title: long read RNA-seq from adrenal gland (ENCLB018BFH)

description:
https://www.encodeproject.org/experiments/ENCSR512EWP/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_215 B6Cast F1 PND4_Male 03_Adrenals
experiment encode accession: ENCSR512EWP
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB018BFH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: adrenal gland

value: B6Cast F1 PND4 Male 04 adrenal gland for Wold core

value: male

value: The Jackson Laboratory

value: ENCBS623ZPY at ENCODE; https://www.encodeproject.org/ENCBS623ZPY/


title: long read RNA-seq from adrenal gland (ENCLB960VMW)

status: Public on Dec 04 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/ENCSR942UFC/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland BL6 male
experiment encode accession: ENCSR942UFC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB960VMW

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J adrenal gland tissue

value: tissue

tag: description

value: RNA Evaluation adrenal gland C57BL6 WT male microRNA-seq from Mortazavi

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

tag: lab

value: Ali Mortazavi, UCI

tag: source

tag: strain

tag: link

value: ENCBS873WBE at ENCODE; https://www.encodeproject.org/ENCBS873WBE/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: PAS-seq from endodermal cell (ENCLB124OYB)

description:
https://www.encodeproject.org/experiments/ENCSR198UNH/
***************
biological replicate number: 3
technical replicate number: 1
description: H1-DE QuantSeq
experiment encode accession: ENCSR198UNH
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB124OYB
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

organism: Homo sapiens

source_name: Homo sapiens male embryo endodermal in vitro differentiated cells

value: endodermal cell

value: in vitro differentiated cells

tag: health state

value: healthy

value: embryonic

value: Barbara Wold, Caltech

value: René Maehr

value: ENCBS971DDS at ENCODE; https://www.encodeproject.org/ENCBS971DDS/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: PAS-seq from endodermal cell (ENCLB599EWH)

description:
https://www.encodeproject.org/experiments/ENCSR198UNH/
***************
biological replicate number: 1
technical replicate number: 1
description: H1-DE QuantSeq
experiment encode accession: ENCSR198UNH
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB599EWH
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: male

value: ENCBS464AKI at ENCODE; https://www.encodeproject.org/ENCBS464AKI/


title: long read RNA-seq from layer of hippocampus (ENCLB152AGW)

description:
https://www.encodeproject.org/experiments/ENCSR472CHU/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_441, ENC4_442 hippocampus_B6Cast F1_18 - 20 months_female_6_ENC4_cDNA513
experiment encode accession: ENCSR472CHU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB152AGW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6CASTF1/J female (18-20 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: female

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS528DMR at ENCODE; https://www.encodeproject.org/ENCBS528DMR/

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


title: PAS-seq from endodermal cell (ENCLB808SNJ)

description:
https://www.encodeproject.org/experiments/ENCSR198UNH/
***************
biological replicate number: 2
technical replicate number: 1
description: H1-DE QuantSeq
experiment encode accession: ENCSR198UNH
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB808SNJ
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: endodermal cell

value: not collected

value: ENCBS012DYC at ENCODE; https://www.encodeproject.org/ENCBS012DYC/


title: long read RNA-seq from adrenal gland (ENCLB268NHJ)

description:
https://www.encodeproject.org/experiments/ENCSR735IBE/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland BL6 female
experiment encode accession: ENCSR735IBE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB268NHJ

value: adrenal gland

value: RNA Evaluation adrenal gland C57BL6 WT female microRNA-seq from Mortazavi

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS525FJF at ENCODE; https://www.encodeproject.org/ENCBS525FJF/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: long read RNA-seq from adrenal gland (ENCLB073ELK)

description:
https://www.encodeproject.org/experiments/ENCSR735IBE/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland BL6 female
experiment encode accession: ENCSR735IBE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB073ELK

value: ENCBS162KCU at ENCODE; https://www.encodeproject.org/ENCBS162KCU/


title: long read RNA-seq from layer of hippocampus (ENCLB713YAL)

description:
https://www.encodeproject.org/experiments/ENCSR060OTU/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD hippo het Female
experiment encode accession: ENCSR060OTU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB713YAL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax layer of hippocampus tissue

value: layer of hippocampus

value: 5xFAD hippo het Female

value: MODEL-AD

value: ENCBS251XQY at ENCODE; https://www.encodeproject.org/ENCBS251XQY/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: long read RNA-seq from left cerebral cortex (ENCLB610LYU)

description:
https://www.encodeproject.org/experiments/ENCSR550KPM/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_471, ENC4_472 B6Cast F1 PND 18-20 months Male 03 L. cortex
experiment encode accession: ENCSR550KPM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB610LYU
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 DPN18-20months

value: female

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS774TTB at ENCODE; https://www.encodeproject.org/ENCBS774TTB/


title: To H3K4me3, developing testis rep 2

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
GSM3403758
Testis.To.merge.CRUP.bw

library_source: genomic

data_processing:
Mapping was performed with the STAR v2.6.1d software41 using settings to enforce unspliced read mapping (--alignEndsType EndToEnd --alignIntronMax 1 --outFilterMatchNminOverLread 0.94). Finally, deduplication was performed via bamUtil (version 1.0.14; option –rmDups, https://github.com/statgen/bamUtil/releases)
Calling of putative enhancer regions was performed for mole and mouse via the software CRUP with replicates merged beforehand. Enhancer regions with a distance <=200bp were merged. To reduce outlier effects in enhancer probability scores, a smoothing over 5 bins of 100bp was applied.
Assembly: mm9 and talOcc4
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Talpa occidentalis

source_name: developing testis

extract_protocol:
Gonads were fixed using 1% formaldehyde and subsequently snap-frozen and stored at -80°C. Chromatin immunoprecipitations were performed using the iDeal ChIP-seq Kit for Histones (Diagenode, Cat. No. C01010051) according to the manufacturer's instructions.
Whole fixed gonads were lysed and subsequently sonicated using a Bioruptor (45 cycles, 30 seconds on, 30 seconds off, at high power) in the provided buffers. 5 µg of sheared chromatin were then used per immunoprecipitation with 1 µg of the following specific histone antibodies: anti-H3K4me3 (Millipore, cat. No. 07-473), anti-H3K4me1 (Diagenode, cat. No. C15410037), anti-H3K27ac (Diagenode, cat. No. C15410174)

tag: cell type

value: developing testis

tag: chip antibody


title: To H3K4me3, developing testis part rep 2

description:
GSM3403760
TestisPortion.To.merge.CRUP.bw

source_name: developing testis part

value: developing testis part

value: anti-H3K4me3 (Millipore, cat. No. 07-473)


title: To H3K4me1, developing testis part rep 2

description:
GSM3403750
TestisPortion.To.merge.CRUP.bw

value: anti-H3K4me1 (Diagenode, cat. No. C15410037)


title: To H3K4me3, developing testis rep 1

description:
GSM3403757
Testis.To.merge.CRUP.bw


title: To H3K4me1, developing testis rep 2

description:
GSM3403748
Testis.To.merge.CRUP.bw


title: To H3K4me3, developing ovary part rep 2

description:
GSM3403754
OvaryPortion.To.merge.CRUP.bw

source_name: developing ovary part

value: developing ovary part


title: To H3K4me1, developing testis part rep 1

description:
GSM3403749
TestisPortion.To.merge.CRUP.bw


title: To H3K4me1, developing ovary part rep 2

description:
GSM3403743
OvaryPortion.To.merge.CRUP.bw


title: To H3K4me1, developing testis rep 1

description:
GSM3403747
Testis.To.merge.CRUP.bw


title: To H3K4me3, developing ovary part rep 1

description:
GSM3403753
OvaryPortion.To.merge.CRUP.bw


title: To H3K4me3, developing testis part rep 1

description:
GSM3403759
TestisPortion.To.merge.CRUP.bw


title: To H3K4me1, developing ovary part rep 1

description:
GSM3403742
OvaryPortion.To.merge.CRUP.bw


title: long read RNA-seq from adrenal gland (ENCLB008ALX)

description:
https://www.encodeproject.org/experiments/ENCSR942UFC/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland BL6 male
experiment encode accession: ENCSR942UFC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB008ALX

value: adrenal gland

value: RNA Evaluation adrenal gland C57BL6 WT male microRNA-seq from Mortazavi

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS004AHE at ENCODE; https://www.encodeproject.org/ENCBS004AHE/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: To H3K27ac, developing testis part rep 1

description:
GSM3403727
TestisPortion.To.merge.CRUP.bw

value: anti-H3K27ac (Diagenode, cat. No. C15410174)


title: long read RNA-seq from layer of hippocampus (ENCLB951YDI)

description:
https://www.encodeproject.org/experiments/ENCSR026WRM/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_415, ENC4_416 hippocampus_B6CastF1_PND14_3x male_7,8,9_ENC4_cDNA499
experiment encode accession: ENCSR026WRM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB951YDI
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6CASTF1/J male (14 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: male

value: 14 day

value: ENCBS299AJA at ENCODE; https://www.encodeproject.org/ENCBS299AJA/

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


title: HUVEC_CNTF_R_VEGF_1

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
STAR aligner (Galaxy Version 2.7.5b) for mapping using standard settings
Merging BAM Files of Flow Cell 1 and 2
featureCounts (Galaxy Version 1.6.4) for generating count matrix using standard settings
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with counts generated by featureCounts and corresponding Ensembl Stable IDs

molecule: polyA RNA

source_name: Human umbilical vein endothelial cells

growth_protocol: 150000 HUVECs (Cat#: C2519A, Lonza Group) were seeded on 6-well plates and incubated overnight

extract_protocol:
Qiazol (Cat#: 79306, Qiagen) and RNeasy Micro Kit (Cat#: 74004, Qiagen) was used for RNA extraction
Librarys were generated by Illumina TruSeq Stranded mRNA Sample Preparation Guide (Cat#: 20020594, Illumina)

treatment_protocol: Cells were stimulated for 24h by cytokines. The following concentrations were used: VEGF (25 ng/mL), OSM+VEGF (100 ng/mL + 25 ng/mL),  CNTF+CNTFR+VEGF (100 ng/mL + 200 ng/mL + 25 ng/mL)

