title: M_6

description: msh1 memory control


title: female_saline_D1_H3K27me3_rep3

status: Public on Jul 08 2022

type: SRA

city: New York

first: Eric

middle: J.

last: Nestler

state: NY

address: 1425 Madison Ave L10-26

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
FS3D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

library_source: genomic

data_processing:
The NGS-Data-Charmer pipeline (Github commit date: June 18, 2020) was used for preprocessing, QC, and alignment of the dataset. Read alignment was performed with Bowtie2 (v2.4.1) (--dovetail --phred33) to the mm10 genome. Duplicated read pairs were subsequently removed using the samtools (v1.10) ‘rmdup’ module.
For generating combined bigwig files, bam files were merge using samtools  ‘merge’ module and corresponding index files were created using samtools ‘index’ module; bigwig files were then generated using Deeptools ‘bamCoverage’ module (bamCoverage --extendReads --ignoreDuplicates --centerReads --normalizeUsing CPM --binSize 10)
For each biological replicate and corresponding IgG control, peaks were called with MACS2 (v2.2.6) (macs2 callpeak -f BAMPE --pvalue 0.05 --keep-dup) and filtered through Irreproducible Discovery Rate (IDR) (v2.0.4.2) using 1% IDR threshold for bulk NAc datasets and 5% IDR threshold for NAc D1- and D2-MSN datasets. IDR output for each group were combined with Bedtools41 (v2.29.2) ‘merge’ module and the output containing high confidence peaks were utilized for further analysis.
Supplementary_files_format_and_content: combined bigwig files
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Mus musculus

source_name: nucleus accumbens

extract_protocol:
Nuclei were prepared through discontinuous sucrose gradient centrifugation, isolated through INTACT approach, and subject to CUT&RUN procedures.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacture instructions.

treatment_protocol: For IP-injection, animals received consecutive 7-day saline or cocaine injection. For self-administration, animals underwent 10-day 2hr per day introvenous self-administration.

tag: genotype

value: wild-type

tag: cell type

tag: Sex

value: female

tag: treatment

value: saline

tag: antibody

value: H3K27me3 (9733, Cell Signaling)

tag: administration

value: IP-injection


title: day 7- only RA treated cells between day 3-5  [R7-Rep1]

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

library_source: transcriptomic

data_processing:
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Removal of low expressed transcripts (minimum of 5 counts for at 10 samples)
Normalization by TMM, regressed for PC1, PC2 and PC3 from picard QC matrix
mm10
Supplementary_files_format_and_content: Significant_geneList_FDR0.1_EdgeR.csv

molecule: total RNA

growth_protocol: mESCs were differentiated as adherant cultures in triplicates under bFGF/CHIR for the first two days to direct NMPs, and then treated with different combinations of RA+BMP4. Differentiations were terminated at day 9 when neuronal morphology was apparent in some samples.

extract_protocol:
At each timepoints, cells were washed with 1X PBS and then cell lysate was collected with RLT buffer (Qiagen). Total RNA was extracted using Rneasy mini kit (Qiagen)
Libraries were constructed with Universal plus mRNA sequencing kit (NuGEN) and sequenced onto 2 lanes of NovaseqS1 to generate 30 million reads/sample.

treatment_protocol: mESC-derived NMPs were treated with three conditions- (1) 100nM RA for 48 hrs between day 3-day 4 (R-conditions) (2) 100nM RA for 24hrs (day 3-day4) followed by 24hr pulse of 100nM RA+ 10ng/ml BMP4 (day 4-day5, B-conditions), (3) combined treatment of 100nM RA+10ng/ml BMP4 for 48 hrs (day3-day 5, C-conditions)

tag: time point

value: day 7

value: mESCs


title: day 5 (day3+48hrs) RA+BMP4 treated  [M5-Rep3]

source_name: day 5 (day3+48hrs) RA+BMP4 treated

value: day 5

value: day 5 (day3+48hrs) RA+BMP4 treated


title: M_5

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: msh1 memory control

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15  with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with  coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the NovaSeq 6000 system.

