title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB565RSP)

description:
https://www.encodeproject.org/experiments/ENCSR614NSH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614NSH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565RSP

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS381JHZ at ENCODE; https://www.encodeproject.org/ENCBS381JHZ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: ATAC-seq from sciatic nerve (ENCLB682GKF)

status: Public on Oct 16 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR619LHF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR619LHF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB682GKF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (47 years) sciatic nerve tissue, preserved by flash-freezing

value: sciatic nerve

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

tag: dev stage

value: adult

tag: age

value: 47 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS182LUZ at ENCODE; https://www.encodeproject.org/ENCBS182LUZ/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: DNase-seq from right cerebral cortex (ENCLB792GBA)

description:
https://www.encodeproject.org/experiments/ENCSR017TAB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR017TAB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792GBA

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J female (14 days) right cerebral cortex tissue

value: right cerebral cortex

tag: description

value: B6Cast F1 PND14 Female 05 right cerebral cortex for Altius Stam biobank

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS189OPC at ENCODE; https://www.encodeproject.org/ENCBS189OPC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: WT_no_treatment_1

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: 150 x 150 cycle paired end sequence

library_source: transcriptomic

data_processing:
Libraries are fed into Novaseq6000 machines according to activity and expected data volume. A paired-end 150 bp sequencing strategy was used and all samples were sequenced to at least 6 Gb.
XPRESSpipe v0.6.3 was used to process sequence files, with the following command: xpresspipe peRNAseq ... -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG --sjdbOverhang 149 --quantification_method htseq --remove_rrna. See supplementary files for XPRESSpipe dependencies and settings used.
Assembly: Ensembl Saccharomyces_cerevisiae release-106
Supplementary files format and content: Tab-delimited text file - processed count data

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae (BY)

growth_protocol: Grown in indicated media overnight and harvested between OD=0.2-0.4, with a total OD of 5 per sample.

extract_protocol:
Direct-zol RNA Miniprep
After the QC procedures, mRNA from eukaryotic organisms is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to I ng/gl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

treatment_protocol: Treatment is indicated above

tag: cell type

value: yeast cells

tag: genotype

value: wild-type

tag: treatment

value: no treatment (ctrl for pho85, rpo41)


title: ali28, scRNA-seq

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

country: China

institute: Zhejiang University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data were demultiplexed with the mkfastq command in cellranger(V5.0.1) to generate Fastq files.
Trimmed sequence files were mapped to the reference genome for humans (GRCh38) provided by 10x Genomics. Read counts were obtained from outputs from Cell Ranger.
Assembly: GRH38
Supplementary files format and content: raw counts table in h5 file.

source_name: WGNT SV20-211

extract_protocol:
WGNT SV20-211 hiPSC-derived aggregates were collected for scRNA-seq analyses: aggregates at fl19 (FACS-sorted whole WG+ fraction [n= 1] or NT+ fraction [n=1]), fl22 (NT+ fraction [n=1]), ali21 (whole WG+ fraction [n=1]) and ali28 (NT+ fraction [n =1]).  Aggregates were dissociated by 0.1% Trypsin/EDTA for 10-15 min at 37 ºC with periodic pipetting. After the reaction was quenched by adding an equal volume of fetal bovine serum, cells were resuspended in FACS buffer (0.1% BSA in PBS). Cell suspension was strained through a 70 µm nylon cell strainer (Thermo Fisher Scientific) to remove cell clumps prior to use. All samples were stained with trypan blue and confirmed to be >85% viable. Cells were loaded into Chromium microfluidic chip B using the Chromium Single Cell 3ʼ Reagent Kit (v3 chemistry) and Chromium Controller (10X Genomics) to generate gel bead emulsions (GEMs). Gelbead emulsion-RT was performed using a C1000 Touch Thermal Cycler equipped with a deep-well head (Bio-Rad).
Subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s instruction.

tag: cell line

value: WGNT SV20-211

value: NT+ fraction


title: ATAC-seq from ureter (ENCLB727KOP)

description:
https://www.encodeproject.org/experiments/ENCSR814RGG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human ureter
experiment encode accession: ENCSR814RGG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB727KOP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) ureter tissue, preserved by flash-freezing

value: ureter

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 47 year

value: ENCBS693JBG at ENCODE; https://www.encodeproject.org/ENCBS693JBG/


title: Pro_wN_3

description: 150 x 150 cycle paired end sequence

value: prototrophic WT

value: grow with nitrogen for 4hr


title: fl22, scRNA-seq

description: 10x Genomics


title: DNase-seq from urinary bladder (ENCLB203VYE)

description:
https://www.encodeproject.org/experiments/ENCSR609SJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR609SJP
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB203VYE

source_name: Mus musculus strain B6CASTF1/J male (10 days) urinary bladder tissue

value: urinary bladder

value: B6Cast F1 PND10 Male 05 urinary bladder for Altius Stam biobank

value: male

value: not collected

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS424FXL at ENCODE; https://www.encodeproject.org/ENCBS424FXL/


title: ATAC-seq from ureter (ENCLB273BFK)

description:
https://www.encodeproject.org/experiments/ENCSR814RGG/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human ureter
experiment encode accession: ENCSR814RGG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB273BFK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ureter

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: DNase-seq from kidney (ENCLB114JCX)

description:
https://www.encodeproject.org/experiments/ENCSR605PMM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR605PMM
assay title: DNase-seq
assembly: mm10
encode release date: 2022-05-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB114JCX

source_name: Mus musculus strain B6CASTF1/J male (14 days) kidney tissue

value: kidney

value: tissue

value: B6Cast F1 PND14 3x Males 05 kidney for Altius Stam core

value: 14 day

value: ENCBS094BGZ at ENCODE; https://www.encodeproject.org/ENCBS094BGZ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Pro_wN_2

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: prototrophic WT

value: grow with nitrogen for 4hr


title: fl19, scRNA-seq, replicate2

description: 10x Genomics

value: WGNT SV20-211

value: whole WG+ fraction [n= 1] or NT+ fraction


title: fl19, scRNA-seq, replicate1

description: 10x Genomics


title: Pro_wN_1

description: 150 x 150 cycle paired end sequence


title: Pro_noN_3

description: 150 x 150 cycle paired end sequence

value: deplete with nitrogen for 4 hr


title: ATAC-seq from heart right ventricle (ENCLB181QRV)

description:
https://www.encodeproject.org/experiments/ENCSR403GBR/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR403GBR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB181QRV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (55 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: adult

value: 55 year

value: Shin Lin

value: ENCBS934SSM at ENCODE; https://www.encodeproject.org/ENCBS934SSM/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: Pro_noN_2

description: 150 x 150 cycle paired end sequence


title: DNase-seq from left cerebral cortex (ENCLB787RBF)

description:
https://www.encodeproject.org/experiments/ENCSR200TAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR200TAZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB787RBF

source_name: Mus musculus strain B6CASTF1/J male (36 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND36 Male 06 left cerebral cortex for Altius Stam biobank

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS193GEQ at ENCODE; https://www.encodeproject.org/ENCBS193GEQ/


title: DNase-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB044BJM)

description:
https://www.encodeproject.org/experiments/ENCSR208YDK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR208YDK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB044BJM

source_name: Homo sapiens male adult (33 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

value: primary cell

value: 33 year

value: John Stamatoyannopoulos, UW

value: StemExpress

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS868OVQ at ENCODE; https://www.encodeproject.org/ENCBS868OVQ/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: fl22, scATAC-seq

description: 10x Genomics

library_source: genomic single cell

data_processing:
scATAC-seq mapping to human reference genome provided by 10X genomics using cellranger-atac-2.0.0 pipeline.
The downstream analysis was performed using Signac (v1.6.0).
Assembly: GRH38
Supplementary files format and content: peak raw counts matirx , h5
Supplementary files format and content: coverage file, bigwig format

extract_protocol:
Cells were sorted out based on WG+ or NT+ fraction. After sorting, count the cells, and isolate nuclei following  the protocol of Nuclei Isolation for Single Cell ATAC Sequencing from 10X genomics.
scATAC-seq libraries were build following protocol of Chromium Single Cell ATAC Reagent Kits User Guide from 10X genomics.

value: WGNT SV20-211

value: whole NT+ fraction


title: ATAC-seq from heart right ventricle (ENCLB620BPV)

description:
https://www.encodeproject.org/experiments/ENCSR403GBR/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR403GBR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB620BPV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: male

