title: SPG, CTRL, APOE27

description: 10X Genomics

tag: Sex

value: female

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: Non-demented control.

value: Terminal pulmonary emphysema/heart failure.

value: 1. Slight senile involutive cortical changes (compatible with the patient's age). 2. Haemorrhagic remainder, in the parietal white matter; whether this is connected with the neuroborreliosis suffered remains unclear.

tag: profession

value: Drawing teacher.


title: SPG, AD, APOE26

status: Public on Jun 04 2024

type: SRA

city: Boston

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were perfomed using CellRanger (version 7.0.0).
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Fresh frozen brain tissue (10 sections of 1cm2 with a thickness of 40µm) were cut and collected and lysed in a sucrose lysis buffer (10 mM Tris-HCL (pH 8.0); 320 mM sucrose; 5 mM CaCl2; 3 μM Mg(Ac)2; 0.1 mM EDTA; 1 mM dithiothreitol (DTT) and 0.1% Triton X-100). Lysates were then filtered through a 70 µm cell strainer. Nuclei were purified by ultracentrifugation (107,000× g for 1.5 h at 4 °C) through a dense sucrose buffer (10 mM Tris–HCL (pH 8.0); 1.8 M sucrose; 3 μM Mg(Ac)2; 0.1 mM EDTA and 1 mM DTT). The supernatants were removed and pellets were re-suspended in 2% BSA/PBS containing RNase inhibitor (0.35 U/μL). The nuclei were incubated with fluorescently-conjugated antibodies directed against the neuronal marker NEUN (RBFOX3/NEUN (1B7) AF647 mouse mAB, Novus Biologicals, NBP1-92693AF647) and the transcription factor OLIG2 for the oligodendrocyte lineage (Anti-OLIG2 clone 211F1.1 AF488 mouse mAb, Merck Millipore, MABN50A4). After washing, the DNA dye DAPI was added and nuclei were sorted on a MoFlo Astrios. For each sample, we collected DAPIposNEUNnegOLIG2neg nuclei for snRNAseq
Library construction was performed to the manufacturer's instuctions (single cell 3' v3.1 single index, 10X Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partioning oil and gel beads to form gel bead-in-emulsion (GEM). tThe poly-A RNA from the nucleus lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, unique molecular identifier (UMI) na dht e 10X barcode. The pooled barcoded cDNA was then cleaned with Silane Dynabeads, amplified by PCR and apropriated size fragments were selected using AMPure XP beads for subsequent library contruction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Brain

value: male

value: AD

value: C

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: AD!

tag: dcode

tag: dcodewk

tag: wcode

value: G-PAR-SUP

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: Alzheimer's disease

value: Cachexia, possible CVA.

value: Compatible with the clinical diagnosis of Alzheimer's disease. Arachnoid cyst in right Sylvian fissure.

tag: diabetes

tag: education

value: Finished his advanced elementary education and followed several evening courses.

value: Civil servant and worked his way up to Chief of Department.


title: SPG, AD, APOE23

description: 10X Genomics

tag: Sex

value: female

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: Alzheimer's disease.

value: Dehydration.

value: Compatible with the clinical diagnosis of (pre)senile dementia of the Alzheimer type.

value: Attended primary school, she doubled one year.

tag: profession

value: Sales person in clothing store.


title: SPG, CTRL, APOE20

description: 10X Genomics

tag: tissue

value: Brain

value: male

value: CTRL

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

tag: diabetes


title: SPG, CTRL, APOE19

description: 10X Genomics

tag: Sex

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: A

tag: braaklb

tag: pmd

tag: ph

value: CONTR

value: ad(2,A); ischemie; meningioma

value: G-PAR-SUP

value: 1. Tuberculosis (1940) 2. Icterus (1955) 3.Ectopic pregnancy (1957) 4. Endometrial cancer (1970) 5. Uterus extirpation (1971) 6. Hepatitis (1971) 7. Depression (1980) 8. Collapse and hyperthermia (1983) 9. Goitre (1987) 10. Bronchitis (1995) 11. Lymphangitis (1999) 12. Arthrosis (2001) 13. Uterine prolapse (2002) 14. Vasovagal syncope (2002) 15. Diverticulitis (2002, 2009) 16. Urinary tract infection (2001, 2002, 2004, 2007, 2010, 2011) 17. Herpes zoster (2003) 18. Rectocele (2004) 19. Presbycusis (2004) 20. Thrombosis (2004) 21. TIA (2006) 22. Breast cancer (2007) 23. Cataract (2008) 24. Metastatic breast cancer (2009) 25. Scoliosis (2011) 26. Atrial fibrillation (2011) 27. Heart failure (2011)

value: Heart failure.

value: 1. Slight senile involutive cortical changes. 2. Small, few, irrelevant ischemic cortical lesions in the vertebrobasilar circulation. 3. Small, irrelevant meningioma.

tag: education

value: Nurse and homemaker.


title: SPG, CTRL, APOE18

description: 10X Genomics

tag: tissue

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

tag: wcode

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: Myocardial infarction.

value: Cardiac arrest, probably due to tamponade.

value: With the exception of slight senile involutive changes in the hipopocampus, compatible with the patient's age, no cerebral abnormalities.

tag: profession


title: SPG, AD, APOE24

description: 10X Genomics

tag: Sex

tag: apoe genotype

tag: disease state

value: AD

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: C

tag: braaklb

tag: pmd

tag: ph

value: AD!

value: 1. Aortal aneurysm 2. Myocardial infarction 3. Duodenal ulcer.

value: Shock due to acute abdomen.

value: Compatible with the clinical diagnosis of Alzheimer's disease.

tag: diabetes

value: Construction foreman.


title: SPG, CTRL, APOE17

description: 10X Genomics

tag: tissue

value: Brain

value: female

value: CTRL

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: CONTR

tag: dcode

tag: dcodewk

tag: wcode

value: G-PAR-SUP

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: Chronical myeloid leukemia.

value: Dyspnea.

value: Substantial senile-involutive cortical changes, possibly a bit much for the age.

tag: education


title: SPG, AD, APOE16

description: 10X Genomics

tag: Sex

value: male

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: superior parietal gyrus

value: plastic bag -80°C

value: 1. Hepatitis Diverticulitis (1983, 1989) 2. Gastritis (1989) 3. Spinal disc herniation (1989) 4. Bursitis (1996, 1998, 2002) 5. Tendinitis (1998. 2002) 6. Folliculitis (2004) 7. CVA (2005) 8.Arthritis (2005) 9. Anemia (2007) 10. Conjunctivitis (2008) 11. Dementia (2008) 12. Alzheimer's disease (2008) 13. Candidiasis or stomatitis (2010) 14. Respiratory infection (2011)

value: Gastrointestinal bleeding.

value: Compatible with the clinical diagnosis of senile dementia of the Alzheimer type. Consistent with this diagnosis, there is some mesiotemporal TDP positivity, but there are no signs of frontotemporal dementia.

tag: profession

value: Consultant.


title: SPG, AD, APOE15

description: 10X Genomics

tag: tissue

value: AD

value: C

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: AD!

tag: dcode

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: Alzheimer's disease.

value: Pneumonia with dehydration.

tag: diabetes

value: Grammar school.

value: Helped in the household at a farm.


title: SPG, AD, APOE13

description: 10X Genomics

value: Brain

tag: Sex

value: female

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

value: G-PAR-SUP

value: Alzheimer's disease

value: Sudden death.

value: Compatible with the clinical diagnosis of Alzheimer's disease.

tag: education

value: Finished elementary education.

value: Doctor's assistant until marriage.


title: SPG, AD, APOE14

description: 10X Genomics

tag: tissue

value: male

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

value: A3B3C3; CERAD score 3 / 3 neuritic plaques; Thal phase 5 / 5; slight caa type 2, stage 1; Lewy bodies in amygdala and entorhinal cortex

tag: wcode

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: 1. Concussion (1975) 2. Nephrolithiasis (1985) 3. Episcleritis (R) (1986) 4. Head trauma (1988) 5. Presbyacussis (L) (1988) 6. External otitis (L) (1992) 7. Bursitis biceps (R) (1995) 8. Cystitis (1996) 9. Contusion shoulder (R) (2000) 10. Hyperlipidemia (2002) 11. Otitis (2005, 2006) 12. Conjunctivitis (L) (2006) 13. Mild cognitive impairment (2010) 14. Tuba-stenosis (2014) 15. Alzheimer's disease 16. (2015) 17. Abnormal glucose tolerance (2016) 18. Hypertension (2016) 19. Constipation (2016)

value: Palliative sedation.

tag: profession

value: Entrepreneur in fruit growing business.


title: SPG, CTRL, APOE37

description: 10X Genomics

tag: Sex

tag: apoe genotype

tag: disease state

value: CTRL

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: O

tag: braaklb

tag: pmd

tag: ph

value: COPSY

value: CONTR

value: hippocampal sclerosis left; small infarctio in substantia nigra app. 2 cm; A0B2C0

value: right

value: 1. Angina pectoris (2001) 2. Constipation

value: Heart failure.

value: 1. Brain with primary age-related tauopathy (Braak stage 3 from 6 for tau without amyloid beta depositions) and only slight amyloid angiopathy but no amyloid beta plaques. 2. Other than that, hippocampal sclerosis (left). 3. In the substantia nigra a small infarction from 0.2 cm. 4. In addition incidental Parkinson's disease (Braak stage 1 of 6 for alpha-synuclein).

tag: diabetes

value: Journalist/writer.


title: SPG, CTRL, APOE9

description: 10X Genomics

tag: tissue

value: Brain

value: female

value: B

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

value: ad(1,B); infarct

tag: wcode

value: G-PAR-SUP

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: No neurologic diagnosis.

value: Multi organ failure after a ruptured abdominal aneurysm.

value: 1. Old posterior infarction, right mdio-temporo-occipitally (TIA is 2000?). 2. Slight senile-involutive cortical changes (Braak stage for tangles = 1, for amyloid = B).

tag: education


title: SPG, CTRL, APOE8

description: 10X Genomics

tag: Sex

value: male

tag: apoe genotype

tag: disease state

value: CTRL

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: A

tag: braaklb

tag: pmd

tag: ph

value: A2B1C0, ARTAG, microscopic infarction putamen right

tag: profession


title: SPG, CTRL, APOE10

description: 10X Genomics

tag: tissue

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: CONTR

tag: dcode

tag: dcodewk

tag: wcode

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

value: NC

tag: storage

value: cryovial -80°C

tag: freezer

value: 1. Focal motor-status epilepticus (1994) 2. Diphteria

value: Septic shock.

value: 1. No signs of cerebral ageing. 2. Metastasis of a large-cellular carcinoma (lung), right temporal.

tag: diabetes


title: SPG, AD, APOE6

description: 10X Genomics

value: Brain

tag: Sex

tag: apoe genotype

tag: disease state

value: AD

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

value: C

tag: braaklb

tag: pmd

tag: ph

value: AD!

value: plastic bag -80°C

value: 1. Tonsillectomy (1972) 2. Presbycusis (2001) 3. MÃ©niÃ¨re's disease (2002) 4. Alzheimer's disease (2006) 5. Frontotemporal dementia (2006) 6. Distal radius fracture (2010)

value: 1. Brain with (possibly hereditary) presenile Alzheimer's disease. There are only few Lewy bodies in the amygdala, as seen always at presenile Alzheimer's.

tag: education

value: Medical school.

value: Language teacher. Doctor in school health service.


