title: Wide type in germ free condition rep2 [WT-GF-2]

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to danRer10 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

organism: Danio rerio

source_name: Wide type in germ free condition

growth_protocol: embryos were incubated at 28.5℃ in E3 egg water (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4)

extract_protocol:
Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: germ free condition was carried out as previously described(Pham et al., 2008).

tag: strain background

value: AB

tag: age

value: 7 days post fertilization

value: Wilde type

value: germ free condition

value: larvae intestine


title: E13-116 AD 3

status: Public on Jan 12 2022

type: RNA

city: Atlanta

first: Ashlyn

middle: G

last: Johnson

state: GA

address: 615 Michael Street NE

department: Neurology

country: USA

institute: Emory University

description: NA indicates data not available.

hyb_protocol: Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA), according to manufacturers instructions.

scan_protocol: Raw data were imported into nSolver 4.0 and analyzed via the nCounter Advanced Analysis plugin (version 2.1.134) to perform quality control checks and normalize the data.

data_processing:
Raw data were imported into nSolver 4.0 and analyzed via the nCounter Advanced Analysis plugin (version 2.1.134) to normalize the data and conduct differential expression, pathway scoring , and cell type profiling analyses. Covariates included disease (control, AD, and FTD-tau) and cartridge ID (to control for batch effects). All samples passed the quality control analysis conducted by the Advanced Analysis plugin.  Differential expression was calculated using disease as the predictor variable and the cartridge ID as the confounder variable.
The complete_normalized_data.txt includes boolean value (true/false, in the below.threshold column) indicating whether the gene met the threshold for pruning due to low count data.

molecule: total RNA

organism: Homo sapiens

source_name: dorsolateral prefrontal cortex

extract_protocol: 30 to 50 milligrams of frozen DLPFC, primarily gray matter, was homogenized in one milliliter of Trizol with a bullet blender. Chloroform and centrifugation were used to obtain an aqueous phase containing RNA. The aqueous phase was mixed 1:1 in 100% ethanol and then processed with the Quick-RNA Miniprep Kit (Zymo Research, USA). RNA was eluted in nuclease free water and stored at -80 ˚C until analysis. Quality of the RNA was determined by the Emory Integrated Genomics Core. All samples had concentrations greater than 20 ng/ul and DV200 values greater than 20%, per manufacturer’s recommendation. Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA).

tag: Sex

value: Female

tag: race

value: white

tag: cartridge id

tag: post mortem interval

tag: apoe genotype

tag: diagnosis

value: AD

tag: tissue

value: dorsolateral prefrontal cortex


title: Wide type in germ free condition rep1 [WT-GF-1]

type: SRA

library_source: transcriptomic

tag: genotype

tag: treatment


title: E08-101 Control 2

description: NA indicates data not available.

label_protocol: Samples from each disease group were randomly distributed across two nCounter Human glial profiling panels (NanoString, USA) and run on an nCounter FLEX Analysis System (NanoString, USA), according to manufacturers instructions.

value: Control


title: E12-06 AD 2

description: NA indicates data not available.

value: Male


title: E05-130 Control 1

description: NA indicates data not available.


title: GSH_RADONC_RectalCancer_043

city: Frankfurt

first: Adele M.

last: Nicolas

state: Deutschland (DEU)

address: Paul Ehrlich StraBe 42 44, Frankfurt Main, Frankfurt Main

country: Germany

institute: Georg Speyer Haus

data_processing:
Sequence reads trimmed by Trimmomatic Software v.0.36
Trimmed reads mapped to Homo sapiens GRCh38 genome by STAR aligner v.2.5.2b
Unique gene hit counts calculated by Subread packages v.1.5.2
Supplementary_files_format_and_content: Raw counts in txt file format

extract_protocol:
Qiagen Rneasy FFPE kit (Qiagen; #73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FFPE material of Patients with advanced rectal cancer treated with neoadjuvant chemoradiotherapy

tag: time

value: Pre-CRT

tag: cancer type

value: Rectal cancer

tag: treatment response pcr vs. non-pcr

value: Non-pCR

tag: disease free survival event

tag: disease free survival time (months)


title: GSH_RADONC_RectalCancer_049


title: srKO 2wk testis, biological replicate 2

city: Clermont-Ferrand

first: Antoine

last: Martinez

address: Faculté de Médecine, CRBC, 28 place Henri Dunant

department: GReD

country: France

institute: CNRS, INSERM, Université Clermont Auvergne

description: gene expression

hyb_protocol: following fragmentation, cDNA were hybridized for 17h at 45°C on GenChip MouseGene2.0 from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GenChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: RMA normalization was performed with R and the BioConductor package.

label: biotin

organism: Mus musculus

source_name: srKO 2-week-old mous testis

label_protocol: biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA (following the GeneChip® WT PLUS Reagent Kit Affymetrix).

extract_protocol: total RNA were extracted from whole adrenal glands using RNAII nucleotide extraction kit from Macherey-Nagel. RNA quality was assessed by Agilent Bioanalyzer chips.

value: srKO

value: Whole testis

value: 2 weeks


title: E04-186 AD 1

description: NA indicates data not available.


title: Wide type in conventionally raised condition rep2 [WT-CV-2]

value: AB

value: conventionally raised condition


title: GSH_RADONC_RectalCancer_042


title: Wide type in conventionally raised condition rep1 [WT-CV-1]

value: 7 days post fertilization

value: Wilde type


title: GSH_RADONC_RectalCancer_041

value: 50,4 + Capecetabine


title: prKO 2wk testis, biological replicate 4

description: gene expression

source_name: prKO 2-week-old mous testis

value: prKO


title: prKO 2wk testis, biological replicate 3

description: gene expression


title: tp53 mutant in germ free condition rep2 [P53-GF-2]

source_name: tp53 mutant in germ free condition

value: tp53e7/e7 mutant

value: germ free condition

value: larvae intestine


title: tp53 mutant in germ free condition rep1 [P53-GF-1]


title: GSH_RADONC_RectalCancer_039


title: tp53 mutant in conventionally raised condition rep2 [P53-CV-2]


title: prKO 2wk testis, biological replicate 2

description: gene expression


title: Brg1-floxed_4OHT_D4_rep1

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2. The ATAC-seq lied within the blacklisted genomic regions for functional genomics analysis were excluded. ChromVAR (v1.10) were used for transcription factor based chromatin accessibility analysis.  321 transcription factors compiled in the Homer database were used for the chromVAR analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: EB

extract_protocol:
EBs were collected at different time points and disaggregated in 0.25% trypsin at 37°C for 3 min incubation with gentle agitation followed by inactivation with culture medium containing 10% FBS. Cells were collected by centrifugation at 500g for 5 minutes, washed once with ice-cold PBS. iHA-Etv2 MEFs were harvested from the culture dishes at different time points by treating the cells with 0.25% trypsin at 37°C for 4 min incubation followed by neutralizing and collecting the cells with culture medium containing 10% FBS. ATAC reaction was performed with 50,000 cells as previously described18 using the Tn5 transposase (Illumina) and libraries were created at the University of Minnesota Genome Center. Libraries were then sequenced on a NextSeq Illumina platform (2x50 bp) aiming for 25 million reads per sample.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

value: Day 4

tag: dox or no dox

value: Dox

value: FALSE


title: GSH_RADONC_RectalCancer_038

value: Pre-CRT

value: Rectal cancer


title: Brg1-floxed_D4_rep2


title: tp53 mutant in conventionally raised condition rep1 [P53-CV-1]

tag: strain background


title: GSH_RADONC_RectalCancer_037

value: Non-pCR


title: Brg1-floxed_4OHT_D4_rep2


title: GSH_RADONC_RectalCancer_036


title: srKO 2wk testis, biological replicate 3

description: gene expression

value: srKO

value: Whole testis

tag: age


title: MEF_Brg1_KD_Dox_D7_S5 [scRNA-seq]

data_processing:
The sequencing reads were mapped to the mouse genome (mm10) using TopHat
The raw read counts were obtained by HTSeq
The single cells were then scaled and normalized by Seruat 3
Genome_build: mm10
Supplementary_files_format_and_content: Summarized experiment and Hierarchical Data Format

extract_protocol: cDNA libraries were prepared according to the manufacturer’s protocol (Single Cell 30v3, 10x Genomics, USA) at the University of Minnesota Genomics Center.

tag: cell type

value: MEF

tag: time point


title: GSH_RADONC_RectalCancer_040

value: pCR


title: Nped9

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

hyb_protocol: The labeled RNA was purified (MicroBioSpin 6, Bio-Rad, 732-6221), hybridized (overnight for 20 hours at 55°C and 20 rpm) and washed (Agilent, 5188-5327) before scanning.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies), to obtain Processed Signals (resulting from all intra-array pre-processing, including background corrections)  corresponding to the transcript levels.

data_processing: The spot images were processed with Feature Extraction Software v10.7.3.1 (Agilent Technologies). Each miRNA microarray was analyzed with respect to signal intensity, background signal, as well as internal control blade and spike in controls.

source_name: Pediatric non-neoplastic adrenal 9

label_protocol: The microRNA library was constructed using 100 ng of total RNA and investigated with the Agilent  Human microRNA Microarray Kit (v3)” (G4470C, Agilent Technologies, Santa Clara, CA, USA) to determine the expression profile of microRNAs according to manufacturer’s instructions. This array contains 866 human and 89 human viral microRNA sequences. Each miRNA species is printed 20 times with replicate probes on the array.

extract_protocol: Fresh surgical tissues were immediately snap-frozen in liquid nitrogen, stored at −80 °C and microdissected prior to RNA extraction and only specimen with at least 80% of tumor cells were included in the study. Total cellular RNA was extracted using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) according to the  anufacturer’s instructions. The RNA was reverse transcribed to single-stranded cDNA using the High Capacity Kit (Applied Biosystems, Foster  City, CA, USA).

