title: Sorted life cells, Bone Marrow, patient1, plate TM961

description: Matrix column names (see plate_wellid) start with: TM961_


title: myeloid cells, wt2

status: Public on Sep 30 2024

type: SRA

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: myeloid cells

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: tissue

value: myeloid cells

tag: genotype

value: wt


title: Sorted life cells, Bone Marrow, patient7, plate TM922

status: Public on Sep 13 2024

city: Utrecht

first: Arjan

last: Boltjes

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center

description: Matrix column names (see plate_wellid) start with: TM922_

library_source: transcriptomic single cell

data_processing:
Raw data was processed with the Sharq pipeline as previously reported: https://www.biorxiv.org/content/10.1101/250811v2
Read mapping was performed using STAR (v2.6.1), on the hg38 Patch 10 human genome
Function featureCounts (v1.5.2) was used to assign reads based on GENCODE (v26) to generate count tables
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: matrix.mtx.gz is a gzipped matrix file built from a sparse matrix in R – as is the usual case with this type of files, second row contains totals for 1. features, 2. cells, 3. non-zero values, third row and further contain 1. row index (features), 2. column index (plate and well ID, 3. counts
Supplementary files format and content: features.tsv.gz is a gzipped tab-delimited text file – this contains the row names of the original sparse matrix; the row indices in matrix.mtx refer to the rows in this file
Supplementary files format and content: plate_wellid.tsv.gz is a gzipped tab-delimited text file – this contains the column names of the original sparse matrix; the column indices in matrix.mtx refer to the rows in this file

organism: Homo sapiens

source_name: Bone marrow including tumour

extract_protocol:
We have made use of the SORT-seq protocol, which is a partially robotized version of the CEL-seq2 protocol, for scRNA-seq. There is no RNA extraction in the classical sense: the cells within the wells are lysed by heat, and the aformentioned primers will hybridize to the poly-A tail of the mRNAs
The following steps take place after primer hybridization: reverse transcription & second-strand synthesis, pooling of wells (one cell per well), in vitro transcription, fragmentation and reverse transcription, PCR amplification of DNA, addition of sequencing adapters: cDNA libraries ready

treatment_protocol: Adrenal gland tissue was cut up and incubated with collagenase I, II and IV for up to one hour, filtered, washed, further dissociated with a dissociation kit. Bone marrow cells did not need dissociation, but were filtered and washed. Cells from both tissues were then FACS sorted into 384-well plates containing 10 μL of mineral oil, 50 nL of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike-Ins. Plates were spun down, snap‐frozen on dry ice, and stored in ‐800C until further processing

value: Bone marrow including tumour

tag: cell type

value: Mixed, but barcoded

tag: treatment

value: None, directly ex vivo


title: Sorted life cells, Bone Marrow, patient3, plate TM907

description: Matrix column names (see plate_wellid) start with: TM907_


title: C42B_siFOXA1

status: Public on Sep 25 2024

city: Sacramento

first: yatian

last: yang

state: CA

country: USA

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

tag: cell line

value: prostate cancer

value: WT

tag: time

value: 48 hours


title: Sorted life cells, Bone Marrow, patient5, plate TM904

description: Matrix column names (see plate_wellid) start with: TM904_


title: Sorted life cells, Bone Marrow, patient6, plate TM915

description: Matrix column names (see plate_wellid) start with: TM915_


title: Sorted life cells, Bone Marrow, patient6, plate TM914

description: Matrix column names (see plate_wellid) start with: TM914_


title: Sorted life cells, Bone Marrow, patient6, plate TM912

description: Matrix column names (see plate_wellid) start with: TM912_


title: Sorted life cells, Bone Marrow, patient6, plate TM913

description: Matrix column names (see plate_wellid) start with: TM913_


title: Sorted life cells, Bone Marrow, patient5, plate TM902

description: Matrix column names (see plate_wellid) start with: TM902_


title: Sorted life cells, Bone Marrow, patient3, plate TM910

description: Matrix column names (see plate_wellid) start with: TM910_


title: Sorted life cells, Bone Marrow, patient3, plate TM495

description: Matrix column names (see plate_wellid) start with: TM495_


title: Sorted life cells, Bone Marrow, patient3, plate TM908

description: Matrix column names (see plate_wellid) start with: TM908_


title: Sorted life cells, Bone Marrow, patient3, plate TM493

description: Matrix column names (see plate_wellid) start with: TM493_


title: Sorted life cells, Bone Marrow, patient5, plate TM905

description: Matrix column names (see plate_wellid) start with: TM905_


title: Sorted life cells, Bone Marrow, patient6, plate TM894

description: Matrix column names (see plate_wellid) start with: TM894_


title: Sorted life cells, Primary, patient4, plate KK092

description: Matrix column names (see plate_wellid) start with: KK092_

source_name: Adrenal gland tissue including tumour

value: Adrenal gland tissue including tumour


title: Sorted life cells, Bone Marrow, patient6, plate TM893

description: Matrix column names (see plate_wellid) start with: TM893_


title: Sorted life cells, Primary, patient4, plate KK089

description: Matrix column names (see plate_wellid) start with: KK089_


title: Sorted life cells, Bone Marrow, patient5, plate TM901

description: Matrix column names (see plate_wellid) start with: TM901_


title: Sorted life cells, Bone Marrow, patient3, plate TM490

description: Matrix column names (see plate_wellid) start with: TM490_


title: Sorted life cells, Bone Marrow, patient7, plate TM898

description: Matrix column names (see plate_wellid) start with: TM898_


title: Sorted life cells, Bone Marrow, patient5, plate TM900

description: Matrix column names (see plate_wellid) start with: TM900_


title: Sorted life cells, Primary, patient5, plate KK081

description: Matrix column names (see plate_wellid) start with: KK081_


title: Sorted life cells, Primary, patient5, plate KK082

description: Matrix column names (see plate_wellid) start with: KK082_


title: Sorted life cells, Bone Marrow, patient3, plate TM489

description: Matrix column names (see plate_wellid) start with: TM489_


title: Sorted life cells, Primary, patient4, plate KK091

description: Matrix column names (see plate_wellid) start with: KK091_


title: Sorted life cells, Bone Marrow, patient6, plate TM895

description: Matrix column names (see plate_wellid) start with: TM895_


title: Sorted life cells, Primary, patient4, plate KK090

description: Matrix column names (see plate_wellid) start with: KK090_


title: Sorted life cells, Primary, patient2, plate KK073

description: Matrix column names (see plate_wellid) start with: KK073_


title: Sorted life cells, Primary, patient2, plate KK071

description: Matrix column names (see plate_wellid) start with: KK071_


title: Sorted life cells, Bone Marrow, patient5, plate TM903

description: Matrix column names (see plate_wellid) start with: TM903_


title: Sorted life cells, Primary, patient1, plate KK069

description: Matrix column names (see plate_wellid) start with: KK069_


title: Sorted life cells, Primary, patient2, plate KK072

description: Matrix column names (see plate_wellid) start with: KK072_


title: Sorted life cells, Bone Marrow, patient3, plate TM909

description: Matrix column names (see plate_wellid) start with: TM909_


title: Sorted life cells, Primary, patient5, plate KK079

description: Matrix column names (see plate_wellid) start with: KK079_


title: Sorted life cells, Primary, patient2, plate KK074

description: Matrix column names (see plate_wellid) start with: KK074_


title: Sorted life cells, Primary, patient3, plate KK055

description: Matrix column names (see plate_wellid) start with: KK055_


title: Sorted life cells, Primary, patient3, plate KK057

description: Matrix column names (see plate_wellid) start with: KK057_


title: Sorted life cells, Primary, patient3, plate KK058

description: Matrix column names (see plate_wellid) start with: KK058_


title: Sorted life cells, Primary, patient1, plate KK066

description: Matrix column names (see plate_wellid) start with: KK066_


title: Sorted life cells, Primary, patient7, plate KK054

description: Matrix column names (see plate_wellid) start with: KK054_


title: Sorted life cells, Primary, patient1, plate KK070

description: Matrix column names (see plate_wellid) start with: KK070_


title: Sorted life cells, Primary, patient1, plate KK067

description: Matrix column names (see plate_wellid) start with: KK067_


title: Sorted life cells, Primary, patient5, plate KK080

description: Matrix column names (see plate_wellid) start with: KK080_


title: Sorted life cells, Primary, patient3, plate KK056

description: Matrix column names (see plate_wellid) start with: KK056_


title: Sorted life cells, Primary, patient1, plate KK068

description: Matrix column names (see plate_wellid) start with: KK068_


title: Sorted life cells, Primary, patient6, plate KK001

description: Matrix column names (see plate_wellid) start with: KK001_


title: Sorted life cells, Primary, patient3, plate KK059

description: Matrix column names (see plate_wellid) start with: KK059_


title: Mouse Skin, Unwounded, 2

status: Public on Sep 11 2024

city: Washington

first: Brett

middle: Adam

last: Shook

state: DC

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

institute: George Washington University

description: 10X Genomics

data_processing:
The de-multiplexing, barcoded processing, gene counting, and aggregation were performed using the CellRanger software v5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Unwounded back skin

extract_protocol:
Unwounded and wounded skin samples were minced in nuclei lysis buffer. They were ground with a loose pestle 22 times, passed through a 200μm pluriStrainer, and further ground with a tight pestle 12 times. Isolated nuclei were incubated in additional nuclei lysis buffer and washed before quality assessment under a microscope and counting. Samples were used immediately afterward for single nuclei RNA sequencing library preparation.
Library preparation was performed using the Single Cell 3' v3.1 protocol from 10X Genomics according to the manufacturer's instructions. Briefly, isolated nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).  Nuclear RNA contained in the gems was retrotranscribed to cDNA, and subsequent cleanup and amplification steps were performed as described in the protocol.

