D/+


title: Kras biological replicate 2


title: Thymus - CD4+ T cells

city: Boston

first: Njabulo

last: Ngwenyama

state: MA

address: 136 Harrison Ave

department: Immunology

institute: Tufts University

data_processing:
Trimmomatic to remove sequencing adaptor
Mixcr align reads to TCR database
Mixcr to export alignment data
Mixcr to assemble clone
Mixcr to export clone
Supplementary_files_format_and_content: tab-delimited text files include TCR beta clone fractions and CDR3 sequences for each Sample

source_name: Thymus - 5000 CD4+ T cells

extract_protocol:
Cell suspensions were derived from lymphoid tissues by mechanical dissociation and from whole LV by Collagenase II enzyme digestion. CD4+CD3+CD4+ cells were FACS sorted  from lymphoid tissues and CD4+CD3+CD4+GFP+ cells were FACS sorted  from the  LV. 5000 purified cells from each site were transfered to isolate RNA for the construction of sequencing libraries..
All sequencing libraries were generated using protocols and reagents included in the SMARTer Mouse TCR a/b Profiling Kit (Takara Bio, Cat. 634403).

treatment_protocol: 8 week old Nur77GFP mice underwent Transverse Aortic Constriction surgery (25G constriction) and were harvested at 8 weeks post-surgery.

tag: surgery

value: Transverse Aortic Constriction

value: Thymus

tag: cell type

value: CD4+ T cells


title: Inguinal Lymph Node - CD4+ T cells

source_name: Inguinal Lymph Node - 5000 CD4+ T cells

value: Inguinal Lymph Node


title: Left Ventricle -  GFP+ CD4+ T cells

source_name: Left Ventricle - 5000 GFP+ CD4+ T cells

value: Left Ventricle


title: Mediastinal Lymph Node -  CD4+ T cells

source_name: Mediastinal Lymph Node - 5000 CD4+ T cells

value: Mediastinal Lymph Node


title: Wild type biological replicate 5

value: villinCreER


title: Apc biological replicate 2

value: villinCreER Apcfl/fl


title: ApcKras biological replicate 2

value: villinCreER Apcfl/fl KrasG12D/+


title: mLiver_Ctcf_2

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

data_processing:
The RNA-seq data passed the quality control conducted using FastQC and MulitQC
Sequencing reads were mapped to the mouse reference genome GRCm38/mm10 using STAR software
Differentially gene expression analysis was performed using the Bioconductor package DESeq2; genes with low read counts (<5) were removed from the analysis
Differential alternative splicing was anlayzed using rMATS
Differential intron retention was analyzed using IRFinder
Genome_build: mm10

source_name: Liver

extract_protocol:
Total RNA from WT and Ctcf+/- tissues (<30 mg weight) were homogenized with TRIzol (Invitrogen) and cleaned up by TURBO DNA-free kit (Invitrogen). The RNA integrity was evaluated using a Bioanalyzer showing an RNA integrity number (RIN) over 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: adult

value: Ctcf haploinsufficiency

value: Liver


title: mLiver_WT_3

value: control


title: Wild type biological replicate 4


title: mBrain_Ctcf_3

source_name: Brain

value: Brain


title: mLiver_Ctcf_3


title: ApcKras biological replicate 3


title: mBrain_Ctcf_2


title: mLiver_WT_1


title: Wild type biological replicate 7


title: Apc biological replicate 3


title: Kras biological replicate 4


title: ApcKras biological replicate 1


title: Apc biological replicate 1


title: Wild type biological replicate 1


title: mLiver_Ctcf_1


title: mLiver_WT_2


title: Kras biological replicate 3


title: Wild type biological replicate 6


title: Wild type biological replicate 3


title: Wild type biological replicate 2


title: mBrain_Ctcf_1


title: mBrain_WT_3


title: mBrain_WT_1


title: IL102

city: Beijing

first: Guangyong

last: Sun

address: Yongan Street 95, Xicheng District

country: China

institute: Beijing Friendship Hospital

description: W/ IL-10 stimulated

data_processing:
Illumina Casava1.7 software used for basecalling.
HISAT2 for read aligment
HTSeq for read counting
Genome_build: GRCm38.90
Supplementary_files_format_and_content: tab-delimited text files include Count values for each Sample

source_name: stimulated with IL-10

extract_protocol:
DNT cells were sorted using FACS Aria II , and then stimulated with IL-10 (50ng/ml) for 24h. And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: double negative T cells


title: IL101

description: W/ IL-10 stimulated


title: C3

description: W/O IL-10 stimulated

source_name: no stimulation


title: IL103

description: W/ IL-10 stimulated


title: C1

description: W/O IL-10 stimulated


title: FB_16: 34-43+_FB_1

city: Melbourne

first: Freya

middle: Faith

last: Bruveris

state: VICTORIA

address: 50 Flemington Rd, Parkville

department: Cell Biology

institute: Murdoch Children's Research Institute

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
The raw reads were mapped to the human genome (hg38) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE Release 19 comprehensive annotation
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 16 columns containing counts for each sample

organism: Homo sapiens

source_name: d2+3 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

value: BMP4, VEGF, SCF, ACTIVIN A

tag: culture medium

value: APEL cell culture medium


title: FB_15: 34+43+_FB_1


title: FB_18: SOX17+34+43-_FB_4


title: FB_14: SOX17+34+43-_FB_3


title: FB_19: 34+43+_FB_2


title: FB_20: 34-43+_FB_2


title: FB_11: SOX17+34+43-_FB_2


title: FB_13: SOX17-34+43-d3_FB_1.1


title: mBrain_WT_2

tag: tissue


title: FB_9: SOX17+34+43-_FB_1


title: LV-rep2

city: Nanjing

first: Shukui

last: Wang

address: No.68, Changle Road, Nanjing

institute: Nanjing First Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table include FPKM values for all Samples.