treatment_protocol: 3 plants from msh1 memory revertant, 2 plants from non-reverant (full-sibs of reverant), and 3 msh1 memory control plants were sequenced. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 2

tag: tissue

value: rosette leaves

tag: developmental stage

value: bolting


title: 105_1

city: Auburn

first: Marie

middle: E

last: Strader

state: AL

address: 101 Rouse Life Sciences, Biological Sciences Department

department: Biological Sciences

institute: Auburn University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Acropora millepora genome (v2.01) using bowtie2(v.2.2.9) --local --no-hd --no-sq --no-unal -k 5
gene counts were compiled using a custom perl script enabling samcounts. Script found at https://github.com/z0on/tag-based_RNAseq
Genome_build: Acropora millepora genome (v2.01)
Supplementary_files_format_and_content: txt files including gene counts values for each sample
Supplementary_files_format_and_content: VCF files for SNP calls

organism: Acropora tenuis

source_name: larval tissue

extract_protocol:
RNAqueous kit (Ambion)
tag-seq: https://github.com/z0on/tag-based_RNAseq

tag: cross

value: SBxSB

tag: temperature treatment

value: Hot

tag: life-stage

value: larval

tag: symbiont


title: day 5 (day3+48hrs) RA+BMP4 treated  [M5-Rep2]


title: M_4

description: msh1 memory control

value: biological rep 1


title: 103_3

value: SBxBK


title: WT_floral_Stem_P3

data_processing:
Illumina for basecalling
Alignments were performed using STAR (version 2.7.3a) with –twopassMode = Basic and –outFilterMultimapNmax = 1  parameters  (Grant et al., 2011)
The read count data were generated from the BAM files by using QoRTs software package (Hartley and Mullikin, 2015) --minMAPQ 25 --dropChrom Pt,Mt
edgeR (version 3.26.8) was used to calculate the differential expression.
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with edgeR

growth_protocol: For leaves and floral stem tissue, seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light). For root tissue, plants were grown on 0.5 MS growth medium for 10 days.

extract_protocol:
Total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.

treatment_protocol: 3 progenies plants from each of the epi populations (epi8, epi24, epi10, epi19) and Col-0 WT were sequenced using either rosette leaves, root, or floral stem. Epi8 and epi 24 were derived from same cross while epi 10 and epi19 were from the same cross. Tissues were flash frozen in liquid nitrogen. Tissues were ground by motor and pestle in liquid nitrogen.

value: biological rep 3

value: floral stem

value: 6-weeks old plant


title: female_saline_D1_H3K27me3_rep1

description:
FS1D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female

value: saline

value: H3K27me3 (9733, Cell Signaling)


title: 103_2


title: day 7- only RA treated cells between day 3-5  [R7-Rep3]

value: day 7

value: mESCs


title: day 5 (day3+48hrs) RA+BMP4 treated  [M5-Rep1]

value: day 5

value: day 5 (day3+48hrs) RA+BMP4 treated


title: 107_1

value: BKxBK

value: Pre


title: day 5 (day 4+24hrs) RA+BMP4 treated  [B5-Rep3]

source_name: day 5 (day 4+24hrs) RA+BMP4 treated

value: day 5 (day 4+24hrs) RA+BMP4 treated


title: 103_1

value: Hot

value: larval


title: female_saline_D1_H3K27ac_rep2

description:
FS2D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27ac (ab4729, Abcam)

value: IP-injection


title: WT_floral_Stem_P2

value: biological rep 2

value: floral stem


title: female_saline_D1_H3K27ac_rep1

description:
FS1D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: day 5 (day 4+24hrs) RA+BMP4 treated  [B5-Rep2]


title: WT_floral_Stem_P1

value: biological rep 1

value: 6-weeks old plant


title: female_cocaine_D1_histone_control_rep1

description:
FC1D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: female

value: cocaine

value: IgG (2729, Cell Signaling)


title: epi_8_floral_Stem_P3

value: biological rep 3


title: 105_2

value: SBxSB


title: 100_2

value: DRxDR


title: female_saline_D1_H3K4me3_rep3

description:
FS3D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: H3K4me3 (13-0041, EpiCypher)