tag: age

value: 8 weeks

value: Unwounded back skin

value: Mixed skin cells

value: wild type

tag: strain


title: Sorted life cells, Primary, patient7, plate KK053

description: Matrix column names (see plate_wellid) start with: KK053_


title: Sorted life cells, Primary, patient7, plate KK052

description: Matrix column names (see plate_wellid) start with: KK052_


title: Mouse Skin, Unwounded, 1

description: 10X Genomics


title: Sorted life cells, Primary, patient7, plate KK051

description: Matrix column names (see plate_wellid) start with: KK051_


title: Mouse Skin, 1dpw, 1

description: 10X Genomics

source_name: Wounded back skin 1dpw

value: Wounded back skin 1dpw


title: ENS6dpf

status: Public on Aug 30 2024

city: PASADENA

first: Can

last: Li

state: California

address: 1200 E.California Blvd MC156-29, Caltech

department: Biology and Biological Engineering

institute: Caltech

description: 10x Genomics

data_processing:
The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10.
Assembly: GRCz10
Supplementary files format and content: h5ad files

organism: Danio rerio

source_name: intestine

extract_protocol:
To isolate ENS cells, we generated a reporter line by inserting mNeonGreen fluorescent protein after the Phox2bb coding sequence, such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2, 3, 4, 5 and 6 dpf were anesthetized by tricaine Methanesulfonate (MS222), followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20, 23, 28, 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system, with pipetting up and down every 5 minutes. After digestion, Accumax was quenched by ice-cold resuspension buffer (1X Hanks' Balanced Salt Solution, no calcium, no magnesium (HBSS);10mM HEPES, adjusted to PH 8.0; 2.5 mg/ml BSA), and samples were then passed through a 70um cell strainer into 50ml conical tube, centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting.
Library was performed following the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics).

value: intestine

value: Cells in the ENS

value: Phox2bb:mNeonGreen Heterozygote


title: ENS5dpf

description: 10x Genomics


title: SAMPLE 24: DNA mehtylation of human stomach with NG_peri-cancer (NG-6 peri-ca)

status: Public on Aug 27 2024

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System

data_processing: The data were analyzed using GenomeStudio Methylation Module Software.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human stomach

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted by standard phenol/chloroform method, and was quantified using a Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).

tag: condition

value: nodular gastritis (NG)

value: Peri-cancerous region


title: ENS3dpf

description: 10x Genomics


title: Mouse Skin, 1dpw, 2

description: 10X Genomics


title: ENS2dpf

description: 10x Genomics


title: Sorted life cells, Primary, patient6, plate KK002

description: Matrix column names (see plate_wellid) start with: KK002_


title: ENS4dpf

description: 10x Genomics


title: SAMPLE 23: DNA mehtylation of human stomach with NG_peri-cancer (NG-4 peri-ca)


title: SAMPLE 25: DNA mehtylation of human stomach with NG_peri-cancer (NG-9 peri-ca)


title: SAMPLE 21: DNA mehtylation of human stomach with NG_peri-cancer (NG-2 peri-ca)


title: SAMPLE 22: DNA mehtylation of human stomach with NG_peri-cancer (NG-3 peri-ca)


title: SAMPLE 16: DNA mehtylation of human stomach with AG (AG-13)

value: atrophic gastritis (AG)

value: Gastric antrum


title: SAMPLE 13: DNA mehtylation of human stomach with AG (AG-5)


title: SAMPLE 19: DNA mehtylation of human stomach with AG (AG-16)


title: SAMPLE 18: DNA mehtylation of human stomach with AG (AG-15)


title: SAMPLE 10: DNA mehtylation of human stomach with NG (NG-11)


title: SAMPLE 15: DNA mehtylation of human stomach with AG (AG-12)


title: SAMPLE 20: DNA mehtylation of human stomach with AG (AG-17)


title: SAMPLE 17: DNA mehtylation of human stomach with AG (AG-14)


title: SAMPLE 14: DNA mehtylation of human stomach with AG (AG-11)


title: SAMPLE 3: DNA mehtylation of human stomach with NG (NG-4)


title: SAMPLE 1: DNA mehtylation of human stomach with NG (NG-2)


title: SAMPLE 12: DNA mehtylation of human stomach with AG (AG-3)


title: SAMPLE 7: DNA mehtylation of human stomach with NG (NG-8)


title: SAMPLE 9: DNA mehtylation of human stomach with NG (NG-10)


title: SAMPLE 8: DNA mehtylation of human stomach with NG (NG-9)


title: YiaT232, E. coli,Replicate 4

status: Public on Aug 22 2024

city: Boston

first: Michal

last: Sheffer

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber

data_processing:
FASTQ files were processed using STAR alignment for the first run and HISAT2 for the second run, followed by DESeq2
Assembly: h38
Supplementary files format and content: tab delimited file with raw gene counts from two RNAseq experiments

source_name: NK cells transduced with MSLN-CAR

growth_protocol: MSLN-CAR NK cells from four different donors (two donor per biological replicate) were cocultured with bacteria YiaT232 (MOI 1000), bacteria YiaT232-hDR18 (MOI 1000), purified hDR18 (100ng/ml) or PBS for 3h

extract_protocol:
RNA was extracted using Maxwell® RSC simplyRNA Cells Kit from Promega for the first run and CWbio RNA extraction kit for second run.
Libraries were constructed using the Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian for the first run and NEBNext Ultra II RNA Library Prep Kit for Illumina, for the second run.

value: NK cells transduced with MSLN-CAR

value: YiaT232, E.coli


title: PBS, Replicate 3

value: PBS


title: PBS, Replicate 4


title: hDR18, Replicate 4


title: hDR18, Replicate 3


title: SAMPLE 5: DNA mehtylation of human stomach with NG (NG-6)


title: SAMPLE 6: DNA mehtylation of human stomach with NG (NG-7)


title: SAMPLE 2: DNA mehtylation of human stomach with NG (NG-3)


title: SAMPLE 4: DNA mehtylation of human stomach with NG (NG-5)


title: YiaT232-hhDR18,  E. coli, Replicate 3

value: YiaT232-hhDR18, E.coli


title: YiaT232-hhDR18,  E. coli, Replicate 2


title: hDR18, Replicate 2


title: SAMPLE 11: DNA mehtylation of human stomach with AG (AG-1)


title: YiaT232-hhDR18,  E. coli, Replicate 4


title: YiaT232, E. coli,Replicate 1


title: YiaT232, E. coli,Replicate 2


title: Patient_21_PBMC_Progression_GEX

status: Public on Aug 11 2024

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0)
FASTQ files were aligned to GRCh38 using Cellranger count (v6.0.1).
For TCR reconstruction, FASTQ files from TCR specific libraries were used as input into CellRanger vdj.
For CITEseq, TotalSeq specific libaries were aligned using CITEseqCount (v1.4.3).
Feature barcodes matrices were read into Seurat (v4.0.5) to create an aggregrated object for downstream analysis. CD8+ T cell were identified and subset from this overall object for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: *_GEX files are tar archives containing a directory with barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CellRanger count).
Supplementary files format and content: *_TCR files are tar archives containing a directory with filtered_contig_annotations.csv (i.e. the output from CellRanger vdj).
Supplementary files format and content: *_CITEseq files are tar archives containing a directory with umi counts for each TotalSeq barcode in the format of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CITEseqCount).

molecule: polyA RNA

source_name: Blood

extract_protocol:
Whole blood was collected by venipuncture into EDTA tubes. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation. Tumor biopsies were collected into RPMI supplemented with 10% fetal bovine serum. Tumor tissue was mechanically disrupted and passed over a 100 micron filter. Live CD45+ cells were sorted from both blood and tumor specimens. Samples were collected at baseline, following four weeks of therapy, and at 12 or 16 weeks or upon evidence of disease progression.
Libraries were created using 10X Genomics 5' GEX and VDJ kits as per the manufacturer's instructions.

treatment_protocol: Patients with advanced melanoma received intravenous infusions of monotherapy with relatlimab (anti-LAG3; 160 mg), montherapy with nivolumab (anti-PD1; 480 mg) or the combination of relatlimab+nivolumab (480 mg + 160 mg, respectively) for a lead-in period of 4 weeks.

value: Blood

tag: timepoint

value: Progression

value: Live CD45+ immune cells

tag: library type

value: Gene expression

tag: disease stage

value: IIIB

tag: biological sex

value: male

value: Nivo


title: Patient_42_PBMC_Baseline_TCR

library_source: other

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0)
FASTQ files were aligned to GRCh38 using Cellranger count (v6.0.1).
For TCR reconstruction, FASTQ files from TCR specific libraries were used as input into CellRanger vdj.
For CITEseq, TotalSeq specific libaries were aligned using CITEseqCount (v1.4.3).
Feature barcodes matrices were read into Seurat (v4.0.5) to create an aggregrated object for downstream analysis. CD8+ T cell were identified and subset from this overall object for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: *_GEX files are tar archives containing a directory with barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CellRanger count).
Supplementary files format and content: *_TCR files are tar archives containing a directory with filtered_contig_annotations.csv (i.e. the output from CellRanger vdj).
Supplementary files format and content: *_CITEseq files are tar archives containing a directory with umi counts for each TotalSeq barcode in the format of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CITEseqCount).
Library strategy: scTCR-seq

molecule: protein

value: Baseline

value: T cell receptor

value: IV

value: female


title: Patient_42_PBMC_Baseline_GEX


title: YiaT232, E. coli,Replicate 3


title: PBS, Replicate 2


title: PBS, Replicate 1


title: hDR18, Replicate 1


title: Patient_41_TIL_Week4_TCR

source_name: Tumor

value: Tumor

value: IIIC

value: Rela+nivo


title: Patient_40_PBMC_TIL_Week4_CITEseq

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0)
FASTQ files were aligned to GRCh38 using Cellranger count (v6.0.1).
For TCR reconstruction, FASTQ files from TCR specific libraries were used as input into CellRanger vdj.
For CITEseq, TotalSeq specific libaries were aligned using CITEseqCount (v1.4.3).
Feature barcodes matrices were read into Seurat (v4.0.5) to create an aggregrated object for downstream analysis. CD8+ T cell were identified and subset from this overall object for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: *_GEX files are tar archives containing a directory with barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CellRanger count).
Supplementary files format and content: *_TCR files are tar archives containing a directory with filtered_contig_annotations.csv (i.e. the output from CellRanger vdj).
Supplementary files format and content: *_CITEseq files are tar archives containing a directory with umi counts for each TotalSeq barcode in the format of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CITEseqCount).
Library strategy: CITE-seq