source_name: HCT116 cells

extract_protocol:
RNA was harvested from HCT116 cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCT116 cells

value: Colorectal cancer cells (CRC)

value: lentiviral vector-mediated miR-1290 inhibitor (LV)


title: LV-rep1


title: NC-rep1

value: lentiviral vector-mediated negative control sequence (NC)


title: NC-rep2


title: LV-rep3


title: NC-rep3


title: FB_7: SOX17-34+43-d2_FB_2

source_name: d2+2 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells


title: FB_4: PDGFRα_FB_2

source_name: d2 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

value: PDGFRα


title: FB_3: PDGFRα_FB_1


title: FB_8: SOX17-34+43-d2_FB_3


title: FB_6: SOX17-34+43-d2_FB_1


title: C2

description: W/O IL-10 stimulated


title: FB_5: PDGFRα_FB_3


title: FB_1038: d6RX1-KO_FB_3

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling
The raw reads were mapped to the human genome (hg39) using the STAR aligner version 2.5.2a in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE Release 19 comprehensive annotation
Genome_build: hg39
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 24 columns containing counts for each sample

source_name: d6 differentiated RUNX1-/- SOX17mCHERRY/w H9 human embryonic stem cells

value: Embryoid bodies

value: BMP4, VEGF, SCF, ACTIVIN A, FGF2, CHIR99012


title: FB_1039: d6RX-SXLSD1i_FB_3

source_name: d6 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

value: BMP4, VEGF, SCF, ACTIVIN A, FGF2, CHIR99012 plus d2 LSD1 Inhbitor


title: FB_1037: d6RX-SX_FB_3


title: FB_17: SOX17-34+43-d3_FB_1.2


title: FB_1040: d6RX1-KOLSD1i_FB_3


title: FB_1022: d6RX1-KOLSD1i_FB_2


title: FB_1021: d6RX-SXLSD1i_FB_2


title: FB_1005: d6RX-SXLSD1i_FB_1


title: FB_1020: d6RX1-KO_FB_2


title: FB_1004: d6RX1-KO_FB_1


title: FB_1019: d6RX-SX_FB_2


title: FB_1010: d4RX1-KOLSD1i_2

source_name: d4 differentiated RUNX1-/- SOX17mCHERRY/w H9 human embryonic stem cells


title: FB_1007: d4RX-SX_FB_2

source_name: d4 differentiated SOX17mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells


title: FB_1003: d6RX-SX_FB_1


title: FB_1009: d4RX-SXLSD1i_FB_2


title: FB_1006: d6RX1-KOLSD1i_FB_1


title: FB_1025: d4RX-SXLSD1i_FB_3


title: FB_997: d4RX-SXLSD1i_FB_1


title: FB_1023: d4RX-SX_FB_3


title: FB_1026: d4RX1-KOLSD1i_3


title: FB-996: d4RX1-KO_FB_1


title: FB_1008: d4RX1-KO_FB_2


title: FB_998: d4RX1-KOLSD1i_1


title: FB_995: d4RX-SX_FB_1


title: FB_1024: d4RX1-KO_FB_3


title: iPSC derived iCD34+ rep 1

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

description:
Differentiated CD34+ cells
iCD34+-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Transcriptome Array 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 3000 7G Scanner.

data_processing: Probe intensities were normalized according to Signal Space Transformation robust multi-array analysis (SST-RMA) method in Transcriptome Analysis Console (TAC) 4.0.

source_name: iPSC

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip WT Pico reagent kit and the standard protocols using 10 ng total RNA.

growth_protocol: Expanded iNK (and NK) cells were cocultured with modified K562s in supplemented B0 media for 2-3 weeks.

extract_protocol: Total RNA was isolated from cells with the PicoPure RNA Isolation kit.

value: iPSC derived CD34+ cells (iCD34+)


title: iPSC from reprogrammed Fibroblast rep 2

description:
Reprogrammed iPSC
iPSC-2

source_name: Fibroblast

value: reprogrammed fibroblast iPSCs


title: Fibroblast rep 2

description:
Fibroblasts
Fibroblast-2

source_name: Foreskin

value: fibroblasts isolated from fetal foreskin


title: Expanded iPSC derived NK cell rep 1

description:
Differentiated iNK cells
Exp iNK-1

value: in vitro expanded iPSC derived NK cells (iNK)


title: NK cell rep 1

description:
CD56+
Adult NK-1

source_name: Primary MNC

value: CD56+ primary NK cells from MNC


title: iPSC from reprogrammed Fibroblast rep 1

description:
Reprogrammed iPSC
iPSC-1


title: Expanded NK cell rep 3

description:
CD56+
Exp Adult NK-3

value: in vitro expanded CD56+ primary NK cells from MNC


title: Fibroblast rep 1

description:
Fibroblasts
Fibroblast-1


title: Central Memory CD4 T cell rep 2

description:
CD4+CD45RA-CCR7+
CD4+Tcm-2

value: CD4+CD45RA-CCR7+ FACS sorted primary T cells from MNC


title: Central Memory CD4 T cell rep 1

description:
CD4+CD45RA-CCR7+
CD4+Tcm


title: Naïve CD4 T cell rep 3

description:
CD4+CD45RA+CCR7+
CD4+Tn-3

value: CD4+CD45RA+CCR7+ FACS sorted primary T cells from MNC


title: Expanded iPSC derived NK cell rep 3

description:
Differentiated iNK cells
Exp iNK-3


title: Expanded iPSC derived NK cell rep 2

description:
Differentiated iNK cells
Exp iNK-2


title: Naïve CD4 T cell rep 1

description:
CD4+CD45RA+CCR7+
CD4+Tn


title: Central Memory CD4 T cell rep 3

description:
CD4+CD45RA-CCR7+
CD4+Tcm-3


title: Expanded NK cell rep 1

description:
CD56+
Exp Adult NK-1


title: iPSC derived NK cell rep 3

description:
Differentiated iNK cells
iNK-3

value: iPSC derived NK cells (iNK)