title: SPG, CTRL, APOE30

description: 10X Genomics

tag: tissue

value: male

value: CTRL

value: B

tag: weight

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

tag: dcode

tag: dcodewk

value: ad(1,B); lb; infarct; poliomyelitis

tag: wcode

value: G-PAR-SUP

tag: region

tag: specific

tag: ocode

tag: storage

tag: freezer

value: 1. Polio. 2. Depression. 3. TIA's. 4. Osteoporosis. 5. Exertion intolerance.

value: Sudden death.

value: 1. Slight senile-involutive cortical changes. 2. Slight alpha-synucleinopathy of the brainstem (medulla oblongata), clinically irrelevant. 3. A few small vascular lesions, probably related to the sustained TIA's (subiculum, putamen, pallidum). 4. Partial loss of motor horn neurons, as a consequence of poliomyelitis many years ago.

tag: profession


title: TL3

status: Public on May 22 2024

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

library_source: transcriptomic

data_processing:
First, the adaptor sequences and polyA sequences were trimmed and filtered out using fastp (ver 0.23.2)
RNAseq reads were aligned to the human reference genome (hg38) using the STAR (v2.7.9) software.
The R Subread package with the featureCount function generated RNA-seq raw counts for quantification (ver2.0.3).
Read count were normalized using RPKM for QC.
Genes expressed at very low levels, with maximum expression <0.1 RPKM from all samples, were excluded from downstream differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

extract_protocol:
Treated Samples were purified using the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared with KAPA mRNA HyperPrep Kit following manufacturer's protocols.

tag: cell line

tag: cell type

value: SCLC

tag: treatment

value: Teriflunomide/Lurbinectedin


title: SPG, CTRL, APOE7

description: 10X Genomics

tag: tissue

value: Brain

tag: Sex

value: female

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

tag: weight

value: CONTR

value: superior parietal gyrus

value: Euthanasia.

value: Shows no cerebral abnormlaities, with the exception of slight senile involutive cortical changes.

tag: diabetes

tag: education


title: L3

tag: cell line

tag: cell type

tag: treatment

value: Lurbinectedin


title: SPG, AD, APOE3

description: 10X Genomics

tag: tissue

tag: Sex

tag: apoe genotype

tag: disease state

value: AD

tag: age

value: C

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: AD!

tag: dcode

tag: dcodewk

tag: wcode

tag: region

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: Pre-senile Alzheimer's disease.

value: Dehydration/cachexia and breast cancer.

value: Brain autopsy:Alzheimer' disease. In addition an inflammatory focus in the medulla oblongata.

value: Elementary school.

tag: profession


title: TL1

tag: cell line

tag: cell type

value: SCLC

tag: treatment


title: SPG, AD, APOE4

description: 10X Genomics

tag: tissue

tag: Sex

value: male

tag: apoe genotype

tag: disease state

tag: age

tag: nbb

tag: sample

tag: donor

tag: autopsy

tag: rin

tag: braak

tag: amyloid

tag: braaklb

tag: pmd

tag: ph

tag: weight

value: G-PAR-SUP

value: 1. Alzheimer's disease. 2. Hernia diaphragmatica (1995) 3. COPD 4. Basal cell carcinoma; surgery (2003 and 2005) 5. Stomach ulcer/volvolus; surgery (2004) 6. Severely enlarged prostate; surgery (2006)

value: Unknown

value: Compatible with the clinical diagnosis of Alzheimer's disease.

tag: diabetes

tag: education

value: Middle school for technical education.

value: Technical drawer.


title: Ovary cortex-medulla, vitrified, slice 1 & 2

status: Public on May 18 2024

city: HK

first: Kun

last: MA

state: Hong Kong

address: No 12 Kam Ling Court Whitty Street Sai Wan HK Island

country: Hong Kong

institute: The University of Hong Kong

data_processing:
We used STOmics Analysis Workflow (SAW), the official data processing pipeline to perform read quality control, genome mapping and gene expression quantification. Prior to genome mapping, we employed the ST_BarcodeMap module for filtering and mapping of chip identifiers (CID) from sequenced reads to their corresponding chip locations, and FastP for quality control and trimming of the reads. The reads were then mapped to the GRCh38 reference genome with STAR and counted for each spot with Bam2Gem.
Assembly: GRCh38
Supplementary files format and content: bin50.rds - bin50 spots of all samples with preprocessed meta data after preprocessing
Supplementary files format and content: fresh.tissue.gem.gz - SAW pipeline output gem file (fresh)
Supplementary files format and content: slow.tissue.gem.gz - SAW pipeline output gem file (slow)
Supplementary files format and content: vitri.tissue.gem.gz - SAW pipeline output gem file (vitri)
Library strategy: Stereo-seq

source_name: ovary

extract_protocol:
Human ovarian tissues were donated from one patient aged 35 years who underwent oophorectomy due to cervical cancer. The ovarian tissues were removed using scissors rather than electrocoagulation. Obtained ovarian tissues were directly placed in sterile transport medium (Leibovitz抯 L-15 Medium supplemented with 1% HSA) and transported on ice to the laboratory. In the laboratory, the ovarian tissues were transferred to 10 cm sterile dishes containing chilled sterile normal saline. The saline was changed several times during the process. After most of the medulla was removed with scalpels, the tissues were cut into 10?? mm pieces and divided into fresh and two cryopreservation groups. According to the Stereo-Seq protocol, one piece of fresh group tissues was fixed in O.C.T. compound (Tissue Tek) for subsequent sequencing, tissues of the two cryopreservation groups were processed after freezing and thawing. The tissue capture area was approximately 10? mm. 10?m tissue sections were cut using cryo-microtome (CM1950, Leica) with head temperature set at -16 癈 and adhered to the Stereo-seq chip (BGI) surface. The sections were then performed histomorphology detection, staining in hematoxylin for 3 min, 10 s in bluing agent, and 1 min in eosin. To release mRNA from the cells, the sections were permeabilized, the optimal time was 22 min. After in situ reverse transcription, the resulting cDNAs were amplified.
PCR products were purified for DNA nanoball (DNB) generation and finally sequenced on MGI DNBSEQ-Tx sequencer; detailed protocols are available on the BGI Stereo-seq website (https://en.stomics.tech/).

tag: tissue

value: ovary


title: Ovary cortex-medulla, fresh, slice 1 & 2


title: Ovary cortex-medulla, slow-frozen, slice 1 & 2


title: Artificial sample

status: Public on May 07 2024

city: Donostia

first: Alex

middle: Martínez

last: Ascensión

state: Gipuzkoa

address: P/ Doctor Begiristain

country: Spain

institute: Biogipuzkoa HRI

description:
ARTIFICIAL
Homo sapiens, Cutibacterium acnes, Dietzia maris, Bifidobacterium bifidum, Lactobacillus acidophilus, Bacteroides fragilis, Roseburia intestinalis, Stenotrophomonas maltophilia, Sphingomonas paucimobilis, Taylorella equigenitalis, Kinneretia asaccharophila, Aspergillus chevalieri, Malassezia restricta, Saccharomyces cerevisiae, Plenodomus lingam, Alternaria alternata, Burzaovirus, Elvirus, Lentivirus, Nickievirus, Lymphocryptovirus
On January 1st, 2025, the raw files for this sample were replaced.

data_processing:
Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample

organism: synthetic construct

source_name: In silico

extract_protocol:
The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.

value: In silico

value: Sample control


title: MNase-ChIP, K9me2 ChIP, NSD RNAi S2 cells, Batch 6, Replicate 1

city: Munich

first: Muhunden

middle: Nallappa

last: Jayakrishnan

state: Munich (city)

address: 57 Nusselstrasse, 57

department: Molecular Biology

country: Germany

institute: Biomedical Center, Ludwig Maximilians University Munich

library_source: genomic

data_processing:
MNase-based paired-end ChIP-seq reads were demultiplexed using JEDemultiplexer and concordantly aligned using Bowtie2 with -X 500 and were filtered using samtools with parameter -q 10. Tag directories and coverage files (normalized to total number of virilis reads and to input) were generated by Homer Software package (Heinz et al. 2010).
Peak calling was performed on replicate-averaged normalized coverages using MACS2 v2.1.2 bdgpeakcall with parameters -l 1000 -c 3
Regions of differential K36me1/2/3 binding upon RNAi were identified using csaw v1.24.3 using BAM files obtained from bowtie2 for all replicates as input. 250bp windows of signficant difference were merged into regions of max 3kb.
Assembly: BDGP6 (dm6), release 104
Supplementary files format and content: For ChIPs, D. virilis scaled and input normalized .bigwig are provided for each individual sample. For inputs, representative D.virilis scaled .bigwig are provided.
Supplementary files format and content: Control K36me1/2/3 peaks as .bed (provided as supplementary to Control RNAi ChIP files)
Supplementary files format and content: csaw output of regions of significant change as .bed (provided as supplementary to HMT RNAi ChIP files except Batch0)

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1mg/mL streptomycin (Sigma‑Aldrich).

extract_protocol:
70 to 130 million RNAi treated S2 cells, resuspended in 20 ml of complete Schneider’s Drosophila Medium, were crosslinked by adding 1:10 of the volume of Fixing Solution (100 mM NaCl, 50 mM Hepes pH 8, 1mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) and rotated at room temperature for 8 min. 1.17 ml of freshly-prepared 2.5 M glycine was added to stop the fixation (final conc. 125 mM). Cells were pelleted at 500 g for 10 min (4°C) and resuspended in 10 mL of ice-cold PBS. 3.5 million of fixed D. virilis cells (fixed as described for D. melanogaster cells) were added for every 70 million D. melanogaster cells. Cells were pelleted at 526 g for 10 min (4°C) and resuspended in 1 ml of PBS + 0.5% Triton-X-100 + 1X cOmplete EDTA-free Protease Inhibitor for every 70 million D. melanogaster cells and rotated at 4°C for 15 min to release nuclei. Nuclei were pelleted at 2000 g for 10 min and washed once with 10 ml of ice-cold PBS. Nuclei were suspended in 1 ml of RIPA buffer (10 mM Tris-HCl pH 8, 140 mM NaCl, 1mM EDTA, 0.1% Na-deoxycholate, 1% Triton-X-100, 0.1% SDS, 1 mM PMSF, 1X cOmplete EDTA-free Protease Inhibitor + Roche 1x PhosSTOP) + 2 mM CaCl2 for every 70 million D. melanogaster cells, divided into 1 ml aliquots and flash-frozen in liquid N2. 1 mL of fixed nuclei was quickly thawed and 1 µL of MNase (to 0.6 units) (Sigma-Aldrich, Cat. No N5386) added. Chromatin was digested for 35 min at 37°C. MNase digestion was stopped by transferring the samples on ice and adding 22 µL of 0.5 M EGTA. Samples were mildly sonicated using a Covaris S220 instrument with the following settings: 50 W peak power, 20% duty factor, 200 cycles/burst, 8 min total time. Insoluble chromatin was removed by centrifugation at 16,000 g for 30 min at 4°C. Soluble chromatin was pre-cleared by incubation with 10 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry (GE Healthcare, Cat. No 17-5280-11 and 17-0618-06) for every 100 µL of chromatin for 1 h at 4°C. 100 µL of pre-cleared chromatin were set aside (input) and kept overnight at 4°C, while each primary antibody was added to 300 µL of chromatin and incubated overnight at 4°C. 40 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry was added for each immunoprecipitation and rotated 3 h at 4°C. Beads were washed 5 times with 1 ml of RIPA (5 min rotation at 4°C, pelleted at 3000 g for 1 min between washes) and resuspended in 100 µL of TE (10 mM Tris pH 8, 1 mM EDTA). 0.5 µL of RNaseA (Sigma-Aldrich, Cat. No. R4875) was added to both input samples and resuspended beads, followed by incubation at 37°C for 30 min. After addition of 6 µL of 10% SDS, protease digestion (250 ng/ µL Proteinase K, Genaxxon, Cat.no. M3036.0100) and crosslink reversal were performed simultaneously at 68°C for 2 hr. DNA was purified using 1.8X Agencourt AMPure XP beads (Beckman Coulter, Cat No A63880) following the standard protocol and eluted in 30 µL of 5 mM Tris-HCl pH 8. Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465). Libraries were sequenced on an Illumina NextSeq 1000 instrument at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU).
Standard Paired-end protocol using 5-10ng input material using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465).  Dual index oligos from NEB (#E6440). Libraries were size selected in 200-500 bp range and validated using Agilent TapeStation system.