source_name: Blood and tumor

value: Blood and tumor

value: CITEseq

value: Rela


title: Patient_40_TIL_Baseline_GEX


title: Patient_40_PBMC_Baseline_TCR

value: Blood


title: YiaT232-hhDR18,  E. coli, Replicate 1

value: NK cells transduced with MSLN-CAR

value: YiaT232-hhDR18, E.coli


title: Patient_21_PBMC_Progression_TCR

value: Progression

value: Live CD45+ immune cells


title: Patient_39_TIL_Week4_TCR

value: male


title: Patient_39_PBMC_TIL_Week16_CITEseq


title: Patient_40_TIL_Baseline_TCR


title: Patient_41_TIL_Week4_GEX

value: Gene expression


title: Patient_38_TIL_Baseline_GEX

value: Baseline


title: Patient_38_TIL_Week4_GEX


title: Patient_40_PBMC_TIL_Week4_GEX


title: Patient_40_PBMC_TIL_Week4_TCR

value: T cell receptor


title: Patient_40_PBMC_Baseline_GEX

value: IV


title: Patient_38_PBMC_TIL_Week16_CITEseq


title: Patient_38_PBMC_Baseline_GEX


title: Patient_39_PBMC_TIL_Week16_GEX


title: Patient_39_PBMC_TIL_Baseline_CITEseq


title: Patient_37_PBMC_Baseline_GEX


title: Patient_37_PBMC_Week4_GEX


title: Patient_38_TIL_Week4_TCR


title: Patient_38_TIL_Baseline_TCR


title: Patient_36_PBMC_Baseline_TCR

value: female

value: Nivo


title: Patient_38_PBMC_TIL_Week16_TCR


title: Patient_38_PBMC_TIL_Week16_GEX


title: Patient_38_PBMC_Baseline_TCR


title: Patient_37_TIL_Baseline_TCR

value: Tumor


title: Patient_37_TIL_Baseline_GEX

value: Rela+nivo


title: Patient_36_PBMC_TIL_Week4_TCR

value: Blood and tumor


title: Patient_37_PBMC_Baseline_TCR


title: Patient_37_PBMC_Week4_TCR


title: Patient_39_PBMC_TIL_Baseline_GEX


title: Patient_36_PBMC_TIL_Week4_CITEseq

value: CITEseq


title: Patient_36_PBMC_Baseline_GEX


title: Patient_34_TIL_Week12_GEX


title: Patient_34_TIL_Week12_TCR


title: Patient_34_PBMC_Week4_TCR


title: Patient_35_PBMC_TIL_Week4_TCR


title: Patient_35_TIL_Week16_GEX


title: Patient_35_PBMC_TIL_Week4_CITEseq


title: Patient_35_TIL_Week16_TCR


title: Patient_33_PBMC_TIL_Week4_GEX

value: Rela


title: Patient_34_TIL_Week4_TCR


title: Patient_33_PBMC_TIL_Week12_GEX


title: Patient_34_PBMC_TIL_Baseline_TCR


title: Patient_34_PBMC_Week4_GEX

value: Blood


title: Patient_32_PBMC_Week4_TCR


title: Patient_36_PBMC_TIL_Week4_GEX


title: Patient_32_PBMC_Week4_GEX


title: Patient_34_TIL_Week4_GEX


title: Patient_34_PBMC_TIL_Baseline_GEX


title: Patient_31_PBMC_Week4_TCR


title: Patient_33_PBMC_TIL_Week12_TCR


title: Patient_33_PBMC_TIL_Week4_TCR


title: Patient_34_PBMC_TIL_Baseline_CITEseq


title: Patient_33_PBMC_TIL_Week4_CITEseq


title: Patient_30_TIL_Baseline_GEX


title: Patient_35_PBMC_TIL_Week4_GEX


title: Patient_32_TIL_Week4_GEX


title: Patient_30_PBMC_TIL_Week4_GEX


title: Patient_30_PBMC_TIL_Week4_TCR


title: Patient_30_PBMC_TIL_Week4_CITEseq


title: Patient_32_TIL_Baseline_TCR


title: Patient_39_TIL_Week4_GEX


title: Patient_30_PBMC_Baseline_TCR


title: Patient_31_TIL_Week4_TCR


title: Patient_32_PBMC_Baseline_TCR


title: Patient_31_TIL_Week4_GEX


title: Patient_32_PBMC_Baseline_GEX


title: Patient_31_TIL_Week16_GEX


title: Patient_29_PBMC_Baseline_GEX


title: Patient_33_PBMC_TIL_Week12_CITEseq


title: Patient_28_TIL_Week4_GEX


title: Patient_30_TIL_Baseline_TCR


title: Patient_31_PBMC_Week4_GEX


title: Patient_31_PBMC_Baseline_GEX


title: Patient_28_TIL_Week16_TCR


title: Patient_28_PBMC_Week4_TCR


title: Patient_28_TIL_Baseline_TCR


title: Patient_29_PBMC_Week16_TCR


title: Patient_30_PBMC_Week16_GEX


title: Patient_28_PBMC_Week4_GEX


title: Patient_29_PBMC_Baseline_TCR


title: Patient_31_PBMC_Baseline_TCR


title: Patient_29_PBMC_Week4_TCR


title: Patient_27_TIL_Week4_GEX


title: Patient_29_PBMC_Week16_GEX


title: Patient_27_TIL_PBMC_Baseline_CITEseq


title: Patient_28_TIL_Baseline_GEX


title: Patient_26_TIL_Week4_GEX


title: Patient_26_PBMC_Week4_GEX


title: Patient_29_PBMC_Week4_GEX


title: Patient_30_PBMC_Baseline_GEX


title: Patient_28_PBMC_Week16_GEX


title: Patient_28_PBMC_Week16_TCR


title: Patient_27_TIL_PBMC_Baseline_TCR


title: Patient_25_TIL_Week16_GEX


title: Patient_25_TIL_PBMC_Baseline_TCR


title: Patient_27_TIL_PBMC_Baseline_GEX


title: Patient_25_TIL_PBMC_Week4_CITEseq


title: Patient_28_TIL_Week4_TCR


title: Patient_27_PBMC_Week4_GEX


title: Patient_26_TIL_Baseline_TCR


title: Patient_25_PBMC_Week16_TCR


title: Patient_26_PBMC_Baseline_TCR


title: Patient_26_TIL_Baseline_GEX


title: HepG2_Glucose Deprivation_rep2

status: Public on Jul 25 2024

city: HEFEI

first: Yang

last: Yang

state: ANHUI

address: NO. 96, JinZhai Road

institute: University of Science and Technology of China

data_processing:
The identification of circRNA candidates was performed utilizing CIRI2, with BSJ reads per million utilized for circRNA level calculation
Differential expression analysis of circRNAs was performed using DESeq2, with criteria set at fold change > 5 or < 0.20 and a Q-value < 0.05 for significance.
Assembly: hg19
Supplementary files format and content: Excel file including readcount and TPM

source_name: Liver

extract_protocol:
Total RNA was extracted from tissue samples by TRIzol reangent, and the concentration and purity of the extracted RNA was examined using Nanodrop 2000. 5ug of total RNA was used for construction of sequnencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeqTM Stranded Total RNA Library Prep Kit following manufacturer's protocols after removing rRNA by Ribo-Zero Magnetic Kit and mRNA by RNase R.

value: Liver

value: WT

value: Glucose free 24h


title: Patient_25_TIL_PBMC_Week4_GEX

value: Live CD45+ immune cells


title: Patient_25_TIL_PBMC_Week4_TCR

value: male


title: Patient_25_TIL_PBMC_Baseline_GEX

value: Gene expression


title: HepG2_Normal_rep1

value: Normal


title: Patient_25_PBMC_Week16_GEX


title: Patient_11_Baseline_TIL_TCR

extract_protocol:
Whole blood was collected by venipuncture into EDTA tubes. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation. Tumor biopsies were collected into RPMI supplemented with 10% fetal bovine serum. Tumor tissue was mechanically disrupted and passed over a 100 micron filter. Live CD45+ cells were sorted from both blood and tumor specimens. Samples were collected at baseline, following four weeks of therapy, and at 12-16 weeks or upon evidence of disease progression.
Libraries were created using 10X Genomics 5' GEX and VDJ kits as per the manufacturer's instructions.

value: Baseline

value: TCR sequencing


title: Microglia AD WT replicate 1

status: Public on Jun 30 2024

first: Zengqiang

last: yuan

address: No. 27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
Assembly: mm10
Supplementary files format and content: RNA-seq read counts in genes (comma-delimited text file)

source_name: microlgia

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
Transcriptome library was prepared following Clontech-SMART-Seq™ v4 Ultra™ Low Input RNA Kit for sequencing using 10ng of total RNA. Then the synthesized cDNA was conducted into library according to Illumina’s library construction protocol. Finally, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

value: microlgia

value: WT AD


title: Patient_11_Baseline_TIL_GEX

value: Tumor

value: IV


title: Microglia WT replicate 1


title: HepG2_Glucose Deprivation_rep1


title: Microglia CKO replicate 2

value: Rack1 CKO


title: Patient_26_PBMC_Baseline_GEX


title: Astrocyte AD WT replicate 1

source_name: Astrocyte

value: Astrocyte


title: Microglia AD WT replicate 2


title: Microglia AD CKO replicate 1

value: Rack1 CKO AD


title: Microglia WT replicate 2


title: Astrocyte AD WT replicate 2


title: Patient_25_TIL_PBMC_Baseline_CITEseq

value: Blood and tumor

value: CITEseq

value: Nivo


title: Microglia AD CKO replicate 2


title: HepG2_Normal_rep2

value: Liver

value: WT


title: Astrocyte WT replicate 1


title: Astrocyte CKO replicate 2


title: Astrocyte AD CKO replicate 2


title: Patient_9_Baseline_PBMC_GEX

value: Live CD45+ immune cells

value: unknown


title: PAO1[pMMBpsrA]

status: Public on Jul 05 2024

city: Hsinchu

first: Li-Ching

last: Kok

address: 101, Section 2, Kuang-Fu Road

department: Institute of Molecular Medicine

country: Taiwan

institute: National Tsing Hua University

data_processing:
CLC Genomics Workbench v9.5
Sequence were trimmed for low quality sequence, ambiguous nuclotides, and adaptoe sequences using CLC Gemonic Workbench v9.5 benchwork
Trimmed sequence reads were mapped to NC_002516 gemone database using CLC Genomics Workbench v9.5
Read count extraction and normalization was performed using CLC Genomics Workbench v9.5
The relative expression level of genes was determined and normalized on the basis of reads per kilo base per million mapped reads (RPKM)
Assembly: NC_002516
Supplementary files format and content: spreadsheet (xls) files includes RPKM values for each sample

organism: Pseudomonas aeruginosa

source_name: plasmid

growth_protocol: P. aeruginosa PAO1 or PAO1 overexpressing PsrA were grown in LB broth supplemented with 500 µg/ml carbenicillin at 37°C for 9 h till late log phase

extract_protocol:
The bacterial RNA was extracted using the TRIzol® reagent and further purified using the PureLink™ RNA Mini kit according to manufacturer’s instructions. The contaminating DNA was removed with DNase I along with an RNase inhibitor. Complementary DNA was synthesized with GeneScript First-Strand Synthesis Kit. Approximately 1 ug of cDNA for each sample was sent for transcriptomic analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PAO1 overexpressing PsrA (plasmid pMMBpsrA) was compared with wild-type PAO1 carrying empty vector pMMB66EH

value: plasmid

value: Overexpression of psrA


title: Hv ribosome footprints, digested with MNR, biol rep 2

status: Public on Jun 22 2024

city: Baltimore

first: Matthew

last: Isada

state: Maryland

address: 3400 N Charles St Levi 235

department: Biology

institute: Johns Hopkins University

description: Ribosomes footprinted with MNR. Libraries prepared from resulting RNA fragments.