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS934SSM at ENCODE; https://www.encodeproject.org/ENCBS934SSM/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: ATAC-seq from heart left ventricle (ENCLB068ZZP)

description:
https://www.encodeproject.org/experiments/ENCSR204PZT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR204PZT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB068ZZP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (41 years) heart left ventricle tissue, preserved by cryopreservation

value: heart left ventricle

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS631SVK at ENCODE; https://www.encodeproject.org/ENCBS631SVK/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: DNase-seq from heart (ENCLB152QZL)

description:
https://www.encodeproject.org/experiments/ENCSR800YHA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR800YHA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB152QZL

source_name: Mus musculus strain B6CASTF1/J female (9 months) heart tissue

value: heart

value: unknown

value: 9 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS104DII at ENCODE; https://www.encodeproject.org/ENCBS104DII/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: FZ,rep2

data_processing:
Raw sequencing data was demultiplexed as Fastq files by bcl2fastq2 (v2.20.0.422),
Adaptor and barcode were removed by Trimmomatic(v0.32).
Fastq files were mapped to human reference genome (GRH38) from UCSC by using STAR (2.7.1a)
Gene count table was generated by featurecounts
Assembly: GRH38
Supplementary files format and content: tab-delimited text files includeraw counts for each Sample

source_name: Fetal Zone

extract_protocol:
The fetal adrenal glands and the heart, hiPSCs, floating and ALI cultured aggregates were used for bulk RNA-sequencing. The fetal tissues were dissociated with Multi Tissue Dissociation Kit 1 (Milteny Biotech) according to the manufacturer’s instruction. Briefly, after tissues were minced into <1 mm fragments by scissors, samples were collected in 15 ml falcon tubes and mixed with dissociation solution (enzyme mix mixed with serum-free DMEM). Then, samples were incubated at 37 ºC for 30 min in water bath with pipetting for every 10 min. At the end of incubation, FBS was added (15% of total volume) and cell suspension were strained through 70 mm cell strainer. Cells were washed once with PBS by centrifugation at 300 g for 5 min, and subsequently treated with Red Blood Cell Lysis Solution (Miltenyi Biotec) for 2 min at room temperature. After addition of 3ml DMEM, cells were centrifuged at 300 g for 5 min and resuspended in FACS buffer before cell number was counted with trypan blue exclusion. In some samples (Fetal adrenal glands at 17 and 19 wpf), cells were subsequently stained with APC-anti-CD10 (also known as MME) antibody and CD10 negative cells were sorted by FACSAria Fusion. Cells were pelleted by centrifugation at 300 g for 5 min and pellets were snap frozen by liquid nitrogen and stored at -80 ºC until used for RNA isolation.
cDNA library preparation was performed using Clontech SMART-Seq® HT Plus Kit (PN R400749) according to manufacturer’s protocol.

tag: tissue

value: Fetal Zone

value: CD10 negative cells

tag: developmental stage

value: 9 wpf

value: male


title: ATAC-seq from heart left ventricle (ENCLB235RIG)

description:
https://www.encodeproject.org/experiments/ENCSR204PZT/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR204PZT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB235RIG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: tissue

value: female

value: adult

value: Michael Snyder, Stanford


title: ali21, scRNA-seq

description: 10x Genomics

value: WGNT SV20-211

value: whole WG+ fraction


title: FZ,rep1


title: cortex, KO, mouse6

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description:
young_mouse_6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v5.0.0).
Cells were filtered based on output from isOutlier function from scater (v1.20.1), genes expressed in less than two cells were discarded, normalisation was performed by deconvulation.
Selection of variable genes, dimensional reduction, batch correctoin (with fastMNN) and clustering (with scran) was performed a first time to subset the oligodendrocytes and a second time with the cells from clusters positive for oligodendrocyte markers (Plp1, Mog, Mag and Mbp).
Assembly: mm10
Supplementary files format and content: tab delimited file containing oligodendrocytes log-normalized counts
Supplementary files format and content: tab delimited file linking each cell to it's metadata variables

source_name: cortex

extract_protocol:
Brains were collected from 6–7-week-old female mice at the same time of day for each animal. Mice were culled via cervical dislocation and brains were dissected, with the olfactory bulbs and cerebellum being removed. Hippocampi from both hemispheres and the remainder of the left hemisphere (without the hippocampus) were collected in ice-cold HBSS (w/o Ca2+ and Mg2+; 14175-053; Gibco) with 5% trehalose (T0167; Sigma Aldrich) and 30 µM actinomycin D (A1410; Sigma Aldrich) and were finely minced using a 22A scalpel. Brains were digested using the Adult Brain Dissociation Kit (130-107-677; Miltenyi Biotec), with the following modifications: (i) tissues were dissociated as described in the “manual dissociation” section of the Neural Tissue Dissociation Kit protocol (130-092-628; Miltenyi Biotec), (ii) enzymatic digestions were performed at 35°C, (iii) half the concentration of enzyme P was used, (iv) actinomycin D was used to limit dissociation-induced transcriptional changes,  (v) 5% trehalose was added in all buffers to increase cellular viability, (vi) cell clusters were removed by filtration through prewetted 70 μm (352350; Falcon) and 40 μm (352340; Falcon) cell strainers, (vii) erythrocyte and myelin debris removal steps were omitted during dissociation steps, and (viii) all centrifugations were performed at 200 g at 4°C. After dissociation, cells were collected in PBS with 0.2% BSA before being sorted on a Sony SH800 cell sorter. Gates were chosen based on forward and side scatter to exclude myelin debris, erythrocytes, and doublets. Non-viable cells were excluded based on Draq7 and/or DAPI staining (Draq7high and/or DAPIhigh cells were classified as non-viable).
single cells were processed through the Chromium Single Cell Platform using the Chromium Next GEM Single Cell 3’ GEM Library and Gel Bead Kit (v3.1 chemistry, PN-1000121, 10x genomics) and the Chromium Next GEM Chip G kit (PN-1000120) and processed following manufacturer’s instructions.

value: cortex

value: FIREdelta/delta  KO

tag: exit age


title: cortex, WT,mouse4

description:
young_mouse_4
10x Genomics

value: WT


title: reg1snf1mct1_2

description:
150 x 150 cycle paired end sequence
Saccharomyces cerevisiae (BY)

data_processing:
NovaSeq 150x150 bp Sequencing:  Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).
Single base mismatch
Build genome index (STAR v2.7.7a): STAR --runMode genomeGenerate … --sjdbOverhang 150 --genomeSAindexNbases 10
Preprocessing (fastp v0.20.1): fastp -l 30 -q 28 --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT  …
Alignment (STAR v2.7.7a): STAR --sjdbOverhang 150 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM ...
Postprocess sort (samtools v1.11): samtools sort …
Postprocess index (samtools v1.11): samtools index …
Count quantification (htseq v0.13.5): htseq-count -q -f bam -m intersection-nonempty -t exon -i gene_id -r pos -s no …
Assembly: Ensembl Saccharomyces_cerevisiae release-100
Supplementary files format and content: Tab-delimited text file - processed count data

source_name: yeast cells

growth_protocol: Cultured in SD-complete overnight; harvested OD between 0.2-0.4.

extract_protocol:
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads.
Stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371) .  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.

treatment_protocol: No treatment.

value: yeast cells

value: reg1 snf1 mct1 deletion


title: hippocampus, WT, mouse4

description:
young_mouse_4
10x Genomics

source_name: hippocampus

value: hippocampus


title: Heart

description: Heart

source_name: Heart

value: Heart


title: cortex, KO, mouse3

description:
young_mouse_3
10x Genomics


title: DNase-seq from left cerebral cortex (ENCLB459KBM)

description:
https://www.encodeproject.org/experiments/ENCSR200TAZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR200TAZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB459KBM

value: left cerebral cortex

value: B6Cast F1 PND36 Male 05 left cerebral cortex for Altius Stam biobank

tag: biosample encode accession

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS447YRF at ENCODE; https://www.encodeproject.org/ENCBS447YRF/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: reg1snf1mct1_3


title: DNase-seq from naive B cell (ENCLB551DHV)

description:
https://www.encodeproject.org/experiments/ENCSR017SBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR017SBI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB551DHV

source_name: Homo sapiens with multiple sclerosis; naive B primary cell, preserved by cryopreservation

value: naive B cell

value: primary cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

tag: Sex

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS073IDQ at ENCODE; https://www.encodeproject.org/ENCBS073IDQ/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: DNase-seq from HCT116 (ENCLB268NUY)

description:
https://www.encodeproject.org/experiments/ENCSR811COL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR811COL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB268NUY

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

tag: line

value: cell line

value: male

tag: health state

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS131GLR at ENCODE; https://www.encodeproject.org/ENCBS131GLR/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: reg1snf1_3

value: yeast cells

value: reg1-snf1 deletion


title: cortex, WT, mouse1

description:
young_mouse_1
10x Genomics

value: cortex

value: WT

value: female


title: Pro_noN_1

description: 150 x 150 cycle paired end sequence

source_name: Saccharomyces cerevisiae (BY)

value: prototrophic WT

value: deplete with nitrogen for 4 hr


title: DNase-seq from immature natural killer cell (ENCLB082KJD)

description:
https://www.encodeproject.org/experiments/ENCSR012RCX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR012RCX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB082KJD

source_name: Homo sapiens immature natural killer primary cell, preserved by cryopreservation

value: immature natural killer cell

value: primary cell

value: not collected

value: healthy

tag: dev stage

tag: age

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS021VJD at ENCODE; https://www.encodeproject.org/ENCBS021VJD/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: reg1snf1mct1_1

value: reg1 snf1 mct1 deletion


title: hiPSC, rep2

source_name: in vitro

value: in vitro

value: WGNT SV20-211

value: male


title: reg1snf1_2

value: yeast cells

value: reg1-snf1 deletion


title: hippocampus, KO, mouse3

description:
young_mouse_3
10x Genomics

value: hippocampus

value: FIREdelta/delta  KO

value: female


title: ATAC-seq from T-helper 17 cell (ENCLB005OIA)

description:
https://www.encodeproject.org/experiments/ENCSR803FKU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR803FKU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-11-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB005OIA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (38 years) T-helper 17 primary cell

value: T-helper 17 cell

value: adult

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS150IQU at ENCODE; https://www.encodeproject.org/ENCBS150IQU/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: reg1snf1_1


title: fl09, scATAC-seq

description: 10x Genomics

source_name: WGNT SV20-211

value: whole WG+ fraction


title: hippocampus, WT, mouse1

description:
young_mouse_1
10x Genomics

value: WT


title: DNase-seq from naive B cell (ENCLB579XCP)

description:
https://www.encodeproject.org/experiments/ENCSR011VHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR011VHK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB579XCP

value: naive B cell

value: primary cell

tag: description

value: B naive CD3- CD14- CD19+ CD27- IgD+

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

tag: link

value: ENCBS306XUQ at ENCODE; https://www.encodeproject.org/ENCBS306XUQ/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: hiPSC, rep1

value: in vitro

value: WGNT SV20-211

value: male


title: sit4snf1mct1_3

tag: cell type

value: yeast cells

tag: genotype

value: sit4-snf1-mct1 deletion


title: DNase-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB510JDI)

description:
https://www.encodeproject.org/experiments/ENCSR009MDC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR009MDC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB510JDI

source_name: Homo sapiens male adult (30 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads, 10 ng/mL Interleukin-2