value: Human umbilical vein endothelial cells

tag: treatment

value: 100 ng/mL CNTF, 200ng/mL CNTFR alpha and 25 ng/mL VEGF for 24h


title: HUVEC_CNTF_R_VEGF_2


title: To H3K27ac, developing testis part rep 2

description:
GSM3403728
TestisPortion.To.merge.CRUP.bw

value: developing testis part


title: To H3K27ac, developing ovary part rep 2

description:
GSM3403722
OvaryPortion.To.merge.CRUP.bw

value: developing ovary part


title: To H3K27ac, developing testis rep 2

description:
GSM3403726
Testis.To.merge.CRUP.bw

value: developing testis


title: To H3K27ac, developing testis rep 1

description:
GSM3403725
Testis.To.merge.CRUP.bw


title: HUVEC_OSM_VEGF_3

value: 100 ng/mL OSM and 25 ng/mL VEGF for 24h


title: VM CD8+ T cells, clean, timestamped at day 28, rep 3 (ATAC-seq)

city: Ithaca

first: David

middle: S

last: Iu

state: NY

address: 427 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Raw reads were evaluated, trimmed, and filtered using trim galore (v0.6.5; -j 8 —quality 20 -gzip —length 50 –paired –fastqc) and aligned to the mouse reference genome (mm10) using bwa mem (-M -R)45, then processed using samtools view (v1.9; -b -h -F 0x0100). The reads were further sorted and indexed using samtools sort and samtools index46. Mitochondrial reads were filtered out using a custom shell script, and then picard MarkDuplicates was used to deduplicate the reads.
Assembly: mm10
Supplementary files format and content: BW

source_name: spleen

extract_protocol:
FACS sorted cells were permeabilized in lysis buffer (10 mM Tris-Cl pH 8.0, 300 mM sucrose, 10 mM NaCl, 2 mM MgAc2, 6 mM CaCl2, 0.2% NP-40 (Igepal), 0.5 mM DTT, 1x Pierce protease inhibitor (Thermo Scientific), and 40 units of RiboLock RNase inhibitor (Thermo Scientific) per 10 mL buffer) by brief aggressive pipetting, washed with buffer W (10 mM Tris-Cl pH 8.0, 300 mM sucrose, 10 mM NaCl, 2 mM MgAc2, 0.008% Tween20, 0.5 mM DTT, 1x protease inhibitor, and 40 units of RiboLock RNase inhibitor per 10 mL buffer), and resuspended in storage buffer (50 mM Tris-Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT, 1x protease inhibitor, and 40 units of RiboLock RNase inhibitor per 10 mL buffer). The cells were pelleted at 1000 g for 8 minutes for each step of buffer change. The permeabilized cells were counted, snap-frozen in liquid nitrogen, and stored at -80°C.
Libraries were prepared by the TREx core at Cornell University from 25,000 permeabilized cells as described in Buenrostro et al. (2015) and Corces et al. (2017). Briefly, frozen permeabilized cells were thawed, washed twice in ATAC-RSBbuffer containing 0.1% Tween20, resuspended in Transposition Mix (Nextera DNA Sample Preparation Kit, Illumina) containing 0.1% Tween20, resuspended in 25 µL Omni-ATAC Transposition Mix (10 mM Tris pH 8, 5 mM MgCl2, 10% DMF, 0.1% Tween20, 0.01% digitonin, 1.25 µL TDE1 enzyme (Illumina), and 8.25 µL PBS in final 25 µL volume per sample), incubated for 30 minutes at 37°C with shaking (900 rpm), with immediate addition of Zymo binding buffer. After Zymo column cleanup, libraries were amplified using Nextera PCR oligos (Nextera Index Kit, Illumina) and 2x HiFi Master Mix (New England Biolabs) with an initial incubation at 72°C for 5 minutes to extend the segmented ends and 11 PCR amplification cycles.  The libraries were cleaned up twice (in series) with a 2:1 ratio of SPRIselect beads (Beckman Coulter).

treatment_protocol:
N/A
Splenic CD8+ T cells were isolated and purified using positive selection with CD8a microbeads (Miltenyi). Purified CD8+ T cells were stained using antibodies against CD4 (Gk1.5), CD44 (IM7), CD122 (TM-B1), CD49d (R1-2), and CD8a (53-6.7). ‘Bulk stamped’ CD8+ populations were sorted for CD4-CD8+CD49dloGFP+, ‘stamped CD44hi’ populations were sorted for CD4-CD8+CD49dloGFP+CD44hi, and ‘stamped CD44lo’ populations were sorted for CD4-CD8+CD49dloGFP+CD44lo. Samples were sorted using a BD FACS Aria Fusion II equipped with four lasers. Samples were sorted using a BD Aria Fusion II equipped with four lasers. Samples were sorted to >95% cell purity as determined by a post-sort check.

tag: transgenic insertions

value: CD8+ T cells

tag: phenotype

tag: tissue

value: spleen

tag: condition

value: specific pathogen-free

tag: timestamp age

value: 28 days

tag: age of animal

value: 8 weeks


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 3 (ATAC-seq)

value: exposed to microbial material


title: HUVEC_OSM_VEGF_2


title: HUVEC_VEGF_3

value: 25 ng/mL VEGF for 24h


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 3 (ATAC-seq)

value: 1 day


title: HUVEC_CNTF_R_VEGF_3


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 3 (ATAC-seq)


title: HUVEC_OSM_VEGF_1


title: HUVEC_VEGF_1


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 3 (ATAC-seq)


title: VM CD8+ T cells, clean, timestamped at day 1, rep 3 (ATAC-seq)


title: HUVEC_VEGF_2


title: TN CD8+ T cells, clean, timestamped at day 1, rep 3 (ATAC-seq)


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 2 (ATAC-seq)


title: To H3K27ac, developing ovary part rep 1

description:
GSM3403721
OvaryPortion.To.merge.CRUP.bw

value: anti-H3K27ac (Diagenode, cat. No. C15410174)


title: TN CD8+ T cells, clean, timestamped at day 28, rep 2 (ATAC-seq)


title: VM CD8+ T cells, clean, timestamped at day 28, rep 2 (ATAC-seq)


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 2 (ATAC-seq)


title: TN CD8+ T cells, clean, timestamped at day 28, rep 3 (ATAC-seq)


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 2 (ATAC-seq)


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 2 (ATAC-seq)


title: VM CD8+ T cells, clean, timestamped at day 1, rep 2 (ATAC-seq)


title: TN CD8+ T cells, clean, timestamped at day 1, rep 2 (ATAC-seq)


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 1 (ATAC-seq)


title: VM CD8+ T cells, clean, timestamped at day 28, rep 1 (ATAC-seq)


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 1 (ATAC-seq)


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 1 (ATAC-seq)


title: TN CD8+ T cells, clean, timestamped at day 1, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 3 (ATAC-seq)


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 2 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 3 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 2 (ATAC-seq)


title: VM CD8+ T cells, clean, timestamped at day 1, rep 1 (ATAC-seq)


title: TN CD8+ T cells, clean, timestamped at day 28, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 3 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 2 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 3 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 1 (ATAC-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 2 (ATAC-seq)


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 3 (RNA-seq)

data_processing:
Raw reads were evaluated, trimmed, and filtered using trim galore (v0.6.5; -j 8 —quality 20 -gzip —length 50 –paired –fastqc) and aligned to the mouse reference genome (mm10) using STAR (v2.7.0e) with default parameters. Quality control metrics were calculated using multiqc (v1.8). Mapped reads were assigned to genes using featureCounts under Rsubread (v2.4.3; minMQS=30, countMultiMappingReads=FALSE, isPairedEnd=TRUE).
Assembly: mm10 (UCSC)
Supplementary files format and content: TXT file reporting counts

extract_protocol:
10,000 FACS sorted cells were placed in Trizol and RNA was purified following the manufacturer's instructions, with the addition of a second chloroform extraction, GlycoBlue carrier when precipitating, and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer.
Libraries were prepared by the TREx core at Cornell University using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs).

treatment_protocol:
N/A
Splenic CD8+ T cells were isolated and purified using positive selection with CD8a microbeads (Miltenyi). Purified CD8+ T cells were stained using antibodies against CD4 (Gk1.5), CD44 (IM7), CD122 (TM-B1), CD49d (R1-2), and CD8a (53-6.7). ‘Bulk stamped’ CD8+ populations were sorted for CD4-CD8+CD49dloGFP+, ‘stamped VMs’ populations were sorted for CD4-CD8+CD49dloGFP+CD44hi, and ‘stamped TN’ populations were sorted for CD4-CD8+CD49dloGFP+CD44lo. Samples were sorted using a BD FACS Aria Fusion II equipped with four lasers. Samples were sorted to >95% cell purity as determined by a post-sort check.


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 3 (RNA-seq)


title: TN CD8+ T cells, clean, timestamped at day 28, rep 3 (RNA-seq)


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 3 (RNA-seq)


title: TN CD8+ T cells, clean, timestamped at day 1, rep 3 (RNA-seq)


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 3 (RNA-seq)


title: VM CD8+ T cells, clean, timestamped at day 28, rep 3 (RNA-seq)


title: VM CD8+ T cells, clean, timestamped at day 1, rep 3 (RNA-seq)


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 2 (RNA-seq)


title: TN CD8+ T cells, clean, timestamped at day 28, rep 2 (RNA-seq)


title: Mm H3K27ac, developing testis rep 2

source_name: mouse developing testis

value: mouse developing testis


title: Mm H3K27ac, developing testis rep 1


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 2 (RNA-seq)


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 1 (RNA-seq)


title: Mm H3K4me1, developing testis rep 2

value: anti-H3K4me1 (Diagenode, cat. No. C15410037)


title: TN CD8+ T cells, clean, timestamped at day 1, rep 2 (RNA-seq)


title: Mm H3K4me1, developing testis rep 1


title: Mm H3K4me1, developing testis rep 3


title: Mm H3K4me3, developing ovary rep 1

source_name: mouse developing ovary

value: mouse developing ovary

value: anti-H3K4me3 (Millipore, cat. No. 07-473)


title: Mm H3K4me1, developing ovary rep 3


title: Mm H3K4me1, developing ovary rep 2


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 3 (RNA-seq)


title: VM CD8+ T cells, clean, timestamped at day 1, rep 1 (RNA-seq)


title: Mm H3K27ac, developing ovary rep 1


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 2 (RNA-seq)


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 2 (RNA-seq)


title: H883

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

institute: Institute of Bioinformatics

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM gene counts for every gene and every sample.

source_name: brain metastases

growth_protocol: All brain metastases samples were obtained with informed consent as approved by the local ethics committee (24/10/05).