data_processing:
All ribosome profiling data were analyzed using previously established methods and the plastid python library (Dunn and Weissman 2016; Gelsinger et al. 2020; Mohammad et al. 2019). In brief, reads were trimmed using trim_galore v. 0.6.10, reads corresponding to rRNA and tRNA were discarded, and the remaining reads were mapped against the Hv NCBI RefSeq genome (taxonomy identification 2246, GCF 000025685.1, ASM2568v1), allowing two mismatches using Bowtie2 v. 2.5.3 (Langmead et al. 2009). Genome-aligned reads were used to generate footprint read length distributions. Distributions from commercial MNase and MNase A were statistically compared within biological replicates by permutation test with scipy v. 1.11.3 (distribution mean as test statistic, two-sided, independent, 10,000 resamples). Plastid was used to construct metagene plots, mapping from either the 5’- or 3’-end of genome-aligned reads.
TPMs - Genome-aligned reads were subset to include only reads subset to coding sequences (CDSs); these data were converted to transcripts per million (TPMs) using Stringtie v. 2.2.3, log-transformed (using a pseudocount of 1), and compared between MNaseA and the commercial nuclease for each biological replicate.
Codon frame - The plastid module psite was used to determine the Hv ribosome P-site offset, or the distance in nucleotides between the P-site (internal to the ribosome footprint) and the 5' end of the ribosome footprint. For the current work, the P-site offset was measured as the distance between the stop codon and a spike of high ribosome density shortly upstream of the stop codon. The P-site offset was found to be 14-17 nt for highly abundant ribosome footprint lengths associated with elongation (14 nt offset for 24 nt footprints; 17 nt offset for 27 nt footprints). A 17 nt P-site offset for 27 nt footprints was used with the plastid module phase_by_size to calculate the positions of ribosome footprint 5'-ends within codons.
Assembly: Hv NCBI RefSeq genome (taxonomy identification 2246, GCF 000025685.1, ASM2568v1)
Supplementary files format and content: MN[X]_biorep[Y]_readlengths.txt: Frequency counts of read lengths for a given sample. Frequency counts generated using samtools. [X] = A or R. [Y] = 1, 2, or 3.
Supplementary files format and content: MN[X]_biorep[Y]_5p_metagene_profile.txt: Mean ribosome density on all genes aligned at their start codon using 5'-end mapped reads. Density values generated using plastid. [X] = A or R. [Y] = 1, 2, or 3.
Supplementary files format and content: tpms.csv: Genome-aligned ribosome profiling reads converted to transcripts per million (TPMs). These are untransformed TPM values, i.e., they have not yet had a pseudocount value added and have not been log-transformed.
Supplementary files format and content: codon_frame.txt: Fractions of ribosome profiling reads corresponding to different positions within a codon, stratified by read length.
Library strategy: Ribo-Seq

organism: Haloferax volcanii

growth_protocol:
Cells collected under standard growth conditions.
H. volcanii DS2 strain H26 (ΔpyrE2) (Hv) single colonies were picked and grown overnight at 42°C with shaking at 220 rpm (Eppendorf Innova S44i) in Hv-YPC medium (https://haloarchaea.com/wp-content/uploads/2018/10/Halohandbook_2009_v7.3mds.pdf) until saturation (OD600 > 1.0). The cultures were then diluted to OD600 = 0.01 in fresh media and grown to OD600 = 0.6.

extract_protocol:
As previously described (Gelsinger et al. 2022), cells were harvested by dispensing culture into liquid nitrogen, forming small pellets. Batches of 50 g of pellets were supplemented with 100 μg/mL anisomycin (Sigma-Aldrich, #A9789) and pulverized in a cryomill (6870 Large Freezer/Mill (Spex)) for 8 cycles (1 min grinding at 10 Hz, 1 min cooling). Cell lysates were thawed at RT and pre-cleared at 10,000 x g for 15 min at 4°C. Ribosomes were pelleted from pre-cleared lysate over a 1 M sucrose cushion [sucrose dissolved in 1× lysis buffer (3.4 M KCl, 100 mM MgCl2, 50 mM CaCl2, 10 mM Tris-HCl pH 7.5)] in an ultracentrifuge with a Type 45 Ti rotor (Beckman Coulter) at 40,000 rpm (185,511 x g) for 3 h at 4°C. Ribosome pellets were resuspended in 200 μL 1x lysis buffer, then pooled for each biological replicate. RNA concentrations of pooled pellets were measured using the Qubit RNA Broad Range assay (ThermoFisher Scientific, #Q10210), then pellets were split back into equal volumes. For each biological replicate, equal amounts of RNA were digested either with Roche MNase (Nuclease S7, Roche, #10107921001) or with MNaseA, for 1 h at 25 °C, at a ratio of 250 U per 1 μg RNA. Digested pellets were loaded onto a 10-50% sucrose gradient (sucrose dissolved in 1× lysis buffer) and ultracentrifuged using a SW41 Ti rotor (Beckman Coulter) at 40,000 rpm (273,620 x g) for 2.5 h at 4°C. Gradients were fractionated into 450 μL fractions to resolve ribosome 30S and 50S subunits, monosomes, and polysomes. Fractions were flash-frozen on dry ice for subsequent RNA extraction.
TRIzol LS (Invitrogen) was used according to manufacturer instructions to extract RNA from sucrose gradient fractions corresponding to 70S monosomes. Library preparation was performed as previously described (Gelsinger et al. 2022). Briefly, 1-5 µg of RNA fragments extracted from 70S monosome fractions were used to purify 10–45 nt RNA fragments by polyacrylamide gel electrophoresis on a 15% TBE-Urea gel; RNA fragments were treated with T4 polynucleotide kinase (NEB, #), ligated to the linker (NEB Universal miRNA Cloning Linker, #S13115S) using T4 RNA ligase (NEB, #M0242), purified by an Oligo Clean and Concentrator kit (Zymo Research, #D4061), and reverse transcribed with SuperScript III (Invitrogen, #18080044) using custom primers previously described (Gelsinger et al. 2022). DNA fragments were gel purified on a 10% TBE-Urea denaturing polyacrylamide gel, circularized using CircLigase (Epicentre, CL4115K), and PCR amplified (8–12 cycles) with Phusion polymerase (NEB) using custom primers (Gelsinger et al. 2022). PCR products were gel extracted from a native 8% TBE gel and analyzed for size and concentration using a BioAnalyzer high-sensitivity DNA kit (standard protocol) before sequencing (Novagene, Novaseq 6000, PE150).

value: digested with MNR


title: Hv ribosome footprints, digested with MNR, biol rep 1


title: Hv ribosome footprints, digested with MNR, biol rep 3


title: PAO1[pMMB66EH]

value: Wild type


title: Hv ribosome footprints, digested with MNA, biol rep 3

description: Ribosomes footprinted with MNA. Libraries prepared from resulting RNA fragments.

value: digested with MNA


title: Hv ribosome footprints, digested with MNA, biol rep 2


title: Microglia CKO replicate 1

value: microlgia


title: Hv ribosome footprints, digested with MNA, biol rep 1


title: Late Log yeast, replicate 2, RNAseq

status: Public on Jun 20 2024

city: Birmingham

first: Catarina

middle: Alexandra

last: Mendes Felgueira

state: AL

address: 1720 University Blvd

institute: University of Alabama at Birmingham

data_processing:
Reads were base-called using bclconvert software.
Read quality was assessed with FastQC (version 0.11.9-Java-11). Reads were then aligned to the yeast genome using STAR with filters "--outFilterMultimapNmax 10" and "--outFilterMatchNmin 12" (version 2.7.3a-GCC-6.4.0-2.28).
Feature counts were obtained using HTseq (version 0.12.3-foss-2018b-Python-3.6.6).
DESeq2 (version 1.42.1) was used to calculate differential gene expression.
Gene set enrichment analysis was conducted using Webgestalt (version 0.4.6).
All subsequent data analysis and visualization was performed with R (version 4.3.1) and Rstudio (version 2024.04.0+735).
Assembly: S. cerevisiae R64-1-1  (GenBank assembly: GCA_000146045.2)
Supplementary files format and content: Processed data are in .txt files with gene feature counts for each sample (output from HTseq).

organism: Saccharomyces cerevisiae

source_name: WT yeast

growth_protocol: Yeast was grown on YPD at 30ºC with nutation until indicated OD600

extract_protocol:
Yeast cells were pelleted and flash frozen. Total RNA was obtained using hot acidic phenol/chloroform extraction followed by DNAse I treatment to deplete DNA from samples. A final acidic phenol/chloroform extraction was perform to remove DNAse I from samples.
rRNA was depleted using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). RNA-seq libraries was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7760) in conjunction with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (NEB #E7600).