value: Non-neoplastic Adrenal


title: MEF_Brg1_KD_NoDox_D7_S6 [scRNA-seq]

value: NoDox


title: WT 2wk testis, biological replicate 8

description: gene expression

source_name: WT 2-week-old mous testis

value: WT

value: 2 weeks


title: Nped8

source_name: Pediatric non-neoplastic adrenal 8


title: mTSC with induced Hand1 expression

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

country: China

institute: Xiamen University

data_processing:
Zebracall software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm10

source_name: mouse TSC

extract_protocol:
mouse TSC differentiating for 2 days without or with induced Hand1 expression by doxycycline treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse TSC

value: 0.6 ug/ml dox


title: mTSC without induced Hand1 expression


title: WT 2wk testis, biological replicate 7

description: gene expression


title: GSH_RADONC_RectalCancer_034


title: MEF_Brg1_KD_Dox_D2_S4 [scRNA-seq]


title: prKO 2wk testis, biological replicate 1

description: gene expression

value: prKO


title: MEF_Brg1_KD_Dox_D1_S3 [scRNA-seq]


title: Brg1-floxed_D4_rep1

value: Day 4


title: GSH_RADONC_RectalCancer_033


title: WT 2wk testis, biological replicate 5

description: gene expression


title: Nped7

source_name: Pediatric non-neoplastic adrenal 7


title: WT 2wk testis, biological replicate 4

description: gene expression


title: WT 2wk testis, biological replicate 6

description: gene expression


title: WT 2wk testis, biological replicate 2

description: gene expression


title: srKO 2wk testis, biological replicate 1

description: gene expression


title: Total RNA from ENKTL108

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

institute: The Ohio State University

data_processing:
For fresh/frozen samples, alignment to human genome (hg38) was done using TopHat. Transcriptome assembly and analysis was performed using Cufflinks and expression was reported as FPKM
For FFPE-derived samples, low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64.  Samples were aligned to Ensemble Human reference GRCh37.97 using the RNA-Seq aligner STAR version 2.6.0c. Features were identified from Ensemble (grch37/release-97). Feature coverage counts were calculated using featureCounts, FPKMs values were generated based on overall alignment. Expression was normalized using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: csv files include FPKM values for each sample

source_name: Tumor

extract_protocol:
For fresh-frozen samples, total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen). Total RNA was extracted from FFPE samples using the RNeasy FFPE kit (Qiagen).
For fresh-frozen samples, directional poly-A RNA sequencing libraries were prepared and sequenced as 42-bp paired-end reads on an Illumina NextSeq 500 instrument (Illumina) to a depth of 33.2-48.0 million read pairs. For FFPE samples, directional RNA sequencing libraries were prepared and sequenced as 150-bp paired-end reads to a depth of ~50 million read pairs per sample.

tag: disease state

value: Tumor

tag: sample type

value: ENKTL

tag: dna isolation type

value: FFPE

tag: pdx-derived

value: No


title: Total RNA from ENKTL58


title: MEF_Brg1_KD_NoDox_S2 [scRNA-seq]

value: TRUE


title: WT 2wk testis, biological replicate 3

description: gene expression

tag: tissue


title: WT 2wk testis, biological replicate 1

description: gene expression

tag: genotype


title: Nped6

source_name: Pediatric non-neoplastic adrenal 6


title: Nped5

source_name: Pediatric non-neoplastic adrenal 5


title: GSH_RADONC_RectalCancer_031

value: Pre-CRT

value: Rectal cancer

value: Non-pCR

tag: treatment


title: MEF_Dox_D7_Flk1pos_S5 [scRNA-seq]

description: processed data file: processed_Etv2_scRNAseq.rds

value: MEF

value: Dox


title: GSH_RADONC_RectalCancer_030

tag: time


title: GSH_RADONC_RectalCancer_035

tag: cancer type


title: Total RNA from ENKTL53


title: MEF_Dox_D7_Flk1pos_S4 [scRNA-seq]


title: GSH_RADONC_RectalCancer_029

tag: treatment response pcr vs. non-pcr


title: Nped4

source_name: Pediatric non-neoplastic adrenal 4

value: Non-neoplastic Adrenal


title: Total RNA from ENKTL48


title: GSH_RADONC_RectalCancer_028

value: pCR

tag: disease free survival event


title: Nped3

source_name: Pediatric non-neoplastic adrenal 3


title: MEF_Dox_D7_S1 [scRNA-seq]

value: FALSE


title: GSH_RADONC_RectalCancer_032

tag: disease free survival time (months)


title: UPN1

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

data_processing:
Whole-transcriptome RNA sequencing data was generated for 34 cell lines derived from lymphoma tumors: 11 from mantle cell lymphoma (MCL), 3 from Burkitt lymphoma, and 20 from diffuse large B-cell lymphoma (DLBCL; 14 of the germinal centre B-cell-like (GCB) subtype and 6 of the activated B-cell-like (ABC) subtype).
The STAR aligner (v2.5.3a_modified) was used to align reads to the GRCh38 reference and produce raw counts per gene.
Raw counts were read into R (v3.6.1) and normalized across all cell lines using a variance-stabilizing transformation in the DESeq2 package (v1.26.0).
Expression of CXCR4 between cell lines was visualized in R, and statistical comparisons between pathologies were performed using Student’s t-tests.
Genome_build: GRCh38

source_name: Cell line

extract_protocol: RNA sequencing data were generated using standard Illumina protocols at the British Columbia Cancer Research Centre from 34 lymphoma cell lines representing multiple pathologies. These datasets were generated at multiple timepoints.

tag: cell line

tag: pathology

value: Mantle Cell Lymphoma


title: MEF_Dox_D1_S5 [scRNA-seq]


title: Nped2

source_name: Pediatric non-neoplastic adrenal 2


title: MEF_Dox_D1_S2 [scRNA-seq]


title: GSH_RADONC_RectalCancer_026


title: Total RNA from ENKTL56


title: Z-138 GSM5710044 (re-analyzed)

description: GSM5710044 (re-analyzed)


title: SU-DHL-8 GSM5710038 (re-analyzed)

description: GSM5710038 (re-analyzed)

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: GSH_RADONC_RectalCancer_025

value: 50,4 + Capecetabine


title: Toledo GSM5710040 (re-analyzed)

description: GSM5710040 (re-analyzed)

value: Toledo

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: ACTped36

source_name: Pediatric adrenocortical tumor 36

value: Tumor

tag: gender

value: Female

tag: age at diagnosis (months)

tag: sandrin stage

tag: metastasis

value: Absent

tag: relapse

value: absent

tag: vital status

value: alive


title: Nped1

source_name: Pediatric non-neoplastic adrenal 1


title: ACTped37

source_name: Pediatric adrenocortical tumor 37


title: MEF_NoDox_S1 [scRNA-seq]

tag: cell type

tag: time point

value: NoDox


title: SU-DHL-5 GSM5710036 (re-analyzed)

description: GSM5710036 (re-analyzed)


title: EB_NoDox_D25_Etv2_rep2 [bulk RNA-seq]

data_processing:
The sequencing reads were mapped to the mouse genome mm10 using TopHat
The raw read counts were obtained by HTSeq
The read counts data were normalized by DESeq2, followed by differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts.txt

extract_protocol: EBs were harvested as described above.

value: EB


title: GSH_RADONC_RectalCancer_024

value: Pre-CRT

value: Rectal cancer

value: Non-pCR


title: EB_NoDox_D25_Etv2_rep1 [bulk RNA-seq]


title: GSH_RADONC_RectalCancer_023


title: ACTped35

source_name: Pediatric adrenocortical tumor 35

tag: tissue


title: SU-DHL-4 GSM5710035 (re-analyzed)

description: GSM5710035 (re-analyzed)


title: MEF_Dox_D2_S3 [scRNA-seq]

value: MEF

tag: treatment

value: Dox


title: GSH_RADONC_RectalCancer_022

tag: time

value: pCR


title: EB_Dox_D25_Flk1pos_Etv2_rep2 [bulk RNA-seq]

value: TRUE


title: SP-53 GSM5710033 (re-analyzed)

description: GSM5710033 (re-analyzed)

value: Mantle Cell Lymphoma


title: GSH_RADONC_RectalCancer_027

tag: cancer type


title: EB_Dox_D25_Flk1pos_Etv2_rep1 [bulk RNA-seq]


title: GSH_RADONC_RectalCancer_021

tag: treatment response pcr vs. non-pcr


title: ACTped33

source_name: Pediatric adrenocortical tumor 33

value: Male


title: ACTped34

source_name: Pediatric adrenocortical tumor 34

value: Present

value: present

value: dead


title: GSH_RADONC_RectalCancer_020

tag: disease free survival event


title: SP-49 GSM5710032 (re-analyzed)

description: GSM5710032 (re-analyzed)


title: EB_Dox_D25_Etv2_rep2 [bulk RNA-seq]

value: FALSE


title: ACTped32

source_name: Pediatric adrenocortical tumor 32

value: Tumor

value: Absent

value: absent


title: GSH_RADONC_RectalCancer_019

tag: disease free survival time (months)


title: REC-1 GSM5710031 (re-analyzed)

description: GSM5710031 (re-analyzed)

tag: cell line


title: EB_Dox_D25_Etv2_rep1 [bulk RNA-seq]

value: EB


title: GSH_RADONC_RectalCancer_018

value: Pre-CRT


title: EB_NoDox_D2_Etv2_rep2 [bulk RNA-seq]

value: NoDox


title: ACTped30

source_name: Pediatric adrenocortical tumor 30

value: Female

value: alive


title: ACTped31

source_name: Pediatric adrenocortical tumor 31


title: Ramos GSM5710030 (re-analyzed)

description: GSM5710030 (re-analyzed)

value: Ramos

tag: pathology

value: Burkitt’s Lymphoma


title: ACTped29

source_name: Pediatric adrenocortical tumor 29

tag: gender


title: Raji GSM5710029 (re-analyzed)

description: GSM5710029 (re-analyzed)

value: Raji


title: GSH_RADONC_RectalCancer_017

value: Rectal cancer

value: Non-pCR


title: SU-DHL-10 GSM5710034 (re-analyzed)

description: GSM5710034 (re-analyzed)

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: EB_NoDox_D2_Etv2_rep1 [bulk RNA-seq]


title: ACTped28

source_name: Pediatric adrenocortical tumor 28

tag: age at diagnosis (months)

value: Present


title: GSH_RADONC_RectalCancer_016


title: EB_Dox_D2_Etv2_rep2 [bulk RNA-seq]

value: Dox


title: ACTped27

source_name: Pediatric adrenocortical tumor 27

tag: sandrin stage


title: GSH_RADONC_RectalCancer_015


title: OCI-Ly3 GSM5710026 (re-analyzed)

description: GSM5710026 (re-analyzed)