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein;

value: ENCBS589RZO at ENCODE; https://www.encodeproject.org/ENCBS589RZO/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: ali21,2125, rep1

tag: cell line

value: NT+ fraction

value: Air-liquid interface  21 days

value: female


title: ali21,211, rep1


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB266YMD)

description:
https://www.encodeproject.org/experiments/ENCSR400YJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR400YJR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB266YMD

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS938EKE at ENCODE; https://www.encodeproject.org/ENCBS938EKE/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: sit4snf1mct1_2

value: yeast cells

value: sit4-snf1-mct1 deletion


title: fl22,211, rep2

value: in vitro

value: WGNT SV20-211

value: floating 22 days

value: male


title: TF ChIP-seq from K562 (ENCLB621PYG)

description:
https://www.encodeproject.org/experiments/ENCSR849LXI/
***************
biological replicate number: 1
technical replicate number: 2
description: eGFP-MTF1 ChIP-seq on human K562
experiment encode accession: ENCSR849LXI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU, ENCSR785AHP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB621PYG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MTF1

tag: antibody

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS512MRM at ENCODE; https://www.encodeproject.org/ENCBS512MRM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: sit4snf1mct1_1


title: TF ChIP-seq from K562 (ENCLB083DZQ)

description:
https://www.encodeproject.org/experiments/ENCSR849LXI/
***************
biological replicate number: 2
technical replicate number: 2
description: eGFP-MTF1 ChIP-seq on human K562
experiment encode accession: ENCSR849LXI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU, ENCSR785AHP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB083DZQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: female

value: ENCBS838OWM at ENCODE; https://www.encodeproject.org/ENCBS838OWM/


title: fl22,211, rep1

tag: tissue

value: NT+ fraction


title: e18.5, mutant, rep2

city: Philadelphia

first: Pablo

middle: G

last: Camara

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

description:
Columns in processed count matrix (all_rna_cells.txt) containing sample title
all_rna.mtx
all_rna_cells.txt
all_rna_genes.txt

data_processing:
Fastq files were aligned to the mm10 mouse reference genome and count matrices were generated using the CellRanger (v2.1) pipeline.
We filtered out cells with less than 2,000-5,000 UMIs based on the inflection point of the log-transformed barcode rank plot of each sample, or more than 15% of the UMIs coming from mitochondrially encoded genes. In total, 249,071 cells passed these filters, with a median of 4,891 UMIs/cell, (interquartile range: 3,795 – 6,372 UMIs/cell), 2,466 genes/cell (interquartile range: 2,092 – 2,943 genes/cell), and 2.7% of UMIs in each cell coming from mitochondrially encoded genes (interquartile range: 2.1 – 3.5%).
Assembly: mm10
Supplementary files format and content: Matrix (mtx) files of gene counts with additional text files for row and column names

molecule: polyA RNA

source_name: embryonic murine prosomere 2 (p2)

extract_protocol:
The thalamus was manually dissected from control (ShhΔSBE1;ΔSBE5/+) and mutant (ShhΔSBE1;ΔSBE5/ΔSBE1;ΔSBE5) brains at four embryonic stages (E12.5, E14.5, E16.5 and E18.5) in ice-cold PBS. The caudal and rostral boundaries of dissection coincided with the cephalic flexure and the mammillary body, respectively. Each thalamus was cut into small pieces and dissociated into a single cell suspension using the Papain Dissociation System (Worthington, LK003153) according to the manufacturer’s protocol. Samples were dissociated in Papain-EBSS solution for 40 minutes at 37ºC. Papain was inactivated with ovomucoid protease inhibitor, and the digested tissue was resuspended in PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/ml). Cell suspensions were stained with Trypan Blue to determine the ratio of viable to damaged cells and counted using a haemocytometer (Thermo Fisher Scientific). Single cell suspensions containing more than 90% viable cells were fixed in methanol for 1 week. Samples were rehydrated at a concentration of 700-1200 cells/l in ice-cold PBS containing 0.04% weight/volume BSA (400 µg/ml) immediately prior to the generation of single-cell RNA sequencing libraries.
Single-cell RNA-seq libraries were generated using the 10X Genomics platform (Chromium Single Cell 3’ library and Gel Bead Kit v3, PN-1000075) and sequenced on a NovaSeq 6000 system (Illumina) at the Center for Applied Genomics (Children’s Hospital of Philadelphia). Three independent libraries were generated for each time point and genotype (n=24 libraries).

value: embryonic murine prosomere 2 (p2)

tag: developmental stage

value: embryo


title: ali28, 211, rep1

value: in vitro

value: Air-liquid interface  28 days


title: e16.5, mutant, rep3


title: fl22, 2121, rep2

value: floating 22 days


title: sit4snf1_3

value: yeast cells

value: sit4-snf1 deletion


title: sit4snf1_2


title: Healthy control, patient with ARPC5 deficiency; mRNA-derived cDNA

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Fastq files were processed using BD's Rhapsody analysis pipeline on the Seven Bridges Platform using default parameters, the GRCh38-PhiX-gencodev29 reference genome and the gencodev29-20181205 transcriptome annotation
Data (molecules per gene per cell based on DBEC error correction) were analyzed using BD SeqGeq v1.8 and the Seurat plug-in to perform dimensionality reduction (UMAP) and differential analysis output for selected cell subsets (CD4+ T cells, CD8+ T cells, NK cells, NKT cells, classical monocytes, intermediate monocytes, non-classical monocytes)
Supplementary files format and content: Comma-separated Assigned Sample Tag for each putative cell
Supplementary files format and content: Comma-separated data table containing molecules per gene per cell based on DBEC error correction
Supplementary files format and content: Data table of gene counts in sparse format
Assembly: GRCh38

source_name: PBMC

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were labeled with sample tags (BD Human Single Cell Multiplexing Kit) and AbSeq antibodies (CD1c, CD3, CD4, CD5, CD8, CD11c, CD14, CD16, CD18, CD19, CD20, CD21, CD23, CD24, CD25, CD27, CD28, CD31, CD38, CD40, CD44, CD45RA, CD45RO, CD56, CD62L, CD123, CD127, CD134, CD137, CD161, CD183, CD185, CD186, CD196, CD197, CD272, CD278, CD279, CD303, CD314, CD337, CD357, CD366, HLA-DR, IgD, IgM,TCRαβ, TCRγ8, Vα24-Jα18).Single-cell capture was performed using the BD Rhapsody Express.

value: PBMC

tag: library type

value: mRNA


title: fl22, 2121, rep1


title: hippocampus, KO, mouse6

description:
young_mouse_6
10x Genomics

value: hippocampus

value: FIREdelta/delta  KO

tag: exit age


title: e18.5, mutant, rep1

tag: Sex


title: Healthy control, patient with ARPC5 deficiency; STO-derived cDNA

description: Sequence Tag library: read1 file contains cell barcode and UMI; read2 file contains Sequence Tag Antibody Derived Tag reads

library_source: other

molecule: protein

value: STO


title: sit4snf1_1


title: e18.5, control, rep3

value: Control


title: fl22, 211, KIKO, rep2

value: WGNT SV20-KIKO19

value: male


title: Healthy control, patient with ARPC5 deficiency; ADT-derived cDNA

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: ADT


title: reg1mct1_3

value: reg1-mct1 deletion


title: e18.5, mutant, rep3

value: embryonic murine prosomere 2 (p2)


title: e18.5, control, rep1

value: embryo

value: female


title: NC 3

city: Qingdao

first: yongchen

last: Bie

address: No. 16, Jiangsu Road, Shinan District, Qingdao

department: Spinal Surgery

institute: The Affiliated Hospital of Qingdao University

data_processing:
Illumina bcl2fastq software used for basecalling.
Reads were  mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
gene expression levels were estimated using RSEM v1.2.15
The trimmed mean of M-values was used to standardize gene expression
Assembly: hg19
Supplementary files format and content: Excel files include TMM values for each Sample

source_name: Peripheral Serum,RNA-seq

extract_protocol:
Total RNA was extracted from serum using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer's instructions
RNA library was  constructed using the SMARTer Stranded Total RNA-Seq kit v.2 (Takara Bio USA, Mountain View, CA, USA).

value: serum

tag: disease state

value: normal control


title: e18.5, control, rep2


title: fl22, 211, KIKO, rep1

value: in vitro

value: NT+ fraction

value: floating 22 days


title: reg1mct1_2

value: yeast cells


title: fl14, rep2

value: WGNT SV20-211

value: floating 14 days


title: reg1mct1_1


title: e16.5, mutant, rep2


title: e16.5, mutant, rep1


title: fl14, rep1


title: reg1_3

value: reg1 deletion


title: fl09, rep1

value: whole WG+ fraction

value: floating 9 days


title: AS 2

value: Ankylosing Spondylitis


title: NC 1


title: AS 3


title: AS 1


title: fl09, rep2

value: male


title: e16.5, control, rep2

value: Control


title: e16.5, control, rep3

value: embryonic murine prosomere 2 (p2)


title: e16.5, control, rep1

value: embryo


title: e14.5, mutant, rep3

value: female


title: sit4mct1_3

value: sit4-mct1 deletion


title: e14.5, mutant, rep2


title: reg1_2


title: reg1_1


title: 5F1_ATM-null

city: Tabuk

first: Sael

middle: M

last: Alatawi

address: Duba Road

country: Saudi Arabia

institute: University of Tabuk

data_processing:
fastq files were aligned to mouse reference genome GRCm38.p5  using the Hisat2 aligner.
Filtered final BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the estimateSizeFactors function in the DESEQ2 package in R
Differentially expressed genes (³2-fold and £5% adjusted p-value) were identified using DESEQ2  with default settings
Assembly: GRCm38.p5
Supplementary files format and content: Comma-separated values file includes the raw count matrix values for each Sample

source_name: splenic B-cells

growth_protocol: Cell lines were established from single-cell suspensions of ATM-/-nu-/- lymphomas, cultured in RPMI containing 15% FCS, 1% pyruvate, 1% NEAA/β-mercaptoethanol (50uM) and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from splenic B-cells using the RNeasy Micro Kit and processed as per manufacturer’s instructions.
RNA-seq libraries were generated using Neoprep mRNA kits, according to the manufacturer’s instructions.

