title: Sample at remission [Constitutional_458rep3]

description:
HiSeq 2000
RNAseq_read_counts.txt

value: male


title: TO_1700

status: Public on Oct 17 2023

type: SRA

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

library_source: transcriptomic single cell

data_processing:
The sequenced data were preprocessed and quantified for gene expression using STAR aligner (v2.5.1b) and RSEM (v1.3.1) tool.
Assembly: GRCh38-3.0.0
Supplementary files format and content: text file includes TPM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Bilaminoid D6

extract_protocol:
Bilaminoids (D6) were manually picked. Each bilaminoid was transferred in a drop of Accutase and incubated at 37℃ for 15-20 min, then dissociated into single cells by repeated pipetting using glass capillaries. Each single cell was transferred into individual PCR tubes and immediately frozen in Smart-seq HT lysis buffer. To collect amnion-like cells(AMLCs), PGC-like cells(PGCLCs), and hematoendothelial progenitor-like cells(HEPLCs), CER1-GFP+ anterior visceral endoderm-like cells(AVELCs) were sorted as single-cells and immediately frozen in Smart-seq HT lysis buffer.
The libraries for scRNA-seq were prepared using the SMART-seq HT kit (Z4436N, Takara), following the manufacture’s instruction. The libraries were then sequenced on an NovaSeq 6000 or NextSeq 2000 with paired-end sequencing.

tag: analysis method

value: scRNA-seq

tag: cell line

value: H9 ESCs

tag: cell type

value: Bilaminoid Day6

tag: protocol

value: manual cell picking


title: ALL sample at diagnosis [ALL_985]

city: Uppsala

first: Olga

last: Krali

address: Husargatan 3

country: Sweden

institute: Uppsala University

description:
HiSeq 2500
RNAseq_read_counts.txt

library_source: transcriptomic

data_processing:
The raw sequencing data were processed together using the nextflow-based (21.02.0.edge) nf-core/rnaseq (3.0) pipeline
The sequencing paired-end reads were trimmed by trimgalore (0.6.6)
Alignment to GRCh38 reference genome with ENSEMBL gene annotation (GRCh38.103) was conducted with STAR
Quantification of the aligned reads at transcript level took place with the help of Salmon (1.4.0)
Transcript level expression values were summarized to gene level with the bioconductor package tximeta (1.8.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw count values for each Sample

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
The RNA was extracted using the AllPrep kit (Qiagen).
RNA sequencing libraries were prepared using the Illumina TruSeq stranded Total RNA (RiboZero human/mouse/rat) kit, Illumina TruSeq RNA Access library preparation kit or Script-Seq kit (EpiCentre), as indicated in each sample information.

tag: tissue

value: Bone Marrow/Peripheral Blood

tag: disease

value: childhood B acute lymphoblastic leukemia

tag: disease state

value: diagnosis

tag: genotype

value: Unclassified BCP-ALL

tag: revised (predicted)_genotype

tag: Sex

value: female

tag: library protocol

value: RNAaccess


title: TO_1697


title: TO_1661


title: ALL sample at diagnosis [ALL_905]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1081]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [KSALL50]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: ALL sample at diagnosis [ALL_S1]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: ALL sample at diagnosis [ALL_1065]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: TruSeq


title: ALL sample at diagnosis - technical replicate 2 [ALL_468_2]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1658


title: TO_1669


title: TO_1724


title: TO_1721


title: TO_1657


title: TO_1640


title: ALL sample at diagnosis [ALL_1062]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1639


title: TO_1638


title: ALL sample at diagnosis [ALL_853]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1023]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1056]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1635


title: TO_1636


title: ALL sample at diagnosis [ALL_1005]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_784]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ALL sample at diagnosis [ALL_170]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1633


title: ALL sample at diagnosis [ALL_761]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1628


title: TO_1656


title: ALL sample at diagnosis [ALL_1039]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1625


title: TO_1622


title: TO_1631


title: ALL sample at diagnosis [ALL_501]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_76]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1026]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1620


title: ALL sample at diagnosis [ALL_604]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1621


title: ALL sample at diagnosis [ALL_829]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1651


title: ALL sample at diagnosis [ALL_808]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_9]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1601


title: TO_1607


title: TO_1599


title: ALL sample at diagnosis [ALL_298]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1598


title: TO_1596


title: ALL sample at diagnosis [ALL_967]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_45]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_986]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_710]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1595


title: TO_1594


title: ALL sample at diagnosis [ALL_944]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1588


title: ALL sample at diagnosis [ALL_942]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1586


title: TO_1592


title: TO_1585


title: TO_1587


title: ALL sample at diagnosis [ALL_17]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_709]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1561


title: ALL sample at diagnosis [ALL_541]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1564


title: ALL sample at diagnosis [ALL_978]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1565


title: TO_1554


title: ALL sample at diagnosis [ALL_976]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_930]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_952]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1544


title: TO_1539


title: TO_1553


title: ALL sample at diagnosis [ALL_168]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_907]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_175]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_564]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1523


title: TO_1533


title: ALL sample at diagnosis [ALL_926]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_901]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_180]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: TO_1509


title: TO_1508


title: ALL sample at diagnosis [ALL_884]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1507


title: TO_1512


title: ALL sample at diagnosis [ALL_543]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_499]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_586]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_717]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1503


title: ALL sample at diagnosis [ALL_593]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_169]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: Ped011

city: St Louis

first: Jichang

last: Han

state: MO

address: 4905 Children's PI

country: USA

institute: Washington University in St Louis

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneal cavity

extract_protocol:
Peritoneal wash was collected at the beginning of the procedure before it was affected by the surgical process. Briefly, about 1 L (for adults) or 200 mL (for children) of sterile saline was flushed into the human peritoneal cavity and the abdomen was massaged for 2 minutes for a thorough wash before the saline containing peritoneal cells were vacuumed out. Live CD45+ immune cells were then FACS sorted for library preparation.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit

value: peritoneal cavity

value: CD45+ immune cell

tag: surgical procedure

value: laparoscopic inguinal hernia repair

tag: age range

tag: gender

value: Female


title: ALL sample at diagnosis [ALL_47]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: TO_1502

value: scRNA-seq

value: H9 ESCs

value: Bilaminoid Day6

value: manual cell picking


title: Ped010

description: 10x Genomics

value: laparoscopic cholecystectomy


title: ALL sample at diagnosis [ALL_24]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_382]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: ALL sample at diagnosis [ALL_357]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female


title: Ped007

description: 10x Genomics

value: Male


title: ALL sample at diagnosis [ALL_16]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_219]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: ALLIUM B-other

value: RNAaccess


title: Ped006

description: 10x Genomics

value: peritoneal cavity

value: CD45+ immune cell

value: laparoscopic G tube placement


title: ALL sample at diagnosis [ALL_567]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: TO_1538

value: scRNA-seq


title: ALL sample at diagnosis [ALL_598]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: male


title: Ped004

description: 10x Genomics

value: laparoscopic converted to open cholecystectomy


title: TO_1506

value: H9 ESCs

value: Bilaminoid Day6

value: manual cell picking


title: ALL sample at diagnosis [ALL_7]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia


title: Ped002

description: 10x Genomics

value: laparoscopic inguinal hernia repair

value: Female


title: ALL sample at diagnosis [ALL_62]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: diagnosis

value: Unclassified BCP-ALL


title: Adu007

description: 10x Genomics

value: Laparoscopic RYGB

value: Male


title: ALL sample at diagnosis [ALL_293]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female

value: ScriptSeq


title: Adu006

description: 10x Genomics

value: peritoneal cavity

value: CD45+ immune cell


title: Adu005

description: 10x Genomics

value: Laparoscopic  sleeve gastrectomy


title: Adu004

description: 10x Genomics

value: Laparoscopic inguinal hernia repair


title: ALL sample at diagnosis [ALL_164]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: male

value: RNAaccess


title: Ped009

description: 10x Genomics

value: laparoscopic fundoplication


title: ALL sample at diagnosis [ALL_878]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: ALLIUM B-other

value: TruSeq


title: Ped008

description: 10x Genomics

value: laparoscopic cholecystectomy


title: ALL sample at diagnosis [ALL_503]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: HeH


title: ALL sample at diagnosis [ALL_492]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_28]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: Adu002

description: 10x Genomics

value: Heller

value: Female


title: ALL sample at diagnosis [ALL_494]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female

value: ScriptSeq


title: ALL sample at diagnosis [ALL_167]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1116]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1159]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: low HeH


title: ALL sample at diagnosis [ALL_202]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_217]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: ALL sample at diagnosis [ALL_1139]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1136]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_317]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: RNAaccess


title: Ped001

description: 10x Genomics

value: peritoneal cavity

value: CD45+ immune cell

value: laparoscopic G tube placement

value: Male


title: ALL sample at diagnosis [ALL_218]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia


title: ALL sample at diagnosis [ALL_1162]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: diagnosis

value: TruSeq


title: ALL sample at diagnosis [ALL_1131]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_1127]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_513]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_4]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_482]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ALL sample at diagnosis [ALL_1187]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_validation_12]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: female


title: ALL sample at diagnosis [ALL_488]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: ALL sample at diagnosis [ALL_1178]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_371]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_629]

description:
HiSeq 2500
RNAseq_read_counts.txt

value: ALLIUM B-other


title: ALL sample at diagnosis [ALL_1058]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1099]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_877]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_874]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1109]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_244]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_319]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1118]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_247]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_368]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_351]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1096]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_444]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1111]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_246]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1086]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_882]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_58]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1019]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_389]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1057]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: low HeH


title: ALL sample at diagnosis [ALL_1034]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_1001]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_172]

description:
HiSeq 2500
RNAseq_read_counts.txt


title: ARC CCI-ION sample 2

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

country: China

institute: Soochow University

data_processing:
Illumina HiseqX system software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using bowtie v1.1.1 with parameters -f -p 20
Use cutadapt (version 1.14) software to remove the connector sequence, fastx_ Toolkit (version 0.0.13) software for quality control of sequences, NGSQCToolkit (version 2.3.3) to filter out reads containing N bases, fastx_ The toolkit (version 0.0.13) to count the number of types of clean reads.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

organism: Rattus norvegicus

source_name: Hypothalamic arcuate nucleus

extract_protocol:
Hypothalamic arcuate nucleus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A trigeminal neuropathic pain model was produced by CCI-ION. After anesthetization, the left ION was dissected near the infraorbital foramen using glass rods. Two loose ligatures (4-0 silk) were placed around the ION using fine forceps. The sham-operated rats received only unilateral nerve exposure using the same procedure without ligation.

