title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E10_S77]

description:
coculture24h_CART_NALM6_5to1_E10_S77
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E10_S221]

status: Public on Jun 09 2022

type: SRA

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

description:
coculture24h_CART_NALM6_5to1_E10_S221
mRNA
052721_countmatrix_scRNAseq.csv

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5'.
Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: scRNA-Seq: 052721_countmatrix_scRNAseq.csv: HTSeq count matrix with raw counts for all individual cells.
Supplementary_files_format_and_content: scATAC-Seq: 052721_countmatrix_scATACseq.csv: Fragments file with fragments for all individual cells; raw counts.

molecule: total RNA

organism: Homo sapiens

source_name: B-cell precursor leukemia cell line NALM-6

growth_protocol: NALM-6 cells were cultured in RPMI-1640 media with 10% of heat-inactivated fetal bovine serum, 100 μM penicillin/streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 1x NEAA, 20 mM HEPES and 0.5 mM 2-mercaptoethanol.

extract_protocol:
Single cells were directly sorted into 96 well plates containing TCL buffer.
Full-length single-cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

treatment_protocol: Cells were treated for 24h with CAR T-cells/uninfected T-cells.

value: CAR T-cells


title: subject WF-023 baseline

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: subject WF-023 baseline

data_processing:
STAR (PMID:23104886) was used to align the raw reads in sample fastq files to reference human genome version GRCh38 using default parameters after adapter sequence trimming by Skewer (https://omicstools.com/skewer-tool/). Raw counts for each mapped gene transcript were generated using the Bioconductor package Rsubreads, and the normalized counts data matrix obtained using the Bioconductor package DESeq2 (https://bioconductor.org/packages /release/bioc/html/ DESeq2.html) default parameters.
Genome_build: GRCh38

source_name: sputum airway cells

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
The cDNA library preparation for total RNA from sputum cells was performed with the Illumina TruSeq Stranded Total RNA (Illumina, Inc., San Diego, CA). Libraries were quality checked by quantification with PicoGreen, size analysis on a Bioanalyzer or TapeStation 2200 (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. 75 bp paired end reads were generated on a HiSeq 2500 flow cell. Libraries are loaded at an empirically determined concentration in order to generate the optimal number of clusters per lane of the flow cell. Samples were sequenced with an average depth of 20 million reads using Illumina HiSeq 2500 GPL27467.

tag: Sex

value: Female

tag: age

tag: bmi

tag: age of asthma diagnosis

tag: asthma severity

value: Mild

tag: fev1 forced expiratory volume in 1 second % predicted pre-bd

tag: fvc forced vital capacity % predicted pre-bd

tag: fev1/fvc % predicted pre-bd

tag: maximum absolute difference in fev1 % predicted post-bd versus pre-bd

tag: immunoglobulin e (iu/ml)

tag: total white blood count (x 10^3 cels/ul)

tag: blood neutrophil count (cells/ul)

tag: blood lymphocyte count (cells/ul)

tag: blood monocyte count (cells/ul)

tag: blood eosinophil count (cells/ul)

tag: blood basophil count (cells/ul)

tag: sputum white blood cells %

tag: sputum differential neutrophil count %

tag: sputum differential eosinophil count %

tag: sputum differential lymphocyte count %

tag: fractional exhaled nitric oxide feno (ppb)


title: subject WF-016 baseline

description: subject WF-016 baseline

tag: Sex

tag: age

tag: bmi

tag: age of asthma diagnosis

tag: asthma severity

value: Moderate


title: subject WF-014 followup

description: subject WF-014 followup

tag: fev1 forced expiratory volume in 1 second % predicted pre-bd

tag: fvc forced vital capacity % predicted pre-bd

tag: fev1/fvc % predicted pre-bd

tag: maximum absolute difference in fev1 % predicted post-bd versus pre-bd


title: subject WF-014 baseline

description: subject WF-014 baseline

tag: immunoglobulin e (iu/ml)

tag: total white blood count (x 10^3 cels/ul)

tag: blood neutrophil count (cells/ul)

tag: blood lymphocyte count (cells/ul)

tag: blood monocyte count (cells/ul)


title: subject WF-035 followup

description: subject WF-035 followup

value: Male

value: Severe

tag: sputum white blood cells %

tag: sputum differential neutrophil count %

tag: sputum differential eosinophil count %


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E11_S229]

description:
coculture24h_CART_NALM6_5to1_E11_S229
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E11_S181]

description:
coculture24h_CART_NALM6_5to1_E11_S181
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-032 baseline

description: subject WF-032 baseline

tag: Sex

tag: age

tag: bmi

tag: age of asthma diagnosis

tag: blood eosinophil count (cells/ul)

tag: blood basophil count (cells/ul)

tag: sputum differential lymphocyte count %

tag: fractional exhaled nitric oxide feno (ppb)


title: subject WF-023 followup

description: subject WF-023 followup

tag: asthma severity

tag: fev1 forced expiratory volume in 1 second % predicted pre-bd

tag: fvc forced vital capacity % predicted pre-bd

tag: fev1/fvc % predicted pre-bd

tag: maximum absolute difference in fev1 % predicted post-bd versus pre-bd


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E11_S133]

description:
coculture24h_CART_NALM6_5to1_E11_S133
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-010 followup

description: subject WF-010 followup

tag: sputum white blood cells %

tag: sputum differential neutrophil count %

tag: sputum differential eosinophil count %


title: subject WF-016 followup

description: subject WF-016 followup


title: subject WF-009 followup

description: subject WF-009 followup


title: subject WF-009 baseline

description: subject WF-009 baseline

tag: immunoglobulin e (iu/ml)

tag: total white blood count (x 10^3 cels/ul)

tag: blood neutrophil count (cells/ul)

tag: blood lymphocyte count (cells/ul)

tag: blood monocyte count (cells/ul)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S348]

description:
coculture24h_CART_NALM6_5to1_D8_S348
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S60]

description:
coculture24h_CART_NALM6_5to1_D8_S60
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E10_S126]

description:
coculture24h_CART_NALM6_5to1_E10_S126
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E10_S173]

description:
coculture24h_CART_NALM6_5to1_E10_S173
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [E10_S125]

description:
coculture24h_CART_NALM6_5to1_E10_S125
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-039 baseline

description: subject WF-039 baseline

tag: Sex

tag: age

tag: bmi

tag: age of asthma diagnosis

tag: blood eosinophil count (cells/ul)

tag: blood basophil count (cells/ul)

tag: sputum differential lymphocyte count %

tag: fractional exhaled nitric oxide feno (ppb)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D9_S356]

description:
coculture24h_CART_NALM6_5to1_D9_S356
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D9_S36]

description:
coculture24h_CART_NALM6_5to1_D9_S36
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D9_S212]

description:
coculture24h_CART_NALM6_5to1_D9_S212
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S108]

description:
coculture24h_CART_NALM6_5to1_D8_S108
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-012 baseline

description: subject WF-012 baseline

tag: asthma severity

tag: fev1 forced expiratory volume in 1 second % predicted pre-bd

tag: fvc forced vital capacity % predicted pre-bd

tag: fev1/fvc % predicted pre-bd

tag: maximum absolute difference in fev1 % predicted post-bd versus pre-bd

tag: sputum white blood cells %

tag: sputum differential neutrophil count %

tag: sputum differential eosinophil count %


title: subject WF-012 followup

description: subject WF-012 followup


title: subject WF-010 baseline

description: subject WF-010 baseline

tag: immunoglobulin e (iu/ml)

tag: total white blood count (x 10^3 cels/ul)

tag: blood neutrophil count (cells/ul)

tag: blood lymphocyte count (cells/ul)

tag: blood monocyte count (cells/ul)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D9_S164]

description:
coculture24h_CART_NALM6_5to1_D9_S164
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S28]

description:
coculture24h_CART_NALM6_5to1_D7_S28
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D9_S116]

description:
coculture24h_CART_NALM6_5to1_D9_S116
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-003 followup

description: subject WF-003 followup

tag: Sex

tag: age of asthma diagnosis

tag: sputum differential lymphocyte count %

tag: fractional exhaled nitric oxide feno (ppb)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S196]

description:
coculture24h_CART_NALM6_5to1_D7_S196
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S32]

description:
coculture24h_CART_NALM6_5to1_D8_S32
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S278]

description:
coculture24h_CART_NALM6_5to1_D8_S278
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-003 baseline

description: subject WF-003 baseline

tag: age

tag: bmi

tag: asthma severity

tag: fev1 forced expiratory volume in 1 second % predicted pre-bd

tag: fvc forced vital capacity % predicted pre-bd

tag: fev1/fvc % predicted pre-bd

tag: blood eosinophil count (cells/ul)

tag: blood basophil count (cells/ul)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D8_S204]

description:
coculture24h_CART_NALM6_5to1_D8_S204
mRNA
052721_countmatrix_scRNAseq.csv


title: subject WF-001 followup

description: subject WF-001 followup

tag: maximum absolute difference in fev1 % predicted post-bd versus pre-bd

tag: sputum white blood cells %

tag: sputum differential neutrophil count %

tag: sputum differential eosinophil count %


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S52]

description:
coculture24h_CART_NALM6_5to1_D7_S52
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S272]

description:
coculture24h_CART_NALM6_5to1_D7_S272
mRNA
052721_countmatrix_scRNAseq.csv


title: 14961, control, rep1

city: La Jolla

first: John

middle: R

last: Kelsoe

state: CA

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California, San Diego

description: Control

data_processing:
quality control using FASTQC
alignment to the human genome using STAR v2.5.1
read quantification using RSEM v1.3.0
low expressed genes were filtered out (CPM<1)
trimmed mean of M-values normalization was applied
Assembly: hg19
Supplementary files format and content: Subjecs in columns, genes in rows, gene counts

source_name: Fibroblast

extract_protocol:
TruSeq Stranded Total RNA Sample Prep Kit (Illumina)
SuperScript™ II reverse transcriptase (Invitrogen) was used to reverse transcribe the depleted RNA into cDNA