treatment_protocol: RNAi against target genes in S2 cells was performed as previously described (Albig et al., 2016) with minor modifications. In brief, double-stranded RNA fragments (dsRNA) were generated with HiScribe T7 kit (NEB) from PCR products. Cells were incubated with 10 µg dsRNA per 1x10e6 cells (2 distinct sequences per target) in either 6 well plates or 75 cm^2 flasks for 1 hour. Two volumes of growth medium were added and cells were incubated at 26°C. Depending on the experiment, total duration of RNAi was 7-12 days with 2-3 rounds of fresh RNAi treatments.

tag: cell line

tag: cell type

value: Late-stage Embryonic

tag: antibody

tag: treatment

value: NSD RNAi


title: MNase-ChIP, K27me3 ChIP, NSD RNAi S2 cells, Batch 7, Replicate 1

value: K27me3 (07-449 Millipore)


title: MNase-ChIP, K27me3 ChIP, Set2 RNAi S2 cells, Batch 7, Replicate 1

value: Set2 RNAi


title: SPG, AD, APOE5

description: 10X Genomics

value: Brain

tag: Sex

value: female

tag: apoe genotype

tag: disease state

value: AD

tag: age

tag: nbb

tag: sample

value: C

tag: csf

tag: barcode

tag: ID

tag: dcodeprot

value: LBV

tag: dcode

value: AD!

tag: dcodewk

value: AD(5,C); infarct

tag: wcode

tag: region

value: superior parietal gyrus

tag: specific

tag: ocode

tag: storage

value: plastic bag -80°C

tag: freezer

value: 1. Laparectomy 2. Diverticulitis (1971) 3. Rheumatoid Polimyalgia Cholelithiasis (1977) Cholecystectomy (1979) 4. Poliposis nasi operation (1981) Degeneration vertebrae L5-S1 (1985) Arthrosis (1992) 5. Gonarthrosis bilateral (1994) 6. Adenocarcinoma - recto-sigmoid resection (1998) Depression (1998) 7. Cataract operations (2002/2003) 8. Diabetes mellitus (insuline sensitive) (1997) Dementia syndrome

value: Mors subitum.

value: Diabetes Mellitus Type II.

tag: profession


title: L1

tag: cell line

tag: cell type

value: SCLC

tag: treatment

value: Lurbinectedin


title: MNase-ChIP, K27me3 ChIP, GST RNAi S2 cells, Batch 7, Replicate 1

value: Late-stage Embryonic

tag: antibody

value: Control RNAi


title: MNase-ChIP, JASPer ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3

tag: chip antibody

value: JASPer (Albig et al., 2019)

value: Set2+NSD RNAi


title: L2


title: TL2

value: Teriflunomide/Lurbinectedin


title: MNase-ChIP, JASPer ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, JASPer ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3

value: NSD RNAi


title: MNase-ChIP, JASPer ChIP, Control RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, JASPer ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2

value: Set2 RNAi


title: MNase-ChIP, JASPer ChIP, Control RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3

value: Msl3 (Albig et al., 2019)


title: MNase-ChIP, JASPer ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, Msl3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K9me2 ChIP, GST RNAi S2 cells, Batch 6, Replicate 1


title: MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, Msl3 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K27me3 ChIP, Ash1 RNAi S2 cells, Batch 7, Replicate 1

value: K27me3 (07-449 Millipore)

value: Ash1 RNAi


title: MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, Msl3 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me1 ChIP, Ash1 RNAi S2 cells, Batch 7, Replicate 2

description: DiffRegions_3kb_tol100_K36Me1_Ash1_KD.bed


title: MNase-ChIP, Msl3 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me1 ChIP, Ash1 RNAi S2 cells, Batch 6, Replicate 1


title: MNase-ChIP, K36me1 ChIP, NSD RNAi S2 cells, Batch 7, Replicate 2

description: DiffRegions_3kb_tol100_K36Me1_NSD_KD.bed


title: MNase-ChIP, K36me1 ChIP, Set2 RNAi S2 cells, Batch 7, Replicate 2

description: DiffRegions_3kb_tol100_K36Me1_Set2_KD.bed


title: MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 7, Replicate 2


title: MNase-ChIP, K36me1 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 1


title: MNase-ChIP, K36me1 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 1


title: MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 6, Replicate 1


title: MNase-ChIP, JASPer ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me1 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 1


title: MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me2 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1

description: DiffRegions_3kb_tol100_K36Me2_NSD_KD.bed


title: MNase-ChIP, K36me1 ChIP, Control RNAi S2 cells, Batch 5, Replicate 1


title: MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3

description: DiffRegions_3kb_tol100_K36Me2_Set2_KD.bed


title: MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me2 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me3 ChIP, DKD (Set2+NSD) RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me2 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 2, Replicate 2

description: DiffRegions_3kb_tol100_K36Me3_NSD_KD.bed


title: MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 5, Replicate 3

description: DiffRegions_3kb_tol100_K36Me3_Set2_KD.bed


title: MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me3 ChIP, Set2 RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 2, Replicate 2


title: MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 7, Replicate 3

value: dMes4 (NSD) (Bell et al., 2007)


title: MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, dMes4(NSD) ChIP, Control RNAi S2 cells, Batch 4, Replicate 2


title: MNase-ChIP, K36me2 ChIP, NSD RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 4, Replicate 2

value: S2Ph-PolII (ab5095)


title: MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 7, Replicate 3


title: MNase-ChIP, IgG ChIP, Control RNAi, Batch 5

value: IgG (CST #2729S)


title: MNase-ChIP, Input, NSD RNAi, Batch 1


title: MNase-ChIP, S2Ph-PolII (ePol) ChIP, Control RNAi S2 cells, Batch 3, Replicate 1


title: MNase-ChIP, Input, Ash1 RNAi, Batch 6


title: CUT&RUN, IgG, WT S2 cells, Replicate 2

value: No treatment


title: MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 1


title: CUT&RUN, H3K36me3, WT S2 cells, Replicate 2


title: CUT&RUN, H3K36me3, WT S2 cells, Replicate 1


title: MNase-ChIP, JASPer ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2


title: CUT&RUN, IgG, WT S2 cells, Replicate 1


title: MNase-ChIP, JASPer ChIP, Control 7-day RNAi, Batch 0, Replicate 1


title: MNase-ChIP, JASPer ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2


title: MNase-ChIP, JASPer ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1


title: MNase-ChIP, K36me2 ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2


title: MNase-ChIP, K36me2 ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1


title: MNase-ChIP, K36me3 ChIP, NSD RNAi S2 cells, Batch 1, Replicate 1


title: MNase-ChIP, K36me2 ChIP, Control 7-day RNAi, Batch 0, Replicate 1


title: MNase-ChIP, K36me3 ChIP, Control RNAi S2 cells, Batch 5, Replicate 3


title: MNase-ChIP, K36me2 ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2


title: MNase-ChIP, K36me3 ChIP, Set2 (1) 7-day RNAi, Batch 0, Replicate 2


title: MNase-ChIP, K36me3 ChIP, Control_2 7-day RNAi, Batch 0, Replicate 2


title: MNase-ChIP, K36me3 ChIP, Control 7-day RNAi, Batch 0, Replicate 1


title: Clover 24hpi sample 3

status: Public on Apr 01 2024

city: Moscow

first: Scott

middle: Stephen

last: Grieshaber

state: ID

address: 875 Perimeter Drive MS 3051

department: Biological Sciences

institute: University of Idaho

data_processing:
Aligned with Bowtie2
Counts generated using Htseq
Differentail gene expression calcualted using Dseq2
Assembly: Alinged to C. trachomatis L2 434/Bu using Bowtie2
Supplementary files format and content: Tab delinated text file of counts

organism: Chlamydia trachomatis

source_name: Cos-7 cells

growth_protocol: Cos-7 cells (CRL-1651) were grown in RPMI-1640, supplemented with 10% FBS and 10 μg/mL gentamicin (Cellgro).

extract_protocol:
Total RNA was isolated from cells infected with the indicated strains. Expression of each protein was induced at 15 hpi with either 0.5 mM theophylline and 30ng/ml anhydrotetracycline (HctB) or 0.5 mM theophylline (Clover, HctA, CtcB and Euo) and the Ctr isolated at 18 and 24 hpi on ice. Briefly, the infected monolayer was scraped into ice cold PBS, lysed using a Dounce homogenizer and the Ctr isolated over a 30% MD-76R pad. Total RNA was isolated using TRIzol reagent (Life Technologies) following the protocol provided and genomic DNA removed (TURBO DNA-free Kit, Invitrogen). The enriched RNA samples were quantified and the libraries built and barcoded by the IBEST Genomics Resources Core at the University of Idaho.
Kapa RNA Hyper Prep

treatment_protocol: Cos-7 Cells were infected with either C. trachomatis L2 434/Bu-clover, L2 434/Bu-euo, L2 434/Bu-hctA, L2 434/Bu-hctB, L2 434/Bu-ctcB

value: Cos-7 cells

value: Clover expression at 15hpi isolated at 24hpi


title: Clover 24hpi sample 1


title: Clover 18hpi sample 2

value: Clover expression at 15 hpi isolated at 18hpi


title: MNase-ChIP, Input, Set2 (KK) 7-day RNAi, Batch 0

value: Late-stage Embryonic


title: MNase-ChIP, Input, Control 7-day RNAi, Batch 0

value: Control RNAi


title: Clover 18hpi sample 3


title: CtcB 24hpi sample 3

value: CtcB expression at 15 hpi isolated at 24hpi


title: CtcB 18hpi sample 2

value: CtcB expression at 15 hpi isolated at 18 hpi


title: CtcB 18hpi sample 1


title: CtcB 18hpi sample 3


title: HctB 24hpi sample 3

value: HctB expression at 15 hpi isolated at 24hpi


title: MNase-ChIP, K36me3 ChIP, Set2 (KK) 7-day RNAi, Batch 0, Replicate 1


title: HctA 24hpi sample 3

value: HctA expression at 15 hpi isolated at 24hpi


title: HctB 18hpi sample 2

value: HctB expression at 15 hpi isolated at 18 hpi


title: HctB 24hpi sample 2


title: HctA 24hpi sample 2


title: HctB 18hpi sample 3


title: HctB 18hpi sample 1


title: HctB 24hpi sample 1


title: HctA 18hpi sample 2

value: HctA expression at 15 hpi isolated at 18 hpi


title: HctA 18hpi sample 1


title: Euo 24hpi sample 3

value: Euo expression at 15 hpi isolated at 24hpi


title: HctA 24hpi sample 1


title: HctA 18hpi sample 3


title: Euo 24hpi sample 2


title: Euo 24hpi sample 1


title: Clover 24hpi sample 2


title: Euo 18hpi sample 3

value: Euo expression at 15 hpi isolated at 18 hpi


title: Euo 18hpi sample 1


title: CtcB 24hpi sample 2


title: CtcB 24hpi sample 1


title: N60_PASmos_LC_library_frog_oocyte_progesterone_7hr_Tail_seq

status: Public on Feb 15 2024

city: Cambridge

first: Kehui

last: Xiang

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: Libraries enriched by antisese oligos before ligaion, followed by reverse transcription and PCR amplification with library-specific primers