tag: strain

value: Sprague-Dawley

value: Hypothalamic arcuate nucleus

tag: age

value: 8-10 weeks

tag: treatment

value: CCI-ION-operation

tag: molecule subtype

value: microRNA


title: ARC CCI-ION sample 3


title: ALL sample at diagnosis [ALL_1031]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_386]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_762]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ARC sham sample 3

value: sham-operation


title: ARC CCI-ION sample 1


title: ALL sample at diagnosis [ALL_388]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: ALL sample at diagnosis [ALL_984]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: TruSeq


title: ALL sample at diagnosis [ALL_125]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ALL sample at diagnosis [ALL_975]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_1000]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: female


title: ARC sham sample 2


title: ALL sample at diagnosis [ALL_988]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ARC sham sample 1


title: ALL sample at diagnosis [ALL_1003]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_61]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: ALL sample at diagnosis [ALL_964]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: ALLIUM B-other


title: ALL sample at diagnosis [ALL_962]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Hh, 1h, biol rep4

city: Shanghai

first: xiufang

last: xin

address: Xuhui

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with default settings.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2(http://ccb.jhu.edu/software/hisat2/index.shtml) software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method.RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: TAIR 10
Supplementary files format and content: Read counts for genes (TAIR 10) were provided.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants  were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.

extract_protocol:
Total mRNA was extracted from leaves using Trizol reagent. Total RNA was treated with DNase I to remove DNA, and purified RNA was recovered with RNeasy® MinElute™ Cleanup kit. A total amount of 1 μg RNA per sample was used as input material for library preparation and Illumina sequencing.
Sequencing libraries were generated using TruSeq™ RNA Library Prep Kit for Illumina®  following manufacturer’s recommendations and sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The 3.5-4 weeks old plants were placed in three chambers, in which humidity was set to 40-45% RH (for low humidity treatment) , 55-60% RH (for moderate humidity treatment) and 95% RH (for high humidity treatment). Temperature was set at 22℃ and photoperiod at 12 h light/12 h dark in all chambers. The plants were treated with different humidity for 1 h.

value: leaf

value: Four-week-old

value: WT

value: Hh, 1h


title: ALL sample at diagnosis [ALL_52]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_1006]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Hh, 1h, biol rep3


title: ALL sample at diagnosis [ALL_57]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_941]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_920]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_913]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_931]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: low HeH


title: ALL sample at diagnosis [ALL_953]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: ALL sample at diagnosis [ALL_113]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia


title: Hh, 1h, biol rep2


title: ALL sample at diagnosis [ALL_950]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_403]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: Mh, 1h, biol rep4

value: Mh, 1h


title: ALL sample at diagnosis [ALL_753]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia


title: Hh, 1h, biol rep1


title: ALL sample at diagnosis [ALL_903]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: diagnosis


title: ALL sample at diagnosis [ALL_378]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: T-ALL


title: Mh, 1h, biol rep3


title: ALL sample at diagnosis [ALL_71]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: TruSeq


title: ALL sample at diagnosis [ALL_888]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_562]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: female


title: Mh, 1h, biol rep2


title: ALL sample at diagnosis [ALL_29]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH

value: ScriptSeq


title: ALL sample at diagnosis [ALL_718]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_234]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Lh, 1h, biol rep4

value: leaf

value: Lh, 1h


title: ALL sample at diagnosis [ALL_63]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: Mh, 1h, biol rep1

value: Four-week-old

value: WT


title: ALL sample at diagnosis [ALL_569]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_11]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_474]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_232]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Lh, 1h, biol rep3


title: ALL sample at diagnosis [ALL_568]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_560]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_477]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: ALLIUM B-other


title: Lh, 1h, biol rep1


title: ALL sample at diagnosis [ALL_174]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: ALL sample at diagnosis [ALL_324]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: Lh, 1h, biol rep2


title: ALL sample at diagnosis [ALL_312]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_194]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_456]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_584]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: sac3b atxr56 CaLCuV inoculated rep2

city: college station

first: Zhen

last: Wang

state: Texas

address: 300 Olsen Blvd,

department: Department of Biochemistry & Biophysics

institute: Texas A & M University

data_processing:
Adapter sequence is trimmed by Trimmomatic/0.39-Java-11 with parameter
Reads were filter with parameter:fa:2:30:10LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Trimmed sequence were mapped to TAIR10 with HISAT2/2.1.0-foss-2018b (default parameter)
Reads count was performed with HTSeq/0.9.1-intel-2017A-Python-2.7.12 (defulat parameter)
Comparasion was performed with DE-seq2
Assembly: Tair 10
Supplementary files format and content: txt files with raw reads count for each sample

source_name: rossete leaves

growth_protocol: A. thaliana plants were grown under cool-white, fluorescent light (120 μmol m-2 s-1) in a short day condition (8 h light/ 16 dark) with 22℃ and 50% humidity.

extract_protocol:
Total RNA was extracted from virus-inoculated and mock-treated plants at 16 dpi with TRIzol and then treated with TURBO Dnase (Thermo Fisher, AM2238).
Messager RNA was enriched with Dynabeads™ Oligo(dT)25 (InvitrogenTM, 61005) according to the manufacturer’s manual. First strand synthesis was completed with Random primer (Invitrogen™, 48190011), RNaseIn (Invitrogen™, AM2696), SuperScript™ III Reverse Transcriptase (Invitrogen™, 18080044) after fragmentation. Second strand synthesis was conducted with dUTP mixure (20mM dUTP, 10mM dATP, dCTP, and dGTP), RNase H (NEB, M0297), DNA polymerase I (NEB, M0209) and E coli DNA ligase (NEB, M0205). End repair was conducted with NEBNext UltraTM End repair/dA-Tailling Module (NEB, E7442) followed by the adapter ligation with ligation mix and adapter (Illumina, TruSeq Kits, 15026773) according to the manufacturer’s manual. Enriched mRNA from 1 μg total RNA was used as starting material and 15 cycles were used to amplify library.

treatment_protocol: Plants were grown on MS plate under 8-h light/16-h dark condition for 10 days and then transferred to soil under 8-h light/16-h dark condition for around 14 days to reach eight-true -leaf developmental stage. Plants with different genotypes were infected by agroinfiltration of CaLCuV infective clones of PNSB1090 DNAA and PNSB1091 DNAB. The symptoms of plants were monitored and evaluated daily since we began to observe the yellow mosaic and chlorosis in viral infected plants.

value: rossete leaves

value: sac3b atxr5 atxr6

value: virus inoculated


title: ALL sample at diagnosis [ALL_130]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: sac3b atxr56 CaLCuV inoculated rep1


title: ALL sample at diagnosis [ALL_595]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: TruSeq


title: ALL sample at diagnosis [ALL_485]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_589]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_248]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_262]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female


title: mbd9 atxr56 CaLCuV inoculated rep2

value: mbd9 atxr5 atxr6


title: ALL sample at diagnosis [ALL_236]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_254]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL

value: ScriptSeq


title: ALL sample at diagnosis [ALL_215]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: mbd9 atxr56 CaLCuV inoculated rep1


title: ALL sample at diagnosis [ALL_544]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_200]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_514]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_529]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_462]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ALL sample at diagnosis [ALL_106]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_141]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_160]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_420]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_410]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: PAX5 P80R


title: atxr56 CaLCuV inoculated rep2

value: atxr5 atxr6


title: ALL sample at diagnosis [ALL_465]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_206]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_221]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_284]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: atxr56 CaLCuV inoculated rep1

value: rossete leaves


title: ALL sample at diagnosis [ALL_321]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: brca1 atxr56 CaLCuV inoculated rep1

value: brca1 atxr5 atxr6


title: ALL sample at diagnosis [ALL_412]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Col-0 CaLCuV inoculated rep2

value: WT

value: virus inoculated


title: ALL sample at diagnosis [ALL_157]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: ALL sample at diagnosis [ALL_602]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Unclassified BCP-ALL