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

treatment_protocol: Samples of brain metastases were collected from patients previously diagnosed with primary breast cancer during neurosurgical removal.

value: brain metastases,primary breast cancer

value: neurosurgical removal


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 2 (RNA-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 3 (RNA-seq)


title: H570


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 3 (RNA-seq)


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 2 (RNA-seq)


title: RJ9018

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies) and then loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 (Illumina) and run for 61 cycles using a single-read recipe according to the manufacturer's instructions.
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option.
The sequencing reads were mapped using Tophat version 2.0.9 supplied by Ensembl reefrence genome (GRCh38) and the annotation file; GRCh38.78.gtf.
Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78).
The raw read counts were normalized by EDAseq.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file, Normalized read counts

source_name: blood

extract_protocol:
RNA was extracted from the PAXgene tubes using QIAsymphony PAXgene Blood RNA Kit as per the manufacturer’s instructions (Qiagen). Optical density values of extracted RNA were measured using NanoDrop to confirm an A260:A280 ratio above 1.9. RNA integrity number was measured using BioAnalyzer (Agilent Technologies). RNA 6000 Nano Kit to confirm RIN above 7.
The cDNA libraries were prepared using the Ovation RNA-seq System V2 (NuGEN, San Carlos, CA) as per the manufacturer’s instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing.

treatment_protocol: Observational study, no treatment intervention.

value: blood

tag: disease state

value: Healthy Control

tag: mtx

value: Not Cur

tag: disease duration


title: TN CD8+ T cells, dirty, timestamped at day 28, rep 2 (RNA-seq)

value: CD8+ T cells

value: spleen


title: H38


title: RJ9017

tag: age


title: VM CD8+ T cells, clean, timestamped at day 28, rep 2 (RNA-seq)

value: specific pathogen-free

value: 28 days


title: Mm H3K4me3, developing testis rep 2


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 2 (RNA-seq)

value: exposed to microbial material

value: 8 weeks


title: VM CD8+ T cells, clean, timestamped at day 1, rep 2 (RNA-seq)

value: 1 day


title: RJ9016


title: VM CD8+ T cells, dirty, timestamped at day 28, rep 1 (RNA-seq)


title: VM CD8+ T cells, clean, timestamped at day 28, rep 1 (RNA-seq)


title: RJ9015


title: Mm H3K4me3, developing ovary rep 2


title: TN CD8+ T cells, clean, timestamped at day 28, rep 1 (RNA-seq)


title: Mm H3K4me3, developing testis rep 1


title: VM CD8+ T cells, dirty, timestamped at day 1, rep 1 (RNA-seq)


title: TN CD8+ T cells, dirty, timestamped at day 1, rep 1 (RNA-seq)


title: shTw2v2_2h_rep2

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: shTw2v2 2h rep2

data_processing:
Aligned to mm39 with hisat2 v2.1.0
Data manipulation with samtools v1.10
Reads sorted into annotations with htseq-count v0.13.5
Assembly: mm39
Supplementary files format and content: raw read counts for each sample for all genes expressed in the data set

growth_protocol: 3T3-L1s were grown in high-glucose DMEM + 10% Newborn Calf Serum + 1% Fetal Calf Serum + 100 U/mL penicillin G sodium + 100 µg/mL streptomycin sulfate

extract_protocol:
Total RNA was extracted from cells using the Direct-zol-96 RNA kit (Zymo Research #R2054)
RNA was sent to Novogene for generation of stranded, poly-A enriched, random-hexamer amplified cDNA libraries

treatment_protocol: For differentiatoin, 3T3-L1s were switched into high-glucose DMEM + 10% Fetal Calf Serum + 100 U/mL penicillin G sodium + 100 µg/mL streptomycin sulfate

tag: cell line

tag: time


title: Mm H3K4me1, developing ovary rep 1


title: RJ9014


title: TN CD8+ T cells, clean, timestamped at day 1, rep 1 (RNA-seq)

tag: strain


title: Mm H3K27ac, developing ovary rep 2

value: anti-H3K27ac (Diagenode, cat. No. C15410174)


title: H218


title: shTw2v2_1h_rep1

description: shTw2v2 1h rep1


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 3 (RNA-seq)


title: H971


title: H82


title: bulk CD8+ T cells, clean, timestamped at day 28, rep 1 (RNA-seq)


title: bulk CD8+ T cells, dirty, timestamped at day 28, rep 1 (RNA-seq)


title: H672


title: RJ0063

value: Controlled RA


title: shTw2v2_0h_rep1

description: shTw2v2 0h rep1


title: H638


title: shTw2v2_0h_rep2

description: shTw2v2 0h rep2


title: H736


title: RJ9020


title: bulk CD8+ T cells, dirty, timestamped at day 1, rep 1 (RNA-seq)


title: H573


title: shTw2v1_4h_rep2

description: shTw2v1 4h rep2


title: RJ0061


title: RJ9021


title: RJ9019


title: BM0069


title: shTw2v1_4h_rep1

description: shTw2v1 4h rep1


title: RJ0059

value: Controlled RA-SDFR


title: RJ0056


title: OregR_06hE rep 2

city: Chapel Hill

first: Markus

last: Nevil

state: NC

address: 3350 Genome Sciences Bldg, CB 7100

department: Biology

institute: University of North Carolina at Chapel Hill

data_processing:
The sequencing quality of each sample was assessed using FASTQC version 0.11.7
Raw paired-end reads were trimmed of adapters using BBDuk from the BBTools software version 38.71 using the parameters: ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Reads were aligned to the BDGP Release 6 of the Drosophila melanogaster genome (dm6)53 using Bowtie2 version 2.3.4.154 and parameters -q --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Duplicate reads were marked using Picard 2.2.4
SAM files were converted to BAM format, filtered for quality (-bq 5), and removed of duplicates (-bF 0x400) using Samtools version 1.9
Replicates were merged (samtools merge) and each genotype was scaled to the diploid Oregon R embryo signal in 5-kb bins: bamCompare -b1 treatment.bam -b2 oregR.bam –-operation first -bs 5000
Genome_build: dm6

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Wild-type (Oregon R) flies were maintained in population cages on agar-grape juice and yeast paste plates at 26°C, 60% humidity with 12-h dark-light cycle. Mutant flies were reared, and crosses were performed at 26°C on standard cornmeal/molasses medium with dry yeast added to the surface.

extract_protocol:
Salivary glands from female wandering third-instar larvae were isolated and flash-frozen in liquid N2 until all samples were collected. Genomic DNA for sequencing was prepared from 25 L3 salivary gland pairs or 10 mg embryos (0-6 h AED) using DNeasy Blood and Tissue kit (Qiagen). Each sample was prepared in triplicate. The tissues were soaked in 180 µl buffer ATL + 20 µl proteinase K (15 mg/ml) and lysed for 2-3 h at 55°C. The reactions were cooled to room temperature, supplemented with 4 µl RNase A, ~40 mg/ml (Sigma Aldrich), and RNA was digested for 10 min at room temperature. The genomic DNA was fragmented with 0.002 units DNase I (Thermo Fisher) in 100-µl reactions containing 10 mM Tris-HCl, pH 7.5, 10 mM MnCl2, 0.1 mM CaCl2, 0.1 mg/ml RNase A and 0.2 mg/ml nuclease-free BSA (1x reaction buffer) for 15 min at 37°C. (DNAse I dilutions were prepared using 1x reaction buffer.) Reactions were stopped by adding 5 µl 0.5 M EDTA, and DNase I was inactivated for 20 min at 65°C. The fragmented DNA was purified on QiaQuick columns using PCR purification kit (Qiagen) and eluted in 40 µl 10 mM Tris-HCl, pH 8.0. The size distribution of DNA fragments (200-600 bp, average ~400 bp) was confirmed and DNA concentration was measured on 2100 BioAnalyzer (Agilent).
Libraries were prepared from 20 ng of fragmented genomic DNA with the ThruPLEX DNA-seq kit using SMARTer® DNA Unique Dual Indexes (TakaraBio)

value: embryos

value: Oregon R


title: MMD4m9_3LW rep 3

source_name: Salivary glands

value: Salivary glands


title: MMD4m9_3LW rep 2


title: shTw2v2_4h_rep2

description: shTw2v2 4h rep2


title: bulk CD8+ T cells, clean, timestamped at day 1, rep 1 (RNA-seq)


title: RJ0060

value: Current


title: H305

value: brain metastases,primary breast cancer

value: neurosurgical removal


title: shTw2v2_4h_rep1

description: shTw2v2 4h rep1


title: H297


title: H281


title: MMD4m9_3LW rep 1


title: H203


title: H176


title: RJ0067

value: blood

value: Not Cur


title: H1299


title: shTw2v2_2h_rep1

description: shTw2v2 2h rep1


title: shTw2v2_1h_rep2

description: shTw2v2 1h rep2


title: RJ0071


title: RJ0065

value: Active RA


title: RJ0072


title: OregR_06hE rep 1


title: SuUR_ES_3LW rep 1

value: SuURES


title: shTw2v1_2h_rep1

description: shTw2v1 2h rep1


title: shTw2v1_2h_rep2

description: shTw2v1 2h rep2


title: w1118_3LW rep 3


title: OregR_06hE rep 3


title: RJ0053


title: SuUR_ES_3LW rep 3


title: shTw2v1_1h_rep1

description: shTw2v1 1h rep1


title: RJ0045


title: shTw2v1_1h_rep2

description: shTw2v1 1h rep2


title: RJ0051


title: w1118_3LW rep 2


title: SuUR_ES_3LW rep 2


title: RJ0035


title: shTw2v1_0h_rep2

description: shTw2v1 0h rep2


title: RJ0048


title: shTw2v1_0h_rep1

description: shTw2v1 0h rep1


title: RJ0047


title: shC_4h_rep2

description: shC 4h rep2

value: shControl


title: RJ0054


title: RJ0044


title: shC_2h_rep2

description: shC 2h rep2


title: w1118_3LW rep 1


title: shC_0h_rep2

description: shC 0h rep2


title: RJ0024


title: HET-R525H-3

city: MADISON

first: Siqi

last: Shen

state: WI

address: 425 Henry Mall

institute: University of Wisconsin - Madison

description: DDX41 R525H-expressing mutant

data_processing:
Use RSEM to generate gene expression from fastq data
Supplementary files format and content: results: txt file containing TPM and FPKM level

source_name: Fetal liver

growth_protocol: Cells were cultured in expansion media containing β-estradiol

extract_protocol:
Qiagen RNeasy Micro Kit (74004)
RNA libraries were prepared through Illumina TruSeq Stranded Total RNA (rRNA reduction) protocol

treatment_protocol: Cells were incubated with retroviruses for 2 d and washed and resuspended in PBS with 2% FBS prior to FACS isolation.