title: Effector CD4 T cell rep 3

description:
CD4+CD45RA-CCR7-
CD4+Te-3

value: CD4+CD45RA-CCR7- FACS sorted primary T cells from MNC


title: iPSC derived NK cell rep 1

description:
Differentiated iNK cells
iNK-1


title: Expanded NK cell rep 2

description:
CD56+
Exp Adult NK-2


title: Effector CD4 T cell rep 1

description:
CD4+CD45RA-CCR7-
CD4+Te


title: Effector CD4 T cell rep 2

description:
CD4+CD45RA-CCR7-
CD4+Te-2


title: iPSC derived iCD34+ rep 2

description:
Differentiated CD34+ cells
iCD34+-2

source_name: IPSC


title: BackgroundPool06_T0_Rep2

description: BackgroundPoolCounts.txt

source_name: primary murine lung tumor organoids


title: Naïve CD4 T cell rep 2

description:
CD4+CD45RA+CCR7+
CD4+Tn-2


title: J82_IGF2BP2_B

city: Århus N

first: Trine Line

middle: Hauge

last: Okholm

address: Palle Juul-Jensens Boulevard 99

department: Department of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

data_processing:
Fastq files demultiplexed using Illumina’s bcl2fastq v2.20.0.422
Adapters removed using Trim Galore v0.4.1
Reads mapped using TopHat2 and Bowtie2 (version 2.1.1)
Read counts were estimated using HTSeq (v0.6.1p1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized abundance measuments

source_name: cell line

extract_protocol:
RNA was extracted from cells dissolved in Trizol (Invitrogen) according to manufacturers protocol except for using two chloroform extractions instead of one.  After isopropanol precipitation RNA pellets were dissolved in nuclease free water (Ambion)
Libraries were prepared for sequencing using the standard protocol QuantSeq 3'mRNA-SEQ Library Prep Kit (Lexogen). Input were 500 ng RNA and 12 PCR cycles were applied.

value: Bladder carcinoma

tag: sirna

tag: triplicate

value: B


title: J82_scr_C

value: scr

value: C


title: J82_IGF2BP2_A

value: A


title: J82_IGF2BP1_B


title: J82_IGF2BP2_C


title: J82_scr_A


title: J82_IGF2BP1_C


title: J82_IGF2BP1_A


title: Central Memory CD8 T cell rep 3

description:
CD8+CD45RA-CCR7+
CD8+Tcm-3

value: CD8+CD45RA-CCR7+ FACS sorted primary T cells from MNC


title: NK cell rep 2

description:
CD56+
Adult NK-2


title: Effector CD8 T cell rep 1

description:
CD8+CD45RA-CCR7-
CD8+Te

value: CD8+CD45RA-CCR7- FACS sorted primary T cells from MNC


title: Central Memory CD8 T cell rep 1

description:
CD8+CD45RA-CCR7+
CD8+Tcm


title: Naïve CD8 T cell rep 2

description:
CD8+CD45RA+CCR7+
CD8+Tn-2

value: CD8+CD45RA+CCR7+ FACS sorted primary T cells from MNC


title: Central Memory CD8 T cell rep 2

description:
CD8+CD45RA-CCR7+
CD8+Tcm-2


title: Effector CD8 T cell rep 3

description:
CD8+CD45RA-CCR7-
CD8+Te-3


title: Naïve CD8 T cell rep 3

description:
CD8+CD45RA+CCR7+
CD8+Tn-3


title: J82_GRWD1_C


title: J82_circCDYL_C

value: circCDYL


title: J82_GRWD1_B


title: J82_scr_B


title: Naïve CD8 T cell rep 1

description:
CD8+CD45RA+CCR7+
CD8+Tn


title: UMUC3_scr_B


title: J82_circCDYL_B


title: UMUC3_IGF2BP2_B


title: UMUC3_scr_C


title: UMUC3_IGF2BP2_C


title: UMUC3_scr_A


title: UMUC3_IGF2BP2_A


title: UMUC3_IGF2BP1_A


title: UMUC3_GRWD1_B


title: UMUC3_GRWD1_A


title: J82_GRWD1_A


title: UMUC3_GRWD1_C


title: J82_circCDYL_A


title: UMUC3_IGF2BP1_B


title: UMUC3_circCDYL_C


title: UMUC3_circCDYL_B


title: UMUC3_circCDYL_A


title: Effector CD8 T cell rep 2

description:
CD8+CD45RA-CCR7-
CD8+Te-2


title: UMUC3_IGF2BP1_C


title: HepG2_scr_C

value: Hepatocellular carcinoma


title: HepG2_scr_A


title: HepG2_circCDYL_B


title: HepG2_circCDYL_A


title: HepG2_circCDYL_C


title: Submissive male 7

city: Mainz

first: Hristo

last: Todorov

address: Hanns-Dieter Hüsch-Weg 15

department: Institute of Human Genetics

country: Germany

institute: Johannes Gutenberg University Mainz

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_14_1400-S1_S14

data_processing:
Raw sequencing files in fastq format were first inspected with FastQC v0.11.8 (Andrews 2010) for quality control. Adapter trimming was performed with cutadapt v1.15 (Martin 2011). Afterwards, quality trimming was conducted with bbduk.sh v38.06 from the BBMap suite with a cutoff of Q10.
The trimmed and cleaned reads were mapped to the reference genome of GRCm38/mm10 using the STAR aligner v2.6.0a with default settings.
After quality checks, a count matrix was created using featureCounts v1.6.2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Submissive_Male_brain right hemishere

extract_protocol:
RNeasy Lipid Tissue Mini Kit (Qiagen) was used following the instructions of the vendor and including the optional DNAse on-column digestion
The Illumina TruSeq stranded total RNA Human/Mouse/Rat kit was used for library preparation containing RiboZero beads for rRNA depletion from total RNA
Sequencing was then realised with the Illumina NextSeq 500 platform and the High Output v2 kit with an average output of 32 million single-end (85 nt) reads per sample.