value: TruSeq


title: Col-0 CaLCuV inoculated rep1


title: brca1 atxr56 CaLCuV inoculated rep2


title: ALL sample at diagnosis [ALL_313]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female


title: ALL sample at diagnosis [ALL_468]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_665]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_646]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_606]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_528]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: ALLIUM B-other


title: sac3b atxr56 Mock treated rep1

value: sac3b atxr5 atxr6

value: Mock treated


title: ALL sample at diagnosis [ALL_431]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_381]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: ALL sample at diagnosis [ALL_621]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_747]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_745]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_373]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_734]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: mbd9 atxr56 Mock treated rep1

value: mbd9 atxr5 atxr6


title: brca1 atxr56 Mock treated rep2


title: ALL sample at diagnosis [ALL_713]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: low HeH


title: ALL sample at diagnosis [ALL_750]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_395]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_557]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: brca1 atxr56 Mock treated rep1


title: ALL sample at diagnosis [ALL_532]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: sac3b atxr56 Mock treated rep2


title: ALL sample at diagnosis [ALL_435]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: ALL sample at diagnosis [ALL_489]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_422]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_609]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_644]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: PAX5 P80R


title: ALL sample at diagnosis [ALL_740]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_683]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_656]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: mbd9 atxr56 Mock treated rep2

value: rossete leaves


title: ALL sample at diagnosis [ALL_268]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Col-0 Mock treated rep2

value: WT


title: ALL sample at diagnosis [ALL_686]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_613]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_460]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_402]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Col-0_Mock_rep2_RPA1A

library_source: genomic

data_processing:
Adapter sequence is trimmed by Trimmomatic/0.39-Java-11 with parameter
The leftover reads later were mapped by bowtie2 (ver. 2.4.4) with perfect matches using Arabidopsis genome TAIR10 (http://www. arabidopsis.org/) as a reference genome. Reads uniquely mapped to genome and reads mapped to multiple locations in the genome were separately extracted by Samtools (ver. 1.15.1) for distinct downstream peak calling analyses. MACS2 (ver. 2.2.5) was used for ChIP-seq peak calling using default parameters, both narrowPeak and broadPeak were called for each sample.
We used the reads mapping to genome which contain sequence mapped to multiple locations in the genome to perform the ChIP signal profile, peak number, peak reads percentage analysis and comparative analysis with DESeq2 (ver.3.15)
The peaks belonging to distinct categories were first extracted with Samtools69, and then reads over peaks from distinct categories were counted with Subread feature Counts (ver. 2.0.0). Total reads of peaks from specific categories were divided by total reads of peaks from all categories to generate peak reads percentages for individual specific categories.
Peaks with P-value < 0.05 were selected for the following analysis, narrowPeak and broadPeak were merged by bedtools
Assembly: Tair 10
Supplementary files format and content: bigWig with noramlized RPKM

molecule: genomic DNA

extract_protocol:
Three grams of materials were crosslinked with 1% formaldehyde for 20 min by vacuum infiltration at 4 degree, and the reaction was stopped with a final concentration of 100 mM Glycine by vacuum infiltration for 10 min at 4 degree. Plants were rinsed 5 times with pre-chilled sterilized water, flash-frozen in liquid nitrogen, and thoroughly grounded with TissueLyser II (QIAGEN, 85300). The powder was suspended in pre-chilled 6 volume (1.5 g with 9 ml) nuclei isolation buffer (15 mM PIPES-KOH pH 6.8, 0.25 M sucrose, 0.9% Triton X-200, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 1 mM PMSF, 1 pellet/50 ml EDTA free Protease inhibitor [Roche] and 25 μM MG132) on ice for 6 min. The mixture was filtered through two-layer of Miracloth and centrifuged at 11000 g for 10min at 4 ℃ and carefully rinsed with 2 ml nuclei isolation buffer after discarding the supernatant. The white pellet was resuspended with 1 ml nuclei lysis buffer (40 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.2% SDS, 0.1% Sodium Deoxycholate, 0.6% Triton X-100, 1 mM PMSF, 1 pellet/50 ml EDTA free Protease inhibitor [Roche] and 25 μM MG132) on ice for 6 min and then sonicated with 30 s ON and 60 s OFF for 16 cycles with Bioruptor Pico sonication device (Diagenode SA, B01060010) at 4 ℃.  Supernatant was collected after centrifuge for 10 min at 15000 rpm at 4 ℃ and diluted with the same volume nuclei dilution buffer (40 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM EDTA. 0.2% Triton X-100, 1 mM PMSF, 1% Glycerol, 1 pellet/50 ml EDTA free Protease inhibitor [Roche] and 25 μM MG132). 100 μl diluted mixture was used as input, then the rest was split into two tubes with addition of 30 μl prewashed Protein A Agarose beads (Sigma, 11134515001), 3 μg anti-RAD51 (PHYTOAB, PHY1804A) and 3 μg anti-RPA1A (PHYTOAB, PHY1813S), and incubated at 4 degree with mild rotation for 6 hours.  The beads-protein-DNA complex was washed as previously described. Elution was repeated twice at 1200 rpm, 65 ℃ with 250 μl elution buffer (0.1 M NaHCO3, 1% SDS) for 30 min. De-crosslinking was performed with 100 NaCl at 65 ℃ for 12 hour, followed by Rnase A treatment and Protease K treatment. Purification was performed with phenol:chlorophorm:isoamyl alcohol (25:24:1, pH 8.0), precipitation of DNA was performed with 1/10 volume of 3 M sodium citrate (pH 5.2), 2.5 volume of Ethyl alcohol and 1μl GlycoBlue (Invitrogen TM, AM9516) and DNA was dissolved in 1×TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0).
ChIP-enriched DNA or one sixth of input DNA were used as starting materials for DNA end repair process for library construction with NEBNext UltraTM End repair/dA-Tailling Module (NEB, E7442). Then the products were ligated to adapters (NEBNEXT Multiplex Oligos for Illumina, E7335, E7500 and E7710) with Blunt/TA Ligase Master Mix (NEB, M0367) according to the manufacturer’s manual. For the library preparation, 9 cycles were used to amplify products from input DNA, 13 cycles were used to amplify RAD51 ChIP-enriched DNA and 16 cycles were sued to amplify RPA1A ChIP-enriched DNA.

value: Mock-treated

tag: antibody


title: Col-0 Mock treated rep1


title: Col-0_Mock_rep1_RPA1A


title: ALL sample at diagnosis [ALL_493]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia


title: ALL sample at diagnosis [ALL_290]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: diagnosis


title: ALL sample at diagnosis [ALL_295]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: atxr56 Mock treated rep2

value: atxr5 atxr6


title: ALL sample at diagnosis [ALL_555]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: HeH

value: female

value: TruSeq


title: ALL sample at diagnosis [ALL_291]

description:
NovaSeq 6000
RNAseq_read_counts.txt


title: Col-0_Ino_rep2_RPA1A

value: virus inoculated


title: atxr56 Mock treated rep1

value: Mock treated


title: scRNA_multiplexedsample3

city: birmingham

first: lin

last: jin

state: alabama

address: 1824 6th ave s

department: Dermatology

institute: university of alabama at birmingham

description:
10X Genomics
CMO310 = HS6
CMO311 = HS7
CMO312 = Normal6

data_processing:
The demultiplexing, barcoded processing, cell multiplex oligo (CMO) processing, gene counting and aggregation were made using the Cell Ranger 'multi' software v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin epidermis

extract_protocol:
HS and healthy skin tissues were cut into small pieces and were digested with 2.5U/ml Dispase-II (Millipores Sigma, Cat#4942078001) in Hanks’ Balanced Salt Solution (HBSS, Corning, Cat#21-022-CM) overnight at 4°C. After digestion, the epidermis was peeled off and minced. The minced epidermis was incubated with 0.05% trypsin-EDTA at 37°C for 40 mins for further digestion. The suspension was then filtered through a 40um cell strainer and spun down at 300g at 4°C for 5 mins. Collected single cells were for the application of SingleCell RNA sequence.
Single epidermal cells were loaded into 10xcontroller and individual cells were be captured into oil droplets to form Gel Bead-In-EMulsions (GEMs). The single cell cDNA libraries were constructed according to manufacturer’s protocol provided by the Chromium NextGEM single cell 3’ reagent kit (10XGenomics, version 3.1).

value: skin epidermis

tag: diagnosis

value: multiplexed sample:HS and Normal


title: ALL sample at diagnosis [ALL_536]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male

value: ScriptSeq


title: ALL sample at diagnosis [ALL_634]

description:
NovaSeq 6000
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: scRNA_multiplexedsample2

description:
10X Genomics
CMO311 = HS3
CMO312 = HS4
CMO303 = HS5
CMO310 = Normal5


title: ALL sample at diagnosis [ALL_620]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: Col-0_Ino_rep1_RPA1A

value: rossete leaves


title: scRNA_Normal3

description:
10X Genomics
CMO302
This sample is not multiplexed.