tag: tissue

value: Fibroblast

tag: cell type

value: IPSC derived Hippocampal neuron

value: Control


title: 11692, lithium, rep1

description: Lithium Responder

value: Lithium


title: subject WF-001 baseline

description: subject WF-001 baseline

tag: Sex

tag: age

tag: age of asthma diagnosis

tag: immunoglobulin e (iu/ml)

tag: total white blood count (x 10^3 cels/ul)

tag: blood neutrophil count (cells/ul)

tag: blood lymphocyte count (cells/ul)

tag: blood monocyte count (cells/ul)

tag: sputum differential lymphocyte count %

tag: fractional exhaled nitric oxide feno (ppb)


title: 14961, lithium, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S148]

description:
coculture24h_CART_NALM6_5to1_D7_S148
mRNA
052721_countmatrix_scRNAseq.csv


title: 14474, control, rep1

description: Lithium Responder


title: 14474, lithium, rep1

description: Lithium Responder


title: 14959, lithium, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D7_S100]

description:
coculture24h_CART_NALM6_5to1_D7_S100
mRNA
052721_countmatrix_scRNAseq.csv


title: 14934, lithium, rep1

description: Lithium Non-Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S188]

description:
coculture24h_CART_NALM6_5to1_D6_S188
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S265]

description:
coculture24h_CART_NALM6_5to1_D6_S265
mRNA
052721_countmatrix_scRNAseq.csv


title: 14959, control, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S44]

description:
coculture24h_CART_NALM6_5to1_D6_S44
mRNA
052721_countmatrix_scRNAseq.csv


title: 11822, lithium, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S24]

description:
coculture24h_CART_NALM6_5to1_D6_S24
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S92]

description:
coculture24h_CART_NALM6_5to1_D6_S92
mRNA
052721_countmatrix_scRNAseq.csv


title: 11822, control, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S140]

description:
coculture24h_CART_NALM6_5to1_D6_S140
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D5_S324]

description:
coculture24h_CART_NALM6_5to1_D5_S324
mRNA
052721_countmatrix_scRNAseq.csv


title: 9691, lithium, rep1

description: Lithium Non-Responder


title: JNJ012, lithium, rep1

description: Control

source_name: Lymphoblast

value: Lymphoblast


title: JNJ001, lithium, rep1

description: Lithium Non-Responder


title: 14934, control, rep1

description: Lithium Non-Responder


title: 9691, control, rep1

description: Lithium Non-Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D5_S84]

description:
coculture24h_CART_NALM6_5to1_D5_S84
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D5_S20]

description:
coculture24h_CART_NALM6_5to1_D5_S20
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D6_S332]

description:
coculture24h_CART_NALM6_5to1_D6_S332
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ011, control, rep1

description: Control


title: 11692, control, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D5_S132]

description:
coculture24h_CART_NALM6_5to1_D5_S132
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ012, control, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D5_S258]

description:
coculture24h_CART_NALM6_5to1_D5_S258
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S76]

description:
coculture24h_CART_NALM6_5to1_D4_S76
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S316]

description:
coculture24h_CART_NALM6_5to1_D4_S316
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S28]

description:
coculture24h_CART_NALM6_5to1_D4_S28
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ011, lithium, rep1

description: Control


title: JNJ001, control, rep1

description: Lithium Non-Responder


title: JNJ007, lithium, rep1

description: Lithium Responder


title: JNJ010, lithium, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S251]

description:
coculture24h_CART_NALM6_5to1_D4_S251
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S172]

description:
coculture24h_CART_NALM6_5to1_D4_S172
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ010, control, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D3_S308]

description:
coculture24h_CART_NALM6_5to1_D3_S308
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D4_S16]

description:
coculture24h_CART_NALM6_5to1_D4_S16
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ009, lithium, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D3_S20]

description:
coculture24h_CART_NALM6_5to1_D3_S20
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ007, control, rep1

description: Lithium Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D2_S237]

description:
coculture24h_CART_NALM6_5to1_D2_S237
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ008, control, rep1

description: Control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D1_S52]

description:
coculture24h_CART_NALM6_5to1_D1_S52
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ002, lithium, rep1

description: Lithium Non-Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D1_S230]

description:
coculture24h_CART_NALM6_5to1_D1_S230
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D3_S12]

description:
coculture24h_CART_NALM6_5to1_D3_S12
mRNA
052721_countmatrix_scRNAseq.csv


title: MCF7-siHuR-UT-n2

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

description: replicate 2

data_processing:
Raw reads were were aligned on the human reference genome (hg19) using STAR (version 2.5.3a) (Dobin et all, 2013).
A coverage track was generated using bamCoverage (Ramírez et al., 2016) for each alignement files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

source_name: Breast cancer cell line

growth_protocol: MCF-7 breast cancer cells were cultured in High Glucose DMEM (Eurobio Scientific, France) supplemented with 10% (v/v) fetal bovine serum (PAN Biotech, Germany), 2 mM L-glutamine (Eurobio Scientific, France) and maintained at 37°C in 5% CO2.

extract_protocol:
RNA from whole cells was extracted with TRIzol Reagent (ThermoFischer Scientific) according to the manufacturer’s instructions, and 1 µl of GlycoBlue (ThermoFisher Scientific) was added for RNA precipitation. RNA was treated with TURBO DNase I (ThermoFisher Scientific) and quantified using a Nanodrop 2000 spectrophotometer (ThermoFischer Scientific). For sequencing, RNA samples were analyzed using an RNA 2100 Bioanalyzer (Agilent).
Total RNA was subjected to DNAse I treatment. 500 ng of good quality RNA (RIN > 9) were used for Illumina compatible library preparation using the TruSeq Stranded total RNA protocol allowing to take into account strand information. A first step of ribosomal RNA depletion was performed using the RiboZero Gold kit (Illumina). After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche). Sequencing was carried out on the NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases) using a S1 flow cell in order to obtain around 100 million clusters (200 million raw paired-end reads) per sample.

treatment_protocol: Reverse transfection of siRNAs (Eurogentec, Belgium) was performed at a final concentration of 25 nM using Lipofectamine RNAimax (ThermoFischer Scientific, France) following the manufacturer's instructions. After 42 hours, cells were treated for 6 hours with or without 3.5 µM doxorubicin hydrochloride (Sigma Aldrich, France) resuspended in water.

tag: transfected sirna

value: siRNA against HuR

value: Vehicle (H2O)

tag: compartment

value: Total cells


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S48]

description:
coculture24h_CART_NALM6_5to1_D12_S48
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line


title: MCF7-siHuR-Doxo-n1

description: replicate 1

tag: treatment

value: Doxorubicin


title: JNJ005, lithium, rep1

description: Lithium Responder


title: MCF7-siCT-Doxo-n1

description: replicate 1

value: negative control siRNA


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D1_S100]

description:
coculture24h_CART_NALM6_5to1_D1_S100
mRNA
052721_countmatrix_scRNAseq.csv

tag: library strategy


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D2_S156]

description:
coculture24h_CART_NALM6_5to1_D2_S156
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S236]

description:
coculture24h_CART_NALM6_5to1_D12_S236
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ008, lithium, rep1

description: Control

tag: tissue


title: JNJ005, control, rep1

description: Lithium Responder

tag: cell type


title: JNJ002, control, rep1

description: Lithium Non-Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D1_S292]

description:
coculture24h_CART_NALM6_5to1_D1_S292
mRNA
052721_countmatrix_scRNAseq.csv


title: JNJ004, lithium, rep1

description: Lithium Non-Responder


title: JNJ004, control, rep1

description: Lithium Non-Responder


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D2_S300]

description:
coculture24h_CART_NALM6_5to1_D2_S300
mRNA
052721_countmatrix_scRNAseq.csv


title: MCF7-siHuR-Doxo-n2

description: replicate 2


title: UT-Tot-IgG-n2

description: replicate 2

data_processing:
For each sample, raw reads were trimmed in their 5’ and 3’ ends to remove uninformative nucleotides.
Trimmed reads were aligned on the human reference genome (hg19) using Bowtie2 (version 2.2.5) (Langmead and Salzberg 2012). Only reads with a mapping quality score (MAPQ) of 20 or more were retained (Samtools version 1.1) for downstream analysis.
Duplicated reads were removed using Picard tools.
Peaks were identified using Piranha (Uren, Bioinformatics 2012) using a cutoff of 0.95.
Genome_build: hg19
Supplementary_files_format_and_content: .bed