value: WT yeast


title: Late Log yeast, replicate 3, RNAseq


title: Late Log yeast, replicate 1, RNAseq


title: Mid Log yeast, replicate 3, RNAseq


title: Astrocyte CKO replicate 1

value: Rack1 CKO


title: Mid Log yeast, replicate 1, RNAseq


title: Astrocyte WT replicate 2

value: Astrocyte


title: Astrocyte AD CKO replicate 1

value: Rack1 CKO AD


title: Early Log yeast, replicate 2, RNAseq


title: Early Log yeast, replicate 3, RNAseq


title: Early Log yeast, replicate 1, RNAseq


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 2

status: Public on Jun 18 2024

city: Evanston

first: Jason

last: Brickner

state: IL

address: Hogan 1-500, 2205 Tech Drive

institute: Northwestern University

library_source: genomic

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq21

extract_protocol:
Ligation and tagmentation. Illumina Nextera XT index adapters sequences
Proteinase K digestion and phenol-choloroform extraction

value: MATa leu2delta0 ura3delta0 met15delta0 CYC1pro-SV40-NLS-MNase:HIS3 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7::kanMX6


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq22


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq25


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq18

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 TOA2-3FLAG-MNase:kanMX6 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq20


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq23


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq17


title: Soluble MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq24


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq16


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq19


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq13

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 TFA1-3FLAG-MNase:kanMX6 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq12


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq9


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq11


title: Mid Log yeast, replicate 2, RNAseq


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq7

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq8


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq6


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq5


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq4


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq2


title: Rpb1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq3


title: BY4741, Ethanol Stress, Replicate 2

data_processing:
library strategy: SLAM-seq
slamdunk
*processed data files format and content: tab-separated file containing RNA counts table generated by slamdunk
Assembly: S288C, R64.3.1

extract_protocol:
QuantSeq 3‘ mRNA-Seq
Proteinase K digestion and phenol-choloroform extraction

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: BY4741, SDC, Replicate 3


title: BY4741, SDC, Replicate 2


title: BY4741, Ethanol Stress, Replicate 3


title: BY4741, Ethanol Stress, Replicate 1


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 2

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq15


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 60min, Replicate 2

value: MATa ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 60min, Replicate 3


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 60min, Replicate 1


title: gcn4-pd-GFP, SDC_noHistidine 60min, Replicate 3

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 gcn4-pd-GFP:kanMX6


title: BY4741, SDC, Replicate 1


title: Toa2-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 1

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq14


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 60min, Replicate 1


title: gcn4-pd-GFP, SDC 60min, Replicate 1


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 60min, Replicate 2


title: Tfa1-MNase, OsTir1 Sua7-AID, YPD, 3IAA NegativeControl 20min, Replicate 3

data_processing:
mapped with bowtie2. Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts. Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq10


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 60min, Replicate 3


title: gcn4-pd-GFP, SDC 60min, Replicate 3


title: gcn4-pd-GFP, SDC_noHistidine 60min, Replicate 1


title: gcn4-pd-GFP, SDC 60min, Replicate 2


title: gcn4-pd-GFP, SDC_noHistidine 60min, Replicate 2


title: GCN4-sm-GFP, SDC_noHistidine 60min, Replicate 3

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 GCN4-sm-GFP:kanMX6


title: GCN4-sm-GFP, SDC 60min, Replicate 3


title: GCN4-sm-GFP, SDC_noHistidine 60min, Replicate 2


title: GCN4-sm-GFP, SDC_noHistidine 60min, Replicate 1


title: GCN4-sm-GFP, SDC 60min, Replicate 1


title: GCN4-sm-GFP, SDC 60min, Replicate 2


title: Soluble MNase, GCN4-sm, SD+Uracil 60min, Replicate 3

data_processing:
library strategy: ChEC-seq2
mapped with bowtie2.  Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
*processed data files format and content: bigwig files contain CPMn noramlized coverage counts.  Repetitive regions are masked.
Assembly: S288C, R64.3.1

extract_protocol:
Ligation and tagmentation.  Illumina Nextera XT index adapters sequences
Proteinase K digestion and phenol-choloroform extraction

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:CYC1pro-SV40-NLS-MNase:TEFpro-kanMX6-TEFterm GCN4-sm


title: Soluble MNase, GCN4-sm, SD+Uracil 60min, Replicate 2


title: Soluble MNase, GCN4-sm, SD+Uracil 60min, Replicate 1


title: Soluble MNase, GCN4-sm, SDC 60min, Replicate 3


title: Soluble MNase, GCN4-sm, SDC 60min, Replicate 1


title: Soluble MNase, GCN4-sm, SDC 60min, Replicate 2


title: Rpb1-MNase, gcn4-pd, SD+Uracil 60min, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 gcn4-pd


title: Rpb1-MNase, gcn4-pd, SD+Uracil 60min, Replicate 3


title: Rpb1-MNase, gcn4-pd, SD+Uracil 60min, Replicate 1


title: Rpb1-MNase, gcn4-pd, SDC 60min, Replicate 3


title: Rpb1-MNase, GCN4-sm, SD+Uracil 60min, Replicate 1

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 GCN4-sm


title: Rpb1-MNase, GCN4-sm, SD+Uracil 60min, Replicate 3


title: Rpb1-MNase, gcn4-pd, SDC 60min, Replicate 2


title: Rpb1-MNase, GCN4-sm, SDC 60min, Replicate 3


title: Rpb1-MNase, GCN4-sm, SD+Uracil 60min, Replicate 2


title: Rpb1-MNase, GCN4-sm, SDC 60min, Replicate 2


title: Rpb1-MNase, gcn4-pd, SDC 60min, Replicate 1


title: Soluble MNase, gcn4∆, SD+Uracil 60min, Replicate 1

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:CYC1pro-SV40-NLS-MNase:TEFpro-kanMX6-TEFterm gcn4delta::TEFpro-HygromycinB-TEFterm


title: Rpb1-MNase, GCN4-sm, SDC 60min, Replicate 1


title: Soluble MNase, gcn4∆, SD+Uracil 60min, Replicate 3


title: Rpb1-MNase, gcn4∆, SD+Uracil 60min, Replicate 3

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 gcn4delta::TEFpro-HygromycinB-TEFterm


title: Rpb1-MNase, gcn4∆, SDC 60min, Replicate 3


title: Rpb1-MNase, gcn4∆, SD+Uracil 60min, Replicate 2


title: Rpb1-MNase, gcn4∆, SD+Uracil 60min, Replicate 1


title: Soluble MNase, gcn4∆, SDC 60min, Replicate 2


title: Rpb1-MNase, gcn4∆, SDC 60min, Replicate 2


title: Rpb1-MNase, gcn4∆, SDC 60min, Replicate 1


title: Soluble MNase, gcn4∆, SDC 60min, Replicate 1


title: Rpb3-MNase, YPD, Replicate 1

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB3-3FLAG-MNase:kanMX6


title: Rpb3-MNase, YPD, Replicate 3


title: Rpb3-MNase, YPD, Replicate 2


title: Spt5-MNase, SDC, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 SPT5-3FLAG-MNase:kanMX6


title: Spt5-MNase, SDC, Replicate 3


title: Spt5-MNase, SDC, Replicate 1


title: Ctk1-MNase, SDC, Ethanol Stress, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 CTK1-3FLAG-MNase:kanMX6


title: Ctk1-MNase, SDC, Ethanol Stress, Replicate 3


title: Ctk1-MNase, SDC, Replicate 3


title: Ctk1-MNase, SDC, Ethanol Stress, Replicate 1


title: Soluble MNase, gcn4∆, SDC 60min, Replicate 3


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 1

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:CYC1pro-SV40-NLS-MNase:TEFpro-kanMX6-TEFterm TEFpro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3MX6


title: Soluble MNase, gcn4∆, SD+Uracil 60min, Replicate 2


title: Ctk1-MNase, SDC, Replicate 2


title: Ctk1-MNase, SDC, Replicate 1


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 2


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 3


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 2


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 3


title: Soluble MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 1


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 3

value: MATa leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 TDH3pro-OsTIR1-ADH1term:LEU2 SUA7-3V5-IAA7:HIS3MX6


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 1


title: Soluble MNase, SDC, Replicate 2 (JVY338)

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:CYC1pro-SV40-NLS-MNase:TEFpro-kanMX6-TEFterm


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 1


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA 20min, Replicate 2


title: Soluble MNase, SDC, Replicate 1 (JVY338)


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 3


title: Ser5pMintbody-MNase, SDC, Ethanol Stress, Replicate 3

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:ADH1pro-Ser5pMintbody-3V5-MNase:natMX6


title: Soluble MNase, SDC, Replicate 3 (JVY338)


title: Ser5pMintbody-MNase, SDC, Ethanol Stress, Replicate 2


title: Ser5pMintbody-MNase, SDC, Ethanol Stress, Replicate 1


title: Ser5pMintbody-MNase, SDC, Replicate 3


title: Ser5pMintbody-MNase, SDC, Replicate 2


title: Ser5pMintbody-MNase, SDC, Replicate 1


title: Ser2pMintbody-MNase, SDC, Ethanol Stress, Replicate 3

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:ADH1pro-Ser2pMintbody-3V5-MNase:natMX6


title: Ser2pMintbody-MNase, SDC, Ethanol Stress, Replicate 2


title: Ser2pMintbody-MNase, SDC, Ethanol Stress, Replicate 1


title: Ser2pMintbody-MNase, SDC, Replicate 1


title: Ser2pMintbody-MNase, SDC, Replicate 3


title: Ser2pMintbody-MNase, SDC, Replicate 2


title: Ser5pMintbody-MNase, kin28is, SDC, CMK, Replicate 3

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:ADH1pro-Ser5pMintbody-3V5-MNase:natMX6 kin28is


title: Ser5pMintbody-MNase, kin28is, SDC, CMK, Replicate 2


title: Ser5pMintbody-MNase, kin28is, SDC, CMK, Replicate 1


title: Ser5pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 2


title: Ser2pMintbody-MNase, kin28is, SDC, CMK, Replicate 2

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:ADH1pro-Ser2pMintbody-3V5-MNase:natMX6 kin28is


title: Ser2pMintbody-MNase, kin28is, SDC, CMK, Replicate 1


title: Ser2pMintbody-MNase, kin28is, SDC, CMK, Replicate 3


title: Ser5pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 3


title: Ser5pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 1


title: Ser2pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 3


title: Ser2pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 1


title: Soluble MNase, kin28is, SDC, CMK, Replicate 2

value: MATa leu2delta0 ura3delta0 met15delta0 his3delta1:CYC1pro-SV40-NLS-MNase:kanMX6 kin28is