title: day 5 (day 4+24hrs) RA+BMP4 treated  [B5-Rep1]

value: day 5

value: mESCs

value: day 5 (day 4+24hrs) RA+BMP4 treated


title: female_saline_D1_H3K27me3_rep2

description:
FS2D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27me3 (9733, Cell Signaling)

value: IP-injection


title: day 5 (day3+48hrs) RA treated  [R5-Rep3]

source_name: day 5 (day3+48hrs) RA treated

value: day 5 (day3+48hrs) RA treated


title: epi_8_floral_Stem_P2

value: biological rep 2

value: floral stem


title: 100_1

value: Hot

value: larval


title: female_saline_D1_H3K27ac_rep3

description:
FS3D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female

value: H3K27ac (ab4729, Abcam)


title: female_saline_D1_H3K4me3_rep1

description:
FS1D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: epi_8_floral_Stem_P1

value: biological rep 1

value: 6-weeks old plant


title: day 5 (day3+48hrs) RA treated  [R5-Rep2]


title: day 5 (day3+48hrs) RA treated  [R5-Rep1]


title: EuMYC , IgM positive, Tumour,  dCas9SAM/sgBCL-2 [21_179_Tumour_IgMp]

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

department: Blood Cells and Blood Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Graphpad Prism software version 8.2.0 and  The R Project for Statistical Computing version 4.1.3
Sequence reads were mapped to GrCM38/mm10 using Rsubread version 2.2.6
Read count extraction and CPM normalization were performed using edgeR Bioconductor package version 3.34.15
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM normalised values for each sample

source_name: primary tissue

growth_protocol: MEF cells were cultured in DMEM supplemented with 10% FBS and 1 mM L-glutamine at 37C with 10% CO2. Lymphoma cells were cultured in FMA media at 37C with 10% CO2. Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.

extract_protocol:
RNA was harvested using Direct-zol RNA Microprep kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries. Leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 1 ug of total RNA was used for sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols.

treatment_protocol: No treatment applied.

value: primary tissue

value: B cells

value: IgM positive, Tumour, EuMYC/dCas9-SAM/sgBCL-2


title: 100_3

value: DRxDR


title: epi_24_floral_Stem_P2


title: female_saline_D1_H3K4me1_rep3

description:
FS3D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: H3K4me1 (ab8895, Abcam)


title: EuMYC tumour, IgM positive, Tumour,  dCas9SAM/sgBCL-2 [20_180_Tumour_IgMp]


title: epi_24_floral_Stem_P3

value: biological rep 3


title: EuMYC cells, IgM negative,  dCas9SAM/sgBCL-2 [19_216_IgMn]

source_name: EuMYC Lymphoma

value: EuMYC Lymphoma

value: IgM negative, EuMYC/dCas9-SAM/sgBCL-2


title: female_saline_D1_H3K4me1_rep2

description:
FS2D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: day 4+6hrs RA+BMP4 treated  [B6hr-Rep3]

source_name: day 4+6hrs RA+BMP4 treated

value: mESCs

value: day 4+6hrs RA+BMP4 treated


title: female_saline_D1_H3K4me1_rep1

description:
FS1D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: WT_root_P3

value: root

value: 10 days old plant


title: epi_24_floral_Stem_P1

value: biological rep 1

value: floral stem


title: day 4+6hrs RA+BMP4 treated  [B6hr-Rep1]


title: EuMYC cells, IgM positive, dCas9SAM/sgBCL-2 [17_213_IgMp]

value: IgM positive, EuMYC/dCas9-SAM/sgBCL-2


title: female_saline_D1_H3K4me3_rep2

description:
FS2D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: female

value: H3K4me3 (13-0041, EpiCypher)


title: day 4+6hrs RA treated  [R6hr-Rep3]

source_name: day 4+6hrs RA treated

value: day 4+6hrs RA treated


title: WT_root_P2

value: biological rep 2


title: day 4+6hrs RA+BMP4 treated  [B6hr-Rep2]