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: EB_Dox_D2_Etv2_rep1 [bulk RNA-seq]

value: FALSE


title: GSH_RADONC_RectalCancer_014


title: 8345_PBMC_GST_S2

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

data_processing:
The quality of RNA-Seq raw reads were evaluated using FastQC quality control tool, filtered using the TrimGalore software (version 0.4.1 with the parameter-illumina), Afterwards, a reference genome index was established using Bowtie2 software.
Sequence reads were trimmed off adaptor sequences and independently aligned using TrimGalore software (version 0.4.1 with the parameter-illumina) with default setting against mRNA  accounting for a maximum of two gaps or mismatches in each sequence
Differential expression, p-value and fold changes for each gene were determined using linear model in R with the package Cuffdiff  (version 2.2.1) according to a design with a single factor comprising all different experimental groups with default parameters.
Genome_build: PlasmoDB Release 33

source_name: PBMCs

growth_protocol: All strains were collected from PBMCs from mice treated with recombinant PbTIP and GST protein

extract_protocol:
Eight C57BL/6 mice were treated with recombinant PbTIP (2mg/Kg) for four consecutive days and eight mice were treated with GST protein (control protein) in similar way. Upon treatment, blood from each mice group is pooled and PBMCs were isolated by percoll density gradient centrifugation. The PBMCs RNA was isolated using Trizol (sigma) and RNA integrity was estimated by its RIN value which was above 8. More than ….ug of RNA was given for transcriptome analysis.
The sequencing library is prepared by random fragmentation of the cDNA sample preparation kit (TruSeq RNA Sample Preparation v2 Guide, Part #15026495 Rev. F.) according to the manufacturer’s instructions. Briefly the total RNA (5µg) were ligated 5’ and 3' adapter using T4 RNA ligase 2 truncated (NEB)and a 5' and 3’ adapter using  T4 RNA ligase 2. The ligation products were reverse transcribed using Superscript II Reverse Transcriptase (Life Technologies) and amplified with  PCR (12 Cycle). The PCR products were purified with electrophoresis of 6% Novex TBE PAGE Gel. The purified cDNA library for each sample was analyzed on Agilent 2100 Bioanalyzer using Agilent DNA high sensitivity kit.

tag: strain

value: PBMCs

value: recombinant GST


title: GSH_RADONC_RectalCancer_013


title: OCI-Ly1 GSM5710024 (re-analyzed)

description: GSM5710024 (re-analyzed)


title: 8344_PBMC_GST_S1


title: ACTped26

source_name: Pediatric adrenocortical tumor 26

value: Tumor

tag: metastasis

value: Absent

tag: relapse

value: absent


title: Mino GSM5710021 (re-analyzed)

description: GSM5710021 (re-analyzed)

value: Mino

value: Mantle Cell Lymphoma


title: ACTped25

source_name: Pediatric adrenocortical tumor 25

value: Female

tag: vital status

value: alive


title: GSH_RADONC_RectalCancer_012

value: Pre-CRT


title: ACTped24

source_name: Pediatric adrenocortical tumor 24


title: MD903 GSM5710019 (re-analyzed)

description: GSM5710019 (re-analyzed)

source_name: Cell line


title: MAVER-1


title: 8349_PBMC_PbTIP_S2

value: recombinant PbTIP


title: GSH_RADONC_RectalCancer_011

value: Rectal cancer

value: Non-pCR


title: 8701_PBMC_PbTIP_S1


title: GSH_RADONC_RectalCancer_010


title: MEF_NoDox_rep2

description:
MEF_NoDox_treat_pileup.bw
MEF_NoDox_summits.bed

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2. The ATAC-seq lied within the blacklisted genomic regions for functional genomics analysis were excluded. ChromVAR (v1.10) were used for transcription factor based chromatin accessibility analysis.  321 transcription factors compiled in the Homer database were used for the chromVAR analysis.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: bed files

source_name: MEF

value: Day 0

tag: dox or no dox

value: NoDox


title: ACTped22

source_name: Pediatric adrenocortical tumor 22

tag: tissue


title: GSH_RADONC_RectalCancer_009

tag: treatment


title: Pfeiffer GSM5710028 (re-analyzed)

description: GSM5710028 (re-analyzed)

value: Pfeiffer

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: Jeko-1 GSM5710010 (re-analyzed)

description: GSM5710010 (re-analyzed)


title: MEF_NoDox_rep1

tag: time

value: FALSE


title: JVM2 GSM5710011 (re-analyzed)

description: GSM5710011 (re-analyzed)


title: HT GSM5710009 (re-analyzed)

description: GSM5710009 (re-analyzed)

value: HT


title: GSH_RADONC_RectalCancer_008

tag: cancer type


title: EB_NoDox_D25_rep2

description:
EB_NoDox_D25_treat_pileup.bw
EB_NoDox_D25_summits.bed

source_name: EB


title: ACTped21

source_name: Pediatric adrenocortical tumor 21

value: Tumor


title: HBL-2


title: ACTped20

source_name: Pediatric adrenocortical tumor 20

value: Absent

value: present

value: dead


title: ACTped23

source_name: Pediatric adrenocortical tumor 23


title: GSH_RADONC_RectalCancer_007

tag: treatment response pcr vs. non-pcr


title: EB_NoDox_D25_rep1


title: ACTped19

source_name: Pediatric adrenocortical tumor 19

value: absent


title: GSH_RADONC_RectalCancer_006

tag: disease free survival event


title: EB_Dox_D25_Flk1pos_rep2

description:
EB_Dox_D25_Flk1pos_treat_pileup.bw
EB_Dox_D25_Flk1pos_summits.bed

value: Dox

value: TRUE


title: ACTped18

source_name: Pediatric adrenocortical tumor 18

value: Male


title: ACTped16

source_name: Pediatric adrenocortical tumor 16

value: Female

value: alive


title: ACTped17

source_name: Pediatric adrenocortical tumor 17


title: GRANTA519 GSM5710005 (re-analyzed)

description: GSM5710005 (re-analyzed)

value: Mantle Cell Lymphoma


title: GSH_RADONC_RectalCancer_005

value: Pre-CRT

value: Rectal cancer

value: Non-pCR

tag: disease free survival time (months)


title: shCtrl

city: Shanghai

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

department: Biochemistry and Molecular Cell Biology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: xlsx file for gene information and FPKM for shCtrl, shSOX9#1 & shSOX9#2
Supplementary_files_format_and_content: xlsx file for transcripts information and FPKM for shCtrl, shSOX9#1 & shSOX9#2

source_name: lentiviral encoding control shRNA transduced Karpas-422 stable cells

growth_protocol: aformentiones stable cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
mRNA was isolated from total RNA using NEB Next poly (A) mRNA Magnetic Isolation Module (NEB, MA, USA) and rRNA was removed using RiboZero Magnetic Gold Kit (Epicentre NY, USA).
RNA library was prepared using KAPA Stranded RNA-SEQ Library Prep Kit (illumina, CA, USA) according to instruction manual prior to subject to sequencing using illumina NovaSeq 6000.

tag: cell line

value: Diffuse large B cell lymphoma cells

tag: transduction

value: control shRNA


title: SOX9 shRNA#2 (Sh2)

source_name: lentivrial encoding SOX9 shRNA#2 transduced Karpas-422 stable cells

value: SOX9 shRNA#2


title: GSH_RADONC_RectalCancer_004

value: pCR


title: EB_Dox_D25_rep2

description:
EB_Dox_D25_treat_pileup.bw
EB_Dox_D25_summits.bed

value: FALSE


title: SOX9 shRNA#1 (Sh1)

source_name: lentiviral encoding SOX9 shRNA#1 transduced Karpas-422 stable cells

value: SOX9 shRNA#1


title: GSH_RADONC_RectalCancer_003


title: ACTped15

source_name: Pediatric adrenocortical tumor 15

value: Tumor

tag: gender

value: Absent


title: EB_Dox_D25_rep1

value: Dox


title: MEF_Dox_D7_Flk1pos_rep2

description:
MEF_Dox_D7_Flk1pos_treat_pileup.bw
MEF_Dox_D7_Flk1pos_summits.bed

value: Day 7

value: TRUE


title: GSH_RADONC_RectalCancer_002


title: HBE FOXA1 FOXA2 KD rep3

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample

source_name: HBE FOXA1 FOXA2 KD rep3

growth_protocol: HBE ALI cells were cultured according to Fulcher et al. 2005

extract_protocol:
Confluent HBE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: Samples were treated with negative control siRNA (sc-37007, Santa Cruz Biotechnology) or siRNA targetting either FOXA1 (sc-37930), FOXA2 (sc-35569), or a combination of the latter two, each at 30nM using RNAiMax transfection reagent (Life Technologies)

value: Human bronchial epithelial cells


title: Total RNA from ENKTL103

data_processing:
For fresh/frozen samples, alignment to human genome (hg38) was done using TopHat. Transcriptome assembly and analysis was performed using Cufflinks and expression was reported as FPKM
For FFPE-derived samples, low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64.  Samples were aligned to Ensemble Human reference GRCh37.97 using the RNA-Seq aligner STAR version 2.6.0c. Features were identified from Ensemble (grch37/release-97). Feature coverage counts were calculated using featureCounts, FPKMs values were generated based on overall alignment. Expression was normalized using DESeq2.
Genome_build: FFPE mapped to GRCh37.97 and fresh/frozen mapped to hg38
Supplementary_files_format_and_content: csv files include FPKM values for each sample

source_name: Tumor

tag: disease state

tag: sample type

value: ENKTL

tag: isolation type

value: FFPE

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: Total RNA from ENKTL101


title: MEF_Dox_D7_Flk1pos_rep1

tag: dox or no dox


title: Total RNA from ENKTL50


title: GSH_RADONC_RectalCancer_001

value: Pre-CRT

value: Rectal cancer


title: HBL-1 GSM5710006 (re-analyzed)

description: GSM5710006 (re-analyzed)

source_name: Cell line

tag: pathology

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: ACTped14

source_name: Pediatric adrenocortical tumor 14

tag: tissue

value: Male

tag: age at diagnosis (months)