tag: background strain

value: ATM -/-


title: 2-593_ATM-null


title: sit4mct1_2

source_name: yeast cells


title: sit4mct1_1


title: e14.5, mutant, rep1


title: 5F3_ATM-null


title: plus-plus_ATM-WT

value: ATM WT


title: sit4_3

value: sit4 deletion


title: e14.5, control, rep3


title: e14.5, control, rep2


title: 53M7_ATM-null


title: sit4_2


title: 1-593_ATM-null


title: sit4_1


title: NC 2

value: serum

value: normal control


title: mct1_3

value: yeast cells

value: mct1 deletion


title: e14.5, control, rep1


title: e12.5, mutant, rep1


title: mct1_1


title: mct1_2


title: 703_ATM-null


title: e12.5, mutant, rep3


title: 55F1_ATM-null


title: 69FS_ATM-null


title: e12.5, control, rep3


title: WT_3

value: wild-type


title: plus-minus_ATM-WT


title: WT_2


title: 36F1_ATN-null


title: 37M3_ATM-null


title: e12.5, control, rep2


title: e12.5, control, rep1


title: WT_1


title: Hippocampus

status: Public on Oct 15 2022

city: London

first: Emil

middle: Karl

last: Gustavsson

address: 20c Guilford St

institute: University College London

data_processing:
guppy for basecalling
pychopper for trimming and orientation
minimap2 for mapping
stringtie to generate GFF annotation
Assembly: hg38 and GENCODE v38
Supplementary files format and content: TXT with gene expression matrix

source_name: Frontal lobe

extract_protocol:
RNA isolated by a modified guanidinium thiocyanate method (1) followed by poly A+ RNA selection with two rounds of oligo(dT)-cellulose columns (2).
direct cDNA sequencing (SQK-DCS109)

value: Frontal lobe

tag: sample type

value: Pooled RNA from 26 individuals


title: 593_ATM-null


title: Frontal lobe

source_name: Hippocampus

value: Hippocampus

value: Pooled RNA from 27 individuals


title: e12.5, mutant, rep2

tag: age


title: lncRNA profile of 163HCC

type: RNA

city: Guangzhou

first: Li-Si

last: Zeng

state: Guangdong

address: 651 Dongfeng Road East

department: Sun Yat-Sen University Cancer Center

institute: Sun Yat-Sen University

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 45°C for 12 to 18 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Firstly, we gridded the microarray image using GenPix Pro 6.0 program, and subtracted background and normalized the data (quantile normalization) using GPR analysis software(edited in-house). Then we computed the average intensity of the duplicated probes and transformed them into log2 value.

label_protocol: In labeling reaction, 400 - 600 ng of total RNAs were used for reverse transcription using GoScript™ Reverse Transcription system (Promega, USA) with random primers and Cyanine-5-dUTP (Cat # ENZ-42502, Enzo Life Sciences, USA). Labeled RNAs were purified using Micro Bio-Spin 30 column (Bio-Rad, USA).

extract_protocol: Total RNA was extracted from 1.5 - 2.0 mL serum using Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Cat # 51000)  according to manufacturer’s instructions (Norgen Biotek, Canada).

value: hepatocellular carcinoma

tag: data set

value: validation


title: lncRNA profile of 164HCC


title: lncRNA profile of 157HCC


title: lncRNA profile of 155LC

value: liver cirrhosis


title: lncRNA profile of 156HCC


title: lncRNA profile of 174HCC


title: lncRNA profile of 149LC


title: lncRNA profile of 151LC


title: lncRNA profile of 175HCC


title: lncRNA profile of 168HCC


title: lncRNA profile of 169HCC


title: lncRNA profile of 171HCC


title: lncRNA profile of 160HCC


title: lncRNA profile of 173HCC


title: lncRNA profile of 161HCC


title: lncRNA profile of 148LC


title: lncRNA profile of 146LC


title: lncRNA profile of 158HCC


title: lncRNA profile of 165HCC


title: lncRNA profile of 167HCC


title: lncRNA profile of 166HCC


title: lncRNA profile of 172HCC


title: lncRNA profile of 159HCC


title: lncRNA profile of 162HCC


title: lncRNA profile of 150LC


title: lncRNA profile of 154LC


title: lncRNA profile of 153LC


title: lncRNA profile of 152LC


title: lncRNA profile of 147LC


title: lncRNA profile of 170HCC


title: lncRNA profile of 144LC


title: lncRNA profile of 142LC


title: lncRNA profile of 143LC


title: lncRNA profile of 145LC


title: lncRNA profile of 141LC


title: lncRNA profile of 140LC


title: lncRNA profile of 138CHB

value: chronic hepatitis B


title: lncRNA profile of 139CHB


title: lncRNA profile of 137CHB


title: lncRNA profile of 135CHB


title: lncRNA profile of 134CHB


title: lncRNA profile of 130CHB


title: lncRNA profile of 136CHB


title: lncRNA profile of 129CHB


title: lncRNA profile of 133CHB


title: lncRNA profile of 119HC

value: healthy control


title: lncRNA profile of 120HC


title: lncRNA profile of 126CHB


title: lncRNA profile of 124HC


title: lncRNA profile of 117HC


title: lncRNA profile of 125CHB


title: lncRNA profile of 121HC


title: lncRNA profile of 122HC


title: lncRNA profile of 127CHB


title: lncRNA profile of 132CHB


title: lncRNA profile of 112HC


title: lncRNA profile of 115HC


title: lncRNA profile of 111HC


title: lncRNA profile of 110HC


title: lncRNA profile of 116HC


title: lncRNA profile of 131CHB


title: lncRNA profile of 108HCC

value: discovery


title: lncRNA profile of 102HCC


title: lncRNA profile of 106HCC


title: lncRNA profile of 107HCC


title: lncRNA profile of 103HCC


title: lncRNA profile of 114HC


title: lncRNA profile of 113HC


title: lncRNA profile of 105HCC


title: lncRNA profile of 104HCC


title: lncRNA profile of 96HCC


title: lncRNA profile of 97HCC


title: lncRNA profile of 95HCC


title: lncRNA profile of 93HCC


title: lncRNA profile of 94HCC


title: lncRNA profile of 101HCC


title: lncRNA profile of 100HCC


title: lncRNA profile of 98HCC


title: lncRNA profile of 99HCC


title: lncRNA profile of 90HCC


title: lncRNA profile of 89HCC


title: lncRNA profile of 91HCC


title: lncRNA profile of 92HCC


title: lncRNA profile of 109HCC


title: lncRNA profile of 88HCC


title: lncRNA profile of 87HCC


title: lncRNA profile of 85HCC


title: lncRNA profile of 86HCC


title: lncRNA profile of 128CHB


title: lncRNA profile of 81LC


title: lncRNA profile of 80LC


title: lncRNA profile of 82LC


title: lncRNA profile of 83LC


title: lncRNA profile of 78LC


title: lncRNA profile of 77LC


title: lncRNA profile of 76LC


title: lncRNA profile of 75LC


title: lncRNA profile of 74LC


title: lncRNA profile of 71LC


title: lncRNA profile of 70LC


title: lncRNA profile of 73LC


title: lncRNA profile of 84HCC


title: lncRNA profile of 69LC


title: lncRNA profile of 68LC


title: lncRNA profile of 67LC


title: lncRNA profile of 79LC


title: lncRNA profile of 62LC


title: lncRNA profile of 66LC


title: lncRNA profile of 72LC


title: lncRNA profile of 59LC


title: lncRNA profile of 61LC


title: lncRNA profile of 60LC


title: lncRNA profile of 58LC


title: lncRNA profile of 63LC


title: lncRNA profile of 57LC


title: lncRNA profile of 52CHB


title: lncRNA profile of 51CHB


title: lncRNA profile of 56LC


title: lncRNA profile of 55LC


title: lncRNA profile of 47CHB


title: lncRNA profile of 64LC


title: lncRNA profile of 45CHB


title: lncRNA profile of 44CHB


title: lncRNA profile of 53CHB


title: lncRNA profile of 41CHB


title: Female_SykFlox_rep1

city: Charlottesville

first: Daniel

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine

description:
single cell RNA from FACS-sorted microglia from mice at 12-18 weeks of age. The mice had received an a MOG injection to induce EAE 35 days prior to harvest.
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
RStudio (v1.2.5033) was used for all downstream analyses and Seurat (v.3.9.9) was used for filtering out low-quality cells, normalization of the data, determination of cluster defining markers and graphing of the data on UMAP.
Low-quality cells were excluded in an initial quality-control (QC) step by removing cells with fewer than 150 unique genes and cells expressing more than 5,000 unique genes in effort to remove doublets and triplets
Cells with transcriptomes that were more than 20% mitochondrial-derived were removed and cells with more than 5% hemoglobin among their expressed genes were also removed.
Using Seurat, genes with high variance were selected using the FindVariableGenes() function, then the dimensionality of the data was reduced by principle component analysis (PCA) and identified by random sampling of 20 significant principal components (PCs) for each sample with the PCElbowPlot() function. Cells were clustered with Seurat’s FindClusters() function.
Next, differential gene expression analysis was performed within the clusters using the ZINB-WaVE (v1.12.0) and DESeq2 (v1.30.0) packages
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: microglia

extract_protocol:
FACS-sorted single cell suspensions were submitted to the University of Virginia Genome Analysis and Technology Core for single-cell RNA sequencing library preparation.
The raw sequencing reads (FASTQ files) were aligned to the UCSC mm10 mouse genome build using Cell Ranger (v1.3.1) which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting.