library_source: other

data_processing:
For gene-specific tail-seq of mRNA reporters, data were processed with a custom script available at https://github.com/coffeebond/MPRA_tail_seq.
For PAL-seq v3 or v4, reads were trimmed with cutadapt v3.7 with the parameters “-m 15 --quality-base=64 -q 20,20 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7”. The trimmed reads were mapped using STAR (v2.7.1a) to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained, the genomic sequences of humans or fish, depending on which spike-in RNAs were used, and the sequences of the poly(A) standards generated previously, with the parameters “--runThreadN 16 --runMode alignReads --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outFilterType BySJout --outSAMattributes All --outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL-seq.
Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4, primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly.
Supplementary files format and content: For gene-specific tail-seq of mRNA reporters, tab-delimited text files with columns indicating 1) sequence of the variable region; 2) median tail length; 3) number of reads; 4–7) tail lengths at quantile 10, 25, 75, and 90.
Supplementary files format and content: For PAL-seq v3 or v4, tab-delimited files with columns indicating 1) gene ID or poly(A) site ID; 2) read cluster ID; 3) tail length
Library strategy: gene-specific tail-seq

molecule: other

source_name: Sythetic mRNA reporter library

extract_protocol:
Frog oocytes and embryos were lysed in ice-cold buffer RL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% [v/v] Triton X-100, 100 µg/ml cycloheximide, cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer], and 200 units/ml SUPERase•In) in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri-reagent for RNA isolation. Fish embryos were de-chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. After removing all E3 medium, Tri-Reagent was added to the embryos for RNA isolation. Mouse GV-oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus-oocyte-complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG-induced mice (16 hr), denuded with 3 mg/ml hyaluronidase for 2 min, washed, and then collected in Tri-reagent for RNA isolation.
For gene-specific tail-seq of reporter libraries, total RNA with reporter mRNA libraries was ligated to a pre-adenylated 3ʹ adapter directly in most cases, but for the N60 library injected into fish embryos and frog oocytes, the N37-PAS-N17 library injected into fish embryos and frog oocytes, and the CPEmos-N60 and N60(LC)-PASmos libraries injected into frog oocytes, reporter library mRNAs were enriched by anti-sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009, 8 pmol KXSH010, and 2x SSC (0.3 M NaCl, 30 mM sodium citrate pH 7.0) in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads (Thermo Fisher, 65002) and incubated for 20 min at 23°C on a thermal mixer, shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined, precipitated with ethanol, and resuspended in 6.5 µl water.
The anti-sense oligo-enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre-adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330, 50 mM HEPES pH 7.5, 10 mM MgCl2, 10 mM dithiothreitol, 1 unit/µl T4 RNA ligase 1 (New England Biolabs, M0204S). The ligation reaction was incubated at 23°C for 150 min. After ligation, RNA was extracted with phenol/chloroform, precipitated with ethanol, and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl, incubated at 65°C for 5 min, and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First-Strand Buffer, 500 µM dNTPs, 5 mM dithiothreitol, 1 unit/µl SUPERase•In, and 200 units SuperScript III (Thermo Fisher, 18080044) at 50°C for 1 hr. After reverse transcription, RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min, followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio-Spin P-30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer (Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR-amplified library was cleaned up twice with AMPure XP beads (Beckman Coulter, A63881) with a beads-to-sample ratio of 1.2.
For sequencing of endogenous mRNA poly(A)-tail length, libraries were prepared with PAL-seq v3 (for frog oocytes) or PAL-seq v4 (for frog embryos, fish embryos, and mouse oocytes) as described previously (PMID: 34213414). When preparing the sequencing libraries of mRNAs from fish embryos, a different 3ʹ adapter (KXS013) was used for 3ʹ-end ligation, and poly(A)-selected mRNA from HeLa cells was used as spike-in, replacing poly(A)-selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer, shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined, precipitated with ethanol, and resuspended in 30 µl water. The oligo-depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample after monitoring consistency.

tag: tissue

value: Sythetic mRNA reporter library

value: 10 uM progesterone 7 hours


title: Clover 18hpi sample 1


title: N60_PASmos_LC_library_frog_oocyte_uninjected_Tail_seq


title: N60_PASmos_library_frog_embryo_stage_12_22hr_post_injection_sucrose_cushion_pellet_Tail_seq

description: Direct ligaion to total RNA, followed by reverse transcription and PCR amplification with library-specific primers.

value: None, stage 12


title: Euo 18hpi sample 2


title: N60_PASmos_library_frog_embryo_stage_6_2hr_post_injection_sucrose_cushion_pellet_Tail_seq

value: None, stage 6


title: N60_PASmos_library_frog_embryo_stage_12_22hr_post_injection_Tail_seq

description: Direct ligaion to total RNA, followed by reverse transcription and PCR amplification with library-specific primers. This dataset alse serves as the input for sucrose cushion at the matched embyonic stage.


title: N60_PASmos_library_frog_embryo_stage_9_6hr_post_injection_Tail_seq

value: None, stage 9


title: N60_PASmos_library_frog_embryo_stage_8_4hr_post_injection_Tail_seq

value: None, stage 8


title: N60_PASmos_library_frog_embryo_stage_7_3hr_post_injection_Tail_seq

value: None, stage 7


title: N60_PASmos_library_frog_embryo_stage_6_2hr_post_injection_Tail_seq


title: N60_PASmos_library_frog_embryo_stage_2_5min_post_injection_Tail_seq

value: None, stage 2


title: N60_PASmos_library_frog_embryo_uninjected_Tail_seq


title: N60_PASmos_library_frog_oocyte_progesterone_7hr_EDTA_sucrose_cushion_input_Tail_seq

description: Direct ligaion to total RNA, followed by reverse transcription and PCR amplification with library-specific primers. Input for sucrose cushion.


title: N60_PASmos_library_frog_oocyte_progesterone_7hr_sucrose_cushion_pellet_Tail_seq

description: Direct ligaion to total RNA, followed by reverse transcription and PCR amplification with library-specific primers. Pellet for sucrose cushion.


title: N60_PASmos_library_frog_oocyte_progesterone_7hr_EDTA_sucrose_cushion_pellet_Tail_seq


title: N60_PASmos_library_frog_oocyte_progesterone_7hr_sucrose_cushion_input_Tail_seq


title: N60_PASmos_library_frog_oocyte_progesterone_5hr_sucrose_cushion_input_Tail_seq

value: 10 uM progesterone 5 hours


title: N60_PASmos_library_frog_oocyte_progesterone_3hr_sucrose_cushion_pellet_Tail_seq

value: 10 uM progesterone 3 hours


title: N60_PASmos_library_frog_oocyte_progesterone_3hr_sucrose_cushion_input_Tail_seq


title: N60_PASmos_library_frog_oocyte_ethanol_7hr_sucrose_cushion_pellet_Tail_seq

value: 0.1% ethanol 7 hours


title: N60_PASmos_library_frog_oocyte_ethanol_3hr_sucrose_cushion_pellet_Tail_seq

value: 0.1% ethanol 3 hours


title: N60_PASmos_library_frog_oocyte_progesterone_7hr_Tail_seq


title: N60_PASmos_library_frog_oocyte_ethanol_5hr_sucrose_cushion_pellet_Tail_seq

value: 0.1% ethanol 5 hours


title: N60_PASmos_library_frog_oocyte_progesterone_5hr_Tail_seq


title: N60_PASmos_library_frog_oocyte_progesterone_3hr_Tail_seq


title: N60_PASmos_library_frog_oocyte_ethanol_3hr_sucrose_cushion_input_Tail_seq


title: N60_PASmos_library_frog_oocyte_uninjected_Tail_seq


title: N60_PASmos_library_frog_oocyte_progesterone_1hr_Tail_seq

value: 10 uM progesterone 1 hour


title: N60_PASmos_library_frog_oocyte_ethanol_5hr_sucrose_cushion_input_Tail_seq


title: YU-030 PDX, residual, rep3

status: Public on Feb 06 2024

city: New Haven

first: Bomiao

last: Hu

state: CT

address: 310 Cedar Street

institute: Yale University

data_processing:
Sequencing reads were trimmed of adaptor sequences using Trim Galore.
Reads were mapped to a combined human (hg38) and mouse (mm10) genome using STAR to separate the components of the two species and to a combined transcriptome (GENCODE v24 for human, vM10 for mouse) to add gene annotation.
The uniquely mapped reads were counted per annotation using featureCounts.
The counting matrix went through DESeq2 package to identify the genes that are differentially expressed between different conditions.
Assembly: Hybrid human (hg38) and mouse (mm10) genome
Supplementary files format and content: csv files including RPKM values for each gene in different PDXs

source_name: Patient-derived xenograft

growth_protocol: Dissociated PDX tissues were implanted subcutaneously into NSG mice. Treatment was started as the tumors grew to appropriate size.

extract_protocol:
Total RNA was extracted from tissue powder using AllPrep DNA/RNA mini kit (Qiagen, 80204).
RNA-seq libraries were constructed using KAPA mRNA HyperPrep Kit (Kapa Biosystems, KR1352).

treatment_protocol: Mice were treated with with osimertinib at 25mg/kg for five consecutive days each week. The treatment lasted for 6 weeks before drug tolerant residual tumor was excised.

value: Patient-derived xenograft

value: Osimertinib for 6 weeks


title: N60_PASmos_library_frog_embryo_stage_10_8hr_post_injection_Tail_seq

value: None, stage 10


title: YU-030 PDX, residual, rep1


title: N60_PASmos_library_frog_embryo_stage_3_1hr_post_injection_Tail_seq

value: Sythetic mRNA reporter library

value: None, stage 3


title: YU-030 PDX, untreated, rep2

value: Untreated


title: N60_PASmos_library_frog_oocyte_progesterone_5hr_sucrose_cushion_pellet_Tail_seq


title: YU-030 PDX, untreated, rep1


title: Organoid_LPM(-)FGF10_biol_rep_2

status: Public on Jan 31 2024

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Pre-processed (post adapter and low-quality sequence removal) paired-end raw fastq sequences received from Nonogene Inc. were analyzed using FastQC 0.11.9 for quality assurance, and aligned against Sus scrofa 11.1 genome using the STAR aligner 2.7.10b in “GeneCounts” mode. Alignment quality for each sample was checked using MultiQC 1.14. Post-quality assurance, the resulting BAM files from STAR aligner were run through featureCounts in “countReadPairs” mode to obtain gene-wise transcript counts for each sample. A gene-wise count matrix was compiled for samples pertaining to each analysis (e.g Organoids Vs Foliate etc.) and subjected to subsequent differential gene expression analysis using DESeq2 available in Bioconductor version 3.17
Assembly: Sus scrofa 11.1
Supplementary files format and content: All processed data files are the default ouput of featureCounts software in txt format