value: Hematopoietic progenitors

tag: genotype

value: Infected with DDX41 R525H vector


title: RJ0040


title: RJ0019


title: HET-R525H-1

description: DDX41 R525H-expressing mutant

tag: cell type


title: HET-R525H-2

description: DDX41 R525H-expressing mutant


title: RJ0020


title: shC_1h_rep1

description: shC 1h rep1


title: shC_4h_rep1

description: shC 4h rep1


title: RJ0021


title: RJ0016


title: RJ0042


title: RJ0014


title: shC_1h_rep2

description: shC 1h rep2


title: HET-G173R-2

description: DDX41 G173R-expressing mutant

value: Infected with DDX41 G173R vector


title: RJ0011


title: HET-G173R-1

description: DDX41 G173R-expressing mutant


title: PAS-seq from F121-9 (ENCLB626IHQ)

description:
https://www.encodeproject.org/experiments/ENCSR944IAR/
***************
biological replicate number: 2
technical replicate number: 1
description: ES QuantSeq
experiment encode accession: ENCSR944IAR
assay title: PAS-seq
assembly: mm10
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB626IHQ
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Mus musculus F121-9 cell line

tag: line

value: cell line

tag: description

value: Cast X 129 F121-9 hybrid mouse ES cells R2 p14

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: lab

value: Barbara Wold, Caltech

tag: source

value: David Gilbert

tag: link

value: ENCBS951CRC at ENCODE; https://www.encodeproject.org/ENCBS951CRC/

value: Derived from ENCODE donor ENCDO817NHY; https://www.encodeproject.org/ENCDO817NHY/


title: RJ0030

tag: tissue

tag: disease state


title: HET-WT3

description: DDX41 WT-expressing mutant

tag: treatment

value: Infected with DDX41 WT vector


title: RJ0010

value: blood

tag: mtx

tag: age

tag: disease duration


title: PAS-seq from F121-9 (ENCLB007ITA)

description:
https://www.encodeproject.org/experiments/ENCSR944IAR/
***************
biological replicate number: 3
technical replicate number: 1
description: ES QuantSeq
experiment encode accession: ENCSR944IAR
assay title: PAS-seq
assembly: mm10
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB007ITA
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: Cast X 129 F121-9 hybrid mouse ES cells R3 p14

value: ENCBS418RDP at ENCODE; https://www.encodeproject.org/ENCBS418RDP/


title: HET-WT2

description: DDX41 WT-expressing mutant


title: RJ0009

value: Active RA

value: Current


title: RJ0008


title: RJ0007

value: Not Cur


title: HET-WT1

description: DDX41 WT-expressing mutant

value: Hematopoietic progenitors


title: HET-E3

description: mutant

value: Infected with empty vector


title: RJ0006

value: Controlled RA


title: HET-E2

description: mutant


title: HET-E1

description: mutant


title: CTRL-E2

description: wild type


title: PAS-seq from layer of hippocampus (ENCLB273HHN)

description:
https://www.encodeproject.org/experiments/ENCSR147WNH/
***************
biological replicate number: 1
technical replicate number: 1
description: Mouse hippocampus QuantSeq
experiment encode accession: ENCSR147WNH
assay title: PAS-seq
assembly: mm10
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB273HHN

source_name: Mus musculus strain B6NCrl adult (6 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: Hippocampus from 6 mo C57BL/6 male

value: adult

value: 6 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS398AWS at ENCODE; https://www.encodeproject.org/ENCBS398AWS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: CTRL-E3

description: wild type


title: CTRL-E1

description: wild type


title: G 70y 15

status: Public on Dec 03 2022

city: Nagoya

first: Tetsuya

last: Magara

address: 1 kawasumi, mizuho-tyo, mizuho-ku, Nagoya

country: Japan

institute: Nagoya City University

data_processing:
NGS analysis was performed using the Ion S5 XL System (Thermo Fisher Scientific).
Data were analyzed on the software application Transcriptome Analysis Console and Gene spring (Thermo Fisher Scientific).
Supplementary files format and content: csv

source_name: skin tumor

extract_protocol:
Total RNA was refined using AllPrep DNA/RNA FFPE Kit (Qiagen) according to the supplier’s instruction.
Libraries were prepared for sequencing using Ion AmpliSeq Library Kit 2.0 (Thermo Fisher Scientific) protocols(Thermo Fisher Scientific).

value: skin tumor

tag: patient

value: G

value: male

tag: lesion

value: primary

tag: tertiary lymphoid_structure

value: positive


title: HET-G173R-3

description: DDX41 G173R-expressing mutant

tag: cell type

value: Hematopoietic progenitors

tag: genotype

value: Infected with DDX41 G173R vector


title: F 72y 14

value: F


title: E 73y 13

value: E

value: recurrence


title: D 62y 11

value: D

value: female

value: negative


title: D 62y 10


title: PAS-seq from F121-9 (ENCLB408PXV)

description:
https://www.encodeproject.org/experiments/ENCSR944IAR/
***************
biological replicate number: 1
technical replicate number: 1
description: ES QuantSeq
experiment encode accession: ENCSR944IAR
assay title: PAS-seq
assembly: mm10
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB408PXV
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

tag: line

value: cell line

tag: description

value: Cast X 129 F121-9 hybrid mouse ES cells R1 p14

tag: biosample encode accession

value: not collected

value: unknown

value: Barbara Wold, Caltech

value: David Gilbert

value: ENCBS648HXY at ENCODE; https://www.encodeproject.org/ENCBS648HXY/

value: Derived from ENCODE donor ENCDO817NHY; https://www.encodeproject.org/ENCDO817NHY/


title: C 81y 9

value: skin tumor

value: C

tag: Sex

value: male

value: primary

value: positive


title: WT11

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 307 Westlake Ave N

department: CGIDR

institute: Seattle Children's Research Institute

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/sturkarslan/DuffyNGS, and https://github.com/sturkarslan/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: H37Rv Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) (WT, STPK knockout, and STPK induction) were grown on Middlebrook 7H9 medium (Difco) with 0.2 % glycerol  and 10% oADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at early stationary phase.

tag: growth phase

value: Stationary

tag: genotype/variation

value: Wildtype


title: B 81y 8

tag: tissue

value: B

value: recurrence 4


title: B 81y 7

value: recurrence 1

value: negative


title: B 81y 6


title: WT10


title: WT6


title: WT8


title: WT9


title: WT5


title: WT4


title: B 81y 2

value: recurrence 2


title: A 74y 17

value: A

value: recurrence


title: E 73y 12

value: E


title: WT2


title: WT1


title: WT3


title: PknL_KO2


title: PknL_KO3


title: PknL_KO1


title: PknL_IND3


title: WT7


title: A 74y 19


title: PknL_IND1


title: C 81y 18


title: PknK_KO2


title: 14-tMOs-6hpf-2

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS)+OLB+GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Reference genome sequences and gene annotation files were downloaded from ENSEMBL (Danio_rerio.GRCz10.86). Hisat2 (v2.1.0)  was used to index reference genome sequence. Raw data were pre-processed by Fastp (v0.12.1) with default parameters. Cleaned data were then aligned to the reference genome via software Hisat2 (v2.1.0). FeatureCounts (v1.5.3) was used to count the reads numbers mapped to each gene.
Genome_build: Danio_rerio.GRCz10.86
Supplementary_files_format_and_content: csv file include TPM values for each Sample.

organism: Danio rerio

growth_protocol: Zebrafish embryos were cultured in Holtfreter’s solution at 28.5°C.

extract_protocol:
Total RNA of each sample was extracted from 30 pooled zebrafish embryos using TRIzol Reagent (Invitrogen).
RNA libraries were prepared for sequencing according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®).

treatment_protocol: Morpholinos were dissolved in nuclease-free water and injected at 2 nl (containing 8 ng MO) per embryo at the one-cell stage using a Narishige IM300 micro-injector. 100 pg of GFP mRNA were co-injected as injection marker.