value: healthy


title: ALL sample at diagnosis [ALL_392]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: scRNA_multiplexedsample1

description:
10X Genomics
CMO303 = HS1
CMO304 = HS2
CMO301 = Normal1
CMO302 = Normal2


title: RNA-seq_HS 3

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw sequence files were trimmed of primer adapters using Trim Galore version 0.6.7 with parameters --paired --trim-n --trim1
Trimmed sequences were aligned to the genome using STAR version 2.7.10a_alpha_220601 with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 2.0.2 with parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode CRCh38 p13 Release 36
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

extract_protocol:
HS and healthy skin tissues were cut into small pieces and were digested with 2.5U/ml Dispase-II (Millipores Sigma, Cat#4942078001) in Hanks’ Balanced Salt Solution (HBSS, Corning, Cat#21-022-CM) overnight at 4°C. After digestion, the epidermis was peeled off and minced. The minced epidermis was incubated with 0.05% trypsin-EDTA at 37°C for 40 mins for further digestion. The suspension was then filtered through a 40um cell strainer and spun down at 300g at 4°C for 5 mins.  Cells were then subjected to remove apoptotic and dead cells by using the Annexin Dead Cell Removal Kit (StemCell Technologies, 17899) and EasySep™ Magnet (StemCell Technologies, 18000). Enriched living cells were stained with APC anti-human CD49f antibody (1:200 Biolegend, Cat# 313616) and incubated for 10 minutes in the dark at 4°C. After washing with sorter buffer (PBS supplemented with 0.5% BSA and 2mM EDTA), each sample was resuspended and incubated with 4 μl of Anti-APC MultiSort MicroBeads (Miltenyi Biotec, Cat# 130-091-255) in 96 μl of sorted buffer for 15 minutes in the dark at 4°C. Samples were then washed, suspended in sorter buffer, and passed over magnetized MS columns. The columns were washed 3 times to remove unlabeled cells. After the last wash, the columns were removed from the magnetic field, and bound cells were eluted in sorter buffer. Collected single cells with high expression of CD49f were  for the application of low input ATAC&mRNA-sequence.
10,000 single cells from each sample were resuspended in transposition mix (25 μl 2×TD buffer, including 2.5 μl Tn5 (Illumina, Cat#15027865), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 1 μl RNase inhibitor, and 4 μl nuclease-free water). Permeabilization/transposition reactions were incubated at 37 °C for 30 min. Once the incubation finished, EDTA and LiCl were added to a final concentration of 10 mM and 0.5 M, respectively, followed by adding 100 μl of Lysis/Binding Buffer in Dynabeads® mRNA DIRECT™ Micro Kit (Invitrogen, Cat# 61021) After complete cell lysis, 20 μl pre-washed Dynabeads® Oligo (dT)25 was added into the cell lysate to enrich mRNA. The sample were then placed on a Dynal magnet to separate the mRNA and genomic DNA (gDNA). The supernatant containing tagmented gDNA was purified with MinElute PCR purification kit (Qiagen, Cat # 28004) and further amplified using NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs, Cat# M0541s) with 10 cycles of PCR. The mRNA captured on beads was washed using Dynabeads® mRNA DIRECT™ Micro Kit. The Dynabeads-mRNA complex was then resuspended in 20 μl of reverse transcription reaction mix without any primer prepared using SuperScript™ IV First-Strand Synthesis System (Invitrogen, Cat #18091050). Direct tagmentation of the mRNA/cDNA hybrids and PCR amplification were performed on beads using Nextera XT DNA Library Prep Kit (Illumina, Cat# FC1311096).

value: Hurley III


title: ALL sample at diagnosis [ALL_504]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia


title: ALL sample at diagnosis [ALL_390]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: diagnosis


title: RNA-seq_HS 1


title: atxr56_Mock_rep1_RPA1A

value: Mock-treated


title: ALL sample at diagnosis [ALL_618]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: RNA-seq_Healthy 3


title: RNA-seq_HS 2

value: Hurley II


title: ALL sample at diagnosis [ALL_693]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: H3K27ac HS 3

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
CUT-RUNTools-2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) was used to trim, align, and call peaks. Used default settings, EXCEPT set "frag_120" to "FALSE".
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --binSize 10
Assembly: Gencode GRCh38 p13 Release 36
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

extract_protocol:
HS and healthy skin tissues were cut into small pieces and were digested with 2.5U/ml Dispase-II (Millipores Sigma, Cat#4942078001) in Hanks’ Balanced Salt Solution (HBSS, Corning, Cat#21-022-CM) overnight at 4°C. After digestion, the epidermis was peeled off and minced. The minced epidermis was incubated with 0.05% trypsin-EDTA at 37°C for 40 mins for further digestion. The suspension was then filtered through a 40um cell strainer and spun down at 300g at 4°C for 5 mins.  Cells were then subjected to remove apoptotic and dead cells by using the Annexin Dead Cell Removal Kit (StemCell Technologies, 17899) and EasySep™ Magnet (StemCell Technologies, 18000). Enriched living cells were stained with APC anti-human CD49f antibody (1:200 Biolegend, Cat# 313616) and incubated for 10 minutes in the dark at 4°C. After washing with sorter buffer (PBS supplemented with 0.5% BSA and 2mM EDTA), each sample was resuspended and incubated with 4 μl of Anti-APC MultiSort MicroBeads (Miltenyi Biotec, Cat# 130-091-255) in 96 μl of sorted buffer for 15 minutes in the dark at 4°C. Samples were then washed, suspended in sorter buffer, and passed over magnetized MS columns. The columns were washed 3 times to remove unlabeled cells. After the last wash, the columns were removed from the magnetic field, and bound cells were eluted in sorter buffer. Collected single cells with high expression of CD49f were  for the application of CUT&RUN sequence.
CUT&RUN experiments were carried out following the protocol of Epicypher CUTANA CUT&RUN kit (version 1.8). Briefly, nuclei from CD49f+ microbeads enriched keratinocytes (1X104) were isolated with Wash Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 1X Roche cOmplete, protease inhibitor). The nuclei were captured with Concanavalin A (ConA) beads and incubated with 0.5 μg primary antibodies, including anti-H3K4me1(Epicypher, Cat#N013-0040), H3K27me3 (Invitrogen, Cat# MA5-11198), H3K27ac ( ActiveMotif, Cat#91193) in Antibody Buffer (Wash Buffer, 0.01% Digitonin, 2 mM EDTA) overnight at 4 °C. Then CUTANA pAG-MNase was added and incubated for 10 min at RT. CaCl2 was next added at a final concentration of 100 mM to activate the enzyme. The reaction was carried out for 2 hours at 4 °C and stopped by STOP buffer (340 mM NaCl, 20 mM EDTA, 4 nM EGTA, 50 μg/mL RNase A, and 50 μg/mL glycogen). Samples were incubated for 10 min at 37 °C in a thermocycler and quick spin down. DNA was purified using the CUANA DNA Purification Kit as the provided instructions. Purified CUT&RUN-enriched DNA was prepared sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Cat# E7645s).

tag: chip antibody


title: Col-0_ Mock_rep2_Input

tag: tissue

value: WT

value: Input


title: atxr56_Mock_rep2_RPA1A

value: atxr5 atxr6


title: Col-0_ Mock_rep1_Input


title: RNA-seq_Healthy 1

value: female


title: RNA-seq_Healthy 2

value: skin epidermis


title: ALL sample at diagnosis [ALL_689]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

tag: disease

value: HeH


title: ALL sample at diagnosis [ALL_539]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

tag: disease state

value: male


title: atxr56_Ino_rep1_RPA1A

tag: genotype

value: virus inoculated


title: ALL sample at diagnosis [ALL_738]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

tag: revised (predicted)_genotype

value: ScriptSeq


title: H3K27ac HS 2

tag: Sex


title: H3K27ac Healthy 2

value: healthy


title: H3K4me3 HS 2

value: Hurley III


title: atxr56_Ino_rep2_RPA1A

value: rossete leaves


title: Col-0_ Mock_rep2_RAD51


title: H3K4me3 HS 3


title: ALL sample at diagnosis [ALL_680]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

tag: library protocol


title: ALL sample at diagnosis [ALL_688]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: H3K4me3 Healthy 1


title: H3K4me1 HS 2


title: H3K4me3 HS 1


title: H3K4me3 Healthy 2


title: ALL sample at diagnosis [ALL_681]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: H3K27ac Healthy 1


title: ALL sample at diagnosis [ALL_735]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: H3K4me1 HS 1

value: Hurley II


title: atxr56_ Mock_rep1_Input

value: Mock-treated


title: H3K4me1 Healthy 2


title: H3K27ac HS 1


title: ATAC-seq_HS 3

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw sequence files were trimmed of primer adapters using Trim Galore version 0.6.7 with parameters --paired --trim-n --trim1
Trimmed sequences were aligned to the genome using Bowtie2 version 2.4.2 with parameters -X 2000
Peaks were called using MACS2 version 2.1.2 with parameters -f BAMPE -g hs -B -q 0.01
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --binSize 10
Assembly: Gencode GRCh38 p13 Release 36
Supplementary files format and content: bigWig, narrowPeak


title: H3K4me1 Healthy 1


title: ALL sample at diagnosis [ALL_682]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: H3K4me1 HS 3


title: ATAC-seq_Healthy 1


title: Col-0_ Ino_rep2_Input

value: WT


title: ATAC-seq_HS 2


title: atxr56_ Mock_rep2_RAD51


title: Col-0_ Ino_rep1_Input

value: Input


title: ALL sample at diagnosis [ALL_314]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC-seq_HS 1