organism: Sus scrofa

source_name: Foliate cell line

growth_protocol: The plated organoid cultures were fed with 2ml fresh LPM every 48hrs. LPM was made by adding the following peptides and small molecules to LGR6 base media (LBM); EGF (50 ng/ml), FGF10 (100 ng/ml), FGF2 (10 ng/ml), R-Spondin-2 (500 ng/ml), Noggin (100 ng/ml), Human SHH (100 ng/ml), Y-27632 (10µM) from Peprotech, hu-Wnt3a (100 ng/ml) from R&D Systems, Insulin (10nM) from Gibco, A-83-01 (0.5µM), SB202190 (10µM), CHIR99021 (2.5µM), Prostaglandin E2 (20nM) from BioGems, Forskolin (1µM) from Tocris, and N-Acetyl-Cysteine (1.25µM), Nicotinamide (10mM) from Sigma-Aldrich. LBM was made by adding the following to DMEM/F12 GlutaMAX from Gibco; Hepes (10mM) and B27 insulin free (2%) from Gibco, N21 Max insulin free (2%) from R&D Systems and Primocin (10µg/ml) from Invivogen

extract_protocol:
Organoid harvesting from 6-well/12-well plates was done using the Cultrex™ Organoid Harvesting Solution (Cat 3700-100-01). Briefly; working on ice the cell culture media was gently aspirated and each well was washed with PBS (2ml/1ml). 1ml of the organoid harvesting solution was added to each well, the domes gently dislodged using a cell scraper/lifter and incubated for 1hr at 4C0 on a rocking shaker (Reliable Scientific Inc.) at a speed of 50, for BME digestion. Post incubation, the organoids were spun down and washed three times with 1ml PBS. Each spin down was done at 400g for 4mins at 4C0. The palleted organoids from each well were lysed in 600µl of RLT Plus lysis buffer (Qiagen) with 6µl of ß-mercaptoethanol (Sigma Life Science Cat# 63689-100ML-F)  and homogenized using ~200µl of  1.0mm Zirconia (BioSpec Cat# 11079110ZX) beads with a single 30 second, 6,000 rpm cycle on a Precellys24 homogenizer (Bertin Corp). Homogenized solution was spun down for 20mins at 8000rpm prior to RNA isolation using RNEasy Plus Mini Kit (Qiagen Cat# 74134/74136) according to manufacturer’s protocol. FP were homogenized in the Extraction Buffer provided in the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems Cat# 12204-01) using the same bead based method described above. RNA extraction followed the recommended Arcturus™ PicoPure™ RNA Isolation Kit protocol without performing the DNAse step since TaqMan probes are at the junctions of gene exons
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Foliate cell line

value: Stem cells/mature taste cells


title: Organoid_LPM_biol_rep_3

value: LPM


title: Organoid_LPM(-)FGF10_biol_rep_3


title: N60_PASmos_library_frog_oocyte_ethanol_7hr_sucrose_cushion_input_Tail_seq


title: Foliate_Organoid_Pig5


title: Organoid_LPM_biol_rep_2


title: Organoid_LPM(-)FGF10_biol_rep_1


title: Foliate_Organoid_Pig4


title: Organoid_LPM_biol_rep_1


title: Foliate_Organoid_Pig2


title: Foliate_Organoid_Pig1


title: Foliate_native_tissue_Pig5

source_name: Foliate tissue

value: Foliate tissue


title: Foliate_Organoid_Pig3


title: YU-030 PDX, residual, rep2


title: Foliate_native_tissue_Pig3


title: Foliate_native_tissue_Pig2


title: Foliate_native_tissue_Pig4


title: Periscope-scRNA-V2mod-Periscope-P07-D0-PL225-15559

status: Public on Jan 21 2024

city: Nijmegen

first: Dimitri

last: Diavatopoulos

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboud University Medical Center

description: 384-well plate containing assorted innate immune cells

data_processing:
Raw FASTQ files (Read1 contains the 8-nucleotide barcode + 8nt UMI and Read2 contains the mRNA sequence) for each plate were mapped to the human transcriptome (HG38) concatanated with ERCC sequences using the STAR aligner v2.7.0f (--limitBAMsortRAM 10000000000 --outSAMmapqUnique 255 --outSAMmultNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outFilterMatchNmin 16 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outStd BAM_SortedByCoordinate --limitBAMsortRAM 10000000000)
Uniquely mapped reads were manually demultiplexed per cell using the known cell barcodes (supplementary file: cell.barcodes.384.txt), of which the mapping to specific wells in the 384-well plate is known (supplementary file: Cell_barcodes_distribution.xlsx).
Unique RNA molecules were manuually counted per cell and summed per gene using the UMI sequence.
Since the mapping of cell types to well positions is known (Supplementary file: Sort_layout.csv), cells were manually labelled according to cell type.
Genome_build: GRch38
Supplementary_files_format_and_content: csv file containing raw gene counts for every gene and every cell. Column names are for each cell, and contain all important metatdata (Plate number, well, cell type, subjectID, Day, and batch)

source_name: Innate immune cells

extract_protocol:
RNA extraction of single-cells in 384 well plates was performed the SORTseq protocol (Muraro et al. 2016), a modified version of the original CEL-Seq2 protocol (Hashimshony, T. et al 2016).
Library preparation was performed per 284-well plate according to the SORTseq protocol (Muraro et al. 2016), a modified version of the original CEL-Seq2 protocol (Hashimshony, T. et al 2016).
RNAseq, libraries were sequenced for on average 30 million reads using NextSeq 500 sequencer.

treatment_protocol: Fresh whole blood was drawn into tubes containing lithium heparin as an anticoagulant. Subsequently, blood was treated with ammonium-chloride-potassium red blood cell lysis buffer for 15 minutes at room temperature, washed,  and then stained with a panel of fluorescently labelled antibodies for single-cell sorting.

value: Contains CD14+ CD16+/- monocytes, CD14- CD16+ monocytes, myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, and neutrophils

value: whole blood

tag: day

value: Day 0

tag: plate code

tag: batch

value: Batch 2


title: Foliate_native_tissue_Pig1


title: Periscope-scRNA-V2mod-Periscope-P07-D1-PL231-15560

value: Day 1


title: Periscope-scRNA-V2mod-Periscope-P05-D1-PL210-15556


title: Periscope-scRNA-V2mod-Periscope-P06-D1-PL213-15558


title: iPSC-derived HOs cultured in three conditions

status: Public on Jan 24 2024

city: Galveston

first: Tatiana

middle: L

last: Fonseca

state: TX

department: Internal Medicine

institute: The University of Texas Medical Branch

description: Parse Bioscience

data_processing:
Parse Bioscience pipeline suite 1.0.4 (https://support.parsebiosciences.com/hc/en-us/articles/360052845451-How-do-I-process-my-data), mkref option used to created the reference genome index (STAR-based)
Parse Bioscience pipeline suite 1.0.4, mode-all option to demultiplex, process barcodes, map  reads and generate the transcript counts per cell
Assembly: GRCh38.108 (hg38)
Supplementary files format and content: barcodes_well_sample.csv: csv table with barcodes and sample per well
Supplementary files format and content: barcode_data.xlsx: Excel file with barcodes per round of barcode tag.
Supplementary files format and content: all_genes.csv: CSV table with features information, gene ENSEMBL ID, name and reference
Supplementary files format and content: cell_metadata.csv: csv tables with metadata for each cell per sample and barcodes per cell
Supplementary files format and content: DEG.mtx: Matrices in matrix market format with counts of transcripts per cell in filtered genes.

source_name: hiPSC-derived Hepatic Organoids

growth_protocol: Human iPSCs were obtained from the Cedars-Sinai Core (CS03iCTR-n3) and cultured on 6 well-plates (coated with Matrigel (Corning)), using serum-free mTeSR+ (Stem Cell Tech-nologies) medium. iPSC culture plates were at 37ºC and 5% CO2. Divergence among the number of passages is three or under of passages is three or under.  Differentiation used the serum-free reagent cocktails (C1-6) previously described in (40). In summary, Day-0 (D-0) iPSCs were treated with STEMdiff™ Definitive Endoderm Kit (Stem Cell Technologies) (C1) containing 50 µM Y-27632 (Tocris) to form differentiated into definitive endoderm (DE). D-4 cells were then treated with 1x Glutamax supplement (Gibco), 1x B27 supplement (Gibco), 20 ng/mL BMP4 (R&D Systems), and 10 ng/mL FGF2 (R&D Systems) in Advanced DMEM/F12 (C2) for 6 days to form the posterior fore-gut (PFG) cells. Subsequently, D-10 cells were lifted using TrypLE™ Express Enzyme (Gib-co) and split into 96 well-plates ultra-low-attachment (ULA, Corning) at 30,000 cells/well in medium (advanced DMEM/F12, including 1x N2 supplement (Gibco), 1x B27, 50 nM A83-01 (Tocris), 30 µM Dexamethasone (Tocris), 5 µM CHIR99021 (Tocris), 500 nM valproic acid (R&D Systems), 50 ng/mL human epidermal growth factor (EGF) (R&D Systems), 20 ng/mL human hepatocyte growth factor (HGF) (R&D Systems), 40 ng/mL Jagged-1 (R&D Systems), 300 ng/mL dbCAMP (Sigma-Aldrich) and 10 µM nico-tinamide (Tocris)) containing 1x Matrigel for 8 days, to promote reorganization into a he-patic intermediate stage. Organoids were then gathered in 6 well-plates ULA (10 organ-oids per well) kept on a multi-platform shaker (Fisherbrand) at 65 rpm, in a modified C3 medium (valproic acid was removed and 25 ng/mL FGF7 (R&D Systems), 50 ng/mL BMP4, and 20 ng/mL BMP7 (R&D Systems) were incorporated (C4)) for the next 8 days. For the hepatic organoids maturation, we used the same reagents as in C4, reducing to 2 µM CHIR99021 and 20 ng/mL BMP4 and removing Jagged-1 (C5). Following 12 days, BMP4, BMP7, and FGF7 were substituted by 25 ng/ml FGF19 (R&D Systems), and 5 µM DAPT (Tocris) for another 8 more days (C6).

extract_protocol:
The reagents were prewarmed at 37ºC. Six organoids (D-45) were recollected in a 15 mL polypropylene (Falcon) tube to wash with PBS twice or thrice. As a dissociation reagent, 1 mL of trypsin 0.5% - EDTA (10X) (Gibco) with 50 µM Y-27632 (Gibco), 40 U/µL RNase inhibitor (Invitrogen), and 1 U DNase I (Thermo Scientific) was added to the organoids and kept on 37ºC in a Vari-Mix™ Platform Rocker (Thermo Fisher) at 30 rpm for 15 min. Every 5 min, we mechanically disrupted the organoids till it was homogenized into single cells. Afterward, we proceeded to the inactivation of trypsin with 1 mL Advanced DMEM/F12 mix containing Bovine Albumin Fraction V (7.5% solution, Gibco) 50 µM Y-27632 (Gibco), 40 U/µL RNase inhibitor (Invitrogen), and 1 U DNase I (Thermo Scientific). We collected and filtered the 2 mL through a 40 µm Cell Strainer (Corning) into a 50 mL tube (Falcon). We then add another 1 mL Advanced DMEM/F12 mix to recover any left cells from the strainer. We carried out the fixation of at least 10^5 required single cells, following the protocol described in the EvercodeTM fixation kit (Parse Bioscience).
Library construction was performed under manufacturer's protocol (Parse Bioscience)

treatment_protocol: iPSC-derived HOs were cultured in three conditions: without thyroid hormones (V-HOs), with free T4 at ~15 pM (T4-HOs) or free T3 at ~10 pM (T3-HOs). Six iPSC-derived HOs were dissociated into single cells at day 45.