tag: developmental stage

tag: morpholino injected


title: 14-tMOs-6hpf-1


title: PknK_KO3


title: B 81y 3

value: recurrence 3


title: PknL_IND2


title: PknK_KO1


title: 14-tMOs-4hpf-2


title: 14-tMOs-4hpf-1


title: PknK_IND3


title: 14-tMOs-2.5hpf-2


title: 14-tMOs-2.5hpf-1


title: PknK_IND2


title: ctrl-MO-6hpf-2

value: ctrl morpholino 8ng


title: ctrl-MO-6hpf-1


title: ctrl-MO-4hpf-2


title: ctrl-MO-4hpf-1


title: ctrl-MO-2.5hpf-2


title: ctrl-MO-2.5hpf-1


title: PknJ_KO3


title: PknJ_IND3


title: PknJ_KO1


title: PknJ_KO2


title: K7M2 cell culture

city: Columbus

first: Ryan

last: Roberts

state: OH

address: Research Building II, 5th Floor WA5108, 700 Children's Drive,

department: Center for Childhood Cancers and Blood Disorders

institute: Nationwide Children's Hospital

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Assembly: hg19, mm10
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every single cell in the specific sample

growth_protocol: OS17 cells in culture were infected with a barcoded lentivirus library synthesized from CloneTracker XPâ¢ 10M Barcode-3' Library with Venus-Puro (plasmid) (Cellecta, BCXP10M3VP-P) as described in Wang and McManus 2009 45 with PEI as the transfection reagent. The barcoded plasmids contain ~10M 38-bp semi-random oligonucleotide sequence that is captured on the Chromium Single Cell 3â²RNA-sequencing system. 48 h post-infection, barcoded OS17 cells were used to inoculate mice intra-tibially and intra-venously to generate primary and metastatic lesions.

extract_protocol:
Tumor harvested from mice were processed using the human tumor dissociation kit (Miltenyi Biotec, 130-095-929) with a GentleMacs Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427). Single cell suspensions in 0.04% BSA-PBS of cell lines, and dissociated tumor tissues were generated and run on Chromium Single Cell 3â²RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions.
Libraries were constructed according to Chromium Single Cell 3â²RNA-sequencing system (10x Genomics) with the Reagent Kit v3 according to the manufacturer's instructions. Briefly, cells were loaded into Chromium Single Cell Chip v3 (10x Genomics) with a targeted cell recovery of 5,000 cells per sample. After performing cDNA purification, amplification, and library construction (sample index PCR 14 cycles) as instructed, we sequenced sample libraries on a half lane of HS4000 (Illumina) to yield (after QA) about 65,000 paired-end reads per cell.

treatment_protocol: Cell lines/mice did not receive any treatment

tag: cell line

tag: treatment


title: PknK_IND1


title: PknJ_IND2


title: F420 cell culture


title: PknJ_IND1


title: mBMN, high, 1

city: Shanghai,

first: Ting

last: Jiang

address: Quxi Road No. 500

country: China

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Quality Control:    In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data
Alignment:    Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2  (v2.0.1)
Expression analysis:    In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data.
Differential expression analysis:    Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative  binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven  prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

growth_protocol: the complete medium Roswell Park Memorial Institute (RPMI) 1640 (Sigma, MO, USA) containing 10% fetal bovine serum (FBS, Gibco, USA) was added to the 3D culture system. Cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer instructions. Samples for RNA-seq were further cleaned up by RNeasy Mini Kit (QIAGEN). RNAseq libraries were prepared with Illumina TruSeq Stranded mRNAseq Sample Prep kit (Illumina), polyadenylated mRNAs were captured with oligodT beads
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

treatment_protocol: neutrophils were encapsuled in GelMA hydrogel with substrates of 1.5 kPa, 2.6 kPa and 5.7 kPa elastic modulus.

value: primary cell

value: murine bone marrow-derived neutrophils (mBMN)

value: wild type

value: cultured in high stiffness hydrogel


title: PknI_IND2


title: PknI_KO1


title: PknI_IND3


title: mBMN, middle, 3

value: cultured in middle stiffness hydrogel


title: PknI_IND1

value: Stationary


title: PknI_KO2


title: Db-derived-neutrophil_5

type: RNA

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

institute: University of Occupational and Environmental Health

description: The expression of circRNA in db-derived neutrophils

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The microarray slides were scanned with an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: neutrophil from bone marrow

label_protocol: The cRNA was linearly amplified and Cy3 labeled by in vitro T7 polymerase transcription using Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from each sample was treated with RNase R to enrich circular RNA. The enriched circular RNA was reverse transcribed with random primers containing a T7 promoter.

treatment_protocol: Bone marrow (BM) was flushed from femurs and tibiae. Neutrophils from the pooled BM of three db or three non-db mice were isolated using a anti-Ly-6G microbead kit (Miltenyi Biotec GmbH, Germany).

tag: gender

value: male


title: mBMN, high, 3


title: mBMN, high, 2


title: Db-derived-neutrophil_6


title: PknI_KO3


title: Db-derived-neutrophil_4


title: PknH_KO3


title: mBMN, middle, 2


title: mBMN, low, 3

value: cultured in low stiffness hydrogel


title: mBMN, middle, 1


title: mBMN, low, 2


title: PknH_KO2


title: PknH_KO1


title: PknH_IND3


title: mBMN, low, 1


title: 40 days, Smurf, 1day [40s1d_r]

city: Paris

last: Rera

state: - None -

address: 8bis Rue Charles V, Center for Research and Interdisciplinarity

country: France

institute: UTELife lab

description:
40s1d_r
Sample_r

data_processing:
FastQC for quality control. No sequence filtering at this step.
Alignement with Hisat2 (Kim et al, 2019) on Drosophila melanogaster BDGP6.95 genome.
Read counts performed with featureCounts (Liao et al, 2014), using the BDGP6.95 gtf annotation file.
Assembly: BDGP6.95
Supplementary files format and content: tab-delimited text files include featureCounts output for each sample (gene in rows and sample in columns). The match between file column names and the initial samples is specified in the Samples section.

source_name: whole body mated females

extract_protocol:
RNA was harvested using TRIzol extraction protocol as in Rio et al, 2010. Approximately 10 ug per sample of total RNA was used sent to Intragen construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Intragen using “TruSeq Stranded mRNA Sample Prep' Illumina” kit.

value: whole body mated females

value: Drs-GFP

value: FD&C #1 blue food dye

tag: condition

value: Smurf

tag: age

value: 40 days

tag: time after_transition

value: 1 day (24 hours)


title: PknH_IND1


title: PknH_IND2


title: Non-db-derived-neutrophil_1

description: The expression of circRNA in non-db-derived neutrophils


title: Non-db-derived-neutrophil_3


title: PknG_KO3


title: 40 days, Smurf, 1day [40s1d_p]

description:
40s1d_p
Sample_p

tag: cell type


title: 40 days, Smurf, 1day [40s1d_q]

description:
40s1d_q
Sample_q

tag: genotype


title: PknG_KO2


title: 40 days, non-Smurf, 1day [40n1d_m]

description:
40n1d_m
Sample_m

value: non – Smurf


title: PknG_IND3


title: PknG_IND1


title: 30 days, Smurf, 1day [30s1d_k]

description:
30s1d_k
Sample_k

value: 30 days


title: PknG_IND2


title: PknG_KO1


title: PknF_KO3


title: 30 days, Smurf, 1day [30s1d_j]

description:
30s1d_j
Sample_j


title: Non-db-derived-neutrophil_2


title: 30 days, non-Smurf, 1day [30n1d_g]

description:
30n1d_g
Sample_g


title: 30 days, non-Smurf, 1day [30n1d_i]

description:
30n1d_i
Sample_i


title: 30 days, non-Smurf, 1day [30n1d_h]

description:
30n1d_h
Sample_h


title: PknF_IND3


title: PknF_KO2


title: PknF_IND2


title: 20 days, Smurf, 1day [20s1d_e]

description:
20s1d_e
Sample_e

value: 20 days


title: shC_0h_rep1

description: shC 0h rep1

value: shControl

tag: time


title: PknF_KO1


title: 20 days, Smurf, 1day [20s1d_f]

description:
20s1d_f
Sample_f


title: PknE_KO3


title: 20 days, Smurf, 1day [20s1d_d]

description:
20s1d_d
Sample_d


title: 40 days, non-Smurf, 1day [40n1d_n]

description:
40n1d_n
Sample_n


title: 40 days, non-Smurf, 1day [40n1d_o]

description:
40n1d_o
Sample_o


title: 40 days, Smurf, 5hours [40s5h_c8]

description:
40s5h_c8
Sample_c8

value: 5 hours


title: 30 days, Smurf, 1day [30s1d_l]

description:
30s1d_l
Sample_l


title: PknE_KO1


title: PknE_KO2


title: 40 days, Smurf, 5hours [40s5h_c7]

description:
40s5h_c7
Sample_c7


title: PknE_IND3


title: 40 days, non-Smurf, 5hours [40n5h_c6]

description:
40n5h_c6
Sample_c6

value: non-Smurf


title: 30 days, Smurf, 5hours [30s5h_c4]

description:
30s5h_c4
Sample_c4


title: 40 days, non-Smurf, 5hours [40n5h_c5]

description:
40n5h_c5
Sample_c5


title: 30 days, non-Smurf, 5hours [30n5h_c2]

description:
30n5h_c2
Sample_c2


title: 30 days, Smurf, 5hours [30s5h_c3]

description:
30s5h_c3
Sample_c3


title: PknF_IND1


title: PknE_IND1


title: PknE_IND2


title: PknD_KO3


title: mouse, blastocysts, ctrl, S10

data_processing:
Libraries with different indices were multiplexed and loaded on an HiSeq instrument according to the manufacturer’s instructions (Illumina, USA). Sequencing was carried out using a 2×150 bp paired-end (PE) reads set.
For data analysis, we pre-processed the raw data by Fastp (v0.12.1) (v0.12.1) with default parameters.
Then cleaned data were then aligned to the reference genome (Mus_musculus. GRCm38) via Hisat2 (v2.1.0).
FeatureCounts (v1.5.3) was used to count the reads numbers mapped to each gene.
The expression levels were determined based on TPM (Transcripts Per Kilobase per Million mapped reads).
Assembly: Mus_musculus. GRCm38
Supplementary files format and content: csv file include TPM values for each Sample.

organism: Mus

source_name: embryo

growth_protocol: Zygotes were collected from the oviduct through a brief treatment with hyaluronidase to wash clean of cumulus cells and then were cultured in KSOM medium at 37°C under 5% CO2 in the air to E4.5 as described (Wang et al., 2017).