tag: sandrin stage

tag: metastasis

value: Present

tag: relapse

value: present

tag: vital status

value: alive


title: MEF_Dox_D7_rep2

description:
MEF_Dox_D7_treat_pileup.bw
MEF_Dox_D7_summits.bed

source_name: MEF

tag: time

value: FALSE


title: Total RNA from ENKTL47

value: Tumor


title: ACTped13

source_name: Pediatric adrenocortical tumor 13

value: Female

value: Absent

value: absent


title: ACTped12

source_name: Pediatric adrenocortical tumor 12


title: EB_Dox_D25_Flk1pos_rep1

source_name: EB

value: Dox

value: TRUE


title: ACTped11

source_name: Pediatric adrenocortical tumor 11


title: MEF_Dox_D7_rep1

value: Day 7


title: ACTped10

source_name: Pediatric adrenocortical tumor 10


title: HBE FOXA1 FOXA2 KD rep1

source_name: HBE FOXA1 FOXA2 KD rep1

value: Human bronchial epithelial cells


title: HBE FOXA1 FOXA2 KD rep2

source_name: HBE FOXA1 FOXA2 KD rep2


title: ACTped9

source_name: Pediatric adrenocortical tumor 9

value: dead


title: MEF_Dox_D2_rep2

description:
MEF_Dox_D2_treat_pileup.bw
MEF_Dox_D2_summits.bed

value: Day 2


title: Total RNA from ENKTL37

value: ENKTL

value: FFPE

value: No


title: HBE FOXA2 KD rep3

source_name: HBE FOXA2 KD rep3


title: ACTped8

source_name: Pediatric adrenocortical tumor 8

value: Present


title: MEF_Dox_D2_rep1


title: Total RNA from ENKTL36


title: HBE FOXA2 KD rep2

source_name: HBE FOXA2 KD rep2


title: ACTped7

source_name: Pediatric adrenocortical tumor 7


title: Total RNA from ENKTL29


title: Total RNA from ENKTL30


title: MEF_Dox_D1_rep1

description:
MEF_Dox_D1_treat_pileup.bw
MEF_Dox_D1_summits.bed

value: Day 1


title: ACTped6

source_name: Pediatric adrenocortical tumor 6

value: present

value: alive


title: MEF_Brg1_KD_NoDox_D7_rep2

description:
MEF_Brg1_KD_NoDox_D7_treat_pileup.bw
MEF_Brg1_KD_NoDox_D7_summits.bed

value: NoDox

value: FALSE


title: Total RNA from ENKTL25

source_name: Tumor

value: Tumor


title: HBE FOXA1 KD rep3

source_name: HBE FOXA1 KD rep3


title: HBE FOXA1 KD rep2

source_name: HBE FOXA1 KD rep2


title: MEF_Brg1_KD_NoDox_D7_rep1

source_name: MEF


title: ACTped5

source_name: Pediatric adrenocortical tumor 5

value: Female

value: Absent

value: absent


title: Total RNA from ENKTL18


title: HBE FOXA1 KD rep1

source_name: HBE FOXA1 KD rep1


title: HBE Negative Control rep3

source_name: HBE Negative Control rep3


title: MEF_Brg1_KD_NoDox_D2_rep2

description:
MEF_Brg1_KD_NoDox_D2_treat_pileup.bw
MEF_Brg1_KD_NoDox_D2_summits.bed


title: Total RNA from ENKTL24


title: ACTped4

source_name: Pediatric adrenocortical tumor 4


title: Total RNA from ENKTL16


title: HBE Negative Control rep2

source_name: HBE Negative Control rep2


title: MEF_Brg1_KD_NoDox_D1_rep2

description:
MEF_Brg1_KD_NoDox_D1_treat_pileup.bw
MEF_Brg1_KD_NoDox_D1_summits.bed


title: Total RNA from ENKTL13


title: MEF_Dox_D1_rep2

value: Dox


title: ACTped3

source_name: Pediatric adrenocortical tumor 3

value: Male


title: HBE FOXA2 KD rep1

source_name: HBE FOXA2 KD rep1

value: Human bronchial epithelial cells


title: ACTped2

source_name: Pediatric adrenocortical tumor 2


title: ACTped1

source_name: Pediatric adrenocortical tumor 1

value: dead


title: HBE Negative Control rep1

source_name: HBE Negative Control rep1


title: MEF_Brg1_KD_NoDox_D1_rep1


title: Total RNA from ENKTL10

value: ENKTL


title: Total RNA from ENKTL3

value: FFPE


title: MEF_Brg1_KD_Dox_D7_rep1

description:
MEF_Brg1_KD_Dox_D7_treat_pileup.bw
MEF_Brg1_KD_Dox_D7_summits.bed

value: Day 7


title: MEF_Brg1_KD_Dox_D2_rep2

description:
MEF_Brg1_KD_Dox_D2_treat_pileup.bw
MEF_Brg1_KD_Dox_D2_summits.bed

value: Day 2


title: MEF_Brg1_KD_NoDox_D2_rep1


title: MEF_Brg1_KD_Dox_D2_rep1


title: EPTH-P1

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St. LRB525

department: Molecular, Cell & Cancer Biology

institute: UMass Medical School

data_processing:
RNA-seq reads were aligned to the human reference genome GRCh38/hg19 by using Tophat2 (version 2.1.1) with minimal and maximal intron length set as 20 bp and 100 kb, respectively.
The resulting BAM files were sorted by name using samtools (1.4.1) and processed by using MMR to assign multi-mapper reads to their most likely genomic locations.
The BAM files output by MMR were input to featureCounts (version 1.5.3) to generated a gene-level count summary table with the following explicit option settings –d 35 –t exon –M and the GTF file for the reference genome GRCh38.89 as the genome annotation file
Genome_build: hg38
Supplementary_files_format_and_content: raw count table in a matrix format: column 1 is the GeneID; the others are raw count per gene generated by featureCounts.

molecule: polyA RNA

growth_protocol: Cells were cultured  in MEBM kit from Lonza

extract_protocol:
RNA was extracted using RNA isolation kit.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq  poly(A) selected kit with 300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.
Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer. 150 bp paired end reads were sequenced on Illumina HighSeq 4000 (Illumnia Inc., San Diego, CA).

treatment_protocol: Cells  were FACS sorted in eoithelial and mesenchymal population using CD24 and ITGB4 antibodies.

tag: cell line

value: HMLER

tag: cell type

value: Epithelial-like, tumorigenic human mammary cells

tag: cell subpopulation

value: epithelial population


title: EPTH-P2


title: MES_P1

value: mesenchymal population


title: MES_P2


title: PFC Setd1a+/- H3K4me3 CUT&RUN Sample1

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
Library strategy: CUT&RUN
Raw reads were first preprocessed to remove low quality reads and adaptor sequences using Trimgalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameter “--paired”. The trimmed reads were then aligned to the mm10 genome using Bowtie2 (v2.3.4.3) [PMID: 19261174]  with parameters “‘--no-unal --no-mixed --no-discordant -I 150 -X 2000”. Samtools (v1.9) [PMID: 19505943]  was used to remove low mapping quality (mapq <10) and unmapped reads. Only uniquely mapped reads were kept for downstream analysis. Bigwig tracks were generated using “bamCoverage” command from deepTools (v3.0.2) [PMID: 24799436]  with parameters “--binSize 20 --extendReads 250 --normalizeUsing RPKM --outFileFormat bigwig  --minMappingQuality 30 --scaleFactor 1”. The bigwigs of the CUT&RUN samples with yeast spiked-in data were scaled based on the number of uniquely mapped reads to the yeast genome normalized to 100,000 reads (saling factor=10^5/[#uniquely mapped spikein reads]). The differential peaks were detected using the R/Bioconductor package Linnorm (v.2.16.0) [PMID: 28981748] for non-spikein CUT&RUN data, and we used the R/Bioconductor package csaw (v1.20.0) [PMID: 26578583] for comparison between spiked-in samples
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: PFC

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
FACS sorted nuclei were used for CUT&RUN experiments. Briefly, Foxp2-Cre or Foxp2-Cre/Setd1a+/- mice were euthanized by inhalation of CO2. Brains were rapidly removed and the prefrontal cortex was dissected and immediately frozen with dry ice and then stored at −80 °C until processing for nuclear isolation. Frozen brain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 20 times with pestle A, followed by 20 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 μm cell strainer (Fisher) and added 1 ml dilution buffer [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6000×g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for FACS. The GFP+ nuclei were directly sorted into CUT&RUN wash buffer with Sony SH800 sorter. The sorted nuclei were immediately used for CUT&RUN experiments.
CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).

tag: strain

value: PFC

tag: Sex

value: male

tag: age

value: 8-10 weeks

tag: treatment

value: Setd1a CRISPR-Cas9

tag: chip antibody

value: H3K4me3 (Cell Signaling 9727S)


title: PFC WT H3K4me3 CUT&RUN Sample2


title: MEF_Brg1_KD_Dox_D1_rep2

description:
MEF_Brg1_KD_Dox_D1_treat_pileup.bw
MEF_Brg1_KD_Dox_D1_summits.bed

value: Day 1

tag: dox or no dox

value: Dox

value: FALSE


title: PFC Setd1a+/- H3K4me3 CUT&RUN Sample2


title: PFC WT H3K4me3 CUT&RUN Sample1


title: MEF_Brg1_KD_Dox_D1_rep1


title: MEF_Brg1_KD_Dox_D7_rep2


title: PFC WT Setd1a CUT&RUN Sample2


title: PFC WT Setd1a CUT&RUN Sample1


title: Sham_2: IR, biological rep2

city: Dalian

first: shi

middle: yong

last: quan

state: Liaoning

address: No.9, west section, lvshunkou district, dalian

institute: DALIAN MEDICAL UNIVERSITY

description: Ischemia reperfusion

hyb_protocol: Following labeling, cDNA was hybridized on a GeneChip Mouse Transcriptom Array 1.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

source_name: Ischemia reperfusion

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: After liver resection, normal water and diet were restored.The regenerated liver tissues were harvested at 6h, 12h and 24h, respectively.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Remove the regenerated liver and freeze it in liquid nitrogen for one hour, then transfer it to the refrigerator at -80 ℃.

value: Regenerative liver


title: Sham_1: IR, biological rep1

description: Ischemia reperfusion


title: IR_per50PHx6h_2: IR+50%PH at 6h, biological rep2

description: Ischemia reperfusion and liver regeneration 6 hours after 50% liver resection


title: IR_per50PHx6h_3: IR+50%PH at 6h, biological rep3

source_name: Ischemia reperfusion and liver regeneration 6 hours after 50% liver resection


title: Sham_3: IR, biological rep3

description: Ischemia reperfusion


title: MEF_Brg1_KD_D0_rep2

description:
MEF_Brg1_KD_D0_treat_pileup.bw
MEF_Brg1_KD_D0_summits.bed

value: Day 0

value: NoDox


title: IR_per50PHx6h_1: IR+50%PH at 6h, biological rep1


title: IR_per50PHx12h_2: IR+50%PH at 12h, biological rep2

description: Ischemia reperfusion and liver regeneration 12 hours after 50% liver resection


title: MEF_Brg1_KD_D0_rep1


title: Rat lung_14d_50mg/kg rep3

city: Jinan

first: Cunxiang

last: Bo

state: Shandong

address: Jingshi road  NO 18877

institute: Shandong Academy of Occupational Health and Occupational Medicine

description: Gene expression after 28d in silica-exposed rat lung

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 14.8 Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis.