title: Soluble MNase, kin28is, SDC, CMK, Replicate 3


title: Soluble MNase, kin28is, SDC, CMK, Replicate 1


title: Ser2pMintbody-MNase, kin28is, SDC, CMK Negative Control, Replicate 2


title: Soluble MNase, kin28is, SDC, CMK Negative Control, Replicate 3


title: Rpb1-MNase, OsTir1 Sua7-AID, SDC, 3IAA NegativeControl 20min, Replicate 2


title: Soluble MNase, kin28is, SDC, CMK Negative Control, Replicate 1


title: Soluble MNase, kin28is, SDC, CMK Negative Control, Replicate 2


title: Rpb1-MNase, kin28is, SDC, CMK Negative Control, Replicate 3

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RPB1-3FLAG-MNase:kanMX6 kin28is


title: Rpb1-MNase, YPD, Replicate 3

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RBP1-3FLAG-MNase:kanMX6


title: Soluble MNase, SDC, Ethanol Stress, Replicate 2

value: MATa leu2delta0 ura3delta0 met15delta0 CYC1pro-SV40-NLS-MNase:HIS3


title: Soluble MNase, SDC, Replicate 3 (JVY141)


title: Soluble MNase, SDC, Ethanol Stress, Replicate 1


title: Rpb1-MNase, kin28is, SDC, CMK, Replicate 2


title: Rpb1-MNase, kin28is, SDC, CMK, Replicate 3


title: Rpb1-MNase, kin28is, SDC, CMK, Replicate 1


title: Rpb1-MNase, kin28is, SDC, CMK Negative Control, Replicate 2


title: Rpb1-MNase, kin28is, SDC, CMK Negative Control, Replicate 1


title: Med1-MNase, SDC, Replicate 3

value: MATalpha ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 MED1-3FLAG-MNase:kanMX6


title: Soluble MNase, SDC, Ethanol Stress, Replicate 3


title: Rpb1-MNase, SDC, Ethanol Stress, Replicate 2


title: Soluble MNase, SDC, Replicate 2 (JVY141)


title: Rpb1-MNase, YPD, Replicate 1


title: Kin28-MNase, SDC, Ethanol Stress, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 KIN28-3FLAG-MNase:kanMX6


title: Med1-MNase, SDC, Replicate 1


title: Kin28-MNase, SDC, Replicate 1


title: Soluble MNase, SDC, Replicate 1 (JVY141)


title: Kin28-MNase, SDC, Replicate 2


title: Rpb1-MNase, SDC, Replicate 1


title: Med1-MNase, SDC, Replicate 2


title: Rpb1-MNase, SDC, Ethanol Stress, Replicate 3


title: Tfa1-MNase, SDC, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 TFA1-3FLAG-MNase:kanMX6


title: Toa2-MNase, SDC, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 TOA2-3FLAG-MNase:kanMX6


title: Kin28-MNase, SDC, Replicate 3


title: Toa2-MNase, SDC, Replicate 3


title: Rpb1-MNase, SDC, Ethanol Stress, Replicate 1


title: Rpb1-MNase, YPD, Replicate 2


title: Tfa1-MNase, SDC, Replicate 1


title: Skin_congenital_melanocytic_nevus_patient_CMN27

status: Public on Jun 17 2024

city: Marseille

first: Daniel

last: Aldea

address: 27 Bd Jean Moulin

country: France

institute: Aix-Marseille University

hyb_protocol: DNAs were hybridized to an Infinium Methylation EPIC v1 BeadChip arrays (Illumina)

scan_protocol: Scanned using an Illumina iSCAN platform.

data_processing: Preprocessing and quality control of the sample intensity data (IDAT) files were performed using the R package Minfi package (v.1.48.0). Sample normalization was done with the preprocessQuantile function. Once our data was combined with publicly available datasets (GSE188593), cell-type deconvolution was performed using the Epidish function, and using a reference library for DNA methylation-based cell-type deconvolution containing melanocyte, keratinocyte, and fibroblast cells. After filtering, normalization, and deconvolution differentially methylated probes were identified through mixed linear regression models using a Limma package from R.

label: Cy3 and Cy5

source_name: Skin

label_protocol: Bisulfite treatment was carried out to convert 500 ng of DNA into unmethylated cytosine nucleotides to uracil using the EpiJET Bisulfite Conversion Kit (ThermoFisher Scientific).

extract_protocol: DNA was extracted from flash-frozen biopsies or paraffin blocks using standard salting-out techniques.

value: Skin

value: Melanocyte, keratinocyte, fibroblast cells, others

value: NRAS Q61R


title: Tfa1-MNase, SDC, Replicate 3


title: Rpb1-MNase, SDC, Replicate 3


title: Skin_congenital_melanocytic_nevus_patient_CMN24


title: Kin28-MNase, SDC, Ethanol Stress, Replicate 3


title: Skin_congenital_melanocytic_nevus_patient_CMN48

value: NRAS Q61K


title: Toa2-MNase, SDC, Replicate 1


title: Saline biol rep 2

status: Public on Jun 07 2024

city: Charleston

first: Alexander

middle: CW

last: Smith

state: SC

address: 173 Ashley Ave, BS403

department: Neuroscience

institute: Medical University of South Carolina

description: 10X Genomics

data_processing:
cellranger v3.1 'cellranger count'
Filtered cells <=5000 and >=200 unique genes
Filtered cells < 5% mitochondrial reads
Filtered out genes expressed in <3 cells
Filtered data scaled to median number of UMIs and log(x+1) transformed
Assembly: mm10-July2020-A
Supplementary files format and content: hdf5, per-molecule information for all molecules that contain a valid barcode, UI, and were assigned with high confidence to a gene or feature barcode. This is a required file to run cellranger aggr.

source_name: Brain

growth_protocol: 8-week old male C57 mice

extract_protocol:
Fresh tissue dissection prior to freezing on dry ice
Per 10X Genomics kit instructions

treatment_protocol: IP injection of saline or 5mg/kg oxycodone

tag: Sex

value: Male

value: 8 weeks

value: Brain

value: Saline IP


title: Skin_congenital_melanocytic_nevus_patient_CMN23


title: Saline biol rep 1

description: 10X Genomics


title: Skin_congenital_melanocytic_nevus_patient_CMN16


title: Skin_congenital_melanocytic_nevus_patient_CMN11


title: Skin_congenital_melanocytic_nevus_patient_CMN10


title: 8_Glom_WT

status: Public on May 27 2024

city: Bethesda

first: Teruhiko

last: Yoshida

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v2.4.11 software was used fro base calling, Bcl2fastq v2.20 was used for sample demultiplexing
The analysis was performed with the Cell Ranger v7.1.0 software using the default parameters with premRNA analysis turned on. The reference was built from mm10 reference genome and HIV-1 virus sequence added.
Assembly: mm10 and HIV-1: NC_001802.1
Supplementary files format and content: tar.gz files contain filtered_features_bc_matrix folder output from CellRanger Count

source_name: Mouse Kidney Glomeruli

extract_protocol:
Nuclei from frozen mouse kidney outer cortex tissue samples and glomeruli-enriched samples were prepared following the protocol. Briefly, ~ 8 mm3 tissue fragments were cut by razor blade in EZlysis buffer (#NUC101-1KT, Sigma, Darmstadt, Germany) and homogenized 30 times using a loose Dounce homogenizer and 5 times by tight pestle. After 5 mins of incubation, the homogenate was passed through a 40 µm filter (PluriSelect, El Cajon, CA) and centrifuged at 500g at 4°C and for 5 min. The pellet was washed with EZlysis buffer (Sigma Aldrich, St Louis, MO) and again centrifuged at 500g at 4°C for 5 min. The pellet was resuspended with DPBS with 1% FBS and passed through a 5 µm filter (PluriSelect, El Cajon, CA) to make final nuclei prep for loading on to a 10xChromium Chip G (10X Genetics, San Francisco, CA) for formation of gel beads in emulsion (GEM).
10x Genomics Chromium 3’ V3.1 mRNA-seq library protocol

treatment_protocol: C16 treatment group mice received 10µg/kg body weight of C16 in 10ml/kg body weight 0.5%DMSO-PBS intraperitoneally three times a week from 6 weeks to 12 weeks of age.

value: Kidney Cortex

value: WT

value: Control


title: 6_Tg26_B

source_name: Mouse Kidney Cortex


title: Oxycodone biol rep 2

description: 10X Genomics

value: 5mg/kg oxycodone IP


title: Oxycodone biol rep 1

description: 10X Genomics


title: 4_Tg26_Glom

data_processing:
Illumina RTA v2.4.11 software was used fro base calling, Bcl2fastq v2.20 was used for sample demultiplexing
The analysis was performed with the Cell Ranger v5.0.0 software using the default parameters with premRNA analysis turned on. The reference was built from mm10 reference genome and HIV-1 virus sequence added.
Assembly: mm10 and HIV-1: NC_001802.1
Supplementary files format and content: tar.gz files contain filtered_features_bc_matrix folder output from CellRanger Count

value: Mouse Kidney Glomeruli


title: 5_WT_B


title: 7_Tg26_C16_B


title: 3_Tg26_C16


title: 1_WT


title: HiC_tissue_DTB-110-BL

status: Public on May 16 2024

city: San Fransisco

first: Felix

last: Feng

address: 1450 3rd Street

institute: University of California

data_processing:
Paired-end raw reads of Hi-C libraries were processed using HiC-Pro62 (version 3.0.0) Singularity container provided by HiC-Pro (https://github.com/nservant/HiC-Pro). Briefly, sequencing reads were first independently aligned to the reference human genome (hg38) using the bowtie263 end-to-end algorithm and ‘-very-sensitive’ option. To rescue the unmapped chimeric fragments spanning the ligation junction, the ligation site was detected using an exact matching procedure and the 5’ fraction of the reads was aligned back to the reference genome. Unmapped reads, multi-mapped reads, and singletons were then discarded. Each pair of aligned reads were then assigned to MboI restriction fragments. Read pairs from uncut DNA, self-circle ligation, and PCR artefacts were filtered out and the valid read pairs involving two different restriction fragments were used to build the contact matrix. Valid read pairs were then binned at 10-kb resolution. The binned contact matrix was then normalized using the iterative correction (ICED) method64 to correct for biases such as GC content, mappability, and effective fragment length in Hi-C data.
Assembly: hg38
Supplementary files format and content: Sparse matrix containing paired locus coordinates and the observed interaction frequency, after ICED normalization.
Supplementary files format and content: A .bed reference file that defines the genomic coordinates used in the HiC matrix files

source_name: tissue

extract_protocol:
As described in Hawley, J. R. et al. Reorganization of the 3D Genome Pinpoints Noncoding Drivers of Primary Prostate Tumors. Cancer Res 81, 5833-5848, doi:10.1158/0008-5472.CAN-21-2056 (2021).
The mCRPC Hi-C libraries were prepared using the SMARTer ThruPLEX DNA-seq library preparation kit (Takara Biosciences) per manufacturer’s protocol, followed by a double-size selection for 300-700 bp fragments using Ampure XP beads. The libraries were then sequenced on a NovaSeq 6000.