extract_protocol:
For preparation of cytosolic and nuclear extracts, cells were washed twice with ice-cold phosphate buffer saline (PBS) and harvested by scraping. Cells from each plate were pelleted in microfuge tubes, resuspended in 200 μL lysis buffer (10 mM Tris-HCl pH 8,140 mM NaCl, 1.5 mM MgCl2, 10 mM EDTA, 0.5% NP40 and protease inhibitor cocktail) and incubated on ice for 5 min followed by centrifugation at 470 g for 5 min at 4 °C. The supernatant was stored as cytosolic fraction and the pellet was washed twice gently with lysis buffer before being resuspended in lysis buffer as nuclear fraction. For total cell lysates, cells were lysed directly by pipetting in lysis buffer. The cell lysate fractions were then sonicated (12 cycles, 30:30) on a Diagenode sonicator.
CLIP-seq procedure (iCLIP): Individual-nucleotide resolution Cross-Linking and Immuno Precipitation (iCLIP) experiments were performed as described (Huppertz et al 2014) with minor modifictaions, as detailed below, using protein lysates (whole cell/ nuclear/cytosolic) from MCF-7 cells treated or not with Doxo for 6 hours (2 replicates per condition). Briefly, 85-90% confluent MCF-7 cells in 10 cm dishes were irradiated with UV- light (254 nM) at 400 mJ/cm2 to crosslink protein-RNA interactions using Stratalinker 1800 (Stratagene). After washing cells with ice-cold PBS, cell fractions were obtained as described above. The lysates were sonicated, incubated with 800 µl RIPA buffer for 30 min. 10 µl RNase 1 (1:250) was added along with 2 µl of turbo DNAse and incubated at 37˚C for 3 min at 1,100 rpm in a table-top Thermomixer (ThermoFischer Scientific) followed by incubation on ice for 3 min. RNAse inhibitor (ThermoFischer Scientific) was added and the lysates were centrifuged at 22,000 rcf for 10 min at 4˚C to remove debris. Immunoprecipitation of HuR-RNA complexes was performed using 5 μg of anti-HuR mAb coupled to protein G dynabeads (ThermoFischer Scientific). IP with anti-mouse IgG (Santa Cruz Biotechnologies) was used as negative control. After washing twice with high-salt buffer RIPA-S (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate) and once with PNK washing buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20), one tenth of the sample were labelled with 32P-ATP using PNK, whereas an RNA Linker was ligated to the rest of the sample after RNA de-phosphorylation. RNA-protein complexes were separated by electrophoresis (SDS-Page) and transferred to nitrocellulose membranes. HuR RNA complexes higher than 55 KDa were marked after visualization by autoradiography. RNA extraction was performed by incubating the nitrocellulose fragment at 37°C for 10 min with proteinase K in PK buffer (100 mM This-Cl pH 7.5, 50 mM NaCl and 10 mM EDTA). 200 μl of PK buffer containing urea (7 M) was added to each sample and further incubated at 37°C for 20 minutes. RNA was isolated by acid-phenol/chloroform extraction and ethanol precipitation. RNA was reverse transcribed into cDNA using RCLIP primers and SuperScript III reverse transcriptase. After cDNA purification using 6% TBE-urea gels, cDNA was circularized and amplified by PCR using Solexa P5/P7 primers (Illumina).
After cDNA purification using 6% TBE-urea gels, cDNA was circularized and amplified by PCR using Solexa P5/P7 primers (Illumina). cDNA libraries from independent experiments were prepared, purified using Agencourt AMPure XP (Beckman Coulter) magnetic beads, quantified with Quant-iT Picogreen dsDNA kit (ThermoFisher Scientific), and run on Experion automated electrophoresis system (BIO-RAD). Pooled libraries were quantitated by qPCR (KAPA Library Quantification Kits Illumina Platforms, Roche), diluted to 12 pM, and subjected to single-end, 50 bp sequencing using the HiSeq 2500 machine (Illumina).

treatment_protocol: Cells were treated for 6 hours with or without 3.5 µM doxorubicin hydrochloride (Sigma Aldrich, France) resuspended in water.


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D1_S148]

description:
coculture24h_CART_NALM6_5to1_D1_S148
mRNA
052721_countmatrix_scRNAseq.csv


title: MCF7-siCT-UT-n2

description: replicate 2


title: MCF7-siCT-Doxo-n2

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D2_S60]

description:
coculture24h_CART_NALM6_5to1_D2_S60
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D3_S244]

description:
coculture24h_CART_NALM6_5to1_D3_S244
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S302]

description:
coculture24h_CART_NALM6_5to1_D12_S302
mRNA
052721_countmatrix_scRNAseq.csv


title: MCF7-siCT-UT-n1

description: replicate 1


title: JNJ009, control, rep1

description: Control


title: MCF7-siHuR-UT-n1

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S140]

description:
coculture24h_CART_NALM6_5to1_D12_S140
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S188]

description:
coculture24h_CART_NALM6_5to1_D12_S188
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S92]

description:
coculture24h_CART_NALM6_5to1_D12_S92
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S84]

description:
coculture24h_CART_NALM6_5to1_D11_S84
mRNA
052721_countmatrix_scRNAseq.csv


title: Doxo-Cyt-HuR-n2

description: replicate 2

value: Cytosol


title: UT-Cyt-HuR-n2

description: replicate 2


title: Doxo-Tot-HuR-n2

description: replicate 2


title: Doxo-Nuc-HuR-n2

description: replicate 2

value: Nucleus


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D12_S380]

description:
coculture24h_CART_NALM6_5to1_D12_S380
mRNA
052721_countmatrix_scRNAseq.csv

value: CAR T-cells


title: UT-Nuc-HuR-n2

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S44]

description:
coculture24h_CART_NALM6_5to1_D11_S44
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S372]

description:
coculture24h_CART_NALM6_5to1_D11_S372
mRNA
052721_countmatrix_scRNAseq.csv


title: UT-Nuc-HuR-n1

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D10_S220]

description:
coculture24h_CART_NALM6_5to1_D10_S220
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D10_S124]

description:
coculture24h_CART_NALM6_5to1_D10_S124
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D10_S290]

description:
coculture24h_CART_NALM6_5to1_D10_S290
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S67]

description:
coculture24h_CART_NALM6_5to1_C9_S67
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S228]

description:
coculture24h_CART_NALM6_5to1_D11_S228
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S35]

description:
coculture24h_CART_NALM6_5to1_C9_S35
mRNA
052721_countmatrix_scRNAseq.csv


title: UT-Tot-HuR-n1

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S180]

description:
coculture24h_CART_NALM6_5to1_D11_S180
mRNA
052721_countmatrix_scRNAseq.csv


title: UT-Tot-IgG-n1

description: replicate 1


title: UT-Tot-HuR-n2

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D10_S40]

description:
coculture24h_CART_NALM6_5to1_D10_S40
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S355]

description:
coculture24h_CART_NALM6_5to1_C9_S355
mRNA
052721_countmatrix_scRNAseq.csv


title: UT-Cyt-HuR-n1

description: replicate 1


title: Doxo-Cyt-HuR-n1

description: replicate 1


title: SR23_Cyt_siHuR_UT

description: replicate 3

data_processing:
Raw reads were trimmed to remove uninformative nucleotides due to primer sequences.
Trimmed reads of 25 bp or more were aligned on the human reference genome (hg19) using Bowtie2 (version 2.2.5) (Langmead and Salzberg 2012). Only reads with a mapping quality score (MAPQ) of 20 or more were retained (Samtools version 1.1) for downstream analysis.
Reads were then clustered along the genome using Bedtools (version 2.17.0) (Quinlan and Hall 2010), allowing a maximum distance of 50 bp and a minimum number of 5 reads per peak.
Peaks with a stretch of 6 consecutive As (or 8 As out of 9 nucleotides) within 50 bp downstream were filtered out, as they are likely due to internal priming of oligo-dT.
Genome_build: hg19
Supplementary_files_format_and_content: .bed

extract_protocol:
For preparation of nuclear and cytosolic (protocol 2) fractions, cells were washed twice with ice-cold phosphate buffer saline (PBS) and harvested by scraping. Cells from each plate were pelleted in microfuge tubes, resuspended in 200 μL lysis buffer (10 mM Tris-HCl pH 8,140 mM NaCl, 1.5 mM MgCl2, 10 mM EDTA, 0.5% NP40 and protease inhibitor cocktail) and incubated on ice for 5 min followed by centrifugation at 470 g for 5 min at 4C.The supernatant was stored as cytosolic fraction and the pellet was washed twice gently with lysis buffer before being resuspended in lysis buffer as nuclear fraction. For total cell lysates, cells were lysed directly by pipetting in lysis buffer. The cell lysate fractions were then sonicated (12 cycles, 30:30) on a Diagenode sonicator and used for RNA isolation or western blot. For preparation of polysomal and cytosolic (protocol 1) fractions, cells were incubated at 37 °C with 100 μg/mL cycloheximide in fresh medium for 5 min. Cells were then washed, scraped into ice-cold PBS supplemented with 100 μg/mL cycloheximide, centrifuged at 3000 r.p.m. for 5 min. The cell pellets were resuspended into 400 μL of LSB buffer (20 mM Tris, pH 7.4, 100 mM NaCl, 3 mM MgCl2, 0.5 M sucrose, 1 mM DTT, 100 U/mL RNasin and 100 μg/mL cylcoheximide). After homogenization, 400 μL LSB buffer supplemented with 0.2 % Triton X-100 and 0.25 M sucrose was added. Samples were stayed on ice for 30 min and centrifuged at 12,000 g for 15min at 4 °C. The supernatant was adjusted to 5 M NaCl and 1 M MgCl2. The lysates were then loaded onto a 5-50 % sucrose density gradient and centrifuged in an SW41 Ti rotor (Beckman) at 36,000 rpm for 2 h at 4 °C. Fractions were monitored and collected using a gradient fractionation system (Isco). RNA was extracted from the four heaviest polysomal fractions (pooled). RNA from whole or fractionated cell lysates were extracted with TRIzol Reagent (TRIzol-LS for polysomes; ThermoFischer Scientific) according to the manufacturer’s instructions, and 1 µl of GlycoBlue (ThermoFisher Scientific) was added for RNA precipitation. RNA was treated with TURBO DNase I (ThermoFisher Scientific) and quantified using a Nanodrop 2000 spectrophotometer (ThermoFischer Scientific). For sequencing, RNA samples were analyzed using an RNA 2100 Bioanalyzer (Agilent).
3’-seq libraries were prepared with QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina (Lexogen) using 250 ng (for polysomal RNA) or 500 ng (for all other samples) of DNase 1 treated RNA (n=3 for each condition) following manufacturer’s instructions. Purified libraries were quantified with Quant-iT Picogreen dsDNA kit (ThermoFisher Scientific) and run on Experion automated electrophoresis system (BIO-RAD). Pooled libraries were quantitated by qPCR (KAPA Library Quantification Kits Illumina Platforms, Roche), diluted to 12 pM, and subjected to single-end, 50 bp sequencing using the HiSeq 2500 machine (Illumina).