treatment_protocol:
We subjected mice to EAE demyelination for 35 days and then performed  scRNAseq on FACS-sorted microglia from whole brains. The microglia from 2 Syk+/+ mice with EAE were pooled as one biological replicate. The microglia from 2 Syk fl/fl mice with EAE were pooled as one biological replicate.
Sykcon-Ai6 and SykMG-Ai6 mice were euthanized on EAE Day 35 with CO2 and immediately transcardially perfused with 20 ml ice cold 1X PBS. Spinal cords were dissected and placed on ice in DMEM + 10% FBS. Tissues were gently homogenized by mashing through a cell strainer then centrifuged at 1500 rpm for 5 min. Pellets were resuspended in 13 ml 37% isotonic Percoll (GE Healthcare, 17-0891-01) in 1X PBS. Samples were centrifuged at 2000 rpm for 12 minutes at room temperature with no brake. After centrifugation, the top myelin layer and supernatant were aspirated and the cell pellet was resuspended in FACS buffer. Cell suspensions were incubated with Fc Block and antibodies for CD45, CD11b, and Gr-1. After two washes with FACS buffer, cells were resuspended in FACS buffer + 0.2 mg/ml DAPI and sorted on DAPI- CD45+ ZsGreen+ cells using an Influx Cell Sorter (Becton, Dickinson & Company) in the University of Virginia Flow Cytometry Core Facility.

value: microglia

tag: strain

value: Ai6 Sykfl/fl Cx3cr1ERT2Cre mice (female)

value: 12-18 weeks old


title: lncRNA profile of 36CHB

value: serum


title: lncRNA profile of 65LC


title: lncRNA profile of 50CHB


title: lncRNA profile of 48CHB


title: lncRNA profile of 49CHB


title: lncRNA profile of 39CHB


title: Male_plus_rep1

value: Ai6 Syk+/+ Cx3cr1ERT2Cre (male)


title: lncRNA profile of 43CHB


title: lncRNA profile of 33CHB


title: lncRNA profile of 34CHB


title: lncRNA profile of 40CHB


title: lncRNA profile of 32CHB


title: lncRNA profile of 42CHB


title: Female_plus_rep1

value: Ai6 Syk+/+ Cx3cr1ERT2Cre (female)


title: lncRNA profile of 37CHB


title: Male_SykFlox_rep1

value: Ai6 Sykfl/fl Cx3cr1ERT2Cre mice (male)


title: lncRNA profile of 38CHB


title: lncRNA profile of 46CHB


title: lncRNA profile of 35CHB


title: C4

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from KKAy Mouse ileum treated intragastrically with water

hyb_protocol: Following labeling, fragmented cDNA was hybridized for 16 hr at 45 ℃ on Clariom ™ S Assay(mouse, Affymetrix). GeneChips were washed and stained in the Affymet-rix Fluidics Station 450.

scan_protocol: All arrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which was installed in GeneChip® Scanner 3000 7G.

data_processing: The raw data(.cel) were normalized by the software TAC (Transcriptome Analysis Console; Vension:4.0.1) with Robust Multichip Analysis (RMA) algorithm using Affy-metrix default analysis settings and global scaling as a normalization method.

label: biotin

source_name: KKAy Mouse treated intragastrically with water

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.

growth_protocol: Male KKAy mice (30 g) aged 14 weeks were housed in a temperature- and humidity-controlled environment at 23 ± 2℃ with a 12-hr light/dark cycle.

extract_protocol: About 4 cm ileum tissue were collected when the mice were sacrificed at the end of treatment. Total RNA was extracted from ileum tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) (n=4 per group) according to manufacturer’s instructions

treatment_protocol: The KKAy mice were fed with high-fat diets (45% of energy from fat; Research Diets, United States) with free access to water.After feeding for 4 weeks of high-fat diets, KKAy mice were treated intragastrically with Voglibose (1mg/kg) or an equivalent volume of water (0.05 ml/10 g body weight) once daily for 8 weeks.

value: KKAy

tag: gender

value: Male

value: Ileum


title: V4

description: Gene expression data from KKAy Mouse ileum treated intragastrically with Voglibose (1mg/kg)

source_name: KKAy Mouse treated intragastrically with Voglibose (1mg/kg)


title: V1


title: C3


title: C2


title: lncRNA profile of 29CHB


title: lncRNA profile of 25CHB


title: lncRNA profile of 24CHB


title: lncRNA profile of 31CHB


title: PFOA high, A9394R1, 24h, blood

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description:
Illumina mRNA-seq
Exp2_Sample7
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz

data_processing:
FastQC (version 11.5) software was used for quality check.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36.
High-quality reads were mapped to the reference M.domestica genome assembly (MonDom5) by Tophat-2.1.1,  Bowtie2 and star-2.7.5.
Gene counts generation were performed with Bedtools -2.30.0.
EdgeR package in R (version 4.1.2) were used to normalize and detect DEGs. The cutoff for detecting significant DEGs were |log2(fold change)| > 1 and FDR < 0.05
Assembly: M.domestica genome assembly (MonDom5) (GenBank: GCA_000002295.1)
Supplementary files format and content: Gzipped, tab-delimited text file including raw gene counts for every gene in all samples in Exp2

organism: Monodelphis domestica

source_name: Monodelphis domestica whole blood

growth_protocol: In the pilot experiment (Exp1), samples were diluted 1:2 and 1:4 with sterile RPMI-1640 culture medium complemented with 2 mM glutamine and antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin). In the main experiment (Exp2), the blood samples were diluted 1:2 with sterile RPMI-1640 culture medium complemented with 2 mM glutamine and antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin). The samples were cultured in sterile 12-well culture plates with lid (USA Scientific, FL) in CO2 incubator at 37 °C under 5 % CO2 atmosphere.

extract_protocol:
DNA/RNA extraction were conducted using Zymo Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, CA) according to the manufacturer’s instructions. DNA/RNA quantity was measured using Qubit Fluorometer 3.0 (Thermo Fisher Scientific, MA) with Qubit RNA BR Assay Kit. Samples with a good RNA quality were selected for RNA sequencing libraries.
RNA sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA). We checked the final concentrations and size distribution of the libraries with Qubit and LabChip GX Touch HT machine (HT DNA NGS 3K Assay) (Perkin Elmer, MA).

treatment_protocol: Perfluorooctanoic acid (PFOA) and ammonium perfluoro(2-methyl-3-oxahexanoate) (GenX) were purchased from Sigma-Aldrich. (Chemical Abstracts Service Registry No. (CASRN) PFOA:335-67-1, GenX:62037-80-3). Stock solutions were prepared by dissolving neat chemical into molecular-grade dimethyl sulfoxide (DMSO) (>99.9%) at various concentrations. DMSO concentration was calculated and adjusted to achieve a final 0.1% volume percent (v/v) in all treatment and control groups. We use two final concentrations for each treatment, PFOA: 400uM/800uM, GenX: 600uM/1200uM.

value: whole blood

value: LSD

tag: treatment

value: PFOA high

tag: cultured time


title: lncRNA profile of 23HC


title: V3


title: lncRNA profile of 27CHB


title: V2


title: lncRNA profile of 30CHB


title: GenX high, A9394R3, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample5
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz

value: GenX high


title: lncRNA profile of 118HC

value: validation


title: Control, A9394R3, 24h, blood

description:
Illumina mRNA-seq
Exp2_Sample4
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz

value: untreated


title: lncRNA profile of 123HC

value: healthy control


title: PFOA low, A9394R2, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample10
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz

value: PFOA low


title: Control, A9394R2, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample2
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: PFOA high, A9394R2, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample8
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 26CHB

value: chronic hepatitis B

value: discovery


title: PFOA low, A9394R1, 24h, blood

description:
Illumina mRNA-seq
Exp2_Sample9
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 18HC

value: serum


title: lncRNA profile of 28CHB


title: Control, A9394R1, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample1
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 17HC


title: C1


title: lncRNA profile of 16HC


title: lncRNA profile of 22HC


title: lncRNA profile of 21HC


title: Control, A9394R2, 24h, blood

description:
Illumina mRNA-seq
Exp2_Sample3
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 19HC


title: A0039, 72h, blood

description:
Illumina mRNA-seq
Exp1_Sample14
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A3538, 72h, blood

description:
Illumina mRNA-seq
Exp1_Sample15
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 13HC


title: A0036, 72h, blood

description:
Illumina mRNA-seq
Exp1_Sample13
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 15HC


title: lncRNA profile of 20HC


title: lncRNA profile of 11HC


title: A3538, 48h, blood

description:
Illumina mRNA-seq
Exp1_Sample12
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A0036, 48h, blood

description:
Illumina mRNA-seq
Exp1_Sample10
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 12HC


title: A0039, 48h, blood

description:
Illumina mRNA-seq
Exp1_Sample11
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 14HC


title: GenX high, A9394R4, 12h, blood

description:
Illumina mRNA-seq
Exp2_Sample6
M.domestica_Exp2_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 10HC


title: lncRNA profile of 8HC


title: lncRNA profile of 9HC


title: lncRNA profile of 7HC


title: A3538, 12h, blood

description:
Illumina mRNA-seq
Exp1_Sample6
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A3538, 0h, blood

description:
Illumina mRNA-seq
Exp1_Sample3
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 5HC


title: A0036, 12h, blood

description:
Illumina mRNA-seq
Exp1_Sample4
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A0039, 12h, blood

description:
Illumina mRNA-seq
Exp1_Sample5
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 4HC


title: A0039, 0h, blood

description:
Illumina mRNA-seq
Exp1_Sample2
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A3538, 24h, blood

description:
Illumina mRNA-seq
Exp1_Sample9
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A0039, 24h, blood

description:
Illumina mRNA-seq
Exp1_Sample8
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: A0036, 0h, blood

description:
Illumina mRNA-seq
Exp1_Sample1
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: lncRNA profile of 2HC


title: C_3, biological replicate3

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression data from CDCA-treated Staphylococcus aureus grown till exponential phase