tag: strain

value: C57B6/J OlaHsd

tag: Sex

value: Male

tag: social hierarchy status

value: Submissive

value: brain right hemishere


title: Submissive male 5

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_10_1398-S2_S10


title: Submissive male 2

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_04_1395-S4_S4


title: Submissive female 4

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_14_Gr2-2_submissive_S14

source_name: Submissive_Female_brain right hemishere

value: Female


title: Dominant female 2

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_10_01280-2_dominant_S10

source_name: Dominant_Female_brain right hemishere

value: Dominant


title: Dominant female 1

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_07_01279-3_dominant_S7


title: Dominant female 3

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_11_Gr1-4_dominant_S11


title: Dominant female 4

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_13_Gr2-4_dominant_S13


title: HepG2_scr_B

tag: cell line


title: Submissive male 4

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_08_1397-S4_S8


title: Submissive female 3

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_12_Gr1-3_submissive_S12


title: Submissive female 2

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_09_01280-1_submissive_S9


title: Submissive male 1

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_02_1394-S3_S2


title: Submissive male 3

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_06_1396-S2_S6


title: Dominant male 7

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_13_1400-D3_S13

source_name: Dominant_Male_brain right hemishere


title: Dominant male 5

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_09_1398-D1_S9


title: Submissive male 6

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_12_1399-S2_S12


title: Dominant male 4

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_07_1397-D2_S7


title: Dominant male 6

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_11_1399-D1_S11


title: db-m-7

first: Yan

last: Huang

address: No.22 Zhong Guan Cun South Street

institute: Peking University School and Hospital of Stomatology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Frozen parotid glands from db/m and db/db mice were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.

treatment_protocol: The fresh parotid glands of mice are preserved at -80 degrees Celsius.

value: parotid gland

tag: gender

value: male


title: Submissive female 1

description:
processed data file: females_RNA_counts.txt
jgu_gerber_2018_01_08_01279-4_submissive_S8


title: db-db-5


title: db-db-1


title: db-db-2


title: db-m-5


title: db-m-2


title: AKorg_h48min_S3

data_processing:
Base calling was performed using Illumina RTA 2.0 software, then samples were demultiplexed using bcl2fastq.
RNAseq reads were aligned to mm10 version 75 using Tophat2 software with the following configurations: --segment-length 18 -r 228 --no-coverage-search
Aligned bam files were sorted using samtools sort with the -n configuration
Raw counts were produced per sample using htseq-count with the following configurations:  --mode=intersection-nonempty --stranded=no --type=exon --idattr=gene_id -f bam
Counts were normalised in DESeq2 using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix of normalised counts

source_name: Cells from whole intestine

extract_protocol:
1cm of proximal intestine was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer.  RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

tag: genotype

value: villinCreER Apc fl/fl Kras G12D/+

tag: time point

value: 48 hours


title: AKorg_h48min_S1


title: db-m-8


title: AKorg_h48min_S2


title: AKorg_h24plus_S3

value: 24 hours


title: Dominant male 2

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_03_1395-D2_S3


title: AKorg_h48plus_S2


title: Apc Kras Vehicle treated replicate 3

source_name: Whole intestine

tag: treatment

value: Vehicle


title: AKorg_h24plus_S1

tag: genetic background


title: Apc Kras Rapamycin treated replicate 4

value: Rapamycin 10 mg/kg


title: Dominant male 3

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_05_1396-D1_S5


title: db-db-8


title: AKorg_h48plus_S3


title: AKorg_h24min_S2


title: AKorg_h24min_S1


title: AKorg_h24plus_S2


title: Apc Kras Vehicle treated replicate 1


title: AKorg_h48plus_S1


title: Apc Kras Vehicle treated replicate 4


title: Apc Kras Vehicle treated replicate 2


title: AKorg_h24min_S3


title: Apc Kras Rapamycin treated replicate 1


title: Apc Kras Rapamycin treated replicate 2


title: Apc Kras Rapamycin treated replicate 3


title: Apc Kras Slc7a5 biological replicate 1

value: villinCreER Apc fl/fl Kras G12D/+ Slc7a5 fl/fl


title: Apc Kras Slc7a5 biological replicate 4


title: Apc Kras Slc7a5 biological replicate 3


title: iPSC derived NK cell rep 2

description:
Differentiated iNK cells
iNK-2

value: iPSC derived NK cells (iNK)


title: Apc Kras Slc7a5 biological replicate 2


title: Apc Kras biological replicate 3


title: Apc Kras biological replicate 2


title: Apc Kras biological replicate 1


title: P30_F SMG scRNA-seq

city: Bethesda

first: Daniel

last: Martin

state: Maryland

address: 30 Convent Dr Bldg 30 Room 320A-3

department: OSD

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v2.0.0 or CellRanger v3.0.1 pipeline using default settings.
Secondary analysis was performed using the Seurat v2, Seurat v3, and Dynverse R packages.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger v2.0.0 or v3.0.1 gene counts matrices.