treatment_protocol: Reverse transfection of siRNAs (Eurogentec, Belgium) was performed at a final concentration of 25 nM using Lipofectamine RNAimax (ThermoFischer Scientific, France) following the manufacturer's instructions, for 48 hours, including 6 or 18 hours with or without 3.5 µM doxorubicin hydrochloride (Sigma Aldrich, France) resuspended in water.

tag: cell compartment

value: Cytosol (protocol 2)


title: Doxo-Nuc-HuR-n1

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S283]

description:
coculture24h_CART_NALM6_5to1_C9_S283
mRNA
052721_countmatrix_scRNAseq.csv


title: SR23_Cyt_sicont_Doxo

description: replicate 3

value: Doxorubicin 6 hours


title: SR23_Cyt_sicont_UT

description: replicate 3


title: SR23_Nuc_sicont_Doxo

description: replicate 3


title: sR23_tot_siHuR_Doxo

description: replicate 3


title: Doxo-Tot-HuR-n1

description: replicate 1


title: SR23_tot_sicont_Doxo

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [D11_S132]

description:
coculture24h_CART_NALM6_5to1_D11_S132
mRNA
052721_countmatrix_scRNAseq.csv


title: sR23_Cyt_siHuR_Doxo

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S211]

description:
coculture24h_CART_NALM6_5to1_C9_S211
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S155]

description:
coculture24h_CART_NALM6_5to1_C8_S155
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S107]

description:
coculture24h_CART_NALM6_5to1_C8_S107
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S163]

description:
coculture24h_CART_NALM6_5to1_C9_S163
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C9_S115]

description:
coculture24h_CART_NALM6_5to1_C9_S115
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C7_S271]

description:
coculture24h_CART_NALM6_5to1_C7_S271
mRNA
052721_countmatrix_scRNAseq.csv


title: SR20_Cyt_sicont_UT

description: replicate 2


title: SR23_Nuc_sicont_UT

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S59]

description:
coculture24h_CART_NALM6_5to1_C8_S59
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C7_S195]

description:
coculture24h_CART_NALM6_5to1_C7_S195
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C7_S147]

description:
coculture24h_CART_NALM6_5to1_C7_S147
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S31]

description:
coculture24h_CART_NALM6_5to1_C8_S31
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S277]

description:
coculture24h_CART_NALM6_5to1_C8_S277
mRNA
052721_countmatrix_scRNAseq.csv


title: SR23_tot_siHuR_UT

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C7_S339]

description:
coculture24h_CART_NALM6_5to1_C7_S339
mRNA
052721_countmatrix_scRNAseq.csv


title: SR23_tot_sicont_UT

description: replicate 3


title: SR20_Cyt_siHuR_UT

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C8_S203]

description:
coculture24h_CART_NALM6_5to1_C8_S203
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C7_S27]

description:
coculture24h_CART_NALM6_5to1_C7_S27
mRNA
052721_countmatrix_scRNAseq.csv


title: sR20_Cyt_siHuR_Doxo

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C6_S264]

description:
coculture24h_CART_NALM6_5to1_C6_S264
mRNA
052721_countmatrix_scRNAseq.csv


title: SR20_Cyt_sicont_Doxo

description: replicate 2


title: SR20_Nuc_sicont_Doxo

description: replicate 2


title: SR20_Nuc_sicont_UT

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C6_S91]

description:
coculture24h_CART_NALM6_5to1_C6_S91
mRNA
052721_countmatrix_scRNAseq.csv


title: SR15_Cyt_siHuR_UT

description: replicate 1


title: sR15_Cyt_siHuR_Doxo

description: replicate 1


title: SR20_tot_sicont_UT

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C4_S250]

description:
coculture24h_CART_NALM6_5to1_C4_S250
mRNA
052721_countmatrix_scRNAseq.csv


title: SR20_tot_sicont_Doxo

description: replicate 2


title: SR20_tot_siHuR_UT

description: replicate 2


title: SR15_Nuc_sicont_Doxo

description: replicate 1


title: SR15_Cyt_sicont_Doxo

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C6_S187]

description:
coculture24h_CART_NALM6_5to1_C6_S187
mRNA
052721_countmatrix_scRNAseq.csv


title: sR20_tot_siHuR_Doxo

description: replicate 2


title: SR15_Nuc_sicont_UT

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C5_S83]

description:
coculture24h_CART_NALM6_5to1_C5_S83
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C5_S131]

description:
coculture24h_CART_NALM6_5to1_C5_S131
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S67]

description:
coculture24h_CART_NALM6_5to1_C3_S67
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C6_S139]

description:
coculture24h_CART_NALM6_5to1_C6_S139
mRNA
052721_countmatrix_scRNAseq.csv


title: SR15_tot_sicont_Doxo

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S307]

description:
coculture24h_CART_NALM6_5to1_C3_S307
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S243]

description:
coculture24h_CART_NALM6_5to1_C3_S243
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C5_S19]

description:
coculture24h_CART_NALM6_5to1_C5_S19
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C4_S15]

description:
coculture24h_CART_NALM6_5to1_C4_S15
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S19]

description:
coculture24h_CART_NALM6_5to1_C3_S19
mRNA
052721_countmatrix_scRNAseq.csv


title: SR15_tot_siHuR_UT

description: replicate 1


title: SR15_Cyt_sicont_UT

description: replicate 1


title: SR15_tot_sicont_UT

description: replicate 1


title: NT6_HP_P_siHuR_Doxo6

description: replicate 3

value: Heavy polysomes


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S11]

description:
coculture24h_CART_NALM6_5to1_C3_S11
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_HP_P_siHuR_UT

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S163]

description:
coculture24h_CART_NALM6_5to1_C3_S163
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_HP_P_siCTRL_Doxo18

description: replicate 3

value: Doxorubicin 18 hours


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C4_S123]

description:
coculture24h_CART_NALM6_5to1_C4_S123
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_HP_P_siCTRL_Doxo6

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C2_S7]

description:
coculture24h_CART_NALM6_5to1_C2_S7
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_HP_P_siCTRL_UT

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C2_S107]

description:
coculture24h_CART_NALM6_5to1_C2_S107
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_cyt_P_siCTRL_Doxo18

description: replicate 3

value: Cytosol (protocol 1)


title: NT6_cyt_P_siHuR_UT

description: replicate 3


title: NT6_cyt_P_siHuR_Doxo6

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C6_S23]

description:
coculture24h_CART_NALM6_5to1_C6_S23
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C1_S229]

description:
coculture24h_CART_NALM6_5to1_C1_S229
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C1_S3]

description:
coculture24h_CART_NALM6_5to1_C1_S3
mRNA
052721_countmatrix_scRNAseq.csv


title: NT6_cyt_P_siCTRL_Doxo6

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C1_S147]

description:
coculture24h_CART_NALM6_5to1_C1_S147
mRNA
052721_countmatrix_scRNAseq.csv


title: sR15_tot_siHuR_Doxo

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S91]

description:
coculture24h_CART_NALM6_5to1_C12_S91
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S47]

description:
coculture24h_CART_NALM6_5to1_C12_S47
mRNA
052721_countmatrix_scRNAseq.csv


title: NT8_HP_P_siCTRL_Doxo18

description: replicate 2


title: NT8_HP_P_siCTRL_Doxo6

description: replicate 2


title: NT8_HP_P_siCTRL_UT

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S301]

description:
coculture24h_CART_NALM6_5to1_C12_S301
mRNA
052721_countmatrix_scRNAseq.csv


title: NT8_cyt_P_siCTRL_Doxo18

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S235]

description:
coculture24h_CART_NALM6_5to1_C12_S235
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C3_S115]

description:
coculture24h_CART_NALM6_5to1_C3_S115
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C1_S51]

description:
coculture24h_CART_NALM6_5to1_C1_S51
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C2_S155]

description:
coculture24h_CART_NALM6_5to1_C2_S155
mRNA
052721_countmatrix_scRNAseq.csv


title: NT8_cyt_P_siCTRL_Doxo6

description: replicate 2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S187]

description:
coculture24h_CART_NALM6_5to1_C12_S187
mRNA
052721_countmatrix_scRNAseq.csv


title: NT8_cyt_P_siCTRL_UT

description: replicate 2


title: NT6_cyt_P_siCTRL_UT

description: replicate 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S83]

description:
coculture24h_CART_NALM6_5to1_C11_S83
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_HP_P_siCTRL_Doxo6

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C12_S139]

description:
coculture24h_CART_NALM6_5to1_C12_S139
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_HP_P_siCTRL_Doxo18

description: replicate 1


title: NT7_HP_P_siHuR_Doxo6

description: replicate 1


title: NT7_HP_P_siHuR_UT

description: replicate 1


title: NT7_Cyt_P_siHuR_Doxo6

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S371]

description:
coculture24h_CART_NALM6_5to1_C11_S371
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S131]

description:
coculture24h_CART_NALM6_5to1_C11_S131
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S227]

description:
coculture24h_CART_NALM6_5to1_C11_S227
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S43]

description:
coculture24h_CART_NALM6_5to1_C11_S43
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C11_S179]

description:
coculture24h_CART_NALM6_5to1_C11_S179
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_Cyt_P_siCTRL_Doxo18

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S75]

description:
coculture24h_CART_NALM6_5to1_C10_S75
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_Cyt_P_siCTRL_Doxo6

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S363]

description:
coculture24h_CART_NALM6_5to1_C10_S363
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S171]

description:
coculture24h_CART_NALM6_5to1_C10_S171
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_Cyt_P_siCTRL_UT

description: replicate 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S289]

description:
coculture24h_CART_NALM6_5to1_C10_S289
mRNA
052721_countmatrix_scRNAseq.csv


title: Bone marrow, KO4

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

country: United Kingdom

institute: Imperial College London

data_processing:
Sequencing data for RNA-Seq samples are adapter trimmed using Fastp v0.20.1 and mapped against a reference transcriptome using splice aware aligner STAR v2.6.0a
We follow the Alternate Protocol 7 from Mapping RNA-seq Reads with STAR and generate both genomic and transcriptomic bam files after aligning fastq files from different lanes and flowcells.
Each lane level bams are tagged with relevant read group information before they are merged together to create a library level bam followed by marking the duplicate reads (without removal) using Picard v2.19
We generate raw counts per gene using the FeatureCounts tool v1.6.4 from the merged genomic bam
Normalized counts are generated using RSEM tool v1.3.1 from the merged transcriptome bam.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw feature counts for each Sample
Supplementary files format and content: tab-delimited text files include normalized counts as TPM and FPKM for each Sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep E6420S following manufacturer's protocols.