organism: Rattus norvegicus

source_name: Rat lung_14d_50mg/kg rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: All the rats grew normally

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

treatment_protocol: Rats in the model group were intratracheally instilled with 50 mg/mL silicon dioxide (1mL per rat) and rats in the control group were treated with 1.0 mL saline (1mL per rat). Lung tissue was analysed 28 days later.

value: lung

tag: gender

tag: agent

value: 50 mg/mL silicon dioxide

tag: time point

value: Wistar


title: PFC Setd1+/- Bulk RNA-Seq Sample2

data_processing:
Raw reads were first preprocessed to remove low quality reads and adaptor sequences using Trimgalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameter “--paired” for paired-end samples. Reads were mapped to the reference genome was performed with STAR (v.2.7.3a) (PMID: 23104886) software. Gene level quantification was done using RSEM (v.1.3.0) (PMID: 21816040). Differential gene expression were performed using the R/Bioconductor package edgeR (3.28.0) (PMID: 19910308).
Bigwig files were generated using deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
For Foxp2+ neuron-specific RNA-Seq, Foxp2-Cre or Foxp2-Cre/Setd1a+/- mice were euthanized by inhalation of CO2. Brains were rapidly removed and the prefrontal cortex was dissected and immediately frozen with dry ice and then stored at −80 °C until processing for nuclear isolation. Frozen brain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 20 times with pestle A, followed by 20 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 μm cell strainer (Fisher) and added 1 ml dilution buffer [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6000×g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for FACS. The GFP+ nuclei were directly sorted into Trizol (Thermo Fisher) with Sony SH800 sorter. The RNA was extracted with Direct-zol RNA Microprep Kits (Zymo) and store at −80 °C upon use.
The RNA-seq library were constructed with Smart-seq V4 reagents following the manufacturer's protocol

tag: tissue


title: WT3_L

city: Ulm

first: Giorgio

last: Caratti

address: Helmholzstraße 8/1

institute: University of Ulm

data_processing:
Index of reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FKPM of each gene was then calculated on the length of the gene and the reads count mapped to this gene.
Differential expression analysis of two conditions/groups (2-3 biological replicates per condition) was performed using the DESeq2 R package.
Genome_build: GRCM38 (mm10)
Supplementary_files_format_and_content: *_fkpm.txt: Tab-delimited text files contain FKPM values per sample.

source_name: Bone-marrow-derived macrophages

growth_protocol: To culture bone-marrow-derived macrophages, total bone marrow was isolated from mice by flushing the femur and tibiae bone marrow with culture medium. Extracted bone marrow was cultured in DMEM high glucose high pyruvate containing 20% of FBS, 1% of penicillin/streptomycin, 1% of fungizone and 30% of L929 conditioned medium for 5 to 7 days.

extract_protocol:
RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene.

treatment_protocol: Differentiated BMDMs exposed to vehicle (DMSO), dexamethasone (100nM), lipopolysaccharide (100ng/ml), DAMPs (1ug/ml) or a combination of lipopolysaccharide and dex, or DAMPs and dex for 24 hours before RNA isolation.

tag: genotype

value: WT

value: Bone-marrow-derived macrophages

value: Lipopolysaccharide


title: WT3_V

value: Vehicle (DMSO)


title: Rat lung_14d_50mg/kg rep1

source_name: Rat lung_14d_50mg/kg rep1

value: male


title: PFC Setd1+/- Bulk RNA-Seq Sample1

value: PFC

value: 8-10 weeks


title: IR_per50PHx12h_1: IR+50%PH at 12h, biological rep1

source_name: Ischemia reperfusion and liver regeneration 12 hours after 50% liver resection


title: IR_per50PHx12h_3: IR+50%PH at 12h, biological rep3


title: PFC WT Bulk RNA-Seq Sample1


title: Rat lung_14d_50mg/kg rep2

source_name: Rat lung_14d_50mg/kg rep2


title: Rat lung_14d_0mg/kg rep3

source_name: Rat lung_14d_0mg/kg rep3

value: 1.0 mL saline


title: WT3_LDe

value: Lipopolysaccharide + Dexamethasone


title: PFC WT Bulk RNA-Seq Sample2


title: WT3_De

value: Dexamethasone


title: WT3_DADe

value: DAMPs + Dexamethasone


title: IR_per50PHx24h_2: IR+50%PH at 24h, biological rep2

description: Ischemia reperfusion and liver regeneration 24 hours after 50% liver resection

value: Regenerative liver


title: IR_per50PHx24h_1: IR+50%PH at 24h, biological rep1

source_name: Ischemia reperfusion and liver regeneration 24 hours after 50% liver resection


title: NAc Setd1+/- scRNA-Seq Sample1

data_processing:
Raw sequencing data were processed with cellranger (v3.0.2) (Zheng et al., 2017) for sample demultiplexing, cell barcode detection and single-cell expression matrices generation. In brief, the “cellranger  mkfastq” command was used to demultiplex the different samples, extract the UMI barcodes and generate the fastq files. The gene-cell expression matrices were then generated for each sample separately using the “cellranger count” command by aligning the reads to the mm10 genome.
We used CellRange (v.3.0.2) (PMID:28091601) to process the libraries generated by the 10x Genomics Single-Cell Chromium Controller. We used the “mkfastq” command to generate demultiplexed FASTQ files from Illumina base call files. Next, the CellRanger command “count” was used to quantify gene expression, identify valid cell-barcodes and generate the initial gene×cell matrix for each sample. We used the R package Seurat (v3.2.0) (PMID: 31178118) for downstream analysis. We kept all the genes that are expressed in at least 3 cells and we filtered out cells expressing less than 800 genes or having more than 10% of their transcriptome coming from mitochondrial genes. Gene expression in each cell was normalized to 10,000 reads, and the top 2,000 variable genes for each sample were identified using function “FindVariableFeatures”. The individual samples of each tissue were combined together using the Canonical Cross-Correlation method (CCA) from Seurat, by calling the function “FindIntegrationAnchors” followed by the function “IntegrateData“ both with parameters “dims=1:30”. The top 30 principle component were used to generate the UMAP dimension reduction representations. Clusters were identified using the function “FindClusters” with a resolution of 0.4. Similar clusters were merged after manual inspection. The R/Bioconductor package DEsingle (v1.12.0) was used to detected differentially expressed genes (FDR < 0.05, FC > 1.5) in each cell type between wild-type and Setd1a heterozygous cells
*_scRNAseq_meta.csv was generated  by combining count expression matrices of WT and Setd1+/- filtered cell.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated files

source_name: NAc

extract_protocol:
For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation . The PFC tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion.
The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp).

value: NAc

value: Setd1a CRISPR-Cas9


title: Rat lung_28d_50mg/kg rep3

source_name: Rat lung 28d 50mg/kg replicate3

value: lung


title: NAc Setd1+/- scRNA-Seq Sample2


title: IR_per50PHx24h_3: IR+50%PH at 24h, biological rep3


title: Rat lung_14d_0mg/kg rep1

source_name: Rat lung_14d_0mg/kg rep1


title: WT3_DA

value: DAMPs


title: Rat lung_14d_0mg/kg rep2

source_name: Rat lung_14d_0mg/kg rep2

value: Wistar


title: NAc WT scRNA-Seq Sample2


title: Rat lung_28d_50mg/kg rep2

source_name: Rat lung 28d 50mg/kg replicate2

value: 50 mg/mL silicon dioxide


title: IR_per85PHx6h_3: IR+85%PH at 6h, biological rep3

description: Ischemia reperfusion and liver regeneration 6 hours after 85% liver resection


title: WT2_V

value: WT

value: Bone-marrow-derived macrophages


title: IR_per85PHx6h_2: IR+85%PH at 6h, biological rep2

source_name: Ischemia reperfusion and liver regeneration 6 hours after 85% liver resection


title: ATAC-seq Day7 Ly6c2+ Rep C

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
For scRNA-seq, sequencing was performed on Illumina HiSeq 4000 (paired end, 50bp).  For bulk RNA-seq, sequencing was performed on Illumina HiSeq 4000 (single end, 50bp).  For ATAC-seq, sequencing was performed on Illumina HiSeq 4000 (paired end, 100bp).
For scRNA-seq, the digital expression matrix was generated by demultiplexing, barcode processing, and gene unique molecular index counting using the Cellranger count pipeline (10X Genomics).  For bulk RNA-seq, the reads were mapped with STAR (version 2.5.3.a) to the mouse genome. The counts for each gene were obtained by using –quantMode GeneCounts commands in STAR, and the other parameters during alignment were set to default.  For ATAC-seq, reads were trimmed to remove low-quality reads and adapters using Cutadapt (version 2.3). The reads were aligned to the reference mouse genome with bowtie2 (version 2.2.9). Peak calling was performed with MACS2 (version 2.1.1). The peaks from all samples were merged into a single bed file, peaks from different samples that were closer than 10bp were merged into a single peak. HTseq (version 0.9.1) was used to count the number of reads that overlap each peak per sample.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts files for every gene/peak and every cell/sample

source_name: ATAC-seq Day7 Ly6c2+

growth_protocol: Mice were bred at UCLA in accordance with the guidelines of the institutional Animal Care and Use Committee (IACUC). The following mouse strains were used this study: C57BL/6 (CD45.2) (Jackson Labs, #000664), B6.SJL (CD45.1) (Jackson Labs, #002114), Ly49H-/- (Ly49H-deficient). Experiments were conducted using 6-8 week old age- and gender-matched mice in accordance with approved institutional protocols.

extract_protocol:
Mice were bred at UCLA in accordance with the guidelines of the institutional Animal Care and Use Committee (IACUC). Experiments were conducted using 6-8 week old age- and gender-matched mice in accordance with approved institutional protocols.
Mouse spleens, livers, lungs, lymph nodes, and blood were harvested and prepared into single cell suspensions. Splenic single cell suspensions were red blood cell lysed and resuspended in EasySep™ buffer (Stemcell). NK cell enrichment was performed with 10 μg per spleen of biotin conjugated antibodies against CD3 (17A2), CD19 (6D5), CD8 (53-6.7), CD88 (20/70), Ly6G (1A8), SiglecF (S17007L), TCR (H57-597), CD20 (SA275A11), CD172a (P84) and magnetically depleted from total splenocyte suspensions with the use of anti-biotin coupled magnetic beads (Biolegend).
scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics). Cells were loaded accordingly to 10X Genomics protocol with an estimated targeted cell recovery of 5000 cells.
bulk RNA-seq libraries were generated using the RNeasy Mini kit (Qiagen).
For ATAC-Seq, 50,000 cells per sample were lysed to collect nuclei and treated with Tn5 transposase (Illumina) for 30 minutes at 37°C with gentle agitation. The DNA was isolated with DNA Clean & Concentrator Kit (Zymo) and PCR amplified and barcoded with NEBNext High-Fidelity PCR Mix (New England Biolabs) and unique dual indexes (Illumina). The ATAC-Seq library amplification was confirmed by real-time PCR, and additional barcoding PCR cycles were added as necessary while avoiding overamplification. Amplified ATAC-Seq libraries were purified with DNA Clean & Concentrator Kit (Zymo). The purified libraries were quantified with Kapa Library Quant Kit (KAPA Biosystems) and quality assessed on 4200 TapeStation System (Agilent).