source_name: P30 Female SMG

extract_protocol:
SMG were dissected with sharp tweezers from 4-7 littermates of E12-E16 ICR mice, and 2-4 littermates of P1 (ICR), P30 (ICR) and adult (C3H mice). E12 and E14 glands were incubated at 37oC for 30 minutes with 500ul of papain (20U/ml in 1mM L-cysteine with 0.5mM EDTA. Glands were dissociated with a pipette in 5-minute intervals. Papain was inactivated with (1:1) albumin-inhibitor solution and the cell suspension was collected by centrifugation at 400g at 4oC for 10 minutes, washed twice and resuspended in Hanks balanced salt solution (HBSS) with 1% BSA.     SMGs from E16 and postnatal day 1 (P1) were isolated and enzymatically dissociated in 5ml of digestion cocktail containing Collagenase II (100mg/ml), Hyaluronidase (50mg/ml), deoxyribonuclease (40mg/ml), and neutral protease (50mg/ml) in HBSS-BSA. Dissociation was performed in a 15ml gentleMACS C tube using a miltenyi gentleMACS Octo Dissociator following their preset dissociation program A (24 seconds of clockwise-counterclockwise spin cycles) followed by 30 min incubation at 37oC. Dissociated cells were centrifuged (400xg) for 10 mins and resuspended in HBSSA-BSA. Then, cells were passed through 100 µm, 40 µm, and 20 µm filters centrifuging (400xg) for 5mins and resuspending in HBSS-BSA after each filtration step. The final cell suspension was centrifuged (400xg) 5 mins and treated with Papain as described above.     For P30 ICR and adult C3H mice, glands were dissociated in a 15ml gentleMACS C tube with 5ml of digestion cocktail prepared with the human tumor dissociation kit (#130-095-929, Miltenyi Biotech, Auburn CA) in RPMI 1640 w/L-Glutamine. 2 SMGs from male and female ICR mice, and 2 SMG from adult female C3H mice were processed individually. Digestion was performed in a Miltenyi gentleMACS Octo Dissociator following the preset 37C_h_TDK_2 program. We added 5ml of RPMI media to the dissociated cells and centrifuged (400xg) for 10 mins. Cells were resuspended in RPMI 1640 w/L-Glutamine with 5% PenStrep (Gibco, USA) and washed twice with RPMI. Next, cells were centrifuged (400g) for 5 minutes and washed with RPMI medium before each filtration step through 70 µm and 40 µm filters. Apart from the enzymatic digestion, all steps were performed on ice.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit v2 and v3 chemistries (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: submandibular gland (SMG)

value: ICR


title: Adult SMG scRNA-seq

source_name: Adult SMG

value: Adult


title: C3H/10T1/2 cells, H2BE113Q, rep1

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

state: New York

address: 1230 York ave

institute: Rockefeller University

description:
TPM_PerSampleTable.csv
TPM_PerGroupTable.csv

data_processing:
Standard Illumina basecalling protocol for Illumina NextSeq was performed.
Quantification of RNA transcripts was performed with the k-mer counting software Salmon (Patro et al., 2017), and a reference genome produced using Illumina’s iGenomes UCSC mm10 package. Expression levels were estimated by counting reads with featureCounts (v1.4.4) using default settings. Read summarization was performed at the gene symbol level using UCSC mm10 known gene exons obtained from the UCSC table browser. The gene symbol-summarized read counts were normalized using the variance stabilized transformation technique (VST), and expression levels clustered using Euclidean distance and hierarchical clustering with the Ward variance minimization algorithm to produce heatmaps. Differentially expressed genes were identified using the DESeq Package (Anders et al., 2012; Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV tables containing TPM values for each group or sample

growth_protocol: C3H10T1/2 (ATCC) were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning) with 10% fetal bovine serum (FBS, Atlanta Biologicals) at 37 °C, 20% oxygen, and 5% CO2. Cells were dissociated with TrypLE Express (Thermo Fisher Scientific) during passaging and regularly tested and found free of mycoplasma.

extract_protocol:
RNA was isolated using a RNeasy Mini Kit (Qiagen).
Libraries were prepared according to the NEBNext Ultra II RNA Library Prep Kit (New Enbland Biolabs) protocol

value: mesenchymal progenitor cell

tag: cell source

value: embryo


title: C3H/10T1/2 cells, H2BE113Q, rep3

tag: cell type


title: E16 SMG scRNA-seq

source_name: E16 SMG

tag: developmental stage


title: E14 SMG scRNA-seq

source_name: E14 SMG


title: P1 SMG scRNA-seq

source_name: P1 SMG


title: E12 SMG scRNA-seq

source_name: E12 SMG


title: C3H/10T1/2 cells, H2BE113Q, rep2


title: C3H/10T1/2 cells, H2BE113K, rep3


title: C3H/10T1/2 cells, H2BE76Q, rep3


title: C3H/10T1/2 cells, H2BE113K, rep2


title: C3H/10T1/2 cells, H2BE76K, rep1


title: C3H/10T1/2 cells, H2BE71Q, rep3


title: C3H/10T1/2 cells, H2BE71Q, rep2


title: C3H/10T1/2 cells, H2BWT, rep3


title: C3H/10T1/2 cells, H2BE76Q, rep2


title: CAST pure rep 3

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University medical school

data_processing:
Sequenced reads were mapped using bowtie2 to the mm9 genome.  Duplicates and reads with a mapping quality below 30 were removed.  Samtools was used to create a pileup indicating the coverage of each base across the genome.  bcftools and the vcfutils.pl script were used to determine SNPs.  Reads were remapped using GSNAP with the predetermined SNP file in order for the CAST reads to be mapped permissibly to the mm9 genome.  SNPs for which neither allele appeared less than 20% or more than 80% in the mapped reads, were used to separate overlapping reads to the appropriate genome.  Reads containing multiple SNPs belonging to both species were removed.
For each allele of each sample, every 200 G1 phase reads were binned and corresponding S phase reads were counted in order to determine an S/G1 ratio for each bin. Ratio data was normalized, smoothed and interpolated using the Matlab csaps function (with a smoothing parameter of 10−16) at a resolution of 100 kb (approximate average size of the windows). Continuous segments containing less than 15 informative windows were removed from the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing normalized replication timing data

source_name: pre-B

growth_protocol: To prepare pre-B-cell clones, Cells isolated from mouse bone marrow (10 weeks old) were grown in RPMI 1640 media (Gibco) supplemented with 10% fetal bovine serum (Hyclone), penicillin–streptomycin (Gibco), L-glutamine (Gibco) and 50 μM of β-mercaptoethanol (Gibco) on irradiated ST2 feeder cells. Recombinant mouse IL-7 (10μg/ml) was added to select for pre-B cell populations (Peprotech, USA). After 10–14 days of IL-7-mediated positive selection, cells were plated on 96-well plates in limiting dilutions to generate single-cell-derived preB-cell clones.