value: hiPSC-derived Hepatic Organoids

value: hiPSC

tag: Sex

value: male

value: mixed sample (without thyroid hormones, free T4 at ~15 pM, and free T3 at ~10 pM)

tag: time

value: Day 45


title: Periscope-scRNA-V2mod-Periscope-P06-D0-PL201-15557


title: Periscope-scRNA-V2mod-Periscope-P05-D0-PL200-15555


title: Periscope-scRNA-V2mod-Periscope-P04-D1-PL290-15554


title: Periscope-scRNA-V2mod-Periscope-P04-D0-PL276-15553


title: Periscope-P06-D1-PL217-15125

value: Batch 1


title: Periscope-P07-D1-PL233-15127


title: Periscope-scRNA-V2mod-Periscope-P03-D1-PL288-15552


title: Periscope-P06-D0-PL205-15124


title: Periscope-scRNA-V2mod-Periscope-P03-D0-PL274-15551


title: Periscope-P05-D0-PL204-15122


title: Periscope-P05-D1-PL215-15123


title: Periscope-scRNA-V2mod-Periscope-P02-D1-PL251-15550


title: Periscope-P07-D0-PL227-15126


title: Periscope-P04-D1-PL294-15121


title: Periscope-P04-D0-PL280-15120


title: Periscope-P01-D1-PL254-15093


title: Periscope-P02-D1-PL255-15094


title: Periscope-P03-D0-PL278-15095


title: Periscope-P01-D0-PL243-15092


title: Periscope-scRNA-V2mod-Periscope-P01-D1-PL249-15547


title: Periscope2_s169_S169_R1_001

data_processing:
Raw FASTQ files were bioinformatically depleted of low-priority sequences that were found to be overrepresented using FASTQC: Poly-G sequences (l > 21), ribosomal 45S rRNA, ribosomal protein S29, RN7SK, hemoglobin and mitochondrial gene sequences, and an unknown gene sequence (l = 63). Before alignment, BBTools was used to filter these sequences from reads and remove low quality (q < 20) and short (l < 40) reads. Reads were then mapped to the human transcriptome (HG38) using the STAR aligner v2.7.0f (default settings) and summation of gene counts per sample was performed with featureCounts v1.6.5 (default settings)
Assembly: GRch38
Supplementary files format and content: .csv file containing raw gene counts for every gene and every sample. Column names are sample names

source_name: Whole blood

extract_protocol:
RNA was isolated from blood samples stored in Paxgene tubes according to the manufacturers’ instructions (Qiagen)
Globin transcripts in blood RNA were blocked with the Ribo-Zero Globin (Illumina) before library preparation. Libraries were prepared using the TruSeq Stranded Total RNA library preparation kit (Illumina)
RNA-Seq, libraries were sequenced on an Illumina Next Seq 550.

value: Whole blood


title: Periscope2_s171_S171_R1_001


title: Periscope2_s168_S168_R1_001


title: Periscope2_s170_S170_R1_001


title: Periscope2_s166_S166_R1_001


title: Periscope-P02-D0-PL244-15097


title: Periscope-scRNA-V2mod-Periscope-P01-D0-PL239-15546


title: Periscope-P03-D1-PL292-15096


title: Periscope2_s163_S163_R1_001


title: Periscope2_s162_S162_R1_001


title: Periscope-scRNA-V2mod-Periscope-P02-D0-PL240-15549


title: Periscope2_s160_S160_R1_001


title: Periscope2_s164_S164_R1_001


title: Periscope2_s157_S157_R1_001


title: Periscope2_s158_S158_R1_001


title: Periscope2_s159_S159_R1_001


title: Periscope2_s154_S154_R1_001


title: Periscope2_s155_S155_R1_001


title: Periscope2_s152_S152_R1_001


title: Periscope2_s150_S150_R1_001


title: Periscope2_s156_S156_R1_001


title: Periscope2_s151_S151_R1_001


title: Periscope2_s149_S149_R1_001


title: 115_BK047_Day 0

data_processing:
Raw FASTQ files were bioinformatically depleted of low-priority sequences that were found to be overrepresented using FASTQC: Poly-G sequences (l > 21), ribosomal 45S rRNA, ribosomal protein S29, RN7SK, hemoglobin and mitochondrial gene sequences, and an unknown gene sequence (l = 63). Before alignment, BBTools was used to filter these sequences from reads and remove low quality (q < 20) and short (l < 40) reads. Reads were then mapped to the human transcriptome (HG38) using the STAR aligner v2.7.0f (default settings) and summation of gene counts per sample was performed with featureCounts v1.6.5 (default settings)
Genome_build: GRch38
Supplementary_files_format_and_content: .csv file containing raw gene counts for every gene and every sample. Column names are sample names

extract_protocol:
RNA was isolated from blood samples stored in Paxgene tubes according to the manufacturers’ instructions (Qiagen)
Globin transcripts in blood RNA were blocked with the Ribo-Zero Globin (Illumina) before library preparation. Libraries were prepared using the TruSeq Stranded Total RNA library preparation kit (Illumina)


title: 112_BK142_Day 1


title: Periscope2_s161_S161_R1_001


title: 108_BK044_Day 1


title: 114_BK143_Day 1


title: 113_BK048_Day 1


title: 111_BK041_Day 1


title: 105_BK039_Day 1


title: 102_BK038_Day 1


title: 107_BK043_Day 1


title: 104_BK041_Day 0


title: 101_BK045_Day 1


title: 109_BK040_Day 1


title: Periscope2_s167_S167_R1_001


title: 100_BK048_Day 0


title: 106_BK042_Day 1


title: 103_BK037_Day 0


title: Periscope2_s153_S153_R1_001


title: 97_BK047_Day 1


title: 98_BK141_Day 1


title: 96_BK040_Day 0


title: 95_BK038_Day 0


title: Periscope2_s148_S148_R1_001


title: 94_BK143_Day 0


title: 93_BK045_Day 0


title: 91_BK044_Day 0


title: Periscope2_s165_S165_R1_001


title: 90_BK043_Day 0


title: 110_BK037_Day 1


title: WT HTZ1-FLAG IP rep 1

status: Public on Jan 13 2024

city: Stony Brook

first: Ed

last: Luk

state: NY

address: 100 Nicolls Rd, Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

description:
LP003
LP003-LP006_v3.bw
WT-swc2_mean_v3.bw
LP003-LP009_mean_v3.bw

data_processing:
Sequencing libraries were pooled and analyzed on a NextSeq 550 platform using paired-end mode with 32 cycles on both ends.
Sequencing data (FASTQ files) were mapped to the S. cerevisiae S288C genome version R64-1-1 using Bowtie2 with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 120 and -X 170
Mapped reads were filtered using Samtools-view with options -q 30 -F 0x4.
Read coverage were calculated using bamCoverage in deepTools with options -binSize 1 -- extendReads --effectiveGenomeSize 11756462 --scaleFactor X (to Read Per Millions) -- blackListFileName Mask_v2.bed (which indicated repetitive sequences in the BED format)
Assembly: R64-1-1
Supplementary files format and content: bigwig format

organism: Saccharomyces cerevisiae

source_name: SWC2 HTZ1-2xFLAG

growth_protocol: Logarithmically growing cells (at 0.5 OD600) cultured in 2 L yeast extract peptone dextrose (YPD) media.

extract_protocol:
Cells were spheroplasted to 80% completion using glucanase and dounced homogenized. Crude chromatin was pelleted by centrifugation and Mnase digested. Solubilized nucleoproteins represent the input fraction of the IP reaction. The input was applied to anti-FLAG M2 affinity gel. The unbound materials were collected as the flow through fraction. The IP fraction represents the eluate after FLAG peptide incubation. Nucleosomal DNA was extracted and purified by the QIAquick spin column (Qiagen)
Sequencing libraries were prepared using the NEBNext Ultra II DNA library prep kit according to the manufacturer protocol (NEB).

treatment_protocol: Yeast cells were harvested by centrifugation, washed, aliquoted, and flash frozen

value: SWC2 HTZ1-2xFLAG

value: yeast

value: anti-flag ChIP-seq


title: 88_BK039_Day 0


title: swc2 HTZ1-FLAG IP rep 1

description:
LP006
LP003-LP006_v3.bw
WT-swc2_mean_v3.bw
LP006-LP012_mean_v3.bw

source_name: swc2delta HTZ1-2xFLAG

value: swc2delta HTZ1-2xFLAG


title: swc2 HTZ1-FLAG IP rep 2

description:
LP012
LP009-LP012_v3.bw
WT-swc2_mean_v3.bw
LP006-LP012_mean_v3.bw


title: WT HTZ1-FLAG IP rep 2

description:
LP009
LP009-LP012_v3.bw
WT-swc2_mean_v3.bw
LP003-LP009_mean_v3.bw


title: SWR Exchange Reaction 15 min FT rep 1

description:
CC015
CC016-CC015_v2.bw
CC_HER_15min_mean.bw

source_name: 2xV5-HHF2 htz1delta swr1delta

value: 2xV5-HHF2 htz1delta swr1delta


title: 99_BK142_Day 0


title: SWR Exchange Reaction 15 min Eluate rep 1

description:
CC016
CC016-CC015_v2.bw
CC_HER_15min_mean.bw


title: SWR Exchange Reaction 15 min FT rep 2

description:
CC017
CC018-CC017_v2.bw
CC_HER_15min_mean.bw


title: SWR Exchange Reaction 30 min Eluate rep 1

description:
CC020
CC020-CC019_v2.bw
CC_HER_30min_mean.bw


title: SWR Exchange Reaction 30 min Eluate rep 2

description:
CC022
CC022-CC021_v2.bw
CC_HER_30min_mean.bw


title: SWR Exchange Reaction 30 min FT rep 1

description:
CC019
CC020-CC019_v2.bw
CC_HER_30min_mean.bw


title: SWR Exchange Reaction 45 min FT rep 1

description:
CC023
CC024-CC023_v2.bw
CC_HER_45min_mean.bw


title: SWR Exchange Reaction 30 min FT rep 2

description:
CC021
CC022-CC021_v2.bw
CC_HER_30min_mean.bw


title: SWR Exchange Reaction 15 min Eluate rep 2

description:
CC018
CC018-CC017_v2.bw
CC_HER_15min_mean.bw


title: SWR Exchange Reaction 45 min Eluate rep 2

description:
CC026
CC026-CC025_v2.bw
CC_HER_45min_mean.bw


title: SWR Exchange Reaction 45 min FT rep 2

description:
CC025
CC026-CC025_v2.bw
CC_HER_45min_mean.bw


title: 92_BK141_Day 0


title: SWR Exchange Reaction 45 min Eluate rep 1

description:
CC024
CC024-CC023_v2.bw
CC_HER_45min_mean.bw


title: NCI-H1975 cells, sgDAMP, ribo-seq, rep2

status: Public on Dec 04 2023

city: Shanghai

first: zhenchuan

last: liu

address: No. 389, Xincun Road

department: Department of Thoracic Surgery

country: China

institute: Shanghai Tongji Hospital Affiliated with Tongji University

description: *library strategy: Ribo-seq

data_processing:
Trimming: Raw reads were subjected to filtering and trimming using Trimmomatic-0.30 based on recommended parameters (Adapter sequences were first trimmed, followed by removing leading pr trailing low quality or N bases, scaning the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 and finally droping reads shorted than minimum length)
Aligning and annotation: Cleaned reads were mapped to genome sequences using HISAT2 (version 2.1.0). The acquired sam files were compressed, sorted and indexed using samtools (version: 1.10). Reads mapped to different genomic features (5'UTR, exon, 3'UTR, CDS) were analyzed and quantified using htseq-count (version 0.11.2).The gene expression level was normalized by using TPM.
Downstream analysis: the edgeR package in R software (http://www.r project.org) was used to conducting differentially expressed genes (DEGs) from obtained count files. Genes with a fold change ≥2 and a false discovery rate (FDR) <0.05 in a comparison were considered as significant DEGs.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited text files including the raw counts for each sample

extract_protocol:
For mRNA-seq, total RNA was isolated using TRIzol (Invitrogen) and quantified by spectrophotometry. For ribo-seq, samples were lysed and subjected to nuclease digestion using the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer's instructions. Lysates were then purified using MicroSpin S-400 HR spin columns (Thermo Fisher). rRNA was then depleted using a Ribo-Zero Plus rRNA Depletion Kit (Illumina).
For mRNA-seq, extracted mRNA was enriched with oligo(dT) beads, subjected to fragmentation, and reverse transcribed into cDNA with random primers. cDNA samples were then purified, subjected to end-repair and oligo(A) added and ligated to Illumina adaptors according to the manufacturer's instructions; For Ribo-seq, rRNA-depleted samples were subjected to purification by PAGE, fragmentation, end repair and 3’ adapter ligation, reverse transcription, and cDNA circularization following a protocol described by Illumina.