value: Ly49H+ NK cells

tag: genotype/variation


title: PFC Setd1+/- scRNA-Seq Sample2

source_name: PFC

value: male


title: PFC Setd1+/- scRNA-Seq Sample1

value: PFC


title: WT2_L

value: Lipopolysaccharide


title: ATAC-seq Day7 Ly6c2+ Rep B


title: Rat lung_28d_0mg/kg rep2

source_name: Rat lung 28d 0mg/kg replicate2

value: 1.0 mL saline


title: WT2_De


title: ATAC-seq Day7 Ly6c2- Rep C

source_name: ATAC-seq Day7 Ly6c2-


title: IR_per85PHx12h_3: IR+85%PH at 12h, biological rep3

description: Ischemia reperfusion and liver regeneration 12 hours after 85% liver resection


title: Rat lung_28d_50mg/kg rep1

source_name: Rat lung_28d_50mg/kg replicate1


title: IR_per85PHx6h_1: IR+85%PH at 6h, biological rep1


title: Rat lung_28d_0mg/kg rep1

source_name: Rat lung_28d 0mg/kg replicate1


title: IR_per85PHx12h_1: IR+85%PH at 12h, biological rep1

source_name: Ischemia reperfusion and liver regeneration 12 hours after 85% liver resection


title: IR_per85PHx12h_2: IR+85%PH at 12h, biological rep2


title: WT2_DADe

source_name: Bone-marrow-derived macrophages


title: PFC WT scRNA-Seq Sample2

value: 8-10 weeks


title: Rat lung_28d_0mg/kg rep3

source_name: Rat lung 28d 0mg/kg replicate3


title: NAc WT scRNA-Seq Sample1


title: WT2_DA


title: ATAC-seq Day7 Ly6c2- Rep A


title: PF_Rep2

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

source_name: female germline stem cells

growth_protocol: Testes from 2- to 7-day postpartum KitW/WV mice were harvested and extracted following a previously described protocol(Bellve, 1993; Bellve et al., 1977). Briefly, after euthanasia by cervical dislocation, testes were collected, decapsulated, cut into small pieces, and then dissociated with collagenase IV (1 mg/ml, Sigma) for 10 min and in 0.05% trypsin (Gibco) for 6 min at 37°C in a shaking water bath. A single cell suspension was obtained after filtration through a 72-µm cell strainer, and cells were collected by centrifugation. KitW/WV mouse testicular cells were directly mixed with FGSCs/SSCs at a ratio of 1:1 or FGSCs/SSCs were seeded on KitW/WV mouse testicular cells that had been cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) FBS for 3 days. From day 0 to day 6, cells were cultured in MEMα (Invitrogen) supplemented with 20% Knockout Serum Replacement (KSR) (Gibco), BMPs-2/4/7 (20 ng/ml each, R&D Systems), retinoic acid (1 μM, Sigma), and activin A (100 ng/ml, R&D Systems). From days 7 to 14, cells were cultured in MEMα (Invitrogen) containing 20% KSR, testosterone (10 mM, Acros Organics), FSH (200 ng/ml, Sigma), and BPE (50 mg/ml, Stem cell). The medium was changed every day. Cells were cultured in 5% CO2 at 37℃.Germ cells of each stage were sorted by flow cytometry, based on being positive for EGFP or EBFP.To compare key stages during in vitro transdifferentiation of FGSCs with those of SSCs, we used FGSC/SSC lines expressing EGFP or EBFP controlled by the cell-specific stimulated by retinoic acid gene 8 (Stra8) (Nayernia et al., 2004) or the protamine 1 (Prm1) promoter (Nayernia et al., 2006; Zambrowicz et al., 1993), respectively.

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014)
DNA libraries were prepared for sequencing using standard Illumina protocols

value: female germline stem cells

tag: passages

tag: restriction enzyme

value: Mbol


title: ATAC-seq Day7 Ly6c2- Rep B


title: WT1_V

value: Vehicle (DMSO)


title: M1-Exos

city: Baoding

first: liu

last: huifang

address: NO.180 Wusi East Road

institute: Hebei University

data_processing:
Hiseq single-end sequencing mode was adopted in this project, and the original data were saved in FASTQ format after the machine was off. Then, the script independently developed by the company was used to remove the joint, and the quality shear was carried out according to the sequence quality, and the original sequence was compared with the window length of 5 bases When the average sequencing quality of bases in the window is lower than 20, the part starting from the front of the window is truncated and discarded, and the sequence is filtered for subsequent analysis.The number of Clean Reads (Total Reads) with sequence length between 18 nt-36 nt was counted, and the identical sequences in a single sample were de-processed and the sequence abundance was counted. These sequences were called Unique Reads for subsequent analysis.The filtered sequences are de-processed, that is, when identical sequences are merged, the corresponding abundance of the sequences is recorded.Genome alignment was performed using miRDeep2 (Mackowiak SD,2011) software, in which mapper.pl program called Bowtie to perform alignment between Unique Reads and reference genome sequences. According to the sequence number of mature miRNA of this species, the Reads Count value of measured miRNA was counted.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: expression; enrichment

source_name: macrophage

extract_protocol:
Exos were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat# NR801) was used with 1 ug of total RNA for the construction of sequencing libraries.
VAHTS small RNA Library Prep   Kit for Illumina
Make 3 ′ and 5 ′ joint connections using ligase
The Superscript II reverse transcriptase reverse transcribes the RNA into a double-stranded cDNA
The PCR was enriched for DNA fragments
Library sorting: Target fragment size products were separated on 15% fragment size according to the P A G E gel,then verify the library

value: 6-10 weeks old

value: wild type


title: WT2_LDe

value: Lipopolysaccharide + Dexamethasone


title: PF_Rep1


title: M0-Exos


title: IR_per85PHx24h_2: IR+85%PH at 24h, biological rep2

description: Ischemia reperfusion and liver regeneration 24 hours after 85% liver resection

value: Regenerative liver


title: PFC WT scRNA-Seq Sample1


title: IR_per85PHx24h_1: IR+85%PH at 24h, biological rep1

source_name: Ischemia reperfusion and liver regeneration 24 hours after 85% liver resection


title: D1_Positive_rep2

data_processing:
library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
Biscuit(v0.3.16) was used to map the sequencing reads to the mouse genome mm10
Methylation information was extracted using Bioscuit(v0.3.16)
Genome_build: mm10
Supplementary_files_format_and_content: bed

extract_protocol: The reagents used in the studies are GpC Methyltransferase (M.CviPI)

value: MEF

tag: time

tag: gpc methyltransferase (m.cvipi)

value: Yes

tag: assay type

value: NOMe


title: IR_per85PHx24h_3: IR+85%PH at 24h, biological rep3

tag: strain


title: D1_Positive_rep1

tag: cell type


title: WT1_LDe

value: WT

value: Bone-marrow-derived macrophages


title: bulk RNA-seq Day7 Ly6c2+ Rep B

source_name: bulk RNA-seq Day7 Ly6c2+

value: Ly49H+ NK cells


title: bulk RNA-seq Day7 Ly6c2+ Rep C


title: SF_Rep2


title: WT1_De

value: Dexamethasone


title: D1_Negative_rep2

value: No


title: SF_Rep1


title: D1_Negative_rep1


title: WT1_DADe

value: DAMPs + Dexamethasone


title: bulk RNA-seq Day7 Ly6c2- Rep C

source_name: bulk RNA-seq Day7 Ly6c2-


title: PS_Rep1

source_name: Spermatogonial stem cells

value: Spermatogonial stem cells


title: D0_Positive_rep2


title: bulk RNA-seq Day7 Ly6c2- Rep B


title: SS_Rep2


title: SS_Rep1


title: bulk RNA-seq Day7 Ly6c2- Rep A


title: D0_Positive_rep1


title: D0_Negative_rep2


title: KO3_LDe


title: KO3_V


title: scRNA-seq Day14

source_name: scRNA-seq Day14


title: PF-H3K27me3-2

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min at room temperature and quenched with 125mM glycine. Cells were then put on ice, resuspended in cold cell lysis buffer (140mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100 and 0.1% SDS and Protease Inhibitors (Roche)). Nuclei were sonicated into 200-1000 bp. The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Milipore).After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

value: female germline stem cells

tag: antibody

value: anti-H3K27me3 (07-449, Milipore)


title: scRNA-seq Day7

source_name: scRNA-seq Day7


title: D0_Negative_rep1


title: PF-H3K27me3-1


title: KO3_De

tag: treatment


title: ref2

type: genomic

city: Wako

first: Junko

last: Ueda

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

hyb_protocol: According to the standard Affymetrix protocol.

data_processing: The signal intensity data was analyzed with the MAT Software, using parameters: Bandwith= 300bp, Max Gap= 300, Min Probe= 10.Pvalue = 1e-3.

source_name: whole genome-amplified DNA

extract_protocol: Standard phenol–chloroform extraction protocols.

treatment_protocol: Fresh brain samples were separated into neuronal and noneuronal nuclei by NeuN-based cell sorting. Enrichment of methylated DNA was performed using MethylCollector (Active Motif).

value: whole genome-amplified DNA

tag: profile

value: Reference

tag: fractions

value: reference


title: ref1

scan_protocol: According to the standard Affymetrix protocol.


title: PF-H3K4me3-2-2

value: anti-H3K4me3 (ab8580, Abcam)


title: 4916_N

source_name: prefrontal cortex, nonneuron, TG mouse

label_protocol: According to the standard Affymetrix protocol.