title: atxr56_ Mock_rep1_RAD51

value: atxr5 atxr6


title: CnR_697_JunB

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
The Nextflow-Core CUT and RUN pipeline (v2.0) was used in spike-in mode to assess quality and map reads to the HG19 (human) and K12-MG1655 (E. coli) reference genomes.
The spike-in normalized .bam files from Nextflow were processed for peak calling with MACS2 using command "macs2 callpeak  -q 0.01 --call-summits --fe-cutoff 2  --gsize 2.7E+9  --format BAMPE  --name ${NAME}  --treatment ${BAM_DIR}/${TREATMENT}  --control ${BAM_DIR}/${CONTROL} --outdir ${OUT_DIR}"
Assembly: hg19
Supplementary files format and content: narrowPeaks from MACS2
Library strategy: CUT and RUN

growth_protocol: RPMI 1640 + 10% serum

extract_protocol: CUT and RUN data were generated using the Epicypher Cutana CUT&RUN kit v3.0 (14-1048) according to the manufacturers provided instructions. Briefly 500k 697 or SUPB15 cells per reaction were bound to 10ml of provided activated ConA beads in 0.2ml PCR tubes. Bead-bound cells were suspended in Antibody Buffer (Wash buffer with 0.1% digitonin, 0.5mM Spermidine, 2mM EDTA, and 1x HALT protease inhibitors) and incubated with 0.5µg targeted or control IgG antibody overnight on a nutator mixer at 4C. The next day after washing, pAG MNase was bound and targeted digestion was carried out for 2 hours at 4C. Digestion was stopped using 33ml Stop buffer + 1ml (0.5ng) E.coli spike-in DNA and then cleaved DNA were released for 10 minutes at 37C. DNA were then purified for library preparation using the included purification kit. >30M 75bp paired end reads were generated per sample using the Illumina Novaseq.

tag: cell line

tag: cell type

value: B-ALL

value: JunB (Cell Signaling 3753)

value: acute lymphoblastic leukemia


title: CnR_697_Fra2

value: Fra2 (Cell Signaling 19967)


title: Col-0_ Mock_rep1_RAD51


title: ATAC-seq_Healthy 2

value: skin epidermis

value: female


title: ALL sample at diagnosis [ALL_376]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: HeH

value: ScriptSeq


title: Col-0_ Ino_rep2_RAD51

value: rossete leaves

value: virus inoculated


title: CnR_697_Jun

value: Jun (Epicypher 13-2019)


title: atxr56_ Mock_rep2_Input


title: CnR_Supb15_Fra2


title: Col-0_ Ino_rep1_RAD51


title: ALL sample at diagnosis [ALL_300]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: male


title: ALL sample at diagnosis [ALL_367]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC-seq_Healthy 3

value: healthy


title: ALL sample at diagnosis [ALL_442]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: CnR_697_IgG

value: IgG (Epicypher 13-0042)


title: CnR_Supb15_Jun

value: B-ALL


title: ALL sample at diagnosis [ALL_372]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: CnR_Supb15_JunB

value: JunB (Cell Signaling 3753)


title: atxr56_ Ino_rep2_Input

value: atxr5 atxr6

value: Input


title: CnR_Supb15_IgG

value: acute lymphoblastic leukemia


title: ALL sample at diagnosis [ALL_679]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: atxr56_ Ino_rep1_Input


title: Input_ChIP_sample_12

data_processing:
Trimming was performed with trim_galore
Trimmed reads were mapped to the hg19 genome with bowtie2
Peak calling was performed using MACS2 with command "callpeak -t H3K27ac_ChIP_NODUPS_NOMT.bam -c Input_Ctrl_NODUPS_NOMT.bam -f BAM -g hs --nomodel --extsize 200 --SPMR -B"
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample

source_name: Lymphoblast

extract_protocol:
Cells were cross-linked, lysed, and sonicated according to the ENCODE project ChIPseq guidelines (https://www.encodeproject.org/about/experiment-guidelines/). 5ug of H3K27ac antibody was used for IP
Libraries were prepared for sequencing using standard Illumina protocols

value: Lymphoblast

value: B-cell acute lymphoblastic leukemia

value: BALL


title: H3K27Ac_ChIP_sample_10

value: H3K27ac Rabbit pAb (Active Motif #39133)


title: ALL sample at diagnosis [ALL_678]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: female

value: ScriptSeq


title: H3K27Ac_ChIP_sample_11


title: atxr56_ Ino_rep2_RAD51

value: rossete leaves

value: virus inoculated


title: H3K27Ac_ChIP_sample_9


title: atxr56_ Ino_rep1_RAD51


title: H3K27Ac_ChIP_sample_8


title: ALL sample at diagnosis [ALL_49]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: HeH


title: H3K27Ac_ChIP_sample_6


title: ALL sample at diagnosis [ALL_669]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_631]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: BTH, Hh, 12h, biol rep4

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with default settings.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method.RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: TAIR 10
Supplementary files format and content: Read counts for genes (TAIR 10) were provided.

treatment_protocol: 3.5-4 weeks old plants were placed in two chambers, in which humidity was set to 40-45% RH (for low humidity treatment) or 95% RH (for high humidity treatment). Temperature was set at 22℃ and photoperiod at 12 h light/12 h dark in both chambers. The plants were pre-treated with different humidity for 24 h and then sprayed with water or BTH solution, and placed back to chambers with different humidity. Samples were taken 12 h and 24 h after BTH treatment.

value: leaf

value: WT

tag: ecotype

value: 95percent RH, BTH, 12h

value: Four-week-old


title: H3K27Ac_ChIP_sample_5


title: BTH, Hh, 12h, biol rep3


title: H3K27Ac_ChIP_sample_2


title: BTH, Hh, 12h, biol rep2


title: H3K27Ac_ChIP_sample_1


title: ALL sample at diagnosis [ALL_627]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL

value: male


title: WT_MNP_D18_Rep1

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

department: GICD

institute: J David Gladstone Institutes

description: scRNA-seq of total RNA in cell type

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite v3.1.0 from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Assembly: hg19
Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format

source_name: Motor neuron progenitor cells

growth_protocol: Cardiac progenitors cells were differentiated from WTC11 hiPSC lines by the WNT modulation protocol.  In brief,  6 uM CHIR were added for 48hours, followed by 5 uM IWP4 for 48 hours. Cells were then grown RPMI with B27 supplement minus insulin until day 10, then with RPMI with B27 plus insulin

extract_protocol:
Single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Detailed in "characteristics: Treatment" to specify different treatments on samples.

value: d18 hiPSC-derived motor neuron progenitor cells

value: untreated


title: IKO_MNP_D18_Rep1

description: scRNA-seq of total RNA in cell type


title: H3K27Ac_ChIP_sample_4

value: Lymphoblast

value: B-cell acute lymphoblastic leukemia

value: H3K27ac Rabbit pAb (Active Motif #39133)


title: H3K27Ac_ChIP_sample_3


title: BTH, Hh, 12h, biol rep1


title: BTH, Lh, 12h, biol rep4

value: 40percent RH, BTH, 12h


title: ALL sample at diagnosis [ALL_624]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: female

value: ScriptSeq


title: ALL sample at diagnosis [ALL_626]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: HeH


title: ALL sample at diagnosis [ALL_612]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: BTH, Lh, 12h, biol rep3

value: leaf

value: WT


title: BTH, Lh, 12h, biol rep1

value: Four-week-old


title: ALL sample at diagnosis [ALL_176]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: BTH, Lh, 12h, biol rep2


title: mock, Hh, 12h, biol rep2

value: 95percent RH, DMSO, 12h


title: H3K27Ac_ChIP_sample_7


title: ALL sample at diagnosis [ALL_702]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: ALL sample at diagnosis [ALL_166]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: mock, Hh, 12h, biol rep3


title: mock, Hh, 12h, biol rep4


title: ALL sample at diagnosis [ALL_633]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: ALL sample at diagnosis [ALL_707]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_622]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: mock, Lh, 12h, biol rep3

value: 40percent RH, DMSO, 12h


title: mock, Hh, 12h, biol rep1


title: ALL sample at diagnosis [ALL_695]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: mock, Lh, 12h, biol rep2


title: mock, Lh, 12h, biol rep1


title: mock, Lh, 12h, biol rep4


title: ALL sample at diagnosis [ALL_299]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_704]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_302]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_619]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_475]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_484]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_466]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_470]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_257]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: NOD, AmericanGW4064, Rep5, RNA

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Alignment (WGBS): TrimGalore/Bismark/Bowtie2
Alignment (RNA-Seq): kallisto
Assembly: mm9
Supplementary files format and content: CpG reports containing methylation information of CpG dinucleotides; abundance files with estimated abundances of gene expression.

organism: Mus musculus

source_name: liver

growth_protocol:
Diet study: 4-week-old A/J, BL6, and NOD mice were acclimated for 2 weeks on a standard laboratory diet, then randomly assigned to  standard or American diet groups for 24 weeks.
Drug study: 9-week-old BL6 and NOD mice were obtained from The Jackson Laboratory and acclimated for 6 weeks on a standard laboratory diet, then randomly assigned to standard-vehicle, American-vehicle, or American-GW4064 treatment groups. Mice were fed their assigned diet for 6 weeks and treated with DMSO or 50 mg/kg GW4064 via intraperitoneal injection twice a week.