treatment_protocol: For ribo-seq, H1975 cells were harvested after treatment with 100 μg/ml cycloheximide.

value: lung adenocarcinoma

value: DAMP knockout


title: NCI-H1975 cells, sgDAMP, ribo-seq, rep3

description: *library strategy: Ribo-seq


title: NCI-H1975 cells, sgControl, ribo-seq, rep3

description: *library strategy: Ribo-seq

value: CRISPR Control


title: NCI-H1975 cells, sgDAMP, ribo-seq, rep1

description: *library strategy: Ribo-seq


title: 89_BK042_Day 0

value: Day 0


title: NCI-H1975 cells, Scramble, ribo-seq, rep2

description: *library strategy: Ribo-seq

value: Scramble


title: NCI-H1975 cells, Scramble, ribo-seq, rep1

description: *library strategy: Ribo-seq


title: NCI-H1975 cells, Scramble, ribo-seq, rep3

description: *library strategy: Ribo-seq


title: NCI-H1975 cells, sgDAMP, input_mRNA, rep3


title: NCI-H1975 cells, sgDAMP, input_mRNA, rep1


title: NCI-H1975 cells, sgControl, input_mRNA, rep1


title: P7_595

status: Public on Nov 09 2023

city: La Jolla

first: Mariko

last: Horii

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.3). Reads were mapped to GRCh38.89 (Ensembl) using STAR (v. 2.5.3a) (Dobin et al., 2013). The STAR parameters used were: --runThreadN 24 --sjdbOverhang 99 --genomeDir ref_ensembl_GRCh38_89/star_index --sjdbGTFtagExonParentGene gene_id --sjdbGTFfile ref_ensembl_GRCh38_89/Homo_sapiens.GRCh38.89.gtf --outSAMtype BAM Unsorted SortedByCoordinate --outReadsUnmapped Fastx --quantMode GeneCounts. Ensembl genes with at least 10 counts in 25% of samples were filtered for the analysis. Normalization and differential expression analysis were performed using R (v. 4.0.3) package DESeq2 (v. 1.30.1) (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID to HUGO gene names (Durinck 2009), and gene set enrichment analysis was done using R (v. 4.0.3) package FGSEA (v. 1.16.0).
Assembly: GRCh38.89(Ensembl)
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample post filtering

source_name: Placenta

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 7.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

value: Placenta

value: African

tag: disease

value: Non-hypertensive control

value: Male


title: NCI-H1975 cells, sgControl, input_mRNA, rep2


title: P7_585

value: European

value: Female


title: NCI-H1975 cells, sgControl, input_mRNA, rep3


title: P679


title: NCI-H1975 cells, sgDAMP, input_mRNA, rep2


title: P687

value: Asian

value: Severe Preeclampsia


title: P660


title: P673


title: NCI-H1975 cells, sgControl, ribo-seq, rep1

description: *library strategy: Ribo-seq


title: P548


title: P1_2969


title: P1_2858


title: P7_2836


title: P1_2591


title: P1_2672


title: NCI-H1975 cells, sgControl, ribo-seq, rep2

description: *library strategy: Ribo-seq


title: P7_2553


title: P7_2371


title: P7_2478


title: P3_2325


title: P1_2263


title: P1_2139


title: P718


title: P7_2109


title: P1958


title: P1956


title: P1950


title: P531


title: P1_2052


title: P1938


title: P1881


title: P1875


title: P7_1907


title: P3_1955


title: P7_1897


title: P9_1805


title: P8_1789


title: P1858


title: P7_2566


title: P1736


title: P9_1796


title: P1_1689


title: P7_1733


title: P9_1672


title: P1666


title: P1719


title: P1653


title: P1620


title: P1586


title: P1584


title: P7_1571


title: P1548


title: P9_1511


title: P1508


title: P1448


title: P1781


title: P1572


title: P3_1536


title: P7_1496


title: P1442


title: P7_1482


title: P1580


title: P1371


title: P7_1382


title: P9_1181


title: P1155


title: P1437


title: P996


title: P990


title: P1028


title: P1_2778


title: P7_988


title: P980


title: P1622


title: P1625


title: P979


title: P976


title: P972


title: P950


title: P7_949


title: P942


title: P1_830


title: P857


title: P818


title: Pr_14354

status: Public on Nov 01 2023

city: Buffalo

first: Henry

middle: G.

last: Withers

state: New York

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Quality control for the raw reads was performed using fastqc
Adapter trimming was done using atropos
Spliced alignments of reads to the reference genome was done using TopHat2 allowing a maximum of 1 mismatch/read
Quality control for this alignment was done using RSeQC
Assembly: Alignment to the mouse genome version mm10
Supplementary files format and content: Raw counts are provided from HTSeq version 0.6.1 using mm10 RefSeq annotation. Columns are sample identifiers, rows are gene symbols in a csv file.

organism: Mus musculus

source_name: Prostate

extract_protocol:
TRIzol total RNA extraction
Illumina TruSeq Stranded Total RNA with RiboZero Gold: The sequencing libraries are prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA.  Following manufacturer’s instructions, the first step depletes rRNA from total RNA.  After ribosomal depletion, the remaining RNA is purified, fragmented and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  AMPure XP beads (Beckman Coulter) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries are amplified by PCR, purified using Ampure XP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).   The DNA libraries are quantitated using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria.

value: Prostate

value: Epithelial

tag: genotype


title: P7_791


title: P801


title: P826


title: P768


title: Pr_14433


title: P7_1162


title: Pr_14345


title: Pr_14273


title: RNAPII-S5P_CUTAC_SL_FLV_8h_(20220509_SB_Mm_050222_SL_FL8_CUTAC)

status: Public on Oct 12 2023

city: Omaha

first: Sandipan

last: Brahma

state: NE

address: 985805 Nebraska Medical Center, DRCI 6054

institute: University of Nebraska Medical Center

description: CUTAC targeting RPB1-S5P in mESCs in SL treated with Flavopridol 8 h

data_processing:
Genome_build: mm10
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked mm10 Mus musculus reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the D. melanogaster alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)

source_name: CUT&Tag

value: Cell Signaling Technology 13523, Antibodies Online ABIN101961

value: AB2.2 mouse embryonic stem cells ATCC SCRC-1023


title: P6_1336


title: RNAPII-S5P_CUTnTag_SL_TRP_2h_(20210326_SB_Mm_ABSL_032421_TR2_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Triptolide 2 h

data_processing:
Genome_build: mm10
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to the UCSC mm10 Mus musculus reference sequence and extracted properly paired fragments from the alignments. 2. We also mapped the reads to NCBI E.coli (Escherichia coli str. K-12 substr. MG1655 U00096.3) with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" and extracted properly paired fragments. 3. We used bedtools 2.30.0 genomecov to make a calibrated mm10 track using E. coli carryover (PMID 31232687) with a scaling factor of (10000/number of fragments mapped to E. coli). (Supplementary file .mm10_ecoli.bw)

extract_protocol:
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827
https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3


title: RNAPII-S5P_CUTnTag_SL_TRP_30m_(20210326_SB_Mm_ABSL_032421_TR30_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Triptolide 30 min


title: RNAPII-RPB3_CUTnTag_SL_(20211229_TL_Mm_AB22_DMSO_Rpb3_TL2_122021)

description: CUT&Tag targeting RPB3 in mESCs in SL

value: Bethyl Laboratories A303-771A, Antibodies Online ABIN101961


title: RNAPII-S5P_CUTAC_SL_0_(20220509_SB_Mm_050222_SL_0_CUTAC)

description: CUTAC targeting RPB1-S5P in mESCs in SL


title: SOX2_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_Sox2)

description: CUT&RUN targeting SOX2 in mESCs in SL

data_processing:
Genome_build: mm10
1. We used Bowtie2 2.4.2 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the paired-end 25bp reads to mm10 Mus musculus reference sequence obtained from UCSC and extracted properly paired fragments. 2. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same reads to Saccharomyces cerevisiae reference sequence obtained from Ensembl masked R64-1-1 and extracted properly paired fragments. 3. We used bedtools 2.30.0 genomecov to make a calibrated mm10 track using the yeast spike-in with a scaling factor of (10000/number of fragments mapped to yeast). (Supplementary file .mm10_yeast.bw)

source_name: CUT&RUN

extract_protocol:
CUT&RUN_Brahma.pdf
CUT&RUN_Brahma.pdf

value: abcam ab192494, Antibodies Online ABIN101961


title: RNAPII-S5P_CUTnTag_SL_FLV_4h_(20210719_SB_MmDmEc_0715_F2_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Flavopiridol 4 h


title: RNAPII-S5P_CUTnTag_SL_FLV_30m_(20210719_SB_MmDmEc_0715_F30_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Flavopiridol 30 m


title: RNAPII-S5P_CUTnTag_SL_FLV_1h_(20210719_SB_MmDmEc_0715_F1_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Flavopiridol 1 h


title: RNAPII-S5P_CUTnTag_SL_DMSO_2_(20210719_SB_MmDmEc_0715_0_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL


title: RNAPII-S5P_CUTnTag_SL_DMSO_(20210326_SB_Mm_ABSL_032421_0_S5P)


title: RNAPII-S5P_CUTnTag_SL_ACT_4h_(20210719_SB_MmDmEc_0715_A4_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Actinomucin D 4 h


title: P850


title: RNAPII-S5P_CUTnTag_SL_ACT_30m_(20210719_SB_MmDmEc_0715_A30_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Actinomucin D 30 m


title: RNAPII-S5P_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_S5P)


title: RNAPII-S5P_CUTnTag_SL_ACT_1h_(20210719_SB_MmDmEc_0715_A1_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Actinomucin D 1 h


title: RNAPII-S5P_CUTnTag_2i_(20200321_SB_Mm_AB2S2i_0319_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in 2i


title: RNAPII-S5P_CUTAC_2i_(20210528_SB_Mm_2i_0506_0_S5_CUTAC)

description: CUTAC targeting RPB1-S5P in mESCs in 2i

data_processing:
Genome_build: mm10
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to the UCSC mm10 Mus musculus reference sequence. 2. We extracted properly paired reads from the alignments. 3.We used bedtools 2.30.0 genomecov to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)


title: RNAPII-S2P_CUTnTag_SL_(20210719_SB_MmDmEc_0715_0_S2P)