value: prefrontal cortex, NeuN-, mC+

value: Control

value: non-neuronal nuclei


title: PF-H3K4me3-2-1


title: 4916_P

source_name: prefrontal cortex, neuron, TG mouse

value: prefrontal cortex, NeuN+, mC+

value: neuronal nuclei


title: PS_Rep2

value: Mbol


title: PF-H3K4me3-1-2


title: KO2_V

value: Bone-marrow-derived macrophages

value: Vehicle (DMSO)


title: WT1_DA

value: WT

value: DAMPs


title: KO2_LDe

value: Lipopolysaccharide + Dexamethasone


title: PF-H3K4me3-1-1

value: female germline stem cells


title: KO2_De

value: Dexamethasone


title: KO2_L

value: Lipopolysaccharide


title: SF-H3K27me3-2

value: anti-H3K27me3 (07-449, Milipore)


title: PF-INPUT


title: 4826_P


title: KO2_DADe

value: DAMPs + Dexamethasone


title: KO3_L


title: SF-H3K27me3-1


title: SF-H3K4me3-2

value: anti-H3K4me3 (ab8580, Abcam)


title: KO2_DA


title: 4772_N

value: prefrontal cortex, NeuN-, mC+


title: KO1_LDe


title: KO1_V


title: 4772_P

value: Control


title: KO3_DA


title: KO3_DADe


title: WSU-DLCL2 GSM5710043 (re-analyzed)

description: GSM5710043 (re-analyzed)

data_processing:
Whole-transcriptome RNA sequencing data was generated for 34 cell lines derived from lymphoma tumors: 11 from mantle cell lymphoma (MCL), 3 from Burkitt lymphoma, and 20 from diffuse large B-cell lymphoma (DLBCL; 14 of the germinal centre B-cell-like (GCB) subtype and 6 of the activated B-cell-like (ABC) subtype).
The STAR aligner (v2.5.3a_modified) was used to align reads to the GRCh38 reference and produce raw counts per gene.
Raw counts were read into R (v3.6.1) and normalized across all cell lines using a variance-stabilizing transformation in the DESeq2 package (v1.26.0).
Expression of CXCR4 between cell lines was visualized in R, and statistical comparisons between pathologies were performed using Student’s t-tests.
Genome_build: GRCh38

source_name: Cell line

extract_protocol: RNA sequencing data were generated using standard Illumina protocols at the British Columbia Cancer Research Centre from 34 lymphoma cell lines representing multiple pathologies. These datasets were generated at multiple timepoints.

tag: cell line

tag: pathology

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: SF-H3K4me3-1-1


title: SU-DHL-6 GSM5710037 (re-analyzed)

description: GSM5710037 (re-analyzed)


title: 4705_N

value: non-neuronal nuclei


title: 4705_P

value: prefrontal cortex, NeuN+, mC+

value: neuronal nuclei


title: KO1_L

value: Bone-marrow-derived macrophages


title: OCI-Ly7 GSM5710027 (re-analyzed)

description: GSM5710027 (re-analyzed)


title: SF-INPUT


title: KO1_De


title: OCI-Ly10 GSM5710025 (re-analyzed)

description: GSM5710025 (re-analyzed)

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: PS-H3K27me4

value: Spermatogonial stem cells


title: 4786_N


title: 4826_N


title: 4704_N


title: KO1_DADe


title: NU-DUL-1 GSM5710023 (re-analyzed)

description: GSM5710023 (re-analyzed)


title: 4704_P


title: KO1_DA

value: DAMPs


title: 4786_P


title: PS-H3K27me3


title: bulk RNA-seq Day7 Ly6c2+ Rep A

value: Ly49H+ NK cells

tag: time point


title: PS-H3K4me3-2


title: 4915_N

value: mutPolg


title: 4915_P


title: SF-H3K4me3-1-2

value: female germline stem cells


title: NU-DHL-1 GSM5710022 (re-analyzed)

description: GSM5710022 (re-analyzed)


title: PS-H3K4me3-1


title: PS-INPUT


title: Karpas422 GSM5710013 (re-analyzed)

description: GSM5710013 (re-analyzed)


title: H1_CXCR4_minus_Rep3

city: Guangzhou

first: Zhijun

last: Ren

address: 74 Zhongshan Rd.2

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4
adapter removed by cutadapt
The frequency of each sgRNA was measured using MAGeCK tools.

growth_protocol: HEK293T (ATCC® CRL-3216™) and A549 (ATCC® CCL-185™) cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (Hyclone, SH30022.01), supplemented with 10% fetal bovine serum (FBS, Hyclone, SH30406.05) and 2 mM GlutaMAX (Gibco, 35050061) at 37 °C with 5% CO2. H1 hESCs (obtained from the WiCell Research Institute) and the TRME hESCs cell line39 were grown in Matrigel (BD, 354277)-coated 6-well plates in E8 medium (Stem Cells Technology, 05940) at 37 °C with 5% CO2. Both cells were authenticated and tested for the absence of mycoplasma contamination using Myco-Blue Mycoplasma Detector (Vazyme).

extract_protocol:
Genomic DNA (gDNA) was extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102) and DNA concentration was measured by Qubit using the Qubit™ dsDNA HS Assay Kit (Invitrogen).
To generate sgRNA amplicons, we used a single-step PCR protocol which was adopted from the protocol published by Julia Joung et al 41. All the gDNA harvested from the screen was used for PCR amplification in 50 µl PCR reactions. Each reaction consisted of 2.5 µg gDNA plus water, 25 μL NEBNext Ultra II Q5 PCR Master Mix, 1.25 μL 10μM stagger forward primer, and 1.25 μL 10μM barcoded reverse primer. PCR reactions were cycling as follow: initial denature 3min at 98℃; followed by 30s denature at 98℃, 10s anneal at 63℃, 25s extension at 72℃, for 23 cycles; and final extension for 2min at 72℃. PCR products were size-selected using VAHTS DNA Clean Beads (Vazyme) according to the manufacturer’s instructions and sequenced on a HiSeq2000 sequencer (Illumina).
sgRNA-seq

tag: treatment/time point


title: 4824_N


title: DOHH-2 GSM5710003 (re-analyzed)

description: GSM5710003 (re-analyzed)


title: 4824_P


title: DB GSM5710001 (re-analyzed)

description: GSM5710001 (re-analyzed)

value: DB


title: SS-H3K27me3-2

value: anti-H3K27me3 (07-449, Milipore)


title: SS-H3K27me3-1


title: 4785_N


title: Peromyscus_polionotus_control_rep3

city: San Francisco

first: Ryan

last: York

address: 1328 6th Avenue

institute: Stanford University

data_processing:
To compare gene expression both across treatments and species, we first removed low-quality and adaptor sequences using SeqPrep (https://github.com/jstjohn/SeqPrep).
The P. maniculatus genome was masked at sites with SNPs using the perl script MaskReferencefromBED (https://github.com/TheFraserLab/ASEr) to avoid reference genome mapping bias. Reads from all F1 hybrid samples were aligned to this masked genome using STAR v 2.4.2a (Dobin et al., 2013) in 2-pass mode.
We determined ASE at the read-level using the script GetGeneASEbyReads in the ASEr package (https://github.com/TheFraserLab/ASEr).
To test for allele-specific expression differences, we first filtered ASE calls from GetGeneASEbyReads requiring at least 1 count per allele from all genes per sample.
After filtering we computed an ASE ratio for each gene by calculating the log2 ratio of P. maniculatus allelic counts compared to P. polionotus allelic counts. Positive values correspond to a P. maniculatus allelic bias while negative values reflect a P. polionotus bias.
Genome_build: pman 1.0
Supplementary_files_format_and_content: Matrix table with allele counts

organism: Peromyscus polionotus

source_name: Whole brain

growth_protocol: All experimental animals were males and housed in standard polysulfone cages (19.7 x 30.5 cm and 16.5 cm high; Allentown, New Jersey, USA) in same sex and genotype groups, until testing adults at approximately 50-80 days of age. Housing cages contained enrichment as previously described (Lewarch and Hoekstra, 2018). We maintained animals at 22 ºC with a 16:8h light:dark cycle and provided them with standard rodent food and water ad libitum. All procedures were approved by the Harvard University Institutional Animal Care and Use Committee (protocol 27-09-3)

extract_protocol:
To capture behavior-relevant gene expression, we focused on the brain. Therefore, at the conclusion of the test trial, we immediately euthanized animals using CO2 inhalation and rapidly dissected whole brains in chilled PBS, flash-froze the sample in liquid nitrogen, and stored it at -80 °C. Later, we homogenized tissues using a TissueLyser (Qiagen, Venlo, Netherlands) in Trizol (ThermoFisher Scientific, Waltham, MA, USA), and extracted total RNA using 5Prime Phase Lock Gel Tubes Heavy (Quantabio, Beverly, MA, USA), followed by clean-up with RNeasy columns (Qiagen, Venlo, Netherlands).
We prepared RNA-seq libraries with a TruSeq Stranded mRNA Library Prep Kit, following manufacturer’s instructions (Illumina, San Diego, CA, USA), and assessed library quality prior to sequencing using a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: We measured burrowing behavior using large sand-filled (Scott Pharma, Marlborough, MA, USA) enclosures (1.2 x 1.5 x 1.1 m) set up as previously described (Weber et al., 2013). We first ran all experimental animals through two “pretest” trials in the enclosures to allow them to acclimate and to confirm individuals burrowed in a species- (or hybrid-) typical manner. Next, we randomly assigned animals to a test trial cohort, “burrowing” or “control”.

tag: tissue

value: Whole brain

tag: condition


title: SS-H3K4me3-2

tag: passages

value: anti-H3K4me3 (ab8580, Abcam)


title: Peromyscus_polionotus_control_rep2


title: 4785_P


title: Selected pop. 4 on standard diet

city: Lausanne

first: Tadeusz

middle: J.

last: Kawecki

address: Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

data_processing:
fastq files from the two lanes for each sample were pooled
Reads were aligned to Dmel genome BDGP6.79 using kallisto v. 0.46.2 with options --single -l 101 -s 10 -b 100 -t 8; the output files are provided ("kallisto_abundance_sample…")
Raw counts per transcript were converted to raw counts per gene with tximport Bioconductor package
Genes with read count greater than 2 per million in at least 6 samples were retained, the rest were filtered out
Abundances were analyzed with limma-voom with implicit EdgeR normalization; normalized log2 expression values (eList$E) are provided as the expression matrix
Genome_build: BDGP6.79
Supplementary_files_format_and_content: Tab-delimited text files "kallisto_abundance_sample??.tsv" contain, for each sample, the FGtr ID of each transcript, its length and effective length, the absolute estimated number of counts (est_counts) and the counts per million (tpm)
Supplementary_files_format_and_content: CarcassesVoomNormlizedLog2Counts.txt: matrix table or voom log2-normalized expression values for each gene (row) and sample (columns)

organism: Drosophila melanogaster

source_name: carcass mated females

growth_protocol: "Standard" diet consisted of 12.5 g dry brewer’s yeast, 30 g sucrose, 60 g glucose, 50 g cornmeal, 0.5 g CaCl2, 0.5 g MgSO4, 10 ml 10% Nipagin, 6 ml propionic acid, 20 ml ethanol and 15 g of agar per liter of water.   The "poor" diet contained 1/4 of the concentrations of yeast, sugars and cornmeal, but the same concentrations of the other ingredients. Flies were raised in bottles seeded with about 200 eggs per 40 ml of food medium.   Adults of all populations and of both sexes were transferred to standard diet on day 1 post-emergence. Females were collected three days later, i.e., they were aged about 4 days.