value: Bone marrow

value: Lin- CD127+

tag: genotype

value: Tref1 -/-


title: Bone marrow, KO3


title: Bone marrow, WT4

value: Trerf1 +/+


title: NT7_Cyt_P_siHuR_UT

description: replicate 1

value: siRNA against HuR


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S123]

description:
coculture24h_CART_NALM6_5to1_C10_S123
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S354]

description:
coculture24h_CART_NALM6_5to1_B9_S354
mRNA
052721_countmatrix_scRNAseq.csv


title: Bone marrow, WT2


title: Bone marrow, KO2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [C10_S39]

description:
coculture24h_CART_NALM6_5to1_C10_S39
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S162]

description:
coculture24h_CART_NALM6_5to1_B9_S162
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S210]

description:
coculture24h_CART_NALM6_5to1_B9_S210
mRNA
052721_countmatrix_scRNAseq.csv


title: Bone marrow, KO1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S282]

description:
coculture24h_CART_NALM6_5to1_B9_S282
mRNA
052721_countmatrix_scRNAseq.csv


title: NT7_HP_P_siCTRL_UT

description: replicate 1

value: Vehicle (H2O)


title: Brain-control-2

city: Madison

first: Junsu

last: Kang

state: WI

address: 1111 Highland Avenue

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

data_processing:
Cutadapt to remove adapter sequences and short reads (less than 10bp)
HISAT2 to align to zebrafish GRCz11 reference genome
FeatureCount
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Brain-control

extract_protocol:
Tissues were homogenized in immediately after dissection and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Ekkwill

value: wild-type

value: Uninjured

tag: protocol

value: 33°C for 1 day

value: Brain


title: Brain-control-1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S114]

description:
coculture24h_CART_NALM6_5to1_B9_S114
mRNA
052721_countmatrix_scRNAseq.csv

value: CAR T-cells


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S346]

description:
coculture24h_CART_NALM6_5to1_B8_S346
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S30]

description:
coculture24h_CART_NALM6_5to1_B8_S30
mRNA
052721_countmatrix_scRNAseq.csv


title: Bone marrow, WT1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S202]

description:
coculture24h_CART_NALM6_5to1_B8_S202
mRNA
052721_countmatrix_scRNAseq.csv


title: Bone marrow, WT3


title: Brain-mutant-2

source_name: Brain-mutant

value: scn8ab(temca) -/-


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B9_S34]

description:
coculture24h_CART_NALM6_5to1_B9_S34
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S106]

description:
coculture24h_CART_NALM6_5to1_B8_S106
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S276]

description:
coculture24h_CART_NALM6_5to1_B8_S276
mRNA
052721_countmatrix_scRNAseq.csv


title: Brain-mutant-1


title: Fin-36hpa-control-1

value: Amputated

value: 33°C for 36 hours

value: Regenerating fin


title: Fin-uninjured-control-2

source_name: Fin-uninjured-control

value: Uninjured fin


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S270]

description:
coculture24h_CART_NALM6_5to1_B7_S270
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B8_S154]

description:
coculture24h_CART_NALM6_5to1_B8_S154
mRNA
052721_countmatrix_scRNAseq.csv


title: Fin-uninjured-control-1


title: Fin-uninjured-mutant-2

source_name: Fin-uninjured-mutant


title: Fin-36hpa-mutant-2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S98]

description:
coculture24h_CART_NALM6_5to1_B7_S98
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S194]

description:
coculture24h_CART_NALM6_5to1_B7_S194
mRNA
052721_countmatrix_scRNAseq.csv


title: Fin-uninjured-mutant-1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S338]

description:
coculture24h_CART_NALM6_5to1_B7_S338
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S26]

description:
coculture24h_CART_NALM6_5to1_B7_S26
mRNA
052721_countmatrix_scRNAseq.csv


title: Fin-36hpa-control-2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B7_S146]

description:
coculture24h_CART_NALM6_5to1_B7_S146
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S186]

description:
coculture24h_CART_NALM6_5to1_B6_S186
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S138]

description:
coculture24h_CART_NALM6_5to1_B6_S138
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S90]

description:
coculture24h_CART_NALM6_5to1_B6_S90
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S330]

description:
coculture24h_CART_NALM6_5to1_B6_S330
mRNA
052721_countmatrix_scRNAseq.csv


title: Gene expression profiling of 4F-treated MSC-Ucs 1

type: RNA

city: Shinjyuku-ku

first: Tomoki

last: Takashina

state: Tokyo

department: Department of Intractable Diseases

country: Japan

institute: National center for Global Health and Medicine

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent SurePrint G3 Human GE microarray (version 3).

scan_protocol: Arrays were scanned on an Agilent scanner (Agilent technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MSC-UCs

label_protocol: Labering was conducted with the Quick-Amp labeling kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Cells were maintained in Cellartis MSC Xeno-Free Basal Medium under humidified conditions with 5% CO2.

extract_protocol: Total RNA was extracted from MSC-Ucs using RNeasy mini kit.

treatment_protocol: Cells were treated with 4F or NE at 0.25 nM twice a day for 5 days and maintained in Cellartis MSC Xeno-Free Basal Medium under humidified conditions with 5% CO2 for additional 2 days.

value: umbilical cord derived


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B5_S130]

description:
coculture24h_CART_NALM6_5to1_B5_S130
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S263]

description:
coculture24h_CART_NALM6_5to1_B6_S263
mRNA
052721_countmatrix_scRNAseq.csv


title: D3

city: changchun

first: Jingyan

last: Ren

state: chaoyang

address: hanseng

country: China

institute: The first hospital of Jilin University

data_processing:
illumina Casava1.7 software used for basecalling
Quality control  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In   this step, clean data (clean reads) were obtained by removing reads containing adapter, reads   1  containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC   content the clean data were calculated. All the downstream analyses were based on the clean   data with high quality.  Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website   directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the   mapping tool for that Hisat2 can generate a database of splice junctions based on the gene   model annotation file and thus a better mapping result than other non-splice mapping tools.  Novel transcripts prediction  The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et   al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well   as an optional de novo assembly step to assemble and quantitate fulllength transcripts   representing multiple splice variants for each gene locus.  Quantification of gene expression level  featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then   FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per   Millions base pairs sequenced, considers the effect of sequencing depth and gene length for   the reads count at the same time, and is currently the most commonly used method for   estimating gene expression levels
Differential expression analysis  (For DESeq2 with biological replicates) Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2   R package (1.20.0). DESeq2 provide statistical routines for determining differential expression   in digital gene expression data using a model based on the negative binomial distribution. The   resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling  the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were   assigned as differentially expressed.  2  (For edgeR without biological replicates) Prior to differential gene expression analysis, for   each sequenced library, the read counts were adjusted by edgeR program package through one   scaling normalized factor. Differential expression analysis of two conditions was performed   using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini &   Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the   threshold for significantly differential expression.
GO and KEGG enrichment analysis of differentially expressed genes  Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented   by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with   corrected Pvalue less than 0.05 were considered significantly enriched by differential   expressed genes. KEGG is a database resource for understanding high-level functions and   utilities of the biological system, such as the cell, the organism and the ecosystem, from  molecular-level information, especially large-scale molecular datasets generated by genome   sequencing and other high-through put experimental technologies  (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical   enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis  Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre_x0002_defined Gene Set can show a significant consistent difference between two biological   states. The genes were ranked according to the degree of differential expression in the two   samples, and then the predefined Gene Set were tested to see if they were enriched at the   top or bottom of the list. Gene set enrichment analysis can include subtle expression   changes. We use the local version of the GSEA analysis tool   http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA  independently.  SNP analysis  GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with   GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o;   FS > 30.0; DP < 10.  3  AS analysis  Alternative Splicing is an important mechanism for regulate the expression of genes and the   variable of protein. rMATS(3.2.5) software was used to analysis the AS event.  PPI analysis of differentially expressed genes  PPI analysis of differentially expressed genes was based on the STRING database, which   known and predicted Protein-Protein Interactions.  Weighted correlation network analysis  WGCNA (Weighted correlation network analysis) is a systematic biological method used to   describe the gene association modes among different samples. it can be used to identify gene   sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic   targets based on the coherence of gene sets and the correlation between gene sets and   phenotypes. The R package WGCNA is a set of functions used to calculate various weighted   association analysis, which can be used for network construction, gene screening, gene cluster   identification, topological feature calculation, data simulation and visualization. WGCNA is   suitable for multisample data. Generally, more than 15 samples are required. One input file is   sample information, that is, a matrix describing the traits of the sample: the traits used for  association analysis must be numeric; If it is a regional or categorical variable, it needs to be   converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing,  FPKM can be used as gene expression data
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: skin

extract_protocol:
Skins were remnoved,fash frozen on dry ice,and RNA was harvested using Trizol reagent.illumina TruSeq RNA Sample Prep Kt (Cati#FC-122-1001)was used wth 1ug of total RNA for the construction
RNA libraries were preparod tor sequencing using standard iIlumina protocols

value: skin

value: bio-multifunctional hydrogel


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B4_S249]

description:
coculture24h_CART_NALM6_5to1_B4_S249
mRNA
052721_countmatrix_scRNAseq.csv