extract_protocol:
Genomic DNA was extracted from liver samples using the Qiagen DNEasy kit, with an additional RNase incubation step (50 μg/sample, 30 minutes) prior to column application to remove RNA.
RNA was isolated from mouse liver using a Maxwell 16 LEV simplyRNA kit.
Whole genome bisulfite sequencing single indexed libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina. Input gDNA was fragmented by Covaris S220 or LE220 Focused-ultrasonicator to average insert size of 350bp. Size selection was performed using AMPure XP beads and insert sizes of 300-400bp was isolated. Samples were bisulfite converted after size selection using EZ DNA Methylation-Gold Kit or EZ DNA Methylation-Lightning Kit.
cDNA was generated using a Transcriptor First Strand cDNA Synthesis Kit (Roche). Strand specific mRNA libraries were generated using the TruSeq Stranded mRNA protocol.

tag: study

value: Drug study

value: liver

tag: strain

value: NOD

tag: diet

value: American


title: ALL sample at diagnosis [ALL_467]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: ScriptSeq


title: ALL sample at diagnosis [ALL_472]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: female


title: ALL sample at diagnosis [ALL_210]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: NOD, AmericanGW4064, Rep2, RNA

tag: treatment


title: NOD, AmericanGW4064, Rep4, RNA


title: NOD, AmericanGW4064, Rep3, RNA


title: ALL sample at diagnosis [ALL_205]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: d60, scRNAseq,pooled

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger version 5.0.1 for each sample
Assembly: GRCh38 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC-derived distal lung organoid

extract_protocol:
We performed scRNA-seq across four developmental time points of our distal lung organoid model- day(d)25,40,60 and 80. D25 organoids were in suspension culture while D40,D60 and D80 were embedded in matrigel. TheD25 samples were collected directly from suspension culture and dissocited into single cells using accutase. The embedded organoids were first released from matrigel using cell recovery reagent (corning Cat# ). The released organoid was dissociated into single cells using accutase and resuspended in IMDM (Cat #)+0.04% BSA(Cat #). The cells from n=3 organoids per time point were pooled, filtered and dead cells were removed using MiltenyiBiotec dead cell removal kit according to manufacturer’s instructions. Cell suspensions were diluted to a concentration of 5000 cells/ul and submitted for sequencing.
Libraries were prepared and sequenced at the JP Sulzberger Columbia Genome Center High-Throughput Screening Center at Columbia University. Sequencing libraries were prepared using 10x Genomics Single Cell Gene Expression 3’ workflow

value: hESC-derived distal lung organoid

value: Rockefeller University Embryonic Stem Cell Line 2 (RUES2)

tag: developmental stage


title: d40, scRNAseq,pooled

description: 10x Genomics Single Cell Gene Expression 3’


title: ALL sample at diagnosis [ALL_542]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: NOD, AmericanVehicle, Rep5, RNA

value: DMSO


title: NOD, AmericanGW4064, Rep1, RNA


title: ALL sample at diagnosis [ALL_495]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ATAC_sample_72

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample include Genomic Intervals

source_name: ALL

extract_protocol:
Cells were transposed following to the Fast-ATAC protocol from the Greenleaf Lab
Libraries were prepared for sequencing using standard Illumina protocols for Nextera adapters

value: ALL


title: d25, scRNAseq,pooled


title: ATAC_sample_96


title: ATAC_sample_141


title: d80, scRNAseq,pooled


title: NOD, AmericanVehicle, Rep4, RNA


title: ALL sample at diagnosis [ALL_537]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

data_processing:
The raw sequencing data were processed together using the nextflow-based (21.02.0.edge) nf-core/rnaseq (3.0) pipeline
The sequencing paired-end reads were trimmed by trimgalore (0.6.6)
Alignment to GRCh38 reference genome with ENSEMBL gene annotation (GRCh38.103) was conducted with STAR
Quantification of the aligned reads at transcript level took place with the help of Salmon (1.4.0)
Transcript level expression values were summarized to gene level with the bioconductor package tximeta (1.8.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw count values for each Sample


title: ATAC_sample_94


title: ATAC_sample_89


title: ALL sample at diagnosis [ALL_486]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: male


title: NOD, AmericanVehicle, Rep3, RNA


title: ATAC_sample_82


title: siERRα-3

type: RNA

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

description: Gene expression of treatment with siERRα

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: TIG113 cells were purchased from Japanese Collection of Research Bioresources Cell Bank. The TIG113 were routinely cultured in DMEM medium supplemented with 10% fetal bovine serum at 37ºC in 5% CO2.

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

treatment_protocol: The expression of the human ERRα gene was silenced by transient transfection with ERRα siRNA (Santa Cruz Biotechnology, Inc.) by using DharmaFECT 1 Transfection Reagent (Horizon Discovery Ltd.). TIG113 cells were incubated with siRNA for 48 h before being used for microarray analysis. For negative control experiments, TIG113 cells were transfected with Silencer® Negative Control #1 siRNA (Thermo Fisher Scientific).

value: Human normal fibroblast from skin (TIG113)


title: siERRα-1


title: siERRα-2


title: siNC-3

description: Gene expression of control


title: ATAC_sample_90


title: ALL sample at diagnosis [ALL_502]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood T acute lymphoblastic leukemia

value: T-ALL


title: ATAC_sample_80


title: ALL sample at diagnosis [ALL_8]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC_sample_81


title: NOD, AmericanVehicle, Rep1, RNA

value: Drug study

value: liver

value: NOD


title: NOD, AmericanVehicle, Rep2, RNA

value: American


title: ATAC_sample_77


title: NOD, StandardVehicle, Rep5, RNA

value: Standard


title: siNC-1

description: Gene expression of control


title: siNC-2

description: Gene expression of control


title: ALL sample at diagnosis [ALL_459]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood

value: childhood B acute lymphoblastic leukemia

value: diagnosis

value: ScriptSeq


title: NOD, StandardVehicle, Rep4, RNA


title: ATAC_sample_76


title: ATAC_sample_75


title: ATAC_sample_156


title: ALL sample at diagnosis [ALL_391]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: female


title: NOD, StandardVehicle, Rep3, RNA

value: DMSO


title: ATAC_sample_74


title: ATAC_sample_73


title: ALL sample at diagnosis [ALL_458]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_5]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ALL sample at diagnosis [ALL_559]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC_sample_155


title: ATAC_sample_154


title: NOD, StandardVehicle, Rep2, RNA


title: ATAC_sample_152


title: ATAC_sample_150


title: ATAC_sample_153


title: NOD, StandardVehicle, Rep1, RNA


title: BL6, AmericanGW4064, Rep5, RNA


title: ALL sample at diagnosis [ALL_563]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Unclassified BCP-ALL


title: ALL sample at diagnosis [ALL_553]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ATAC_sample_130

value: ALL


title: FIB5-226

first: Kelechi

last: Ndukwe

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript (RGSC 6.0/rn6) set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15[2]. TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program[3].
Assembly: rn6
Supplementary files format and content: rsem_count.txt => Expected read count produced by RSEM for each gene in each sample.
Supplementary files format and content: TMM_normalized_reads_count_per_million.txt => Normalized gene expression data by TMM method

source_name: Female, TgF-344AD transgenic rat, Ibudilast chow

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
Kapa Stranded mRNA Kit (Roche, cat. KK8421) to generate strand-specific RNA-seq libraries

value: Left Hippocampus Brain

tag: gender

value: Tg-AD

value: Ibudilast


title: FIB4-211


title: ALL sample at diagnosis [ALL_310]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

extract_protocol:
The RNA was extracted using the AllPrep kit (Qiagen).
RNA sequencing libraries were prepared using the Illumina TruSeq stranded Total RNA (RiboZero human/mouse/rat) kit, Illumina TruSeq RNA Access library preparation kit or Script-Seq kit (EpiCentre), as indicated in each sample information.