extract_protocol:
RNA was extracted from the carcass samples using "Total RNA Purification Plus" by Norgen Biotek (#48300, 48400).
cDNA libraries (TrueSeq Standard RNA) were generated and sequenced on two lanes of Illumina HiSeq4000 (single read, 150 bp)

treatment_protocol: Female flies were collected in the morning and dissected in PBS. The abdomen was separated, and the gonads, the gut and the bulk of Malpighian tubes were removed, producing the "carcass", consisting of the abdominal fat body attached to the body wall, as well as any hemolymph, oenocytes, neurons and fragments of Malpighian tubes that remained embedded in the fat body.

tag: larval diet

value: poor

tag: evolutionary regime

value: Selected

tag: replicate population

tag: age

value: 4 days

value: carcass

tag: Sex

value: female


title: Selected pop. 1 on standard diet

value: Control


title: Selected pop. 6 on standard diet


title: Selected pop. 2 on standard diet


title: Selected pop. 3 on standard diet


title: SS-H3K4me3-1

tag: cell type

tag: strain


title: Peromyscus_polionotus_control_rep1


title: Control pop. 6 on standard diet


title: SS-INPUT

tag: antibody


title: 4771_P

value: prefrontal cortex, NeuN+, mC+

tag: profile

value: neuronal nuclei


title: Peromyscus_polionotus_burrowing_rep3

value: Burrowing


title: Control pop. 5 on standard diet


title: 4702_N

value: prefrontal cortex, NeuN-, mC+

tag: fractions

value: non-neuronal nuclei


title: Selected pop. 5 on standard diet


title: Control pop. 4 on standard diet


title: 4702_P

value: mutPolg


title: Peromyscus_polionotus_burrowing_rep1


title: 4701_N


title: 4701_P


title: Mir_rep2

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

data_processing:
Sequencing reads were aligned using HISAT2 v2.1.0 {Kim, 2015} to mm10 mouse genome. Integrative Genomics Viewer {Robinson, 2011} was used to visualize aligned reads and normalized coverage tracks (RPM). Reads overlapping annotated genes (Ensemble GRCm38.93) were counted using HTSeq v0.11.0 {Anders, 2015}. Differentially expressed genes (DEGs) were detected using DESeq2 v1.18.1 package {Love, 2014} in R {Ihaka, 1996}. Genes with Adj. p < 0.01 were considered significantly differentially expressed. For some comparisons, mRNA abundance of RNA-seq data was obtained using transcript per million normalization (TPM) {Wagner, 2012}.
Genome_build: GRCm.38/mm10 (Ensembl 93)
Supplementary_files_format_and_content: Tab-delimited text files of gene counts per sample.

source_name: Cortical progenitors

extract_protocol:
RNA was extracted using Arcturus PicoPureTM RNA isolation kit (Thermo Fischer Scientific, Cat # KIT0202) according to the manufacturer´s protocol. RNA integrity was analysed using Bioanalyzer (Agilent 2100) and samples with RIN values above 9.5 were selected for RNA sequencing.
For each biological replica, cells from two embryos were pooled together, and three independent replicas per condition were sequenced. Libraries were prepared with the SMART-seq v4 Library Prep Kit and sequenced on Illumina HISeq 2500 sequencer using 50bp single reads.

treatment_protocol:
Wild-type mice in ICR background were obtained from a breeding colony at the Animal Facility of the Instituto de Neurociencias. The day a vaginal plug was detected was considered embryonic day (E) 0.5. Animals were treated according to Spanish (RD 53/2013) and European regulations
For gain-of-function experiments, we used pCAG-GFP expressing green fluorescent protein under the CAG promoter, mixed with psil-pre-miR3607 encoding premiR3607-5p under the U6 promoter, or with psil-pre-miRScr under U6 as control. Oligos encoding pre-miR3607 (5´GATCCGACTGATTTCCTTCATGTCAAGCTTCAAGAGAGCATGTGATGAAGCAAATCAGTTTTTTT3´; SIGMA) were designed with BamHI-HindIII sites and cloned into pSilencer2.1-U6 puro (Thermo Fisher Scientific, Cat# AM5762). pSilencer puro negative control plasmid provided with the kit was used as psil-pre-miRScr, encoding an siRNA sequence not found in the mouse, human,or rat genome databases. Plasmid DNA was purified with a NucleoBond Xtra Midi kit (Cultech, 22740410.50) and resuspended in nuclease-free water (SIGMA).
In utero electroporation was performed as described elsewhere {Cardenas, 2018 #9991}. Briefly, timed-pregnant females were deeply anesthetized with Isoflurane, the abdominal cavity was open and the uterine horns exposed. DNA solution (1μl) was injected into the lateral ventricle using pulled glass micropipettes, and square electric pulses (35V for E12.5, 45V for E14.5, 50ms on – 950ms off, 5 pulses) were applied with an electric stimulator (Cuy21EDIT Bex C., LTD) using round electrodes (CUY650P5, Nepa Gene). Plasmid concentrations for gain-of-function experiments were: GFP (0.7µg/µl), miRScr (1µg/µl), miR3607 (1µg/µl). Uterine horns were placed back into the abdominal cavity, suture closed, and the pregnant female was allowed to fully recover on a heating pad before returning to the home cage.
Electroporated mouse embryos with similar rostro-caudal and latero-medial location of GFP fluorescence in the neocortex were selected and the GFP+ cortical area was dissected out in ice-cold HBSS (Thermo Fisher Scientific). Dissected tissue was dissociated with Trypsin diluted in HBSS in the presence of DNAse at 37˚C for 8 minutes. HBSS supplemented with 10% FBS and 1% penicillin/streptomycin (P/S) was then added, and tissue was gently triturated. The cell suspension was centrifuged, and cells in pellet were resuspended in 500µl of medium, filtered and FACS sorted (FACS Aria II, BD). Cells with high GFP intensity were collected in Neurobasal medium supplemented with 10% FBS, and 1% P/S.

value: cortex

tag: development stage

tag: genotype/variation


title: Mir_rep1


title: Mir_rep3


title: Control pop. 1 on standard diet


title: Control pop. 3 on standard diet


title: Control pop. 2 on standard diet


title: Pancreatic Islets, ICRH125

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Pancreatic Islets

extract_protocol:
Fresh pancreatic islets were dissociated to single cells, Chromium Single Cell 3’ Library & Gel Bead Kit v2 was used to construct the sequencing libraries.
Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2
single cell RNA-Seq

value: Pancreas

tag: gender

value: Male

value: 29 years


title: Scr_rep3

value: control


title: Scr_rep2


title: Selected pop. 5 on poor diet

value: standard


title: Selected pop. 6 on poor diet

value: Selected


title: Scr_rep1


title: Brg1_KD_D7_Etv2_Repeat_rep2

city: Minneapolis

first: Daniel

last: Garry

address: 2231 6th Street SE, 4th Floor

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ChIP-seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files

source_name: MEF

extract_protocol:
EB or MEF cells were harvested as described above. ChIP assays for ETV2 and H3K27ac were performed from 2 x 106 MEFs or 1 x 107 EB cells, respectively. Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M.  For the BRG1 ChIP-seq, cells were first crosslinked in 2 mM disuccinimidyl glutarate (DSG; Life Technologies: Cat. #20593) for 30 min then in 1% formaldehyde for 10 min, quenched with glycine for 5 min.  The remainder of the ChIP protocol was performed following the protocol described by Magli et al19. We used antibodies against H3K27ac (Abcam, ab4729), ETV2 (Abcam, ab181847), and BRG1 (Abcam ab110641) for the respective pulldowns. For both of the pulldowns, protein A Dynabeads were added to the ChIP reactions and incubated for 30 minutes at room temperature. Magnetic beads were washed and chromatin was eluted. After crosslinking reversal, RNase A, and proteinase K treatment, ChIP DNA was extracted with the Min-Elute PCR purification kit (Qiagen). ChIP DNA was quantified with Quant-it PicoGreen dsDNA Assay Kit (Life Technologies). Sequencing libraries were prepared using equal amount of ChIP DNA per sample as per instructions of SMARTer® ThruPLEX® DNA-Seq Kit (Takara R400675) and SMARTer® DNA Unique Dual Index Kit - 24U Set A (Takara R400665). Sequencing was performed at the University of Minnesota Genome Center with the The NextSeq 550 high-throughput benchtop sequencer.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: time point

tag: dox or no dox

value: Dox


title: Brg1_KD_D7_Etv2_Repeat_rep


title: 4771_N


title: Brg1_KD_D7_Input_Repeat

value: input


title: Selected pop. 4 on poor diet

value: 4 days

tag: tissue

value: carcass

value: female


title: M6_Lung_C2

city: Heidelberg

first: Delphine

last: Merino

state: Victoria

address: Level 5, ONJ Centre, 145 Studley Rd, Heidelberg

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

data_processing:
Base calling used Real-Time Analysis on board software v2.4.6
Demultiplexed into fastq files using bcl2fastq software v2.15.0.4
Reads were filtered using cutadapt
Reads were mapped to GRCh38 genome using STAR
Reads were quantified using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files with raw gene counts for every gene and every sample

source_name: Sorted subclone 2 - Lung metastasis, Retransplantation experiment

extract_protocol:
Qiagen miRNeasy micro Kit with in column DNAse treatment
Illumina TruSeq RNA Library Prep Kit v2

tag: sample type

value: Sorted metastatic subclone

tag: subclone

tag: organ

value: Lung metastasis

tag: cell line

tag: mouse number

tag: retransplantation

value: TRUE


title: M6_Liver_C2

source_name: Sorted subclone 2 - Liver metastasis, Retransplantation experiment

value: Liver metastasis


title: Brg1_KD_D1_Etv2_Repeat_rep2

value: day 1