extract_protocol:
DNA was extracted from cells using DNeasy-kit (QIAGEN) and eluted twice with 2 × 200 µl of the kit elution buffer (AE), concentrated using 1.8x Agencourt AMPure XP beads (Beckman Coulter) and eluted in 50 µl EB (Qiagen). DNA concentrations were measured using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).  DNA samples were sonicated   in the M220 Focused-ultrasonicator (Covaris) using 50 W, 20% Duty Factor at 20°C for 120 s, in order to reach an average target peak size of 250 bp as verified with the D1000 or D1000 High Sensitivity ScreenTape using the Electrophoresis 2200 TapeStation system (Agilent).
Library preparation was carried out as described [Yehuda, 2018 #6334]. Briefly, sonicated DNA was subjected to a 50 µl end repair reaction using 1 µl End repair mix (E6050L, NEB), cleaned by 1.8× Ampure XP beads, followed by a 50 µl A-tail reaction using 2 µl Klenow fragment exo- (M0212L, NEB). The products were cleaned by 1.8× beads and ligated by 2 µl quick ligase (M2200, NEB) to 0.75 µM Illumina compatible forked indexed adapters. Ligation products were size selected by 0.7× PEG (considering the PEG in the ligation buffer) in order to remove free adaptors. 12–19 cycles of amplification were performed by PFU Ultra II Fusion DNA polymerase (600670, Agilent) with the following Primers:   P7: 5' AATGATACGGCGACCACCGAGATCTACACT CTTTCCCTACACGAC 3'; P5: 5' CAAGCAGAAGACGGCATACGAGAT 3'. Amplified DNA was size selected for 300–700 bp fragments by taking the supernatant after using 0.5× beads (which removed fragments greater than 700 bp) followed by a 1.0× cleaning to remove remaining primers and adapter dimers. The final quality of the library was assessed by Qubit and TapeStation. Libraries were pooled and sequenced on NextSeq (Illumina) by 75 bp paired-end sequencing, generating 10 M reads per library.

treatment_protocol: Cells were sorted by FACS to S and G1 phase portions.


title: C3H/10T1/2 cells, H2BE113K, rep1


title: C3H/10T1/2 cells, H2BE76K, rep3


title: C3H/10T1/2 cells, H2BE76Q, rep1


title: C3H/10T1/2 cells, H2BE76K, rep2


title: Clone 3 rep 1


title: Clone 8 rep 2


title: CAST pure rep 2


title: Clone 3 rep 2


title: C3H/10T1/2 cells, H2BE71K, rep3


title: C3H/10T1/2 cells, H2BE71Q, rep1


title: Clone 8 rep 1


title: C3H/10T1/2 cells, H2BE71K, rep2


title: C3H/10T1/2 cells, H2BE71K, rep1


title: Dominant male 1

description:
processed data file: males_RNA_counts.txt
um_endres_2018_01_01_1394-D2_S1

value: C57B6/J OlaHsd

value: Male

value: brain right hemishere


title: C3H/10T1/2 cells, H2BWT, rep2


title: Clone 2 rep 1


title: E5 rep 2


title: E5 rep 3


title: Clone 8 rep 3


title: P30_M SMG scRNA-seq

source_name: P30 Male SMG


title: Clone 2 rep 3


title: Clone 3 rep 3


title: Clone 2 rep 2


title: PN_48h_GH146_P12_P5

city: Stanford

first: Qijing

last: Xie

address: Bass Biology Building, Room 334

department: Department of Biology

institute: Howard Hughes Medical Institute

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11505

data_processing:
de-mutiplexd (bcl2fastq 2.19.0.316)
alignment (STAR 2.5.4)
gene count (HTseq 0.11.2, default settings except ‘‘-m  536 intersection-strict’)
normalization (gene counts were rescaled to counts per million reads (CPM), and log transformed to Log2(CPM+1) for processed data)
filtering (cells with fewer than 100,000 uniquely mapped reads were excluded, and cells with high expression of neuronal markers are retained for processed data)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: annotated .h5ad files of high-quality neurons

organism: Drosophila melanogaster

extract_protocol: Modified SMART-seq2 (Li et al. 2017)

value: neuron

tag: Stage

value: 48h APF

tag: number of cells


title: PN_48h_GH146_P12_P7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11507


title: PN_48h_GH146_P12_P9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11509


title: CAST pure rep 1


title: E5 rep 1


title: PN_48h_GH146_P12_P8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11508


title: PN_48h_GH146_P12_P6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11506


title: PN_48h_GH146_P12_P4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11504


title: PN_48h_GH146_P12_P2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11502


title: PN_48h_GH146_P12_P3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11503


title: PN_48h_GH146_P12_P24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11501


title: PN_48h_GH146_P12_P23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11500


title: C3H/10T1/2 cells, H2BWT, rep1


title: PN_48h_GH146_P12_P21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11498


title: PN_48h_GH146_P12_P20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11497


title: PN_48h_GH146_P12_P19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11495


title: PN_48h_GH146_P12_P22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11499


title: PN_48h_GH146_P12_P18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11494


title: PN_48h_GH146_P12_P17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11493


title: PN_48h_GH146_P12_P15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11491


title: PN_48h_GH146_P12_P16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11492


title: PN_48h_GH146_P12_P14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11490


title: PN_48h_GH146_P12_P13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11489