tag: ega

value: tissue


title: HiC_tissue_DTB-008-BL


title: HiC_tissue_DTB-004-BL


title: HiC_tissue_DTB-265-PRO


title: HiC_tissue_DTB-148-BL


title: HiC_tissue_DTB-035-BL


title: HiC_tissue_DTB-090-PRO


title: HiC_tissue_DTB-030-BL


title: 2_Tg26


title: HiC_tissue_PR-040-BL


title: HiC_tissue_DTB-011-BL


title: HiC_tissue_DTB-085-BL


title: HiC_tissue_DTB-063-BL


title: HiC_tissue_DTB-135-PRO


title: HiC_tissue_DTB-124-BL


title: HiC_tissue_DTB-091-BL


title: HiC_tissue_DTB-172-BL


title: HiC_tissue_DTB-129-BL


title: HiC_tissue_DTB-019-PRO


title: HiC_tissue_DTB-090-BL


title: HiC_tissue_DTB-080-PRO


title: HiC_tissue_DTB-055-PRO2


title: HiC_tissue_DTB-040-BL


title: HiC_tissue_DTB-143-BL


title: HiC_tissue_DTB-119-PRO


title: HiC_tissue_DTB-032-BL


title: HiC_tissue_DTB-034-BL


title: HiC_tissue_DTB-141-BL


title: HiC_tissue_DTB-128-BL


title: HiC_tissue_DTB-149-BL


title: HiC_tissue_DTB-126-BL


title: HiC_tissue_DTB-167-PRO


title: HiC_tissue_DTB-053-BL


title: HiC_tissue_DTB-135-BL


title: HiC_tissue_DTB-009-BL


title: HiC_tissue_DTB-125-BL


title: HiC_tissue_DTB-156-BL


title: HiC_tissue_DTB-019-BL


title: HiC_tissue_DTB-206-BL


title: HiC_tissue_PR-095-BL


title: HiC_tissue_DTB-097-BL


title: HiC_tissue_PR-120-BL


title: HiC_tissue_DTB-173-BL


title: HiC_tissue_DTB-146-BL


title: HiC_tissue_DTB-098-BL


title: HiC_tissue_DTB-083-BL


title: HiC_tissue_DTB-218-BL


title: HiC_tissue_DTB-060-BL


title: HiC_tissue_DTB-167-BL


title: HiC_tissue_DTB-069-BL


title: HiC_tissue_DTB-111-PRO


title: HiC_tissue_DTB-080-BL


title: HiC_tissue_DTB-183-BL


title: HiC_tissue_DTB-061-BL


title: HiC_tissue_DTB-222-BL


title: HiC_tissue_DTB-097-PRO


title: HiC_tissue_DTB-138-BL


title: HiC_tissue_DTB-064-BL


title: HiC_tissue_DTB-022-BL


title: HiC_tissue_PR-056-BL


title: HiC_tissue_DTB-037-BL


title: HiC_tissue_DTB-092-BL


title: HiC_tissue_DTB-044-BL


title: HiC_tissue_DTB-059-BL


title: HiC_tissue_PR-081-BL


title: HiC_tissue_DTB-259-BL


title: HiC_tissue_DTB-036-BL


title: HiC_tissue_DTB-176-BL


title: HiC_tissue_DTB-176-PRO


title: HiC_tissue_DTB-170-BL


title: HiC_tissue_DTB-127-PRO


title: HiC_tissue_DTB-127-BL


title: HiC_tissue_DTB-104-BL


title: HiC_tissue_DTB-071-BL


title: HiC_tissue_DTB-077-PRO


title: HiC_tissue_DTB-021-BL


title: HiC_tissue_DTB-140-BL


title: HiC_tissue_DTB-005-BL


title: DPSC + DMP1, sorted, Day 7, biol rep 2

status: Public on May 07 2024

city: Chicago

first: Anne

last: George

address: 801 S Paulina St

institute: University of Illinois Chicago College of Dentistry

data_processing:
Cutadaptand perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
HISAT2 was used to map reads to the genome and StringTie was used to assemble mapped reads for each sample
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
R package edgeR was used to calculate CPM values and conduct differential analysis between samples
Assembly: hg19
Supplementary files format and content: text file containing raw counts for each sample

source_name: DPSC

growth_protocol: The DPSCs were placed in wells coated with HUVEC-ECM at a density of 0.3x10^6 cells per well. They were then cultured in EBM-2 media supplemented with 10% FBS and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from Pre-sorted and post-sorted DPSCs treated with DMP1 was extracted using Trizol reagent (Invitrogen, Waltham, MA) according to the manufacturer’s instructions. The quality and integrity of the total RNA were determined using a Nano drop 2000 spectrophotometer.
Poly(A) RNA libraries were prepared using Illumina’s TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol:
DPSCs were cultured on the HUVEC-ECM with or without DMP1 (500 ng/ml). Following a 7-day culture period, the cells were harvested, washed with PBS, and subsequently incubated with endothelial-specific antibodies CD31 and C144 in the dark at ambient conditions for 40 minutes.
The cells were then subjected to flow cytometry sorting using a Moflo Astrios EQ device (UIC RRC facility).

value: DPSC

value: mesenchymal stem cells

tag: treatment/time point

value: DPSC + DMP1, sorted, Day 7


title: DPSC + DMP1, sorted, Day 7, biol rep 1


title: DPSC, control, biol rep 2

value: DPSC, control


title: DPSC + DMP1, unsorted, Day 7, biol rep 2

value: DPSC + DMP1, unsorted, Day 7


title: DPSC, control, biol rep 1


title: HUVEC, Day7, biol rep 1

source_name: HUVEC

value: HUVEC

value: endothelial cells

value: HUVEC, Day7


title: IMR90_Control3_rep1(RNA-seq)

status: Public on May 01 2024

city: Beijing

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

data_processing:
The raw sequencing data were processed using trim_galore (version 0.6.10) to remove adapters and low-quality reads
The trimmed reads were then mapped to the hg38 or mm10 reference genome using hisat2 (version 2.2.1), and the SAM files were converted to sorted BAM files using samtools (version 1.7)
The gene expression count matrix was obtained using featureCounts (version 2.0.6) and normalized with DESeq2 (version 1.34.0)
Assembly: hg38, mm10
Supplementary files format and content: Tab-delimited text files include normalized values for each sample

source_name: lung

extract_protocol:
Total RNA was extracted from cells for the construction of sequencing libraries using TRIzol® (Invitrogen, 15596018)
RNA libraries were prepared for sequencing using Illumina protocols

value: lung

value: Fibroblast


title: IMR90_Control3_rep2(RNA-seq)


title: IMR90_MS-275_rep1(RNA-seq)


title: IMR90_MS-275_rep2(RNA-seq)


title: IMR90_Control2_rep1(RNA-seq)


title: IMR90_A485_rep2(RNA-seq)


title: HiC_tissue_DTB-101-BL


title: HUVEC, Day7, biol rep 2


title: HiC_tissue_DTB-074-BL


title: IMR90_A485_rep1(RNA-seq)


title: Muscle_MS-275_rep2(RNA-seq)

source_name: muscle

value: muscle


title: Muscle_MS-275_rep1(RNA-seq)


title: IMR90_Control1_rep2(RNA-seq)

data_processing:
The raw sequencing data were processed using trim_galore (version 0.6.10) to remove adapters and low-quality reads
The trimmed reads were then mapped to the hg38 or mm10 reference genome using hisat2 (version 2.2.1), and the SAM files were converted to sorted BAM files using samtools (version 1.7)
The gene expression count matrix was obtained using featureCounts (version 2.0.6) and normalized with DESeq2 (version 1.34.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized values for each sample

value: Hypoxia


title: IMR90_Control1_rep1(RNA-seq)

value: WT


title: HiC_tissue_DTB-130-BL


title: DPSC + DMP1, unsorted, Day 7, biol rep 1


title: IMR90_2-DG_rep1(RNA-seq)


title: IMR90_2-DG_rep2(CUT&Tag)

data_processing:
library strategy: CUT&Tag
Clean data were mapped to the hg38 reference genome using bowtie2 (version 2.2.5).The sorted bam files were converted to bigwig format using bamCoverage (version 3.5.1)
The normalized signal was visualized in Integrative Genomics Viewer (IGV, version 2.11.3). In addition, deepTools (version 3.5.1) was used to calculate signal between ±3 kb from the transcriptional start site
Peak calling was performed using MACS2 (version 2.2.7.1). The DESeq2 (version 1.34.0) was used to identify altered peaks
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
CUT&Tag experiments were performed according to the CUT&Tag Assay Kit manual (Vazyme, TD903). Briefly, cell pellets were collected at 600 × g for 5 min, washed with wash buffer, and incubated with ConA beads for 10 min at room temperature in 8-strip tubes. Subsequently, the cell–ConA bead complexes were incubated with anti-H3K9la (PTM BIOLABS, PTM1419RM) at 4℃ overnight and a secondary antibody for 1 h at room temperature. The pA/G-Tnp transposon mediated the transposition reaction, and TTBL mediated DNA fragmentation. DNA extraction beads were used to extract CUT&Tag-enriched DNA
CUT&Tag libraries were prepared for sequencing using established protocols