extract_protocol:
Total RNAs of each E4.5 mouse embryo were extracted following the Geo-seq methods (Chen J, 2017).
5 ng PCR products were used for the following library preparation. Next-generation sequencing library preparations were constructed according to the manufacturer’s protocol (Nextera XT DNA Sample Preparation Kit, Illumina, FC-131-1096).

treatment_protocol: Rbm14+/-  female mice were superovulated by injecting 5-7 IU of pregnant mare serum gonadotropin (PMSG), followed by 5-7 IU of human chorionic gonadotropin (hCG) 48 h later. Superovulated female mice were mated to Rbm14+/- male mice.

value: embryo

value: blastocysts

value: ctrl

tag: strain


title: PknD_KO1

value: Stationary


title: mouse, blastocysts, Rbm14 ko, S9

value: Rbm14 ko


title: 30 days, non-Smurf, 5hours [30n5h_c1]

description:
30n5h_c1
Sample_c1

value: whole body mated females


title: mouse, blastocysts, Rbm14 ko, S8


title: PknD_IND3


title: mouse, blastocysts, Rbm14 ko, S7


title: mouse, blastocysts, Rbm14 ko, S6


title: 20 days, non-Smurf, 1day [20n1d_c]

description:
20n1d_c
Sample_c

value: Drs-GFP


title: mouse, blastocysts, ctrl, S5


title: 20 days, non-Smurf, 1day [20n1d_b]

description:
20n1d_b
Sample_b

value: FD&C #1 blue food dye


title: mouse, blastocysts, Rbm14 ko, S4


title: 20 days, non-Smurf, 1day [20n1d_a]

description:
20n1d_a
Sample_a


title: hFOB1.19 Osteoblasts


title: PknD_IND1


title: PknB_KD3


title: PknD_KO2


title: 40 days, Smurf, Mixed [40sM_16]

description:
40sM_16
Sample_16

value: Smurf

value: Mixed (unknown)


title: mouse, blastocysts, ctrl, S2


title: 40 days, non-Smurf, Mixed [40nM_13]

description:
40nM_13
Sample_13

value: 40 days


title: PknB_KD2


title: PknB_KD1


title: PknD_IND2


title: KO, liver, rep2

city: Tokyo

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Assembly: mm10
Supplementary files format and content: BED = standard BED file containing MACS peaks

source_name: liver

extract_protocol:
Samples were digested by Proteinase K at 55⁰C overnight and genomic DNA was extracted using the Quick-gDNA MiniPrep kit (Zymo Research).
Genomic DNA (100ng) was digested with TaqaI at 65⁰C for 2h followed by MspI at 37⁰C overnight. Following enzymatic digestion, samples were used for library generation using the Ovation RRBS Methyl-Seq System (Tecan). In brief, digested DNA was randomly ligated, and, following fragment end repair, bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen). After conversion and clean-up, samples were amplified resuming the Ovation RRBS Methyl-Seq System protocol for library amplification and purification. Libraries were measured using Agilent 2200 TapeStation System and quantified using the KAPA Library Quant Kit ABI Prism qPCR Mix (Roche).

value: liver

value: 6-weeks old


title: 32 days, Smurf, Mixed [32sM_10]

description:
32sM_10
Sample_10

value: 32 days


title: KO, liver, rep1


title: PknB_IND3


title: 32 days, non-Smurf, Mixed [32nM_7]

description:
32nM_7
Sample_7

value: non – Smurf


title: WT, liver, rep2


title: 20 days, Smurf, Mixed [20sM_4]

description:
20sM_4
Sample_4

value: 20 days


title: PknB_IND1


title: mouse, blastocysts, Rbm14 ko, S3


title: aortic aneurysm BAV 4

status: Public on Dec 02 2022

city: Linz

first: Christian

last: Doppler

address: Krankenhausstraße 5

country: Austria

institute: Johannes Kepler University Linz

description: Gene expression from smooth muscle cells from aortic aneurysm tissue with a BAV.

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

scan_protocol: GeneChips were scanned using the Affymetrix  GeneArray Scanner 3000.

data_processing: The microarray analysis was performed using Transcriptome Console Software (Thermo, Version 1.2.1). Primary data (CEL files) were normalized at the transcript level using the robust multi-array average method.

label: biotin

source_name: Smooth muscle cells aortic aneurysm tissue BAV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tunica media was separated mechanically followed by an enzymatic collagenase-elastase treatment, which allowed the cells to settle into cell culture dishes. Before starting experiments all cell lines were tested for possible cellular contaminations like endothelial cells or fibroblasts by Western blot analyses.

extract_protocol: Total RNA was extracted using TRIzol reagent and purified with the RNeasy mini kit according to the manufacturers’ instructions.

treatment_protocol: All cells were incubated under identical conditions under 37°C and 5% CO2 using growth Media 231 (Thermo Fisher Scientific).

value: smooth muscle cells

tag: patient diagnosis

value: aortic aneurysm


title: aortic aneurysm BAV 5


title: 20 days, non-Smurf, Mixed [20nM_1]

description:
20nM_1
Sample_1


title: aortic aneurysm TAV 3

description: Gene expression from smooth muscle cells from aortic aneurysm tissue with a TAV.

source_name: Smooth muscle cells aortic aneurysm tissue TAV


title: aortic aneurysm BAV 2


title: aortic aneurysm BAV 1


title: A2780 (R-RAS2 KO) rep3

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from A2780 R-RAS2 KO cell line

hyb_protocol: Clariom S arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.4.1.2).

source_name: A2780 cell line

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: A2780 ovarian carcinoma cells were cultured in RPMI media supplemented with 10% fetal bovine serum, 1% L-glutamine, penicillin (10 ug/ml) and streptomycin (100 ug/ml).

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

treatment_protocol: No treatment was performed

value: R-RAS2 KO

value: Ovarian carcinoma


title: aortic aneurysm TAV 2


title: A2780 (control) rep3

description: Gene expression data from A2780 control cell line

value: Control


title: aortic dissection 4

description: Gene expression from smooth muscle cells from Stanford A dissection tissue.

source_name: Smooth muscle cells Stanford A dissection tissue

value: Stanford A dissection


title: A2780 (R-RAS2 KO) rep2


title: PknB_IND2

value: Stationary


title: shC_2h_rep1

description: shC 2h rep1

value: shControl


title: A2780 (control) rep2


title: aortic dissection 3


title: aortic dissection 1


title: WT, liver, rep1


title: A2780 (control) rep1


title: A2780 (R-RAS2 KO) rep1


title: control 2

description: Gene expression from smooth muscle cells from healthy aortic tissue.

source_name: Smooth muscle cells healthy aortic tissue

value: healthy control


title: control 1


title: aortic aneurysm BAV 3


title: control 3


title: aortic dissection 2


title: 9-hom

city: Berlin

first: Andreas

last: Franz

state: Berlin

address: Tarkustraße 6

department: Institut fuer Chemie, Biochemie, Pharmazie

institute: Freie Universität Berlin

data_processing:
Reads were aligned to the GRCm38 genome using the STAR aligner (v.2.7.9a) and gene expression patterns were analyzed using Salmon (v1.8.0).
Assembly: GRCm38
Supplementary files format and content: Salmon output file (TPM, NumReads)

source_name: Cerebellum

extract_protocol:
Mouse cerebellum was dissected, total RNA extracted using RNATri (Bio&Sell) and analyzed via RNA-Seq.
total RNA (Ribo-)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebellum

tag: model

value: mouse model of humanized Camk2b alternative splicing

value: homozygous mutant

tag: Sex

value: male


title: 11-hom


title: 7-het

value: heterozygous mutant

value: female


title: 5-het


title: 12-hom


title: 4-wt

value: wild type


title: 10-hom


title: 8-het


title: 3-wt


title: 2-wt


title: aortic aneurysm TAV 1


title: 1-wt


title: 14 Lauria-001 - (Early Expanding, EEs)

city: Tampa

first: Asmaa

last: Elkenawi

state: Fl

address: 12902 Magnolia Drive

department: Radiation Oncology

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapped against reference genome, hg19 if human using STAR v2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region associated with each gene
Gene expression data are provided as raw read counts and normalized read counts.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Lung

growth_protocol: Cells were maintained and cultured according to their suggested protocols using RPMI with L-glutamine supplemented with 10% fetal bovine serum (FBS), antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed with PBS then each plate containing cells was frozen at -80 °C until further collection of RNA. RNA and DNA were simultaneously isolated from the indicated clones from plates 1-4  using AllPrep DNA/RNA Kit (#catalogue: 80284, Qiagen) according to manufacturer’s protocols.
RNA extracted from cell lines was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA)
The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (NuGEN Technologies, San Carlos, CA)
The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the P3-200 cycle reagent kit in order to generate approximately 50M million 100-base read pairs per sample (Illumina, Inc., San Diego, CA)

treatment_protocol: 2μM Erlotinib for 3, 19, 27, 75 days

value: Lung

value: NSCLC

value: WT

value: Erlotinib


title: 12 Erlotinib-Day-75-002 - Descendant of Persisters (DPs)


title: 13 Erlotinib-Day-75-003 - Descendant of Persisters (DPs)


title: 15 Lauria-002 - (Early Expanding, EEs)


title: 11 Erlotinib-Day-75-001 - Descendant of Persisters (DPs)


title: 10 Erlotinib-Day-3-003 - Treated- (3 days)


title: 9 Erlotinib-Day-3-002 - Treated- (3 days)


title: 8 Erlotinib-Day-27-003 - Persisters (P)


title: 6 Erlotinib-Day-27-001 - Persisters (P)


title: 5 Erlotinib-Day-19-003 - Persisters (P)


title: 7 Erlotinib-Day-27-002 - Persisters (P)


title: 6-het


title: 4 Erlotinib-Day-19-002 - Persisters (P)


title: 2 Control-002


title: 1 Control-001


title: RNA-6h-IAA-G2-R2

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

institute: GENyO

description: mRNA-seq

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
BamCompare 3.1.3 used to normalize with BPM method and to apply a smoothing of 10 bp. For ChIP-Seq samples, signal from input samples was sustracted to the samples signal. For RNA-Seq samples, signal from the reverse strand was sustracted to the signal in the forward strand.
genome build: mm9
processed data files format and content: Bigwig files containing Reads per Million (RPM) with a 10 bp smoothing. ChIP-Seq signal was normalized against input signal. For RNA-Seq, signal in forward strand has positive values, while signal in reverse strand has negative values.