title: PN_48h_GH146_P12_P10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11486


title: PN_48h_GH146_P12_O9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11485


title: PN_48h_GH146_P12_O8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11484


title: PN_48h_GH146_P12_P11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11487


title: PN_48h_GH146_P12_O6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11482


title: PN_48h_GH146_P12_O7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11483


title: PN_48h_GH146_P12_O5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11481


title: PN_48h_GH146_P12_O3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11479


title: PN_48h_GH146_P12_O2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11478


title: PN_48h_GH146_P12_O24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11477


title: PN_48h_GH146_P12_O4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11480


title: PN_48h_GH146_P12_O21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11474


title: PN_48h_GH146_P12_O22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11475


title: PN_48h_GH146_P12_O23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11476


title: PN_48h_GH146_P12_P1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11496


title: PN_48h_GH146_P12_O20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11473


title: PN_48h_GH146_P12_O1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11472


title: PN_48h_GH146_P12_O19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11471


title: PN_48h_GH146_P12_O18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11470


title: PN_48h_GH146_P12_P12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11488


title: PN_48h_GH146_P12_O13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11465


title: PN_48h_GH146_P12_O14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11466


title: PN_48h_GH146_P12_O15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11467


title: PN_48h_GH146_P12_O12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11464


title: PN_48h_GH146_P12_N9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11461


title: PN_48h_GH146_P12_O11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11463


title: PN_48h_GH146_P12_O17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11469


title: PN_48h_GH146_P12_N5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11457


title: PN_48h_GH146_P12_N6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11458


title: PN_48h_GH146_P12_N7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11459


title: PN_48h_GH146_P12_N3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11455


title: PN_48h_GH146_P12_N8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11460


title: PN_48h_GH146_P12_N23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11452


title: PN_48h_GH146_P12_N24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11453


title: PN_48h_GH146_P12_N21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11450


title: PN_48h_GH146_P12_N20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11449


title: PN_48h_GH146_P12_N22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11451


title: PN_48h_GH146_P12_N1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11448


title: PN_48h_GH146_P12_O16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11468


title: PN_48h_GH146_P12_N18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11446


title: PN_48h_GH146_P12_N17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11445


title: PN_48h_GH146_P12_N15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11443


title: PN_48h_GH146_P12_N14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11442


title: PN_48h_GH146_P12_N16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11444


title: PN_48h_GH146_P12_M9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11437


title: PN_48h_GH146_P12_N19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11447


title: PN_48h_GH146_P12_M8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11436


title: PN_48h_GH146_P12_N12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11440


title: PN_48h_GH146_P12_N13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11441


title: PN_48h_GH146_P12_M6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11434


title: PN_48h_GH146_P12_O10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11462


title: PN_48h_GH146_P12_M7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11435


title: PN_48h_GH146_P12_N4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11456


title: PN_48h_GH146_P12_M4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11432


title: PN_48h_GH146_P12_N2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11454


title: PN_48h_GH146_P12_N10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11438


title: PN_48h_GH146_P12_M3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11431


title: PN_48h_GH146_P12_M24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11429


title: PN_48h_GH146_P12_M21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11426


title: PN_48h_GH146_P12_M23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11428


title: PN_48h_GH146_P12_M22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11427


title: PN_48h_GH146_P12_M20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11425


title: PN_48h_GH146_P12_M2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11430


title: PN_48h_GH146_P12_M19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11423


title: PN_48h_GH146_P12_M18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11422


title: PN_48h_GH146_P12_M17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11421


title: PN_48h_GH146_P12_M1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11424


title: PN_48h_GH146_P12_M13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11417


title: PN_48h_GH146_P12_M12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11416


title: PN_48h_GH146_P12_M10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11414


title: PN_48h_GH146_P12_L6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11410


title: PN_48h_GH146_P12_L5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11409


title: PN_48h_GH146_P12_L9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11413


title: PN_48h_GH146_P12_L7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11411


title: PN_48h_GH146_P12_M16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11420


title: PN_48h_GH146_P12_L3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11407


title: PN_48h_GH146_P12_L24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11405


title: PN_48h_GH146_P12_L2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11406


title: PN_48h_GH146_P12_M15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11419


title: PN_48h_GH146_P12_L23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11404


title: PN_48h_GH146_P12_L22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11403


title: PN_48h_GH146_P12_L21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11402


title: PN_48h_GH146_P12_M11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11415


title: PN_48h_GH146_P12_L20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11401


title: PN_48h_GH146_P12_L8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11412


title: PN_48h_GH146_P12_L1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11400


title: PN_48h_GH146_P12_L4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11408


title: PN_48h_GH146_P12_M5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11433


title: PN_48h_GH146_P12_L16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11396


title: PN_48h_GH146_P12_L19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11399


title: PN_48h_GH146_P12_L14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11394


title: PN_48h_GH146_P12_N11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11439


title: PN_48h_GH146_P12_L18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11398


title: PN_48h_GH146_P12_L17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11397


title: PN_48h_GH146_P12_L12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11392


title: PN_48h_GH146_P12_L15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11395


title: PN_48h_GH146_P12_M14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11418


title: PN_48h_GH146_P12_L13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11393


title: PN_48h_GH146_P12_K8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11388


title: PN_48h_GH146_P12_L11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11391


title: PN_48h_GH146_P12_K7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11387


title: PN_48h_GH146_P12_K6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11386


title: PN_48h_GH146_P12_K9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11389


title: PN_48h_GH146_P12_K5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11385


title: PN_48h_GH146_P12_L10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11390


title: PN_48h_GH146_P12_K4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11384


title: PN_48h_GH146_P12_K3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11383


title: PN_48h_GH146_P12_K22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11379


title: PN_48h_GH146_P12_K23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11380


title: PN_48h_GH146_P12_K24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11381


title: PN_48h_GH146_P12_K19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11375