title: D1


title: Gene expression profiling of NE-treated MSC-Ucs 2

value: NE


title: Gene expression profiling of 4F-treated MSC-Ucs 2


title: Gene expression profiling of NE-treated MSC-Ucs 1


title: Gene expression profiling of 4F-treated MSC-Ucs 3


title: Gene expression profiling of non-treated MSC-Ucs 2

value: untreated


title: Gene expression profiling of non-treated MSC-Ucs 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B6_S22]

description:
coculture24h_CART_NALM6_5to1_B6_S22
mRNA
052721_countmatrix_scRNAseq.csv


title: C1

value: control


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B4_S14]

description:
coculture24h_CART_NALM6_5to1_B4_S14
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B5_S82]

description:
coculture24h_CART_NALM6_5to1_B5_S82
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B5_S256]

description:
coculture24h_CART_NALM6_5to1_B5_S256
mRNA
052721_countmatrix_scRNAseq.csv


title: Fin-36hpa-mutant-1

value: Ekkwill


title: Gene expression profiling of NE-treated MSC-Ucs 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B4_S314]

description:
coculture24h_CART_NALM6_5to1_B4_S314
mRNA
052721_countmatrix_scRNAseq.csv


title: D2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S242]

description:
coculture24h_CART_NALM6_5to1_B3_S242
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B5_S18]

description:
coculture24h_CART_NALM6_5to1_B5_S18
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B4_S170]

description:
coculture24h_CART_NALM6_5to1_B4_S170
mRNA
052721_countmatrix_scRNAseq.csv


title: miRPK2cvp2cvl1 Rep2

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Illumina Casava1.8 software was use for basecalling.
FASTQ file generation and demultiplexing was done by the Functional Genomic Center Zurich.
adapter sequences were remove using Trimmomatic (v0.39) with options SE -phred33 ILLUMINACLIP:trimmed/NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:50.  Trimmed reads were then aligned onto Arabidopsis thaliana TAIR10 Ensembl genome and genes annotation using HISAT2 (v2.2.1) with options -k 10 --max-intronlen 1000.
Counts for annotated gene (TAIR10 EnsemblGenomes release 27) were generated using the featureCounts function from the Subread package with options -O -M -T 10 --largestOverlap --minOverlap 10 --primary
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file of reads count values.

organism: Arabidopsis thaliana

source_name: embryo

growth_protocol: Seeds were surface-sterilized, stratified at 4˚C and grown vertically on 0.5x MS plates under standard continuous-light growth conditions. Seedlings were transferred to soil and grown in  5x5 cm pots in peat-based compost medium in a walk-in chamber at constant 23˚C, 65% humidity in a 16h photoperiod and light intensity of 250μmol photons m-2 sec-1 until flowering until siliques were collected to extract embryos.

extract_protocol:
50 torpedo staged embryos of each genetic background were manually dissected out of the ovule with needles and immediately placed in TRIzol reagent (Ambion) and grounded with a sterile pestle. All samples were frozen in TRIzol and kept at -80ºC until RNA extraction. RNA extraction was completed by incubating samples at 60ºC for 30 minutes and then purified according to Palovaara J, et al. 2017 (Nature Plants 3(11):894-904). The resulting RNA was cleaned up and concentrated using the RNeasy MinElute Cleanup Kit Qiagen.
Extracted RNA was processed into sequencing libraries and sequenced at the FGCZ (https://fgcz.ch/, Switzerland) using the Illumina Novaseq sequencer

tag: ecotype

value: cvp2cvl1 containing a transgene expressing a artificial miRNA targeting RPK2

value: embryo

tag: development stage

value: early to late Torpedo stage


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S114]

description:
coculture24h_CART_NALM6_5to1_B3_S114
mRNA
052721_countmatrix_scRNAseq.csv


title: C2


title: cvp2cvl1 Rep2


title: cvp2cvl1 Rep1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S306]

description:
coculture24h_CART_NALM6_5to1_B3_S306
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S66]

description:
coculture24h_CART_NALM6_5to1_B3_S66
mRNA
052721_countmatrix_scRNAseq.csv


title: Gene expression profiling of non-treated MSC-Ucs 1


title: miRPK2cvp2cvl1 Rep1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S162]

description:
coculture24h_CART_NALM6_5to1_B3_S162
mRNA
052721_countmatrix_scRNAseq.csv


title: cvp2cvl1 Rep3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B2_S58]

description:
coculture24h_CART_NALM6_5to1_B2_S58
mRNA
052721_countmatrix_scRNAseq.csv


title: MCT-PAH2_SGC-CBP30-Nebulization

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for subsequent analyses.
Trimmed and filtered reads were aligned versus Rattus norvegicus genome version rn6 (Ensembl release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1”.
Duplicate reads were removed with Picard 2.21.7.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Counts were normalized using DESeq2 version 1.30.0.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: pul31_rnaseq.txt: Tab-delimited text file contains DESeq normalized counts.

source_name: Lung

growth_protocol: Rats were maintained under normoxic conditions.

extract_protocol:
RNA was isolated from rat lungs using the miRNeasy mini kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
4µg total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacturer's protocol (Vazyme).

treatment_protocol: Rats exposed to Monocrotaline were treated with SGC-CBP30 (intratracheal nebulization 275 nmol/kg in 4% DMSO + PBS) or with DMSO vehicle.

tag: diagnosis

value: Monocrotaline-induced pulmonary arterial hypertension (MCT-PAH)

value: Lung


title: C3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B2_S235]

description:
coculture24h_CART_NALM6_5to1_B2_S235
mRNA
052721_countmatrix_scRNAseq.csv

value: CAR T-cells


title: MCT-PAH1_SGC-CBP30-Nebulization


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B2_S6]

description:
coculture24h_CART_NALM6_5to1_B2_S6
mRNA
052721_countmatrix_scRNAseq.csv


title: SEM::EGR3 input

city: Frankfurt am Main

first: Marius

last: Külp

address: Theodor-Stern-Kai 7

department: Department of Medicine II, Hematology/Oncology

institute: Goethe University Hospital Frankfurt

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using Trim_galore version 0.6.4_dev
ChIP-seq reads were aligned to the ENSEMBL hg38 genome using Bowtie version 2.3.5.1.
To create ChIP-seq coverage representing continuous signals along the genome, the function "bamcoverage" from the tool "deepTools" was used and signal files in the bigwig format were created.
Peaks were called uing macs3 3.0.0a6 with the option BAMPE active because of paired end reads. Significance cut-off q-value <=0.2
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: SEM

growth_protocol: SEM cells were maintained in RPMI 1640 (RPMI-HA, Capricorn Scientific) supplemented with 10% FBS (FBS-11A, Capricorn Scientific), 2 mM L-glutamine (STA-B, Capricorn Scientific), 100 U/ml penicillin and 100 μg/ml streptomycin (PS-B, Capricorn Scientific). Cells were kept at 37°C in 5% CO2 and a relative humidity of 95%.

extract_protocol:
2x10^7 SEM::EGR3 underwent ChIP procedure as described by Kühn et al., 2016.
The ChIP-Seq library was prepared using the Accel-NGS® 2S plus DNA library kit (21024, Swift Biosciences) together with Swift Unique Dual Indexing Primer Kit (X9096, Swift Biosciences) and Accel-NGS 2S Truncated Adapters (28196, Swift Biosciences) according to the manufacturer’s recommendations with indexing by PCR (10 cycles).

value: SEM

value: B cell precursor leukemia

tag: chip antibody

value: DYKDDDDK Tag (D6W5B) Rabbit, monoclonal antibody, unconjugated, Cell Signaling Technology Cat# 14793, RRID:AB_2572292


title: SEM::EGR3 FLAG

value: DYKDDDDK Tag (D6W5B) Rabbit, monoclonal antibody, unconjugated, Cell Signaling Technology Cat# 14793, RRID:AB_2572291


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B2_S154]

description:
coculture24h_CART_NALM6_5to1_B2_S154
mRNA
052721_countmatrix_scRNAseq.csv


title: Col-0WT Rep4

value: WT


title: cvp2cvl1 Rep4


title: Col-0WT Rep1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B2_S10]

description:
coculture24h_CART_NALM6_5to1_B2_S10
mRNA
052721_countmatrix_scRNAseq.csv


title: Control2_Untreated

value: Healthy

value: Untreated


title: DCTNRAS SADBE 3

city: Charlestown

first: David

last: Fisher

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
All extracted RNA samples possessed RIN > 8.0 by Agilent TapeStation System with High Sensitivity RNA Screen Tape (Agilent Technologies) and proceeded for NGS library construction with Illumina Stranded mRNA Prep, Ligation kit (Illumina). Each amplified then bead-cleaned library was assessed for its quality and quantity by Agilent Tapestation with High Sensitivity D1000 ScreenTape and Qubit fluorometer 4.0.(Invitrogen), respectively. Each library was normalized at 4 nM, then pooled, denatured, and loaded onto the Illumina NextSeq550 at 2x74 base-pair specification. The generated FastQ files were processed under DRAGEN FastQC bioinformatic pipeline (Illumina) to assess the overall quality of the data for adapter contaminations or GC contents.  .We performed read alignment using STAR (PMID: 23104886), followed by transcript quantification using Salmon (PMID:28263959), and differential analysis using DESeq2 (PMID: 25516281) that compares SADBE-treated samples and control samples. The set of differentially expressed genes were determined using absolute LogFoldChange>1 and FDR<0.01. To investigate macrophage-related genes, we obtained macrophage gene lists from LM22 (PMID: 25822800) which include markers for macrophage states M0, M1, and M2. We also obtained from TIDE (PMID: 30127393) the gene correlation scores with tumor M2 macrophage level. For the systematic pathway analysis on differentially expressed genes, we performed gene-set enrichment analysis using R packages fgsea (doi: https://doi.org/10.1101/060012 )  and clusterProfiler ( doi: 10.1089/omi.2011.0118 )
Supplementary files format and content: csv: gene counts and salmon tpm
Supplementary files format and content: txt: Gene tpm with converted gene names