source_name: Ring1a-/-; AID::Ring1b mESCs

growth_protocol: AID::Ring1b;FUCCI mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco) and hygromycin B (InvivoGen) as described previously (Asenjo et al, 2020)

extract_protocol:
RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer’s instructions
Libraries were generated from 300 ng of Total RNA using the TruSeq stranded mRNA Library Prep kit for Illumina according to the manufacturer’s instructions

treatment_protocol: Cells were plated in complete ESC media without LIF and RA to a final concentration of 5 µM. To induce the degradation of Ring1b, cells were treated with IAA at 500 µM final concentration. Cell-cycle sorting using an Aria Fusion cell sorter.

tag: cell-type

value: Mouse embryonic stem cells


title: RNA-6h-IAA-G2-R1

description: mRNA-seq


title: RNA-6h-IAA-S-R2

description: mRNA-seq


title: RNA-6h-IAA-G1-R2

description: mRNA-seq


title: RNA-6h-IAA-G1-R1

description: mRNA-seq


title: RNA-6h-UNT-G2-R2

description: mRNA-seq


title: RNA-6h-IAA-S-R1

description: mRNA-seq


title: RNA-6h-UNT-S-R2

description: mRNA-seq


title: RNA-6h-UNT-G2-R1

description: mRNA-seq


title: RNA-6h-UNT-G1-R2

description: mRNA-seq


title: RNA-6h-UNT-G1-R1

description: mRNA-seq


title: RNA-0h-G2-R2

description: mRNA-seq


title: RNA-0h-G2-R1

description: mRNA-seq


title: RNA-6h-UNT-S-R1

description: mRNA-seq


title: RNA-0h-S-R2

description: mRNA-seq


title: RNA-0h-G1-R2

description: mRNA-seq


title: RNA-0h-G1-R1

description: mRNA-seq


title: RNA-0h-S-R1

description: mRNA-seq


title: T cells, After Treatment, Relapse [SEQADJ022]

city: Aurora

first: Ann

last: Strange

state: CO

address: 12801 E. 17th Ave, 8th floor

department: Division of Medical Oncology

institute: CU Anschutz

data_processing:
Paired end sequencing adapters were removed using Trimmomatic.
Alignment and mapping were performed using HISAT2.
HTseq generated a gene count matrix.
Merge counts_P and counts_U count matrices to perform differential gene expression analysis using DESeq2
Stats and vizualizations performed with Prism and R code
Assembly: Ensembl GRCh38 ver 104
Supplementary files format and content: counts_P.table as tab delimited raw counts from paired end alignment
Supplementary files format and content: counts_U.table as tab delimited raw counts from unpaired reads

source_name: melanoma tumor

extract_protocol:
T-cells were isolated from patient PBMC samples by a StemCell EasySep negative isolation kit.
RNA-Seq was performed using the SMARTer Stranded Total RNA-Seq Kit and sequenced using 150-base paired-end sequencing by Azenta Life Sciences to a depth of ~30 million reads per sample.

tag: tissue

value: melanoma tumor

value: CD8+ T-cell

tag: patient id

value: After

tag: outcome

value: Relapse

value: IPI/NIVO, followed by NIVO


title: T cells, Before Treatment, Relapse [SEQADJ021]

value: Before


title: T cells, After Treatment, NED [SEQADJ020]

value: NED


title: T cells, Before Treatment, NED [SEQADJ013]


title: 3 Erlotinib-Day-19-001 - Persisters (P)

tag: cell line


title: T cells, Before Treatment, NED [SEQADJ011]

tag: treatment


title: T cells, After Treatment, NED [SEQADJ014]


title: T cells, Before Treatment, NED [SEQADJ015]


title: T cells, Before Treatment, NED [SEQADJ017]


title: T cells, Before Treatment, NED [SEQADJ019]


title: T cells, After Treatment, NED [SEQADJ018]


title: T cells, After Treatment, NED [SEQADJ012]


title: T cells, After Treatment, NED [SEQADJ016]


title: T cells, Before Treatment, Relapse [SEQADJ007]


title: T cells, After Treatment, Relapse [SEQADJ004]


title: T cells, After Treatment, Relapse [SEQADJ008]


title: T cells, After Treatment, Relapse [SEQADJ006]


title: T cells, Before Treatment, Relapse [SEQADJ003]


title: T cells, Before Treatment, Relapse [SEQADJ005]


title: HPC5_ATAC

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ATAC-seq

data_processing:
BWA mem mapping to mm9
Duplicated and multi-mapped reads were removed using samtools (v0.17).
BigWiggle files were generated using DeepTools (v3.2.0). Footprint analysis was performed using HINT-ATAC (v0.12.1) with correction of strand-specific Tn5 cleavage bias (--atac-seq --paired-end).
Genome_build: mm9
Supplementary_files_format_and_content:bigwiggle

growth_protocol: HPC5 cells were maintained in Iscove’s modified Dulbecco’s media with GlutaMax (IMDM) (Gibco; Carlsbad, CA) supplemented with 5% fetal bovine serum (FBS) (Atlanta Biologicals; Flowery Branch, GA), 1.5x10−4 M monothiolglycerol (MTG) (Sigma-Aldrich; St. Louis, MO), 100 ng/mL murine stem cell factor (SCF) (PeproTech; Rocky Hill, NJ) and 10 ng/mL human interleukin-6 (hIL-6) (PeproTech; Rocky Hill, NJ).

extract_protocol:
100,000 Nfix+/+ HPC5 cells were lysed and nuclei were resuspended using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (20034197, Illumina; San Diego, CA). Following purification with Zymo DNA Clean and Concentrator-5 kit (D4014, Zymo; Irvine, CA), libraries were amplified using NEBnext PCR master mix (M0541S, New England BioLabs; Ipswich, MA) and custom Nextera PCR primers for five cycles (custom primers from Buenrostro et al.70) .
The degree of library amplification to reduce GC and size bias was determined using quantitative PCR using SYBR Gold reagents (S11494, Invitrogen; Waltham, MA). A total of 9-10 cycles were performed and libraries were purified using a Zymo DNA Clean and Concentrator-5 kit (D4014, Zymo; Irvine, CA) or Qiagen MinElute Kit (28004, Qiagen; Hilden, Germany). Eluted libraries were further purified using the E-Gel system (Invitrogen; Waltham, MA). An E-Gel 2% agarose gel (G402002, Thermo Fisher; Waltham, MA) was run and fragments between 100bp and 1000bp were excised followed by clean up with Zymo Clean Gel DNA (D4008, Zymo; Irvine, CA). Purified libraries were submitted to the Hartwell Center for Biotechnology for sequencing.

tag: sample type

value: ATAC-seq


title: wt_p7_pu1

description: ChIP-seq

data_processing:
BWA mem mapping to mm9
Multi-mapped reads were removed using samtools
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content:bigwiggle

extract_protocol: 20 million HPC5 cells were fixed with 1% formaldehyde (Sigma-Aldrich; St. Louis, MO) for 10 minutes at room temperature with gentle stirring. Fixing was quenched with 2M glycine (Sigma-Aldrich; St. Louis, MO) and further stirring for five minutes at room temperature. Cells were collected by centrifugation and snap frozen for storage at -80°C. Cells were then resuspended in buffer L1 (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with one Protease Inhibitor tablet (Roche; Basel, Switzerland). During lysis, samples were kept on ice for 10 minutes with gentle agitation every two minutes. Samples were centrifuged at 1693 rcf for 10 minutes at 4°C in a swing bucket rotor. Supernatant was removed and cells were resuspended in buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA, 10mM Tris pH8.0) supplemented with one Protease Inhibitor tablet (Roche; Basel Switzerland). Samples were rocked at room temperature for 10 minutes. Nuclei were isolated by centrifugation at 1693 rcf for 10 minutes at 4°C. Supernatant was carefully removed and 1X RIPA buffer was added to samples. Nuclei were sonicated using a cell disruptor (SFX250) (Branson Ultrasonics Corporation; Brookefield, CT). Lysate was clarified with centrifugation at 18879 rcf for 15 minutes at 4°C. The supernatant was carefully transferred to a 15mL conical vial. Samples were incubated with protein A/G sepharose beads (Pierce; Waltham, MA) overnight to preclear supernatant. 20µg of anti-PU.1 (sc-390405, Santa Cruz; Dallas, TX), and anti-NFIX (clone: 7B5.3) antibodies were also pre-bound to protein A/G agarose beads (Pierce; Waltham, MA) for overnight incubation. Pre-cleared chromatin was centrifuged at 1000 rcf for three minutes at 4°C. Pre-cleared chromatin was added to respective antibody-bead complex in Eppendorf tubes while some pre-cleared chromatin was reserved for input. Samples were rotated at 4°C for four hours. After incubation, samples were centrifuged at 5418 rcf for five minutes at 4°C. Supernatant was aspirated and beads were washed with various buffers: once with IP Wash Buffer I (20mM Tris pH8.0, 50mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with IP High Salt Wash Buffer (20mM Tris pH8.0, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), once with IP Wash Buffer II (10mM Tris pH8.0, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% deoxycholic acid), and twice with TE buffer. DNA:protein complexes from beads were eluted twice with freshly made elution buffer (1% SDS, 100mM sodium bicarbonate). To reverse crosslinking, 5M NaCl (final concentration 370mM), 10mg/mL RNase (final concentration 0.45mg/mL), and 20mg/mL proteinase-K (final concentration 0.26mg/mL) were added to eluates and input samples. Incubate samples at 37°C for 30 minutes, 45°C for 30 minutes, and 65°C overnight. DNA was eluted using the Qiagen MinElute (Hilden, Germany) kit following manufacturer’s protocol except DNA was eluted in 28uL with provided EB buffer. DNA was quantified using the Quant-iT PicoGreen assay (Life Technologies; Carlsbad, CA) Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific; Waltham, MA) or SpectraMax Quant AccuBlue Pico dsDNA assay kit (Molecular Devices; San Jose, CA). Libraries were prepared with KAPA HyperPrep Library Preparation Kits (KK8504) (Roche; Basel, Switzerland). Libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies; Santa Clara, CA), 5300 Fragment Analyzer System HS Large Fragment Kit (Agilent Technologies; Santa Clara, CA), 4200 TapeStation D1000 ScreenTape assay (Agilent Technologies; Santa Clara, CA) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer; Waltham, MA). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies; Carlsbad, CA) or low pass sequencing with a MiSeq nano kit (Illumina; San Diego, CA). Single read 50 cycle sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA) or NextSeq 550 (Illumina; San Diego, CA).