title: PN_48h_GH146_P12_K21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11378


title: PN_48h_GH146_P12_K18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11374


title: PN_48h_GH146_P12_K17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11373


title: PN_48h_GH146_P12_K1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11376


title: PN_48h_GH146_P12_K15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11371


title: PN_48h_GH146_P12_K14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11370


title: PN_48h_GH146_P12_K13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11369


title: PN_48h_GH146_P12_K11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11367


title: PN_48h_GH146_P12_K12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11368


title: PN_48h_GH146_P12_J8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11364


title: PN_48h_GH146_P12_J7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11363


title: PN_48h_GH146_P12_K16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11372


title: PN_48h_GH146_P12_J2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11358


title: PN_48h_GH146_P12_J5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11361


title: PN_48h_GH146_P12_J6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11362


title: PN_48h_GH146_P12_J4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11360


title: PN_48h_GH146_P12_J23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11356


title: PN_48h_GH146_P12_K2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11382


title: PN_48h_GH146_P12_J21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11354


title: PN_48h_GH146_P12_J3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11359


title: PN_48h_GH146_P12_J20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11353


title: PN_48h_GH146_P12_J24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11357


title: PN_48h_GH146_P12_J22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11355


title: PN_48h_GH146_P12_K10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11366


title: PN_48h_GH146_P12_J1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11352


title: PN_48h_GH146_P12_J19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11351


title: PN_48h_GH146_P12_K20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11377


title: PN_48h_GH146_P12_J18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11350


title: PN_48h_GH146_P12_J17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11349


title: PN_48h_GH146_P12_J16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11348


title: PN_48h_GH146_P12_J13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11345


title: PN_48h_GH146_P12_J10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11342


title: PN_48h_GH146_P12_J12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11344


title: PN_48h_GH146_P12_J11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11343


title: PN_48h_GH146_P12_I9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11341


title: PN_48h_GH146_P12_I8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11340


title: PN_48h_GH146_P12_I7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11339


title: PN_48h_GH146_P12_I6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11338


title: PN_48h_GH146_P12_I5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11337


title: PN_48h_GH146_P12_I4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11336


title: PN_48h_GH146_P12_I2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11334


title: PN_48h_GH146_P12_I1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11328


title: PN_48h_GH146_P12_I18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11326


title: PN_48h_GH146_P12_I22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11331


title: PN_48h_GH146_P12_I20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11329


title: PN_48h_GH146_P12_I17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11325


title: PN_48h_GH146_P12_I21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11330


title: PN_48h_GH146_P12_I3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11335


title: PN_48h_GH146_P12_J15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11347


title: PN_48h_GH146_P12_J14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11346


title: PN_48h_GH146_P12_I13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11321


title: PN_48h_GH146_P12_I14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11322


title: PN_48h_GH146_P12_I12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11320


title: PN_48h_GH146_P12_H9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11317


title: PN_48h_GH146_P12_I10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11318


title: PN_48h_GH146_P12_H8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11316


title: PN_48h_GH146_P12_H7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11315


title: PN_48h_GH146_P12_H5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11313


title: PN_48h_GH146_P12_I24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11333


title: PN_48h_GH146_P12_I23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11332


title: PN_48h_GH146_P12_H4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11312


title: PN_48h_GH146_P12_H2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11310


title: PN_48h_GH146_P12_H3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11311


title: PN_48h_GH146_P12_I19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11327


title: PN_48h_GH146_P12_I16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11324


title: PN_48h_GH146_P12_H21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11306


title: PN_48h_GH146_P12_H22

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11307


title: PN_48h_GH146_P12_H19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11303


title: PN_48h_GH146_P12_H20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11305


title: PN_48h_GH146_P12_H18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11302


title: PN_48h_GH146_P12_H17

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11301


title: PN_48h_GH146_P12_H14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11298


title: PN_48h_GH146_P12_H16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11300


title: PN_48h_GH146_P12_H6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11314


title: PN_48h_GH146_P12_H1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11304


title: PN_48h_GH146_P12_H11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11295


title: PN_48h_GH146_P12_H13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11297


title: PN_48h_GH146_P12_H10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11294


title: PN_48h_GH146_P12_H15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11299


title: PN_48h_GH146_P12_G8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11292


title: PN_48h_GH146_P12_G7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11291


title: PN_48h_GH146_P12_I15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11323


title: PN_48h_GH146_P12_H24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11309


title: PN_48h_GH146_P12_G6

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11290


title: PN_48h_GH146_P12_H23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11308


title: PN_48h_GH146_P12_G5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11289


title: PN_48h_GH146_P12_G3

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11287


title: PN_48h_GH146_P12_G24

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11285


title: PN_48h_GH146_P12_G2

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11286


title: PN_48h_GH146_P12_G23

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11284


title: PN_48h_GH146_P12_I11

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11319


title: PN_48h_GH146_P12_G21

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11282


title: PN_48h_GH146_P12_G20

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11281


title: PN_48h_GH146_P12_G1

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11280


title: PN_48h_GH146_P12_G19

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11279


title: PN_48h_GH146_P12_G9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11293


title: PN_48h_GH146_P12_G18

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11278


title: PN_48h_GH146_P12_G16

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11276


title: PN_48h_GH146_P12_G14

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11274


title: PN_48h_GH146_P12_G12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11272


title: PN_48h_GH146_P12_G10

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11270


title: PN_48h_GH146_P12_G13

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11273


title: PN_48h_GH146_P12_G15

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11275


title: PN_48h_GH146_P12_F9

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11269


title: PN_48h_GH146_P12_H12

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11296


title: PN_48h_GH146_P12_F8

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11268


title: PN_48h_GH146_P12_F5

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11265


title: PN_48h_GH146_P12_F7

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11267


title: PN_48h_GH146_P12_F4

description:
single cell
adata_all_panPN_annotated_final.h5ad
Sample 11264