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT.
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method Bowtie2 and RSEM were used for differential expression analysis
Genome_build: Staphylococcus aureus COL
Supplementary_files_format_and_content: RPKMs, DEGs

organism: Staphylococcus aureus

source_name: Exponential phase bacterial culture of Staphylococcus aureus treated by CDCA

growth_protocol: Bacterial cells were grown for 12 hr at 37C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

treatment_protocol: Bacterial cells were collected and kept on ice to extract RNA.

value: CDCA-treated Staphylococcus aureus strain in LB medium

tag: growth phase

value: Exponential phase

tag: genotype

value: wild type


title: lncRNA profile of 1HC


title: C_1, biological replicate1


title: Control_3, biological replicate3

description: Gene expression data from Staphylococcus aureus grown till exponential phase

source_name: Exponential phase bacterial culture of Staphylococcus aureus

value: Staphylococcus aureus strain in liquid LB medium


title: C_2, biological replicate2


title: Control_2, biological replicate2


title: lncRNA profile of 3HC


title: A0036, 24h, blood

description:
Illumina mRNA-seq
Exp1_Sample7
M.domestica_Exp1_transcriptomes_raw_counts.txt.gz


title: Control_1, biological replicate1


title: lncRNA profile of 6HC


title: Bd21-3 LL ZT24 biol rep3

city: Tuxtepec, OAX

first: Julian

last: Pena-Castro

state: South America

address: Circuito Central 200

department: Biotechnology

country: Mexico

institute: Universidad del Papaloapan

data_processing:
RNA-sequencing FASTQ files were mapped to B. distachyon genome (Bdistachyon_314_v3.0.fa.gz: JGI version 3.0 assembly) using HISAT2 (version 2.1.0; Kim et al., 2019) to generate Binary Alignment File (BAM) files.
For libraries with more than one FASTQ files, the resulting BAM files were combined using SAMTools (version 1.12; Li et al., 2019). Libraries that failed to produced 80% read alignment were discarded.
BAM files were subjected to read count by HTseq python library (version 1.0) (Anders et al., 2015).
Gene expression and count per million (CPM) values were calculated using the edgeR program (Robinson et al., 2010), with the GLM (generalized linear model) method using an FDR cutoff of <0.05.
Assembly: B. distachyon genome (Bdistachyon_314_v3.0.fa.gz: JGI version 3.0 assembly)
Supplementary files format and content: tab-delimited XLS files include CPM values for each sample

organism: Brachypodium distachyon

source_name: Total green tissue

growth_protocol: Seeds were sown horizontally in substrate (1:4 v/v perlite:Cosmopeat) previously autoclaved for 2 h, cooled down and mixed with 2% w/w slow liberation fertilizer (NPK 15:15:17; Nitrofoska). Germination and growth were under long-day conditions (16 h light/8 h dark, 150 μE m−2 s−1, 50% humidity) in a growth room, with irrigation every 3 d using filtered tap water.

extract_protocol:
Aboveground tissue was collected, frozen immediately in liquid nitrogen and stored at − 80ºC. Tissue was ground to powder with a mortar and pestle with liquid nitrogen, avoiding thawing. Total RNA was extracted with the kit Direct-zol RNA mini prep kit (Zymo Research, R2050) and digested in-column with provided DNAse I.
RNA libraries for RNA-seq were prepared using TruSeq RNA sample prep v2 following manufacturer's protocols (Illumina).

treatment_protocol: Brachypodium plants (14-day-old, 6 leaves stage) were randomly arranged and submerged (S samples) in filtered tap water (30-cm deep) inside opaque-walled plastic tanks filled 24 h before the experiment. Plants collected at each indicated time were always grown in the same tank. Light reached the plants subjected to submergence stress (S) at 70 μE m−2 s−1. Normal growth controls (NG) were left at 150 μE m−2 s−1, while low-light controls (LL) were moved to plastic tanks without submergence side-by-side to submergence tanks.

value: Total green tissue

value: Low Light control ZT24


title: Bd21-3 S ZT24 biol rep1

value: Submergence Stress ZT24


title: Bd21-3 LL ZT24 biol rep2


title: Bd21-3 S ZT24 biol rep2


title: Bd21-3 LL ZT24 biol rep1


title: Bd21-3 NG ZT24 biol rep3

value: Normal growth control ZT24


title: Bd21-3 NG ZT24 biol rep2


title: 5xFAD_SykMG_rep4

data_processing:
The raw sequencing reads (FASTQ files) were aligned to the UCSC mm10 mouse genome build using the splice-aware read aligner HISAT2.
Samtools was used for quality control filtering/ PCR duplicate removal.
Reads were sorted into features with HTSeq, produing the processed .txt files.
Assembly: mm10
Supplementary files format and content: Microsoft Excel Open XML Spreadsheet include RPKM values for each Sample

extract_protocol:
Mice were euthanized with CO2 and immediately transcardially perfused with 20 ml 1X PBS. For AD experiments, brains were collected and their meninges and choroid plexus removed then the MACS-sorting protocol was used to isolate microglia as described (Norris et al., 2018). Tissues were homogenized by gently mashing through a 70 um cell strainer.  After centrifugation the cell pellet was resuspended in MACS buffer (Miltenyi Biotec, 130-0910376) to proceed with column purification of microglia using CD11b microbeads (Miltenyi, 130-093-634). We then performed sorting utilizing LS columns and a QuadroMACS magnet (Miltenyi, 130-042-401 and 130-091-051) according to manufacturer’s instructions. Column-bound cells were analyzed for purity by flow cytometry and submitted for RNA-seq.
RNA libraries were prepared for sequencing by GENEWIZ

treatment_protocol: We performed bulk RNA sequencing on the MACs-sorted microglia harvested from control (5xFAD null), SYK deficient (Sykfl/flCX3CR1ert2cre), 5xFAD, and 5xFAD Sykfl/flCx3CR1ert2cre brains at 20 weeks of age

tag: cell line

value: microglia

tag: cell type

value: RNA from microglia harvested from the mouse brain, female, 20 weeks

value: 5xFAD Sykfl/fl Cx3cr1ERT2cre


title: Bd21-3 NG ZT24 biol rep1

tag: tissue


title: 5xFAD_SykMG_rep2


title: 5xFAD_SykMG_rep3


title: Bd21 S ZT24 biol rep2


title: 5xFAD_SykMG_rep1


title: Bd21-3 S ZT24 biol rep3


title: Bd21 S ZT24 biol rep3


title: Bd21 S ZT24 biol rep1


title: 5xFAD_rep4


title: Bd21 LL ZT24 biol rep2


title: 5xFAD_rep3


title: Bd21 LL ZT24 biol rep1


title: 5xFAD_rep2


title: Bd21 NG ZT24 biol rep3


title: Bd21 NG ZT24 biol rep2


title: SykMG_rep4

value: Sykfl/fl Cx3cr1ERT2cre


title: Bd21 NG ZT24 biol rep1


title: Bd21-3 S ZT20 biol rep3

value: Submergence Stress ZT20


title: SykMG_rep1


title: SykMG_rep3


title: Control_rep4

value: WT (Control)


title: Bd21-3 LL ZT20 biol rep3

value: Low Light control ZT20


title: lncRNA profile of 54LC

value: liver cirrhosis

value: discovery


title: Control_rep3


title: SykMG_rep2


title: Bd21-3 LL ZT20 biol rep2


title: Control_rep1


title: Bd21-3 S ZT20 biol rep1


title: Control_rep2


title: Bd21-3 LL ZT20 biol rep1


title: Bd21-3 S ZT20 biol rep2


title: Bd21-3 NG ZT20 biol rep1

value: Normal growth control ZT20


title: Bd21-3 NG ZT20 biol rep3


title: Bd21-3 NG ZT20 biol rep2


title: PRVL89

city: Aubiere

first: Pierre

last: Val

address: 24 avenue des Landais

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
reads were filtered and trimmed using cutadapt v3.2 and checked with FASTQC v0.11.7
Illumina reads were aligned to mouse reference genome mm10 with Hisat v 2.2.1
Reads were annotated using R function "summarizeOverlaps() and RPKM were caluclated for each gene
Differential expression analysis with multiple testing correction was conducted using the R Bioconductor DESeq2 package v 1.34.0
Assembly: mm10
Supplementary files format and content: XLSX table containing RPKM  for each gene (row) in each sample (column)

source_name: Total RNA from mouse adrenals extracted with Macherey Nagel RNA extraction columns

extract_protocol:
Total RNA from whole mouse adrenals were extracted with Macherey Nagel NucleoSpin RNA columns
RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Whole adrenal glands from control wild-type mice and mice with conditionnal ablation of Znrf3 within steroidogenic cells (Sf1-Cre;Znrf3F/F) were collected at different timepoints