source_name: Skin

extract_protocol: RNeasy Plus Universal Kit

value: SADBE

value: DCT NRAS


title: MCT-PAH3_SGC-CBP30-Nebulization


title: Col-0WT Rep3


title: Col-0WT Rep2


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B1_S2]

description:
coculture24h_CART_NALM6_5to1_B1_S2
mRNA
052721_countmatrix_scRNAseq.csv


title: MCT-PAH2_Vehicle-Nebulization

value: Vehicle-Nebulization


title: DCTNRAS SADBE 2


title: Control3_Untreated


title: Control1_Untreated


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B1_S50]

description:
coculture24h_CART_NALM6_5to1_B1_S50
mRNA
052721_countmatrix_scRNAseq.csv


title: HiC_stage4_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: HiC experiment

data_processing:
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks). PUBMED: TADbit (28723903) and GEM (26094690)
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw and normalized counts at 100Kb resolution are stored as tab-separated files with chromosome in first column, coordinates of first bin as second column, and number of contacts to the second bin  of the same chromosome in the third column.
Assembly: mm10
Supplementary files format and content: Raw and normalized interaction matrices are stored in the following format:  chromosome, left-bin and right-bin positions (only cis interactions are included)

growth_protocol: Bone marrow lineage negative hematopoietic stem/progenitor cells from 8-10-week-old female mice were harvested and infected with high-titer retroviruses expressing either an empty PINCO-3xFlag vector or a PINCO–PML-RARa-3xFlag vector carrying human PML-RARa. GFP+ cells transformed with empty vector or PML-RARa-3xFlag vector were sorted by FACS and correspond to stage 0 and stage I, respectively. Stage I cells were then plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 2 weeks (stage II) and 4 weeks (stage III). In parallel, approximately 1 million of GFP+ PML-RARa-3xFlag transduced lineage negative cells (stage I) were transplanted via tail vein injection into lethally irradiated (9 Gy) syngeneic mice (129SvEv) . The animals were monitored periodically for signs of disease and presence of blasts as evaluated by complete blood counts (CBC) and peripheral blood smears. Leukemic mice were humanely euthanized and bone marrow blasts (Mac1+) were isolated for subsequent experiments (stage IV).

extract_protocol:
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547).
Libraries were prepared according to Illumina instructions.

value: Primary mouse bone marrow cells

tag: Stage

value: stage 4


title: HiC_stage2_R1

description: HiC experiment

source_name: Bone marrow lineage negative hematopoietic stem/progenitor cells from 8-10-week-old female mice

value: stage 2


title: MCT-PAH1_Vehicle-Nebulization


title: DCTNRAS Acetone 3

value: Acetone


title: HiC_stage1_R1

description: HiC experiment

value: stage 1


title: HiC_stage3_R1

description: HiC experiment

value: stage 3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S90]

description:
coculture24h_CART_NALM6_5to1_B12_S90
mRNA
052721_countmatrix_scRNAseq.csv

source_name: B-cell precursor leukemia cell line NALM-6

value: CAR T-cells


title: MCT-PAH3_Vehicle-Nebulization

value: Monocrotaline-induced pulmonary arterial hypertension (MCT-PAH)

value: Lung


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S46]

description:
coculture24h_CART_NALM6_5to1_B12_S46
mRNA
052721_countmatrix_scRNAseq.csv


title: RNAseq_KLF4-PMLRAR_OE

data_processing:
RNA-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm10) using TOPHAT (PubMed ID 22383036) with the option -g 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each RNA-seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome.
Assembly: mm10
Supplementary files format and content: Files *.bdg.gz (BedGraph, genome-wide RNA-seq)
Supplementary files format and content: RNAseq_KLF4_OE.bedgraph.gz
Supplementary files format and content: RNAseq_KLF4-PMLRAR_OE.bedgraph.gz

source_name: Bone marrow derived lineage-negative cells

growth_protocol: Cells have been growth in STEM span medium cytokine enriched and then spin-infected with KLF4-retroviral vectors. After 48 hours, GFP positive cells have been sorted.

extract_protocol:
RNA-seq: RNA extraction was performed using the miRNA kit (Qiagen) following manufacturer’s instruction.
Libraries were prepared according to Illumina instructions.

value: Lin-

tag: vector


title: HiC_stage4_R1

description: HiC experiment


title: Tumor Tyr-CreERT2 NrasQ61R/Q61R  147

description: Tumor Tyr-CreERT2 NrasQ61R/Q61R

data_processing: Extracted RNA quality was assessed by the Agilent Bioanalyzer system with Eukaryote Total RNA Pico assay (Agilent Technologies, Santa Clara, CA). The overall quantity was measured by Nanodrop 2000 Spectrophotometer followed by Quant-it RiboGreen RNA Assay (Promega, Madison, WI) to optimize inputs for NGS library construction. The maximum input of 1 ug was processed for library construction with Stranded total RNA with ligation with Ribozero plus kit (Illumina, San Diego, CA). Each amplified then bead-cleaned library was assessed for its quality and quantity by Agilent TapeStation with High Sensitivity D1000 ScreenTapes and Qubit fluorometer 4.0. (Invitrogen, Waltham, MA), respectively. Each library was normalized at 4 nM, then pooled, denatured, and loaded onto the Illumina NextSeq550 targeting 80 million reads per sample at 1x76 base-pair specification. The generated FastQ files were processed under DRAGEN FastQC bioinformatic pipeline (Illumina) to assess the overall quality of the data for adapter contaminations or GC contents. .We performed read alignment using STAR (PMID: 23104886), followed by transcript quantification using Salmon (PMID:28263959), and differential analysis using DESeq2 (PMID: 25516281) that compares SADBE-treated samples and control samples. The set of differentially expressed genes were determined using absolute LogFoldChange>1 and FDR<0.01. To investigate macrophage-related genes, we obtained macrophage gene lists from LM22 (PMID: 25822800) which include markers for macrophage states M0, M1, and M2. We also obtained from TIDE (PMID: 30127393) the gene correlation scores with tumor M2 macrophage level. For the systematic pathway analysis on differentially expressed genes, we performed gene-set enrichment analysis using R packages fgsea (doi: https://doi.org/10.1101/060012 )  and clusterProfiler ( doi: 10.1089/omi.2011.0118 )

source_name: Tumor

extract_protocol: RNA FFPE Miniprep kit (Zymo Research, Irvine, CA)

value: Tyr-CreERT2 NrasQ61R/Q61R

value: Tumor


title: HiC_stage3_R2

description: HiC experiment


title: DCTNRAS Acetone 2


title: HiC_stage1_R2

description: HiC experiment


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B1_S146]

description:
coculture24h_CART_NALM6_5to1_B1_S146
mRNA
052721_countmatrix_scRNAseq.csv

data_processing:
Adapter trimming was performed using trimmomatic version 0.36. Sequence quality was assessed using fastqc version 0.11.5. Sequencing reads were aligned to the human genome using STAR version 2.5.2b using following parameters ‘-- twopassMode Basic --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5'.
Raw counts were obtained from aligned bam files using htseq version 0.9.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: scRNA-Seq: 052721_countmatrix_scRNAseq.csv: HTSeq count matrix with raw counts for all individual cells.
Supplementary_files_format_and_content: scATAC-Seq: 052721_countmatrix_scATACseq.csv: Fragments file with fragments for all individual cells; raw counts.

extract_protocol:
Single cells were directly sorted into 96 well plates containing TCL buffer.
Full-length single-cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B1_S228]

description:
coculture24h_CART_NALM6_5to1_B1_S228
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S378]

description:
coculture24h_CART_NALM6_5to1_B12_S378
mRNA
052721_countmatrix_scRNAseq.csv


title: Tumor Tyr-CreERT2 NrasQ61R/Q61R  138

description: Tumor Tyr-CreERT2 NrasQ61R/Q61R


title: RNAseq_Stage4_Replicate1

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles  were normalized by the total number of reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm10 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. RNA-seq genome-wide profiles  were normalized by the total number of reads of each sample in plus and minus strands.
Genome_build: mm10
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)

extract_protocol:
(ChIP-seq)  ChIP experiments were carried out following a standard protocol in the lab (PubMed ID: 30224650)
(RNA-seq) RNA was extracted with the RNeasy kit (Qiagen) following manufacturer's instructions
Libraries were prepared according to Illumina instructions.


title: 4Fd5

type: genomic

description: SAMPLE 4

hyb_protocol: Bisulphite converted DNA was anplified, fragmented and hybridised to Illumina Infinium Methyl EPIC BeadChip.

scan_protocol: Arrays were imaged using iScan using standardrecommended Illumina scanner setting.

data_processing: R program (version 3.3.2) using minfi package (version 12.0.2) provided through Bioconductor.