description: CUT&Tag targeting RPB1-S2P in mESCs in SL

value: Cell Signaling Technology 13499, Antibodies Online ABIN101961


title: OCT4_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_Oct4)

description: CUT&RUN targeting OCT4 in mESCs in SL

value: abcam ab181557, Antibodies Online ABIN101961


title: OCT4_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_Oct4)

description: CUT&RUN targeting OCT4 in mESCs in 2i


title: RNAPII-S5P_CUTAC_SL_(20210528_SB_Mm_SL_0506_0_S5_CUTAC)

description: CUTAC targeting RPB1-S5P in mESCs in SL


title: NANOG_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_NAN2)

description: CUT&RUN targeting NANOG in mESCs in 2i

value: Bethyl Laboratories A300-397A, Antibodies Online ABIN101961


title: KLF4_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_Klf4)

description: CUT&RUN targeting KLF4 in mESCs in 2i

value: R&D Systems AF3158, Antibodies Online ABIN101961


title: RNAPII-S5P_CUTnTag_SL_TRP_1h_(20210326_SB_Mm_ABSL_032421_TR1_S5P)

description: CUT&Tag targeting RPB1-S5P in mESCs in SL treated with Triptolide 1 h


title: NANOG_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_NAN2)

description: CUT&RUN targeting NANOG in mESCs in SL


title: IgG_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_IgG)

description: CUT&Tag without a primary antibody (control) in mESCs in SL

value: Antibodies Online ABIN101961


title: SOX2_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_Sox2)

description: CUT&RUN targeting SOX2 in mESCs in 2i


title: IgG_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_IgG)

description: CUT&RUN without a primary antibody (control) in mESCs in 2i


title: KLF4_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_Klf4)

description: CUT&RUN targeting KLF4 in mESCs in SL


title: H3K4me1_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_K4m1)

description: CUT&Tag targeting H3K4me1 in mESCs in SL

value: abcam ab8895, Antibodies Online ABIN101961


title: H3K9me3_CUTnTag_SL_(20200526_SB_Mm_G4X40_0514_K9m3)

description: CUT&Tag targeting H3K9me3 in mESCs

value: abcam ab176916, Antibodies Online ABIN101961


title: H3K4me3_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_K4m3)

description: CUT&Tag targeting H3K4me3 in mESCs in SL

value: Active Motif 39915, Antibodies Online ABIN101961


title: H3K27me3_CUTnTag_SL_DMSO_(20210702_SB_Mm_0625_0_K27m)

description: CUT&Tag targeting H3K27me3 in mESCs in SL

value: Cell Signaling Technology 9733, Antibodies Online ABIN101961


title: IgG_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_IgG)

description: CUT&RUN without a primary antibody (control) in mESCs in SL


title: BRG1_IgG_CUTnRUN.ChIP_SL_FLV_(20210628_SB_MmSc_0620_FL8_Brg_IgG)

description: CUT&RUN targeting BRG1 followed by native ChIP with isotype control antibody in mESCs treated with Flavopiridol 8 h in SL

value: abcam ab110641, Antibodies Online ABIN101961, ab172730


title: H3K27me3_CUTnTag_SL_FLV_8h_(20210702_SB_Mm_0625_FL8_K27m)

description: CUT&Tag targeting H3K27me3 in mESCs treated with Flavopiridol 8 h


title: H3K27me3_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_K27m3)


title: BRG1_IgG_CUTnRUN.ChIP_2i_(20210104_SB_MmScEc_2i_1217_BRG1_IgG)

description: CUT&RUN targeting BRG1 followed by native ChIP with isotype control antibody in mESCs in 2i


title: BRG1_H3K4me3_CUTnRUN.ChIP_SL_FLV_(20210628_SB_MmSc_0620_FL8_Brg_K4m3)

description: CUT&RUN targeting BRG1 followed by H3K4me3 native ChIP in mESCs treated with Flavopiridol 8 h in SL

value: abcam ab110641, Antibodies Online ABIN101961, EpiCypher 13-0028


title: BRG1_IgG_CUTnRUN.ChIP_SL_DMSO_(20210628_SB_MmSc_0620_0_Brg_IgG)

description: CUT&RUN targeting BRG1 followed by native ChIP with isotype control antibody in mESCs in SL


title: BRG1_H3K4me3_CUTnRUN.ChIP_SL_DMSO_(20210628_SB_MmSc_0620_0_Brg_K4m3)

description: CUT&RUN targeting BRG1 followed by H3K4me3 native ChIP in mESCs in SL


title: BRG1_H3K4me3_CUTnRUN.ChIP_2i_(20210104_SB_MmScEc_2i_1217_BRG1_K4m3)

description: CUT&RUN targeting BRG1 followed by H3K4me3 native ChIP in mESCs in 2i


title: BRG1_H3K4me1_CUTnRUN.ChIP_SL_FLV_(20210628_SB_MmSc_0620_FL8_Brg_K4m1)

description: CUT&RUN targeting BRG1 followed by H3K4me1 native ChIP in mESCs treated with Flavopiridol 8 h in SL

value: abcam ab110641 Antibodies Online ABIN101961, abcam ab8895


title: BRG1_H3K4me3_CUTnRUN.ChIP_SL_(20210104_SB_MmScEc_SL_1217_BRG1_K4m3)


title: BRG1_H3K27me3_CUTnRUN.ChIP_SL_DMSO_(20210628_SB_MmSc_0620_0_Brg_K27m3)

description: CUT&RUN targeting BRG1 followed by H3K27me3 native ChIP in mESCs in SL

value: abcam ab110641, Antibodies Online ABIN101961, Cell Signaling Technology 9733


title: BRG1_H3K27me3_CUTnRUN.ChIP_SL_(20210104_SB_MmScEc_SL_1217_BRG1_K27m3)


title: BRG1_IgG_CUTnRUN.ChIP_SL_(20210104_SB_MmScEc_SL_1217_BRG1_IgG)


title: BRG1_H3K27me3_CUTnRUN.ChIP_SL_FLV_(20210628_SB_MmSc_0620_FL8_Brg_K27m3)

description: CUT&RUN targeting BRG1 followed by H3K27me3 native ChIP in mESCs treated with Flavopiridol 8 h in SL


title: BRG1_CUTnTag_SL_TRP_30m_(20210326_SB_Mm_ABSL_032421_TR30_BRG)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Triptolide 30 min

value: abcam ab110641, Antibodies Online ABIN101961


title: BRG1_H3K27me3_CUTnRUN.ChIP_2i_(20210104_SB_MmScEc_2i_1217_BRG1_K27m3)

description: CUT&RUN targeting BRG1 followed by H3K27me3 native ChIP in mESCs in 2i

value: AB2.2 mouse embryonic stem cells ATCC SCRC-1023


title: BRG1_CUTnTag_SL_FLV_4h_(20210719_SB_MmDmEc_0715_F4_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Flavopiridol 4 h


title: BRG1_CUTnTag_SL_FLV_1h_(20210719_SB_MmDmEc_0715_F1_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Flavopiridol 1 h


title: BRG1_CUTnTag_SL_ACT_4h_(20210719_SB_MmDmEc_0715_A4_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Actinomucin D 4 h


title: BRG1_CUTnTag_SL_TRP_2h_(20210326_SB_Mm_ABSL_032421_TR2_BRG)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Triptolide 2 h


title: BRG1_CUTnTag_SL_FLV_30m_(20210719_SB_MmDmEc_0715_F30_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Flavopiridol 30 m


title: BRG1_CUTnTag_SL_ACT_1h_(20210719_SB_MmDmEc_0715_A1_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Actinomucin D 1 h


title: BRG1_CUTnTag_SL_ACT_30m_(20210719_SB_MmDmEc_0715_A30_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Actinomucin D 30 m


title: BRG1_CUTnTag_2i_(20200321_SB_Mm_AB2S2i_0319_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in 2i


title: BRG1_CUTnRUN_SL_DMSO_(20210628_SB_MmSc_0620_0_Brg_in)

description: CUT&RUN targeting BRG1 in mESCs in SL


title: BRG1_CUTnRUN_SL_(20210104_SB_MmScEc_SL_1217_BRG1_in)

description: CUT&RUN targeting BRG1 in mESCs in SL


title: BRG1_CUTnTag_SL_DMSO_(20210326_SB_Mm_ABSL_032421_0_BRG)

description: CUT&Tag targeting BRG1 in mESCs in SL


title: BRG1_CUTnTag_SL_DMSO_2_(20210719_SB_MmDmEc_0715_0_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL


title: BRG1_CUTnRUN_SL_FLV_(20210628_SB_MmSc_0620_FL8_Brg_in)

description: CUT&RUN targeting BRG1 in mESCs in SL treated with Flavopiridol 8 h


title: BRG1_H3K4me1_CUTnRUN.ChIP_SL_DMSO_(20210628_SB_MmSc_0620_0_Brg_K4m1)

description: CUT&RUN targeting BRG1 followed by H3K4me1 native ChIP in mESCs in SL

value: abcam ab110641, Antibodies Online ABIN101961, abcam ab8895


title: S8tetMYCDOXPOS_3

status: Public on Oct 11 2023

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2)
Reads were mapped to human genome (GRCh38) by STAR (version 2.7.3a)
The number of fragments in each known gene from GENCODE (version 25) were quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data in supplementary tab-delimited file contains a matrix of raw read counts for each gene accession number (rows) and sample (columns)

source_name: epithelial breast

growth_protocol: For 2D growth, human BT-549 BRCA1 wild-type TNBC (ATCC) cells were cultured in RPMI1640 medium (Thermo Fisher Scientific) containing 10% fetal bovine serum (GEMINI BioProducts), 100 µg/ml streptomycin, 100 U/ml penicillin and 10 µg/ml insulin. For culture of 3D mammospheres, BT-549 cells were seeded at 2.5-5×103/well in 6-well ultra-low attachment culture plates (Corning) using the MammoCult Human Medium Kit (Stemcell Technologies).

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
TruSeq Stranded mRNA (Illumina) was used for library preparation

value: epithelial breast

value: TNBC cell line

value: WT

value: 500 ng/ml doxycycline

tag: growth format

tag: shRNA

value: tet-MYCshRNA

tag: shRNA info

value: MISSION shRNA TRCN0000039642


title: S8tetMYCDOXPOS_2


title: BRG1_H3K4me1_CUTnRUN.ChIP_SL_(20210104_SB_MmScEc_SL_1217_BRG1_K4m1)


title: S8tetMYCDOXPOS_1


title: BRG1_H3K4me1_CUTnRUN.ChIP_2i_(20210104_SB_MmScEc_2i_1217_BRG1_K4m1)

description: CUT&RUN targeting BRG1 followed by H3K4me1 native ChIP in mESCs in 2i


title: S8tetMYCDOX-_3

value: 0.1% DMSO


title: S8tetMYCDOX-_2


title: BRG1_CUTnTag_SL_TRP_1h_(20210326_SB_Mm_ABSL_032421_TR1_BRG)

description: CUT&Tag targeting BRG1 in mESCs in SL treated with Triptolide 1 h


title: S8tetMYCDOX-_1


title: BT549-S6-t8-DOXplus_3

value: MISSION shRNA TRCN0000122938


title: BT549-S6-t8-DOXplus_2


title: BT549-S6-t8-DOX-_1


title: BRG1_CUTnTag_SL_(20200321_SB_Mm_AB2SL_0319_BRG1)

description: CUT&Tag targeting BRG1 in mESCs in SL


title: BT549_S6_GO-203_3