value: Female

value: KO

tag: age (weeks)


title: PRVL88


title: PRVL86


title: PRVL85

value: WT


title: Bd21 S ZT20 biol rep3

value: Total green tissue


title: PRVL84


title: Bd21 S ZT20 biol rep2


title: 5xFAD_rep1


title: Bd21 S ZT20 biol rep1


title: Bd21 LL ZT20 biol rep3


title: PRVL83


title: Bd21 LL ZT20 biol rep2


title: PRVL82


title: PRVL49


title: Bd21 NG ZT20 biol rep3


title: Bd21 NG ZT20 biol rep1


title: PRVL87


title: Bd21 NG ZT20 biol rep2


title: Bd21-3 S ZT16 biol rep3

value: Submergence Stress ZT16


title: PRVL47


title: Bd21-3 S ZT16 biol rep2


title: PRVL46


title: PRVL43


title: PRVL42


title: Bd21-3 LL ZT16 biol rep3

value: Low Light control ZT16


title: PRVL73


title: Bd21-3 LL ZT16 biol rep2


title: Bd21-3 NG ZT16 biol rep3

value: Normal growth control ZT16


title: Bd21-3 S ZT16 biol rep1


title: PRVL71


title: Bd21-3 LL ZT16 biol rep1


title: PRVL70


title: PRVL72


title: Bd21-3 NG ZT16 biol rep1


title: Bd21-3 NG ZT16 biol rep2


title: PRVL48


title: PRVL68


title: PRVL69


title: Bd21 LL ZT20 biol rep1


title: Bd21 S ZT16 biol rep2


title: PRVL45


title: PRVL66


title: Bd21 LL ZT16 biol rep2


title: Bd21 LL ZT16 biol rep1


title: PRVL67


title: PRVL64


title: Bd21 LL ZT16 biol rep3


title: Bd21 NG ZT16 biol rep3


title: PRVL62


title: Bd21 S ZT16 biol rep1


title: Bd21 NG ZT16 biol rep2


title: PRVL61


title: PRVL65


title: PRVL59


title: Bd21-3 S ZT8 biol rep3

value: Submergence Stress ZT8


title: PRVL58


title: PRVL44


title: Bd21 S ZT16 biol rep3


title: Bd21-3 S ZT8 biol rep1


title: PRVL63


title: PRVL57


title: Bd21-3 LL ZT8 biol rep3

value: Low Light control ZT8


title: PRVL56


title: PRVL55


title: Bd21-3 LL ZT8 biol rep2


title: Bd21-3 LL ZT8 biol rep1


title: Bd21-3 NG ZT8 biol rep3

value: Normal growth control ZT8


title: Bd21-3 NG ZT8 biol rep2


title: PRVL53


title: Bd21 NG ZT16 biol rep1


title: Bd21-3 NG ZT8 biol rep1


title: Bd21 S ZT8 biol rep3


title: PRVL81

value: Male


title: Bd21 S ZT8 biol rep1


title: Bd21 S ZT8 biol rep2


title: PRVL50


title: Bd21-3 S ZT8 biol rep2


title: Bd21 LL ZT8 biol rep1


title: PRVL79


title: PRVL80


title: PRVL77


title: Bd21 LL ZT8 biol rep2


title: Bd21 NG ZT8 biol rep3


title: PRVL78


title: PRVL76


title: Bd21 NG ZT8 biol rep2


title: PRVL54


title: Bd21 NG ZT8 biol rep1


title: PRVL74


title: PRVL33


title: Bd21-3 S ZT0 biol rep3

value: Submergence Stress ZT0


title: PRVL52


title: Bd21-3 S ZT0 biol rep2


title: PRVL51


title: PRVL32


title: Bd21-3 S ZT0 biol rep1


title: Bd21 LL ZT8 biol rep3


title: PRVL31


title: Bd21-3 LL ZT0 biol rep3

value: Low Light control ZT0


title: Bd21-3 LL ZT0 biol rep2


title: PRVL30


title: PRVL29


title: Bd21-3 LL ZT0 biol rep1


title: PRVL75


title: PRVL28


title: Bd21-3 NG ZT0 biol rep3

value: Normal growth control ZT0


title: Bd21-3 NG ZT0 biol rep2


title: PRVL25


title: PRVL24


title: Bd21-3 NG ZT0 biol rep1


title: Bd21 S ZT0 biol rep3


title: PRVL4


title: PRVL23


title: Bd21 S ZT0 biol rep1


title: PRVL2


title: PRVL3


title: PRVL1


title: Bd21 LL ZT0 biol rep3


title: Bd21 LL ZT0 biol rep2


title: PRVL8


title: PRVL9


title: Bd21 LL ZT0 biol rep1


title: Bd21 NG ZT0 biol rep2


title: PRVL6


title: PRVL5


title: Bd21 NG ZT0 biol rep1


title: PRVL17


title: PRVL15


title: PRVL12


title: PRVL13


title: Bd21 S ZT0 biol rep2


title: WL1

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

description: 75 bp

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with Tophat v.2.1.0
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Assembly: mm10
Supplementary files format and content: normalized abundance measurements provided as edgeR output files

source_name: liver

extract_protocol:
Total RNA was isolated using RNAseqy MicroKit (Qiage) according to the manufacturer's recommendations
Libraries were constructed using Nugen's Ovation Ultralow Library systems and were subsequently sugject to 76 cycles of NextSeq500 sequencing

value: liver


title: WT1

description: 75 bp

source_name: thymus

value: thymus


title: PRVL10


title: WL2

description: 75 bp


title: PRVL11


title: WT3

description: 75 bp


title: WS3

description: 75 bp

source_name: spleen

value: spleen


title: WS2

description: 75 bp


title: WS1

description: 75 bp


title: PRVL14


title: PRVL16


title: EBd6_c

city: CB2 0RE

first: Giorgia

last: Battistoni

address: Robinson Way

department: CRUK-CI

institute: University of Cambridge

data_processing:
cellranger-2.0.1
Genome_build: mm10
Supplementary_files_format_and_content: compressed cell ranger output

source_name: dissociated Embryoid body induced towards germ cell differentiation

extract_protocol: 10x Genomics Single cell gene Expression 3' v2

value: differentiated

value: germ cell differentiated Embryoid Body


title: Bd21 NG ZT0 biol rep3


title: EBd6_b


title: eNPCs, pooled input [re-used]

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

data_processing:
For data pre-processing, FASTQ files were adaptor-trimmed by TrimGalore [https://github.com/FelixKrueger/TrimGalore] with default parameters and aligned to either hg19 or mm10 genome by Bowtie2.
Trimmed FASTQ files were then aligned to Dm6 genome for later calculation of scaling factors. Calculation of scaling factors and aligned BAM files were down-sampled by Picard.
To identify differential binding regions for SMARCA4/BRG1, respectively, down-sampled BAM files were transformed into BED format by Bedtools.
Differential binding regions were then called by diffReps with a window size of 100bp.
Data visualization was done using BigWig files for SMARCA4/BRG1 signal, generated by the bamCompare command in deepTools using input signal as control.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

source_name: primary NPCs

growth_protocol: Cells were grown under standard cell culture conditions.

extract_protocol: Active Motif

tag: chip antibody

value: SMARCA4/BRG1, ab110641, abcam

value: primary NPCs


title: EBd6_a


title: mEPILCs

source_name: induced mouse Epiblast like cells

value: mouse Epiblast like cells


title: eNPCs, BCL7A KO, SMARCA4/BRG1

value: BCL7A KO


title: eNPCs, pooled input

data_processing:
For data pre-processing, FASTQ files were adaptor-trimmed by TrimGalore [https://github.com/FelixKrueger/TrimGalore] with default parameters and aligned to either hg19 or mm10 genome by Bowtie2.
Trimmed FASTQ files were then aligned to Dm6 genome for later calculation of scaling factors. Calculation of scaling factors and aligned BAM files were down-sampled by Picard.
To identify differential binding regions for H3K27me3, respectively, down-sampled BAM files were transformed into BED format by Bedtools.
Differential binding regions were then called by diffReps with a window size of 300bp for H3K27me3.
Data visualization was done using BigWig files for H3K27me3 signal, generated by the bamCompare command in deepTools using input signal as control.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig

value: H3K27me3, AB_2561020, Actife Motif


title: E13.5_r1

source_name: male gonad

extract_protocol:
FACSorting, 10x Genomics Single cell gene Expression 3' v2
10x Genomics Single cell gene Expression 3' v2

tag: mouse background

tag: fluorescent reporter

value: male gonad


title: mESCs

source_name: cultured naïve mouse ES

value: undifferentiated

value: naive mouse embryonic stem cell


title: eNPCs, wt, SMARCA4/BRG1

value: wt


title: WT2

description: 75 bp


title: eNPCs, BCL7A KO, H3K27me3


title: WL3

description: 75 bp


title: eNPCs, BCL7A KO, 48h differentiation [Sample14_7800_ko_Dif2]

data_processing:
Samples were demultiplexed and base call files were converted into Fastq format using bcl2fastq2 v2.20 software (Illumina) before alignment to the mouse genome mm10 build GRCm38 using STAR aligner. Data analysis was performed using Shyni-Seq (Sundararajan et al, 2019).
Assembly: mm10
Supplementary files format and content: count table

extract_protocol:
At the indicated time points, cells were scraped, collected and pelleted in PBS. Cell pellets of approximately 500,000 cells were then lysed in Trizol, snap-frozen and stored at -80 °C until use RNA was quantified via HS RNA assay on a Tapestation4200 instrument (Agilent).
Approximately 100 ng of extracted ribosomally bound RNA was used as an input for RNA-Seq library preparation according to the TruSeq Stranded mRNA kit (Illumina) following manufacturer's instructions. NGS libraries were quantified via Qubit HS dsDNA assay (Invitrogen) and library size distribution was determined using a HS D1000 assay on a Tapestation4200 instrument (Agilent). Libraries were equimolarly pooled, clustered at 1.8 pM concentration and sequenced SR 75 cycles using High Output v2 chemistry on a NextSeq500 instrument (Illumina).