title: Ring1bflfl-G1-Six2-prom

data_processing:
Reads were assigned to samples based on the first 10 bases of the read.
Primer sequence was removed from the read and the remaining sequence starting before the restriction site for NlaIII (CATG) was trimmed to 41 bases.
41 bases were aligned to the mouse reference genome (mm10) using HISAT2
RPM (reads per million) normalized bedgraph files were generated for downstream visualization and analysis
genome build: mm10
processed data files format and content: rpm normalized bed/bedGraph
Library strategy: 4C-seq

growth_protocol: FUCCI-Ring1bfl/fl mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco) and hygromycin B (InvivoGen) as described previously (Asenjo et al, 2020)

extract_protocol:
Extraction protocol from 4 million cells was carried out as described previously in (Pachano et al., 2021) from G1 and G2-sorted FUCCI-Ring1bfl/fl cells.
For libraries generation, DNA products were amplified by inverse PCR using the Expand Long Template PCR system (Roche) with primers designed within the Six2 promoter.

treatment_protocol: Treatment with 800 nM 4-hydroxytamoxifen (Tmx, Sigma) for 48 hours and collected for downstream analyses 24 hours later (72 hours total). 4-thiouridine labelling during 1 hour 37ºC. Cell-cycle sorting using an Aria Fusion cell sorter.

value: Derived from male blastocysts in (Endoh et al 2008)

tag: developmental stage


title: Ring1bflfl-G2-Six2-prom


title: DS1-NCSCs

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

source_name: DS1-hiPSC-derived neural crest stem cells (sample1)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

tag: sample name

value: hiPSC-derived neural crest stem cells

tag: disease state

value: Down syndrome


title: wt_p7_input

description: ChIP-seq

value: input


title: RNA-Ring1bKO-G2

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2025
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: RNA-Ring1bKO-S

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2024
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: wt_p9_pu1

data_processing:
BWA mem mapping to mm9
Multi-mapped reads were removed using samtools
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bigwiggle

growth_protocol: Nfix+/+ and Nfix-/- HPC5 cells were maintained in Iscove’s modified Dulbecco’s media with GlutaMax (IMDM) (Gibco; Carlsbad, CA) supplemented with 5% fetal bovine serum (FBS) (Atlanta Biologicals; Flowery Branch, GA), 1.5x10−4 M monothiolglycerol (MTG) (Sigma-Aldrich; St. Louis, MO), 100 ng/mL murine stem cell factor (SCF) (PeproTech; Rocky Hill, NJ) and 10 ng/mL human interleukin-6 (hIL-6) (PeproTech; Rocky Hill, NJ).

extract_protocol: 20 million Nfix+/+ and Nfix-/- HPC5 cells were fixed with 1% formaldehyde (Sigma-Aldrich; St. Louis, MO) for 10 minutes at room temperature with gentle stirring. Fixing was quenched with 2M glycine (Sigma-Aldrich; St. Louis, MO) and further stirring for five minutes at room temperature. Cells were collected by centrifugation and snap frozen for storage at -80°C. Cells were then resuspended in buffer L1 (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with one Protease Inhibitor tablet (Roche; Basel, Switzerland). During lysis, samples were kept on ice for 10 minutes with gentle agitation every two minutes. Samples were centrifuged at 1693 rcf for 10 minutes at 4°C in a swing bucket rotor. Supernatant was removed and cells were resuspended in buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA, 10mM Tris pH8.0) supplemented with one Protease Inhibitor tablet (Roche; Basel Switzerland). Samples were rocked at room temperature for 10 minutes. Nuclei were isolated by centrifugation at 1693 rcf for 10 minutes at 4°C. Supernatant was carefully removed and 1X RIPA buffer was added to samples. Nuclei were sonicated using a cell disruptor (SFX250) (Branson Ultrasonics Corporation; Brookefield, CT). Lysate was clarified with centrifugation at 18879 rcf for 15 minutes at 4°C. The supernatant was carefully transferred to a 15mL conical vial. Samples were incubated with protein A/G sepharose beads (Pierce; Waltham, MA) overnight to preclear supernatant. 20µg of anti-PU.1 (sc-390405, Santa Cruz; Dallas, TX), and anti-NFIX (clone: 7B5.3) antibodies were also pre-bound to protein A/G agarose beads (Pierce; Waltham, MA) for overnight incubation. Pre-cleared chromatin was centrifuged at 1000 rcf for three minutes at 4°C. Pre-cleared chromatin was added to respective antibody-bead complex in Eppendorf tubes while some pre-cleared chromatin was reserved for input. Samples were rotated at 4°C for four hours. After incubation, samples were centrifuged at 5418 rcf for five minutes at 4°C. Supernatant was aspirated and beads were washed with various buffers: once with IP Wash Buffer I (20mM Tris pH8.0, 50mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with IP High Salt Wash Buffer (20mM Tris pH8.0, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), once with IP Wash Buffer II (10mM Tris pH8.0, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% deoxycholic acid), and twice with TE buffer. DNA:protein complexes from beads were eluted twice with freshly made elution buffer (1% SDS, 100mM sodium bicarbonate). To reverse crosslinking, 5M NaCl (final concentration 370mM), 10mg/mL RNase (final concentration 0.45mg/mL), and 20mg/mL proteinase-K (final concentration 0.26mg/mL) were added to eluates and input samples. Incubate samples at 37°C for 30 minutes, 45°C for 30 minutes, and 65°C overnight. DNA was eluted using the Qiagen MinElute (Hilden, Germany) kit following manufacturer’s protocol except DNA was eluted in 28uL with provided EB buffer. DNA was quantified using the Quant-iT PicoGreen assay (Life Technologies; Carlsbad, CA) Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific; Waltham, MA) or SpectraMax Quant AccuBlue Pico dsDNA assay kit (Molecular Devices; San Jose, CA). Libraries were prepared with KAPA HyperPrep Library Preparation Kits (KK8504) (Roche; Basel, Switzerland). Libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies; Santa Clara, CA), 5300 Fragment Analyzer System HS Large Fragment Kit (Agilent Technologies; Santa Clara, CA), 4200 TapeStation D1000 ScreenTape assay (Agilent Technologies; Santa Clara, CA) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer; Waltham, MA). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies; Carlsbad, CA) or low pass sequencing with a MiSeq nano kit (Illumina; San Diego, CA). Single read 50 cycle sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA) or NextSeq 550 (Illumina; San Diego, CA).

tag: antibody


title: wt_p9_input


title: histone_input_HPC5_combined


title: Cbx7-S

description: ChIP-seq

source_name: FUCCI-mESCs

growth_protocol: FUCCI-mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco)  and hygromycin B (InvivoGen) as described previously (Asenjo et al. 2020)

extract_protocol:
ChIP assays were mainly performed as described previously (Asenjo et al, 2020).
ChIP-seq libraries were generated from 1-5 ng of immunoprecipitated DNA with the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Cell-cycle sorting using an Aria Fusion cell sorter

value: Mixed background:129/Sv / C57BL/C6


title: RNA-Ring1bflfl-G1

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2020
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: 1706666_MW127_H3K27ac


title: DS2-NCSCs

source_name: DS2-hiPSC-derived neural crest stem cells (sample2)

tag: cell type


title: 1706667_MW127_KO0423_INPUT


title: RNA-Ring1bflfl-S

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2021
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: T cells, After Treatment, Relapse [SEQADJ002]

tag: time


title: Cbx7-G2

description: ChIP-seq

tag: strain


title: 1706664_MW127_H3K4me3


title: 1706665_MW127_H3K27ac


title: 1706663_MW127_H3K4me3


title: RNA-Ring1bflfl-G2

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2022
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: 1706662_MW127_H3K4me1


title: RNA-Ring1bKO-G1

extract_protocol:
4su experiments were carried out as described in Asenjo et al, 2023
Libraries were generated from 20 ng of 4sU-RNA using the TruSeq stranded mRNA Library Prep kit according to manufacturer’s instructions.


title: Cbx7-G1

description: ChIP-seq


title: Rybp-H2AK119ub1-Cbx7-Input

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
bamCoverage 3.5.0 used to normalize with BPM method a with default parameters.
Assembly: mm9
Supplementary files format and content: Bigwig files containing Reads per Million (RPM) values.


title: 1706659_MW127_KONFIX_0417

value: NFIX


title: H2AK119ub1-G1

description: ChIP-seq


title: 1706661_MW127_H3K4me1


title: T cells, Before Treatment, Relapse [SEQADJ001]


title: H2AK119ub1-S

description: ChIP-seq


title: 1706657_MW127_KONFIX_0423


title: H2AK119ub1-G2

description: ChIP-seq


title: 1706669_MW127_KO0417_INPUT


title: 1678573_MW120_P13_Input


title: Rybp-G2

description: ChIP-seq


title: Rybp-G1

description: ChIP-seq


title: 1678572_MW120_P13_NFIX


title: Rybp-S

description: ChIP-seq


title: Ring1b-MBL-G2

description: ChIP-seq


title: Ring1b-MBL-S

description: ChIP-seq


title: 1678570_MW119_P8_NFIX


title: Ring1b-MBL-G1

description: ChIP-seq