title: IMR90_2-DG_rep1(CUT&Tag)


title: IMR90_Normoxia_rep1(CUT&Tag)

value: Normoxia


title: IMR90_Hypoxia_rep1(CUT&Tag)


title: IMR90_Young_rep2(CUT&Tag)


title: IMR90_Hypoxia_rep2(CUT&Tag)


title: Muscle_Control4_rep2(RNA-seq)


title: IMR90_Control2_rep2(RNA-seq)


title: Muscle_Control4_rep1(RNA-seq)


title: IMR90_Senescent_rep1(CUT&Tag)


title: IMR90_Senescent_rep2(CUT&Tag)


title: IMR90_Normoxia_rep2(RNA-seq)


title: IMR90_Young_rep1(CUT&Tag)


title: IMR90_Normoxia_rep1(RNA-seq)


title: IMR90_Hypoxia_rep1(RNA-seq)


title: IMR90_Young_rep2(RNA-seq)


title: IMR90_2-DG_rep2(RNA-seq)


title: IMR90_Hypoxia_rep2(RNA-seq)


title: IMR90_Senescent_rep2(RNA-seq)


title: IMR90_Senescent_rep1(RNA-seq)


title: IMR90_Control1_rep2(CUT&Tag)


title: IMR90_Young_rep1(RNA-seq)


title: IMR90_Control1_rep1(CUT&Tag)


title: NC7

status: Public on Apr 24 2024

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

data_processing:
Initial raw data quality controls was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were trimmed using Trim Galore! (v0.4.2) http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove 3’ ends with base quality below 20 as well as adapter sequences. Reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013, v2.5.2a) with per sample 2-pass mapping strategy. PCR duplicates were detected using MarkDuplicate from Picard tools (version 1.115; http://broadinstitute.github.io/picard/). Reads aligned to mm10 were summarized to Gencode annotation vM2 (Harrow et al., 2012) with featureCounts (Liao et al., 2014, v1.5.0-p3) and using (Li and Dewey, 2011, v1.3.1) counting primary alignments only.
Assembly: mm10
Supplementary files format and content: Patch-seq_TPM.txt

source_name: neuron

extract_protocol:
Preparation of RNase-free internal solution and cleaning of the equipment was performed as described (Cadwell et al., 2017). Coronal brainstem slices were prepared (Hirtz et al., 2011) and in vitro electrophysiological recordings were performed at 36.5  1 °C (Müller et al., 2019). The internal solution contained 0.8 % RNase inhibitor . Electrophysiological characterization was limited to 10-15 min to minimize mRNA degradation; thereafter, total RNA was extracted into the patch pipette by aspirating the neuron’s cytoplasm via gentle suction. Shrinkage of the soma and entering of the nucleus into the pipette were monitored visually under DIC optics (Suppl. Fig. 1 A1 - A3). Upon successful harvesting, atmospheric pressure was reinstalled, and the pipette was slowly removed from the soma (Suppl. Fig. 1 B). In case of contamination by extracellular material on the pipette, absence of a membrane patch at the pipette tip or soma swelling, samples were discarded (Suppl. Fig. 1 C1, C2, D1, D2). The content of the pipette was collected in a reaction tube containing 2 μl lysis buffer . Samples were stored at -80 °C and processed further en bloc (library preparation and sequencing). From a total of 263 patched neurons, 103 remained for further analysis (ultimately, 86 neurons surpassed RNA quality control, see below). One negative control was collected per experimental day. To do so, a pipette filled with internal solution was moved to touch the slice with its tip. It was then retracted, and the pipette’s content was processed as for harvested cells.
Libraries were generated using a modified Version of Smartseq2 followed by Illumina Nextera XT library preparation.
RNA-seq (Patch-seq)

value: Negative Control

value: lateral superior olive of the auditory brainstem

value: neuron


title: NC8


title: NC9


title: IMR90_Normoxia_rep2(CUT&Tag)


title: NC6


title: NC1


title: NC3


title: NC2


title: cell_8

tag: vrest [mv]

tag: rin [mω]

tag: ƭmembrane [ms]

tag: capacitance [nf]

tag: rheobase [pa]

tag: sag_amplitude [mv]

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_9

tag: tissue

tag: cell type


title: NC10


title: Rpb1-MNase, SDC, Replicate 2

tag: cell line

tag: genotype

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RBP1-3FLAG-MNase:kanMX6


title: cell_86

tag: vrest [mv]

tag: rin [mω]

tag: ƭmembrane [ms]

tag: capacitance [nf]


title: cell_84

tag: rheobase [pa]

tag: sag_amplitude [mv]

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_85

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_82

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_81

tag: tissue

tag: cell type


title: cell_79

tag: vrest [mv]

tag: rin [mω]


title: cell_78

tag: ƭmembrane [ms]

tag: capacitance [nf]


title: cell_80

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_76

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_75

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_74

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_77

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_73

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: NC5

tag: tissue

tag: cell type


title: cell_72

tag: rin [mω]


title: cell_71

tag: ƭmembrane [ms]


title: cell_6

tag: vrest [mv]

tag: capacitance [nf]


title: NC4


title: cell_70

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_69

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: Kin28-MNase, SDC, Ethanol Stress, Replicate 1

tag: cell line

tag: genotype

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 KIN28-3FLAG-MNase:kanMX6


title: cell_68

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_83

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_7

tag: rin [mω]

tag: ƭmembrane [ms]

tag: tissue

tag: cell type


title: cell_66

tag: vrest [mv]

tag: capacitance [nf]

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_62

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_65

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_60

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_63

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_67

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_64

tag: rin [mω]

tag: ƭmembrane [ms]


title: cell_5

tag: tissue

tag: cell type


title: cell_59

tag: vrest [mv]

tag: capacitance [nf]


title: cell_61

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_57

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_54

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_55

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_58

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_53

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_56

tag: rin [mω]

tag: ƭmembrane [ms]


title: cell_50

tag: tissue

tag: cell type


title: cell_51

tag: vrest [mv]

tag: capacitance [nf]


title: cell_52

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_4

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_46

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_44

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_48

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_45

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_49

tag: rin [mω]

tag: ƭmembrane [ms]


title: cell_47

tag: tissue

tag: cell type


title: cell_43

tag: vrest [mv]

tag: capacitance [nf]


title: cell_41

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_42

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_40

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_38

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_36

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_39

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_3

tag: rin [mω]

tag: ƭmembrane [ms]


title: cell_34

tag: tissue

tag: cell type


title: cell_32

tag: vrest [mv]

tag: capacitance [nf]


title: cell_31

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_35

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_30

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_28

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_29

tag: tau_decay_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_27

tag: rise_time_sipsc [ms]

tag: tau_decay_sipsc [ms]


title: cell_26

tag: rin [mω]

tag: ƭmembrane [ms]


title: cell_25

tag: tissue

tag: cell type


title: cell_24

tag: vrest [mv]

tag: capacitance [nf]


title: cell_2

tag: rheobase [pa]

tag: sag_amplitude [mv]


title: cell_21

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]


title: cell_19

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: cell_17

tag: amplitude_sepsc [pa]

tag: rise_time_sepsc [ms]


title: cell_1

tag: amplitude_sipsc [pa]


title: cell_23

tag: tau_decay_sepsc [ms]

tag: rise_time_sipsc [ms]


title: cell_20

tag: rin [mω]

tag: tau_decay_sipsc [ms]


title: cell_22

tag: ƭmembrane [ms]

tag: tissue


title: cell_16

tag: vrest [mv]

tag: cell type


title: cell_37

tag: capacitance [nf]

tag: rheobase [pa]


title: cell_33

tag: sag_amplitude [mv]

tag: ap peak latency at rheobase [ms]


title: cell_14

tag: ap_amplitude [mv]

tag: ap_halfwidth [ms]


title: cell_18

tag: ap_threshold [mv]

tag: amplitude_sepsc [pa]


title: cell_13

tag: rise_time_sepsc [ms]

tag: amplitude_sipsc [pa]


title: cell_12

tag: tau_decay_sepsc [ms]

tag: rise_time_sipsc [ms]


title: cell_15

tag: rin [mω]

tag: tau_decay_sipsc [ms]


title: H9 WT D15 RNAseq Replicate 2

status: Public on Apr 17 2024

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b).
Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file containing raw counts for each sample

source_name: ventrally patterned neuronal precursors

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Vitronectin coated cultureware.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (Takara Bio)
RNA-seq library preparation was performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) per the manufacturer’s instructions.

value: ventrally patterned neuronal precursors

tag: stem cell_source

value: H9 hESC

tag: passage

tag: timepoint


title: H9 WT D15 RNAseq Replicate 4

tag: cell type


title: cell_11

tag: vrest [mv]

tag: ƭmembrane [ms]

tag: capacitance [nf]

tag: rheobase [pa]

tag: tissue


title: cell_10

tag: sag_amplitude [mv]

tag: ap peak latency at rheobase [ms]

tag: ap_amplitude [mv]

tag: ap_halfwidth [ms]

tag: ap_threshold [mv]


title: H9 WT D15 RNAseq Replicate 3


title: H9 WT D15 RNAseq Replicate 1


title: H9 WT D0 RNAseq Replicate 3

source_name: embryonic stem cells

value: embryonic stem cells


title: H9 WT D0 RNAseq Replicate 2


title: WT D35 H3K27me3 Replicate 3

data_processing:
Raw reads were processed using AIAP (v1.1) for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file
Supplementary files format and content: narrowPeak or broadPeak file containing output from MACS2 peakcalling
Library strategy: CUT&Tag

source_name: immature cortical interneurons

extract_protocol:
Genomic DNA was processed using CUT&Tag (Epicypher) and isolated using phenol-chloroform follow by the NucleoSpin® Gel and PCR Clean-Up kit (Macherey-Nagel).
After PCR amplification samples with unique dual-end indexes were pooled in equimolar concentrations.

value: immature cortical interneurons

tag: antibody


title: H9 WT D0 RNAseq Replicate 4


title: WT D35 H3K27me3 Replicate 2


title: H9 WT D0 RNAseq Replicate 1


title: WT D35 H3K27me3 Replicate 1


title: WT D15-V H3K27me3 Replicate 1


title: WT D15-V H3K27me3 Replicate 2


title: WT D15-V H3K27me3 Replicate 3