value: childhood T acute lymphoblastic leukemia

value: T-ALL

value: male


title: FIB3-067


title: ALL sample at diagnosis [ALL_546]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC_sample_124


title: ATAC_sample_127


title: BL6, AmericanGW4064, Rep2, RNA

value: Drug study

value: liver

value: American


title: BL6, AmericanGW4064, Rep3, RNA


title: FIB2-063


title: ATAC_sample_123


title: FIB1-052


title: BL6, AmericanGW4064, Rep1, RNA


title: BL6, AmericanVehicle, Rep5, RNA


title: ALL sample at diagnosis [ALL_171]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: Bone Marrow/Peripheral Blood


title: ALL sample at diagnosis [ALL_365]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: childhood B acute lymphoblastic leukemia

value: diagnosis


title: BL6, AmericanGW4064, Rep4, RNA


title: ATAC_sample_115


title: ATAC_sample_122


title: BL6, AmericanVehicle, Rep4, RNA


title: F5-213

source_name: Female, TgF-344AD transgenic rat, rodent chow

value: female

value: No Treatment


title: ATAC_sample_149


title: F4-210


title: ATAC_sample_114


title: ALL sample at diagnosis [ALL_358]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: ScriptSeq


title: F3-093


title: ALL sample at diagnosis [ALL_243]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt

value: HeH


title: ALL sample at diagnosis [ALL_464]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: F2-065


title: ALL sample at diagnosis [ALL_363]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: ATAC_sample_95

value: ALL


title: BL6, StandardVehicle, Rep5, RNA

value: Standard

value: DMSO


title: ALL sample at diagnosis [ALL_380]

description:
HiSeq 2000/2500
RNAseq_read_counts.txt


title: BL6, AmericanVehicle, Rep1, RNA


title: MIB5

description: Male, TgF-344AD transgenic rat, Ibudilast chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq.gz2 v 2.17 program.
reads were first mapped to the latest UCSC transcript (RGSC 6.0/rn6) set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15[2]. TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program[3].
Assembly: rn6
Supplementary files format and content: rsem_count.txt => Expected read count produced by RSEM for each gene in each sample.
Supplementary files format and content: TMM_normalized_reads_count_per_million.txt => Normalized gene expression data by TMM method

source_name: Left Hippocampus Brain

value: Left Hippocampus Brain

value: Tg-AD

value: Ibudilast


title: F1-064


title: ATAC_sample_71


title: BL6, StandardVehicle, Rep4, RNA


title: ATAC_sample_70


title: BL6, AmericanVehicle, Rep3, RNA


title: BL6, StandardVehicle, Rep3, RNA


title: EB, day 7, R2-clones, Capture-C_R3

city: Oxford

first: Emily

last: Georgiades

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

data_processing:
All data was processed using the CapCruncher tool (https://github.com/sims-lab/CapCruncher), with viewpoints listed in mm39_LPx6_oligofile.bed.
restriction_enzyme: dpnii
reporter_exclusion_zone: 1000
aligner: bowtie2, index_flag: -x, options: -p 6 --very-sensitive
Normalisation scale_factor: 1000000
Assembly: mm39
Supplementary files format and content: bigwig

source_name: Erythroid

extract_protocol:
Cells were grown, treated and processed as described in the Methods section of the paper.
Capture-C library was generated as described in the Methods section of the paper and sequenced on the Illumina Nextseq platform using a 300-cycle paired-end kit (NextSeq 500/550 Mid Output Kit v2.5: 20024905)

value: Erythroid

tag: origin cell_line

value: E14TG2a.IV mouse ES cells

tag: differentiation day

value: Day 7


title: EB, day 7, WT, Capture-C_R2

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.


title: ATAC_sample_151


title: ATAC_sample_105


title: BL6, StandardVehicle, Rep2, RNA

value: Drug study

tag: tissue

value: liver


title: MIB3


title: ATAC_sample_69


title: KPNKF Tumour Rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 1 x 80mg/kg intraperitoneal injection of Tamoxifen. Tissues were harvested at clinical endpoint.

value: Male

value: Small Intestine

value: VilCreER KrasG12D/fl p53fl/fl Notch1Tg/+

tag: sample type

value: Primary tumour


title: KPNKF Tumour Rep 4

value: Female

tag: genotype


title: MIB1


title: MIB2


title: ATAC_sample_125


title: NOD, American, Rep4, RNA

value: Diet study

value: NOD

value: American

value: untreated


title: ATAC_sample_99

value: ALL


title: NOD, American, Rep3, RNA


title: KPNKF Tumour Rep 1


title: BL6, StandardVehicle, Rep1, RNA

value: Standard

value: DMSO


title: KPN Tumour Rep 4

value: VilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: M3

description: Male, TgF-344AD transgenic rat, rodent chow

value: Left Hippocampus Brain

value: Tg-AD

value: No Treatment


title: NOD, American, Rep2, RNA

value: liver


title: ATAC_sample_88


title: ATAC_sample_91


title: MIB4

value: Ibudilast


title: M4


title: NOD, American, Rep1, RNA


title: ATAC_sample_86


title: KPN Tumour Rep 3

value: Small Intestine


title: M1


title: ATAC_sample_85


title: KPN Tumour Rep 2


title: KPNKF Tumour Rep 2

value: Male

value: VilCreER KrasG12D/fl p53fl/fl Notch1Tg/+


title: KPN Tumour Rep 1

value: Primary tumour


title: M5


title: mANK-101, replicate 3

city: Cambridge

first: Sailaja

last: Battula

state: MA

address: 245 Main St, 2nd Floor

institute: ANKYRA Therapeutics

description:
R22018701
10X Genomics

data_processing:
The 10X Cell Ranger Software Suite (Version 5.0.1) was used to perform sample de-multiplexing, barcode processing, and single-cell 3′ UMI counting with mouse GRCm38 as the reference genome. Normalization, feature selection, integration of all samples data and dimensionality reduction were conducted using Seurat (version 4.1.1) with default settings.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: tumor tissue

extract_protocol:
On Day 7, freshly collected tumor sample from each mouse was minced separately, and digested with mixed enzymes in C tubes. C tubes were attached onto the sleeve of gentle MACS dissociator before running the program 37C_m_TDK_1. Digested tissues were filtered through 70 μm cell strainers. Cells were then suspended with 1 x Red Blood Cell Lysis Solution and washed twice with DPBS + 1% BSA. The collected cells were transferred into a 2ml microcentrifuge tube. Centrifuge at 300 rcf for 10min. Remove the supernatant without disrupting the cell pellet. Add an appropriate volume of 1X DPBS + 1% BSA to obtain a concentration of 700-1,200 cells/μl.
Library generation was conducted as outlined by the Single Cell 3′ Reagent Kits v3.1 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). In brief, the samples were washed and re-suspended in DPBS (Corning) + 1% BSA (Sigma-B2064) and then the appropriate volume for each sample was calculated for a target capture of 8000 cells. Following cell counting, samples were adjusted to ~1000 cells/μl and loaded onto a 10x Genomics Chip G-single cell. After GEMs (Gel Bead-In-EMulsions) generation and retrieval, samples were transferred into a PCR 8-tube strip (Eppendorf) and heat-sealed. Reverse transcription was performed using a thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead cleanup (Thermo Fisher) according to user guide. Purified cDNA was amplified for 12 cycles before cleaning up using SPRIselect beads (Beckman). Finally, libraries were sequenced on the NovaSeq 6000 Illumina platform with a 150-base pair (bp) paired-end, targeting a median sequencing depth of 50,000 read pairs/cell for each sample.

value: tumor tissue

value: tumor cell line

value: mANK-101, 5ug


title: mANK-101, replicate 4

description:
R22018702
10X Genomics


title: NOD, Standard, Rep1, RNA

value: Diet study

value: NOD

value: untreated


title: ATAC_sample_68

value: ALL


title: ATAC_sample_67


title: mANK-101, replicate 2

description:
R22018700
10X Genomics


title: NOD, Standard, Rep2, RNA

value: Standard


title: NOD, Standard, Rep4, RNA


title: NOD, Standard, Rep3, RNA


title: KPNKF Tumour Organoid Rep 1

value: Female

value: Organoid from Primary Tumour


title: ATAC_sample_66


title: AJ, American, Rep4, RNA

value: A/J

value: American


title: mANK-101, replicate 1

description:
R22018699
10X Genomics


title: M2

value: Left Hippocampus Brain

value: Tg-AD

value: No Treatment


title: KPN Tumour Organoid Rep 4

value: Small Intestine

value: VilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: Vehicle, replicate 4

description:
R22018698
10X Genomics

value: tumor tissue

value: Veh


title: AJ, American, Rep3, RNA

value: liver


title: ATAC_sample_78


title: BL6, AmericanVehicle, Rep2, RNA

value: Drug study

value: DMSO


title: ATAC_sample_64


title: AJ, American, Rep2, RNA

value: Diet study

value: untreated


title: ATAC_sample_63

value: ALL


title: KPN Tumour Organoid Rep 2

value: Male


title: KPNKF Tumour Organoid Rep 2

value: VilCreER KrasG12D/fl p53fl/fl Notch1Tg/+

value: Organoid from Primary Tumour


title: AJ, American, Rep5, RNA

value: A/J

value: American


title: Vehicle, replicate 2

description:
R22018696
10X Genomics

value: tumor cell line


title: KPN Tumour Organoid Rep 3


title: AJ, American, Rep1, RNA


title: Vehicle, replicate 1

description:
R22018695
10X Genomics


title: ATAC_sample_131


title: AJ, Standard, Rep5, RNA

value: Standard


title: AJ, Standard, Rep4, RNA


title: KPN SI Tumour Rep 9

value: Small Intestine

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+

value: Primary Tumour


title: KPN SI Tumour Rep 8


title: ATAC_sample_117


title: AJ, Standard, Rep3, RNA


title: Control Sample25 - VDJ

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description:
GG-25-TCR
10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1) pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Cell Ranger's default settings
Gene expression level of genes were quantified using Cell Ranger's default settings
Contig annotations (TCR) were quantified using Cell Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: tab-separated file with 10x barcodes
Supplementary files format and content: features.tsv.gz: tab-separated file with features (genes)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: filtered_contig_annotations.csv: comma-seprated file with high-level annotations of each high-confidence contigs from cell-associated barcodes