tag: sample id

tag: time


title: eNPCs, wt, H3K27me3


title: E10.5_r1

source_name: posterior embryo

value: posterior embryo


title: eNPCs, wt, 48h differentiation [Sample10_7788_wt_Dif2]


title: eNPCs, BCL7A KO, 48h differentiation [Sample13_7797_ko_Dif2]


title: eNPCs, BCL7A KO, 48h differentiation [Sample11_7791_ko_Dif2]


title: eNPCs, BCL7A KO, 48h differentiation [Sample15_7803_ko_Dif2]


title: WI30min-3

city: Hangzhou

first: jia

last: Luo

address: qingchun road

institute: 浙江大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Rattus_norvegicus.Rnor_6.0 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
RNA was havested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequence libraries.
RNA libraries wered prepared using SMARTER mRNA-Seq library Prep Kit following manufacturers protocols  were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR   amplification, the PCR product was purified by AMPure XP beads, and the library was   finally obtained.

tag: Sex

value: male

value: warm ischemic 30min


title: eNPCs, wt, 48h differentiation [Sample8_7782_wt_Dif2]


title: HOPE1h-1

value: liver

value: warm ischemic 30min+ SCS3h+HOPE1h


title: HOPE1h-3


title: HMP1h-3

value: warm ischemic 30min+ SCS3h+HMP1h


title: SCS4h-2

value: warm ischemic 30min +SCS4h


title: HOPE1h-2


title: WI30min-1


title: HMP1h-2


title: eNPCs, BCL7A KO, undifferentiated [Sample4_7790_ko_Dif0]


title: eNPCs, BCL7A KO, undifferentiated [Sample5_7796_ko_Dif0]


title: eNPCs, wt, 48h differentiation [Sample7_7779_wt_Dif2]


title: eNPCs, BCL7A KO, 48h differentiation [Sample12_7794_ko_Dif2]


title: WI30min-2


title: Day 7 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2

city: Lebanon

first: Xiao feng

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

data_processing:
Library strategy: CUT&RUN
Reads were deduplicated with the clumpify tool using flag -dedupe -subs=2, and subsequently trimmed with bbduk using parameters --ktrim=r --k=21 --mink=11 --hdist=1 --tpe --tbo.
The trimmed fastq files were then aligned to the Hg19 human genome using Bowtie2 aligner. Specifically, we used parameter “--end-to-end --very-sensitive --no-mixed --no-discordant -q -I 10 -X 700 --phred33” for the alignment.
Bam files were converted to bed files after removing chrM, chrUn, and reads containing “random” as chromosome position. Bed files were further cleaned by removing regions contained in the hg19 blacklist from ENCODE (v2)
Epic2 software (v.0.0.41) was used for calling histones and SWI/SNF peaks with parameters at default
Genome_build: hg19
Supplementary_files_format_and_content: CUT_RUN_peak.bed, which includes the peaks for all SWI/SNF subunits and AP-1 samples, is linked to the SuperSeries GSE196960 record.

source_name: G401 cell line

growth_protocol: G401 cell lines were purchased from American Type Culture Collection. Cell lines were cultured in DMEM with 10% FBS. SMARCB1 inducible re-expression stable G401 cell line was created previously and is maintained in media with Tet-free FBS (Gibco, Cat.# 16140071).

extract_protocol:
DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (Cat.# 15593031, ThermoFisher) and purified using ProNex Purification System (Cat.#NG2003, Promega).
CUT&RUN library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat.# E7645L, New England Labs). Libraries were paired-end sequenced with read lengths of 150 bp (PE 2X150 on the Illumina HiSeq Genome Analyzer). Average of 10 million reads per sample.

treatment_protocol: To induce SMARCB1 re-expression, cells were treated with doxycycline (1 μg/ml, EMD Millipore) for indicated time.

value: G401 cell line

value: SMARCB1 +/+ G401 cell line

tag: cut&run antibody

tag: time point


title: HMP1h-1


title: Day 7 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: eNPCs, BCL7A KO, undifferentiated [Sample6_7793_ko_Dif0]

value: primary NPCs


title: SCS4h-3


title: eNPCs, wt, 48h differentiation [Sample9_7785_wt_Dif2]


title: SCS4h-1


title: eNPCs, wt, undifferentiated [Sample2_7784_wt_Dif0]


title: Day 7 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: eNPCs, wt, undifferentiated [Sample1_7778_wt_Dif0]


title: DeltaLN_siNrf2_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: Breast cancer cells

growth_protocol: PyMT-1099 LT, Py2T LT and MT∆Ecad mesenchymal cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. 5g of RNA was then subjected to rRNA depletion using the Ribozero magnetic gold kit (Epicentre, MRZG12324) followed by concentrating it using the  RNeasy MinElute Cleanup Kit (Qiagen, 74204).
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. RNA quality control was performed with an RNA ScreenTape on the Agilent 4200 TapeStation and the concentration measured by using the Quanti-iT RiboGreen RNA assay Kit (Life Technologies). 200 ng of RNA were subjected to rRNA depletion and utilized for library preparation with the Truseq Stranded Total RNA Library Prep kit with Ribo-Zero Gold (Illumina). Library QC was performed with a Fragment Analyzer (AATI) using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473). RNA-seq libraries were sequenced SR81 with NextSeq 500 High Output v2 kit (Illumina) on an Illumina NextSeq 500 using protocols defined by the manufacturer; primary data analysis was done using Illumina RTA Version: 2.4.11.

treatment_protocol: For Nrf2 ablation, PyMT-1099 LT, Py2T LT and MT∆Ecad mesenchymal cells were transfected with Nrf2-targeting siRNA (siNrf2) for 48 hours. Non-targeting siRNA transfected cells served as control (siCtl).

tag: strain

value: MMTV-Neu

value: Tumor developed in mammary gland

tag: used sirna

tag: sirna manufacturer

value: Dharmacon

tag: treatment length

value: 48 hours


title: Day 7 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2

tag: treatment


title: Day 3 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2

tag: cell line


title: Day 3 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: eNPCs, wt, undifferentiated [Sample3_7787_wt_Dif0]

tag: cell type

tag: genotype


title: Py2T_LT_siCtl_2

value: MMTV-PyMT

tag: tissue

value: siCtl


title: Day 3 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: 1099_LT_siNrf2_2


title: DeltaLN_siNrf2_1


title: Py2T_LT_siNrf2_1


title: DeltaLN_siCtl_2


title: Day 1 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: 1099_LT_siCtl_2


title: Day 0 SMARCC1 CUT&RUN profiling in SMARCB1 -/- G401 cell line Rep2

value: SMARCB1 -/- G401 cell line


title: Day 0 BRD9 CUT&RUN profiling in SMARCB1 -/- G401 cell line Rep2


title: Day 3 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: DeltaLN_siCtl_1


title: Day 1 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: Py2T_LT_siCtl_1


title: 1099_LT_siNrf2_1


title: PRVL60

value: Female

value: WT

tag: age (weeks)


title: Day 0 PBRM1 CUT&RUN profiling in SMARCB1 -/- G401 cell line Rep2


title: 1099_LT_siCtl_1


title: Day 0 ARID1A CUT&RUN profiling in SMARCB1 -/- G401 cell line Rep2


title: MTflEcad_I80_replicate_2

growth_protocol: MTflEcad cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

treatment_protocol: For the H2O2 treatment, MTflEcad epithelial cells were daily treated during 7 months with 80 µM and 150 µM H2O2 (MTflEcad I80 and MTflEcad DI150 cells respectively). Untreated cells served as control and were named MTflEcad PBS.

tag: h2o2 concentration

value: 80 uM

value: daily, 7 months


title: Day 7 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line

value: IgG


title: Day 1 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: Day 1 SMARCC1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep2


title: Py2T_LT_siNrf2_2


title: Day 3 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line


title: MTflEcad_DI150_replicate_1


title: MTflEcad_PBS_replicate_2

value: PBS

value: 0 uM


title: Day 1 IgG CUT&RUN profiling in SMARCB1 +/+ G401 cell line

value: G401 cell line


title: Day 0 IgG CUT&RUN profiling in SMARCB1 -/- G401 cell line


title: Py2T_I60_replicate_2

growth_protocol: Py2T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

treatment_protocol: For the H2O2 treatment, Py2T epithelial cells were daily treated during 4 months with 40 µM and 60 µM H2O2 (Py2T C40 and Py2T I60 cells respectively). Untreated cells served as control and were named Py2T PBS.

value: 60 uM

value: daily, 4 months


title: Py2T_I60_replicate_1


title: Day 7 ARID1A CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep1

value: SMARCB1 +/+ G401 cell line


title: Day 7 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep1


title: MTflEcad_I80_replicate_1

value: MMTV-Neu

value: Tumor developed in mammary gland


title: Py2T_C40_replicate_1

value: 40 uM


title: MTflEcad_PBS_replicate_1


title: Day 7 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep1


title: Py2T_C40_replicate_2


title: Day 3 PBRM1 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep1


title: Day 3 BRD9 CUT&RUN profiling in SMARCB1 +/+ G401 cell line Rep1


title: MTflEcad_DI150_replicate_2


title: Py2T_PBS_replicate_1