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from cells using Quick gene DNA tissue kit.

treatment_protocol: Cells were treated with 4F at 0.25 nM twice a day for 3 or 5 days and maintained in Cellartis MSC Xeno-Free Basal Medium under humidified conditions with 5% CO2 for additional 2 days. For control cells, cells were treated with NE at 0.25 nM twice a day for 5 days and maintained in Cellartis MSC Xeno-Free Basal Medium under humidified conditions with 5% CO2 for additional 2 days.

value: umbilical cord derived

value: 4F day5


title: RNAseq_Stage3_Replicate2


title: HiC_stage0_R2

description: HiC experiment

value: stage 0


title: DCTNRAS SADBE 1

value: SADBE

value: DCT NRAS


title: HiC_stage2_R2

description: HiC experiment

value: Primary mouse bone marrow cells


title: DCTNRAS Acetone 1


title: HiC_stage0_R1

description: HiC experiment


title: NE

description: SAMPLE 2


title: Tumor Tyr-CreERT2 NrasQ61R/Q61R  2

description: Tumor Tyr-CreERT2 NrasQ61R/Q61R


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S300]

description:
coculture24h_CART_NALM6_5to1_B12_S300
mRNA
052721_countmatrix_scRNAseq.csv


title: RNAseq_Stage4_Replicate2


title: 4Fd3

description: SAMPLE 3

value: 4F day3


title: ear Skin Tyr-CreERT2 (normal skin control) TRY1L

value: Ear


title: ChIPseq_InputforH3K27ac_stage3


title: NC

description: SAMPLE 1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S234]

description:
coculture24h_CART_NALM6_5to1_B12_S234
mRNA
052721_countmatrix_scRNAseq.csv


title: RNAseq_Stage2_Replicate2


title: ear Skin Tyr-CreERT2 (normal skin control) TRY2L


title: RNAseq_KLF4_OE


title: ChIPseq_Input_stage4


title: ear Skin Tyr-CreERT2 (normal skin control) TRY3L


title: RNAseq_Stage3_Replicate1


title: RNAseq_Stage2_Replicate1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S186]

description:
coculture24h_CART_NALM6_5to1_B12_S186
mRNA
052721_countmatrix_scRNAseq.csv


title: RNAseq_Stage1_Replicate2


title: ChIPseq_Input_stage1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B3_S10]

description:
coculture24h_CART_NALM6_5to1_B3_S10
mRNA
052721_countmatrix_scRNAseq.csv


title: Tumor Dct-Cre NrasQ61R/+ 159

description: Tumor Dct-Cre NrasQ61R/+

value: Dct-Cre NrasQ61R/+


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B12_S138]

description:
coculture24h_CART_NALM6_5to1_B12_S138
mRNA
052721_countmatrix_scRNAseq.csv


title: RNAseq_Stage1_Replicate1


title: RNAseq_Stage0_Replicate2


title: RNAseq_Stage0_Replicate1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S226]

description:
coculture24h_CART_NALM6_5to1_B11_S226
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S42]

description:
coculture24h_CART_NALM6_5to1_B11_S42
mRNA
052721_countmatrix_scRNAseq.csv


title: ear Skin Tyr-CreERT2 NrasQ61R/Q61R  82M10L

description: ear Skin Tyr-CreERT2 NrasQ61R/Q61R


title: ChIPseq_H3K4me1_stage3

value: Abcam, ab8895


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S370]

description:
coculture24h_CART_NALM6_5to1_B11_S370
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_InputforH3K27ac_stage2


title: ChIPseq_InputforH3K27ac_stage1


title: ear Skin Tyr-CreERT2 NrasQ61R/Q61R  L62F3

description: ear Skin Tyr-CreERT2 NrasQ61R/Q61R


title: ChIPseq_InputforH3K27ac_stage0


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S294]

description:
coculture24h_CART_NALM6_5to1_B11_S294
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_H3K4me1_stage1


title: Normal B6 ear Skin B63L

description: Normal B6 ear Skin


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S362]

description:
coculture24h_CART_NALM6_5to1_B10_S362
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_Input_stage3


title: ear Skin Tyr-CreERT2 NrasQ61R/Q61R  L15F6

description: ear Skin Tyr-CreERT2 NrasQ61R/Q61R


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S288]

description:
coculture24h_CART_NALM6_5to1_B10_S288
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_H3K4me3_stage3

value: Diagenode, C15410003


title: ChIPseq_Input_stage2


title: Normal B6 ear Skin B61L

description: Normal B6 ear Skin


title: Tumor Dct-Cre NrasQ61R/+ 160

description: Tumor Dct-Cre NrasQ61R/+


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S130]

description:
coculture24h_CART_NALM6_5to1_B11_S130
mRNA
052721_countmatrix_scRNAseq.csv

value: CAR T-cells


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B11_S178]

description:
coculture24h_CART_NALM6_5to1_B11_S178
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_H3K4me1_stage4


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S170]

description:
coculture24h_CART_NALM6_5to1_B10_S170
mRNA
052721_countmatrix_scRNAseq.csv


title: ear Skin Dct-Cre NrasQ61R/+ 155

description: ear Skin Dct-Cre NrasQ61R/+


title: ChIPseq_H3K4me1_stage2


title: Tumor Dct-Cre NrasQ61R/+ 148

description: Tumor Dct-Cre NrasQ61R/+


title: ChIPseq_Input_stage0


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S38]

description:
coculture24h_CART_NALM6_5to1_B10_S38
mRNA
052721_countmatrix_scRNAseq.csv


title: ear Skin Dct-Cre NrasQ61R/+ 153

description: ear Skin Dct-Cre NrasQ61R/+


title: ChIPseq_H3K4me3_stage2


title: ChIPseq_H3K4me1_stage0


title: ChIPseq_H3K4me3_stage4


title: ChIPseq_H3K27me3_stage0

value: Millipore, 07-449


title: ChIPseq_H3K4me3_stage1


title: ChIPseq_H3K27ac_stage4

value: Millipore 07-360


title: ear Skin Dct-Cre NrasQ61R/+ 169

description: ear Skin Dct-Cre NrasQ61R/+


title: ChIPseq_H3K27ac_stage1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A9_S113]

description:
coculture24h_CART_NALM6_5to1_A9_S113
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S218]

description:
coculture24h_CART_NALM6_5to1_B10_S218
mRNA
052721_countmatrix_scRNAseq.csv


title: ChIPseq_H3K4me3_stage0


title: ChIPseq_H3K27ac_stage0


title: ChIPseq_H3K27me3_stage4


title: Bangor_Tank_Riverine_2_WGBS

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

institute: University of Basel

description:
Total DNA from homogenized tissue
Riverine_tank_n2_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)

data_processing:
RNAseq reads were mapped to MZ_UMD2a and transcript expression values (tpm) were calculated using kallisto (see methods)
WGBS and RRBS reads were mapped to MZ_UMD2a and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see Methods).
Genome_build: GCF_000238955.4_M_zebra_UMD2a_genomic.fa
Supplementary_files_format_and_content: bw files containing mean mCG/CG levels averaged over 50bp non-overlapping bins and across samples for each group. Only CG with ≥4x coverage were used.
Supplementary_files_format_and_content: GeneQuant_tpm_Masoko_wild_liver.txt contains gene expression values (tpm) for all RNAseq samples.
Supplementary_files_format_and_content: Common_mCG_RRBS.txt file contains methylation values at common CG sites across all RRBS samples (min. 4x coverage in all CGs of all samples)

organism: Astatotilapia calliptera

source_name: homogenized adult liver

extract_protocol:
Genomic DNA extracted using silica column based approach (see methods)
DNA strand-specific library using methylated adaptor (NEB) followed by bisulfite conversion (Imprint, Sigma), according to manusfacturer's instructions. WGBS libraries contain lambda genome spike-in control (0.2% w/w).

tag: ecomoprh

value: Riverine

tag: Sex

value: male

tag: type

value: tank-reared

value: liver


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A8_S57]

description:
coculture24h_CART_NALM6_5to1_A8_S57
mRNA
052721_countmatrix_scRNAseq.csv

tag: cell line

tag: treatment


title: ChIPseq_H3K27me3_stage3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [B10_S122]

description:
coculture24h_CART_NALM6_5to1_B10_S122
mRNA
052721_countmatrix_scRNAseq.csv

tag: library strategy


title: ChIPseq_H3K27me3_stage2


title: Normal B6 ear Skin B62L

description: Normal B6 ear Skin

tag: tissue


title: ChIPseq_H3K27me3_stage1


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A9_S281]

description:
coculture24h_CART_NALM6_5to1_A9_S281
mRNA
052721_countmatrix_scRNAseq.csv


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A8_S201]

description:
coculture24h_CART_NALM6_5to1_A8_S201
mRNA
052721_countmatrix_scRNAseq.csv


title: Glucose+Catechol RepB (Strss)

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

hyb_protocol: Agilent hybridisation kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing:
GeneSpring 14.9 GC, Feature extraction,
Normalization: Shift to 75.0 percentile
Baseline Transformation: median of all samples
Statistical analysis (moderated t-test, Benjamini-Hochberg FDR, p_corr < 0.05, 2fold change), export

organism: Pseudomonas putida KT2440

source_name: cell biomass

label_protocol: Agilent labeling kit (one color)

growth_protocol: baffeled 1L shake flask, 100 mL E2 minimal medium (40 mM glucose), 30°C, 230 rpm, initial OD600 = 0.4

extract_protocol: mRNA extracted from harvested cell pellets (2 mg DCW) using Qiagen RNeasy kit and Turbo DNAfree kit

treatment_protocol: cells (2 mg) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

tag: treatment/time point

value: after 1h of 5 mM catechol addition

tag: sample group

value: catechol shock


title: Bangor_Tank_Benthic_1_WGBS

description:
Total DNA from homogenized tissue
Benthic_tank_n2_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)

value: Benthic


title: ChIPseq_H3K27ac_stage3


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A9_S161]

description:
coculture24h_CART_NALM6_5to1_A9_S161
mRNA
052721_countmatrix_scRNAseq.csv


title: Glucose RepC (Ctrl)

value: OD2 before catechol addition

value: exponential growth


title: Glucose+Catechol RepA (Strss)


title: ChIPseq_H3K27ac_stage2

value: Primary mouse bone marrow cells


title: G10E07_wild_Benthic_2_run2_WGBS

description:
Total DNA from homogenized tissue
Benthic_wild_n3_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)

value: wild caught


title: Glucose+Catechol RepC (Strss)


title: Bangor_Tank_Riverine_1_WGBS


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A8_S275]

description:
coculture24h_CART_NALM6_5to1_A8_S275
mRNA
052721_countmatrix_scRNAseq.csv


title: G09D05_wild_Riverine_2_run2_WGBS

description:
Total DNA from homogenized tissue
Riverine_wild_n2_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)


title: NALM-6_CARTtreated_24h_SMARTseq2_0001 [A7_S97]

description:
coculture24h_CART_NALM6_5to1_A7_S97
mRNA
052721_countmatrix_scRNAseq.csv