source_name: Liver containing metastases of CRC origin

extract_protocol:
Liver metastases were isolated and dissociated into single cells by physical (chopping the tissue into small pieces) and enzymatic (collagenase, Dispase II and DNAse) digestion followed by a filtering step using a 0.4mm cell strainer. No antibody staining was performed, single cells were resuspended in autoMACS running buffer containing 7AAD (BioLegend/ 420404) in a 1/50 dilution. Viable cells were sorted based by gating on single 7AAD negative cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1, 10x Genomics, ref. CG000204). Briefly, sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: feature type

value: VDJ

value: Control


title: KPN SI Tumour Rep 7

tag: Sex


title: Control Sample25 - Gene expression

description:
GG-25-GEX
10X Genomics

value: Liver containing metastases of CRC origin

value: GEX


title: ATAC_sample_110


title: Vehicle, replicate 3

description:
R22018697
10X Genomics

value: tumor tissue

value: Veh


title: ATAC_sample_109

value: ALL


title: AJ, Standard, Rep2, RNA

value: Diet study

value: liver

value: untreated


title: KPN SI Tumour Rep 6

value: Male


title: AJ, Standard, Rep1, RNA

value: A/J


title: ATAC_sample_62


title: KPN Tumour Organoid Rep 1

value: VilCreER KrasG12D/+ p53fl/fl Notch1Tg/+

value: Organoid from Primary Tumour


title: ATAC_sample_108


title: IFNa + aCTLA4 Sample22 - VDJ

description:
GG-22-TCR
10X Genomics

value: IFNa + aCTLA4


title: BL6, American, Rep5, RNA

value: American


title: KPN SI Tumour Rep 4

value: Small Intestine

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+

value: Primary Tumour


title: IFNa + aCTLA4 Sample22 - Gene expression

description:
GG-22-GEX
10X Genomics

value: Liver containing metastases of CRC origin


title: ATAC_sample_104


title: ATAC_sample_79


title: IFNa Sample23 - VDJ

description:
GG-23-TCR
10X Genomics

value: VDJ

value: IFNa


title: BL6, American, Rep4, RNA


title: ATAC_sample_61


title: BL6, American, Rep3, RNA


title: KPN SI Tumour Rep 3


title: ATAC_sample_60


title: IFNa Sample18 - Gene expression

description:
GG-18-GEX
10X Genomics

value: GEX


title: IFNa Sample18 -VDJ

description:
GG-18-TCR
10X Genomics


title: KPN SI Tumour Rep 2


title: IFNa Sample23 - Gene expression

description:
GG-23-GEX
10X Genomics


title: BL6, American, Rep2, RNA


title: BL6, American, Rep1, RNA


title: Control Sample11 - VDJ

description:
GG-11-TCR
10X Genomics

value: Control


title: ATAC_sample_59

value: ALL


title: KPN SI Tumour Rep 5


title: BMT2 SI Tumour Rep 5

value: Female

value: vilCreER BrafV600E/+ Mlh1fl/fl Tgfbr2fl/fl


title: BL6, Standard, Rep5, RNA

value: Diet study

value: liver

value: Standard

value: untreated


title: Control Sample11 - Gene expression

description:
GG-11-GEX
10X Genomics


title: ATAC_sample_58


title: BMT2 SI Tumour Rep 4


title: KO_msE9.5_forebrain_3

city: Ann Arbor

first: Elizabeth

middle: Anne

last: Werren

state: MI

address: 1137 Catherine St.

institute: University of Michigan

description:
mouse_gene_counts.txt
mouse_ercc_counts.txt

data_processing:
FASTQ files were trimmed with Cutadapt v4.1 using default parameters. Read quality was assessed by FASTQC v0.11.9. MultiQC v1.7 was used to visualize FASTQC outputs and compare samples. ERCC spike-in FASTA and GTF annotation files were merged with human GRCh38.p13 reference genome FASTA with GTF release 39 or mouse GRCm39 reference genome FASTA with GTF release M28. FASTQ reads were then mapped to merged files using STAR alignment with parameter ‘--outSAMtype BAM SortedByCoordinate’.
Count analysis was performed on sorted BAM files using RSEM with paired-end alignment specified.
Differential expression analysis was carried out using DESeq2 v1.34.0 in R v4.1.2. ERCC spike-in counts were used to estimate size factors for each sample for DESEq2 analysis.
Alternative splicing analysis was performed on sorted BAM files using rMATS v4.1.2 with the following parameters: ‘-t paired --readLength 150 --variable-read-length --nthread 4’
Assembly: GRCh38/GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes ERCC spike-in counts for each sample

source_name: E9.5 forebrain tissue

growth_protocol: Human ESC and iPSC lines were cultured using feeder free conditions on Matrigel (Corning) with mTeSR-1 (STEMCELL Technologies). Passaging was performed using mTeSR-1 supplemented 1 nM ROCK inhibitor (BD Biosciences 562822) to prevent differentiation. Both manual and chemical dissociation with Versene (Gibco 15040066) were performed for splitting. All mice were maintained according with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and were approved by the Case Western Reserve Institutional Animal Care and Use Committee. CRISPR genome editing was performed in the University of California, San Diego Transgenic and Knockout Mouse Core. C57BL/6JN hybrid mice (Jackson Laboratory, 005304) were used for CRISPR editing of the Thoc6 locus. Founder mice with the Thoc6fs/+ allele were intercrossed with C57BL/6JN mice (Jackson Laboratory, 005304) for line maintenance. All ex vivo analyses were performed on tissue collected from mice of both sexes at embryonic day (E) 8.5-10.5. Sex-dependent differences were not assessed.

extract_protocol:
Total RNA was extracted from cultured hNPCs (two biological replicates per genotype) using TRIzol Reagent (Invitrogen 15596026) followed by DNAse column treatment using PureLink RNA extraction kit (Invitrogen 12183018A). Total RNA from dissected E9.5 mouse forebrain tissue (three biological replicates per genotype) was extracted using Picopure RNA isolation kit (Applied Biosystems KIT0204) according to manufacturer’s recommendations. hNPC and E9.5 mouse forebrain RNA samples were ribo-depleted followed by 151 bp paired-end sequencing on the Illumina NovaSeq 300 cycle, ~20-30 million reads per sample.
Library preparation and sequencing was conducted by the Advanced Genomics Core (AGC) at the University of Michigan using Illumina Total RNA library prep kit following manufacturer's instructions. ERCC spike-ins (Invitrogen 4456740) were added for sequencing controls at starting concentrations according to the manufacturer’s instructions.

treatment_protocol: human ESCs/iPSCs were passaged into 96-well V-shaped bottom ultra-low attachment cell culture plates (PrimeSurface® 3D culture, MS-9096VZ) to achieve a starting cell density of 600-1,000 cells per well in 30 µl of mTesRTM1 with 1 nM ROCK inhibitor. After 36 hours, 150 µl of N-2/SMAD inhibition media (cocktail of 1X N-2 supplement (Invitrogen 17502048), 2 μM A-83-01 inhibitor (Tocris Bioscience 2939), and 1 mM dorsomorphin (Tocris Bioscience 309350) in DMEM-F12 (Gibco 11330032)) was added for neural induction. On day 7, EBs were transferred to Matrigel-coated plates to enrich for neural rosettes at a density of 20-30 EBs per well of a 6-well plate, and media was changed to neural differentiation media (0.5X N-2 supplement, 0.5X B-27 supplement (Invitrogen 17504044) with 20 pg/μl bFGF and 1mM dorsomorphin inhibitor in DMEM/F-12). For monolayer NPC differentiation, neural rosettes were scored and uplifted on day 14, dissociated in Accutase (Gibco A1110501), and re-plated on poly-L-ornithine (PLO)/Laminin-coated plates for NPC expansion, selection, and passaging. 15 μg/mL PLO (Sigma-Aldrich P4957) diluted in DPBS (Gibco 14040-133); 10 μg/mL laminin (Sigma-Aldrich L2020) diluted in DMEM/F-12.

value: E9.5 forebrain tissue

value: Thoc6 fs/fs


title: ATAC_sample_106


title: BL6, Standard, Rep4, RNA


title: KO_msE9.5_forebrain_2


title: BL6, Standard, Rep3, RNA


title: BMT2 SI Tumour Rep 3

value: Small Intestine


title: KPN SI Tumour Rep 1

value: Male

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: BMT2 SI Tumour Rep 2

value: Primary Tumour


title: KO_msE9.5_forebrain_1


title: ATAC_sample_56


title: AKPT SI Tumour Rep 4

value: vilCreER Apcfl/fl KrasG12D/+ p53fl/fl Tgfbr1fl/fl


title: NOD, American, Rep3, WGBS

value: NOD

value: American


title: ATAC_sample_55


title: HET_msE9.5_forebrain_1

value: Thoc6 +/fs


title: HET_msE9.5_forebrain_2


title: AKPT SI Tumour Rep 3


title: NOD, American, Rep2, WGBS


title: AKPT SI Tumour Rep 2


title: ATAC_sample_53

value: ALL


title: AKPT SI Tumour Rep 1

value: Female


title: ATAC_sample_54


title: WT_msE9.5_forebrain_3

value: wildtype


title: NOD, American, Rep1, WGBS

value: Diet study