title: EuMYC cells, IgM negative,  dCas9SAM/sgBCL-2 [18_214_IgMn]

value: B cells


title: day 4+6hrs RA treated  [R6hr-Rep2]


title: EuMYC cells, IgM positive, dCas9SAM/sgBCL-2 [16_202_IgMp]


title: female_saline_D1_histone_control_rep2

description:
FS2D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: IgG (2729, Cell Signaling)


title: female_saline_D1_histone_control_rep3

description:
FS3D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: EuMYC cells, IgM positive, dCas9SAM/sgBCL-2 [15_180_IgMp]

value: EuMYC Lymphoma


title: WT_root_P1


title: day 4+6hrs RA treated  [R6hr-Rep1]


title: female_saline_D1_histone_control_rep1

description:
FS1D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: EuMYC cells, IgM positive, dCas9SAM/sgBCL-2 [14_179_IgMp]


title: male_cocaine_D1_H3K27me3_rep3

description:
MC3D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: cocaine

value: H3K27me3 (9733, Cell Signaling)


title: day 4 (day3+24hrs) RA+BMP4 treated  [M4-Rep3]

source_name: day 4 (day3+24hrs) RA+BMP4 treated

value: day 4

value: mESCs

value: day 4 (day3+24hrs) RA+BMP4 treated


title: MEF cells, WT [13_WT_MEFs_2]

source_name: Mouse embryonic fibroblasts

tag: cell line

value: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblast cells

value: WT


title: epi_8_root_P2

value: root

value: 10 days old plant


title: male_cocaine_D1_H3K27me3_rep2

description:
MC2D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: MEF cells, WT [11_WT_MEFs_1_1]


title: day 4 (day3+24hrs) RA+BMP4 treated  [M4-Rep2]


title: male_cocaine_D1_H3K27me3_rep1

description:
MC1D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: epi_24_root_P3

value: biological rep 3


title: male_cocaine_D1_H3K27ac_rep3

description:
MC3D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27ac (ab4729, Abcam)


title: MEF cells, BCL2 [10_MEFs_2_BCL2_2]


title: epi_24_root_P2

value: biological rep 2


title: day 4 (day3+24hrs) RA+BMP4 treated  [M4-Rep1]


title: MEF cells, BCL2 [9_MEFs_2_BCL2_1]


title: day 4 (day3+24hrs) RA treated  [R4-Rep3]

source_name: day 4 (day3+24hrs) RA treated

value: day 4 (day3+24hrs) RA treated


title: male_cocaine_D1_H3K27ac_rep2

description:
MC2D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: day 4 (day3+24hrs) RA treated  [R4-Rep2]


title: epi_8_root_P3


title: male_cocaine_D1_H3K27ac_rep1

description:
MC1D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: MEF cells, BCL2 [7_MEFs_1_BCL2_1]


title: WT_leaf_P3

value: rosette leaves

value: bolting


title: MEF cells, BCL2 [8_MEFs_1_BCL2_2]


title: day 4 (day3+24hrs) RA treated  [R4-Rep1]

value: day 4


title: male_cocaine_D1_H3K4me3_rep3

description:
MC3D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: H3K4me3 (13-0041, EpiCypher)


title: male_cocaine_D1_H3K4me3_rep2

description:
MC2D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: epi_8_root_P1

value: biological rep 1


title: MEF cells, Non-targeting controls [5_MEFs_2_NTC1]

value: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblast cells

value: dCas9-SAM/Non-targeting controls


title: WT_leaf_P1


title: NMPs [D3-Rep2]

source_name: NMPs

value: day 3

value: mESCs

value: NMPs


title: MEF cells, Non-targeting controls [3_MEFs_1_NTC1]

value: dCas9-SAM/ Non-targeting controls


title: male_cocaine_D1_H3K4me3_rep1

description:
MC1D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: epi_8_leaf_P3

value: biological rep 3


title: male_cocaine_D1_H3K4me1_rep3

description:
MC3D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)

value: IP-injection


title: MEF cells [2_MEFs_2]


title: MEF cells [1_MEFs_1]


title: NMPs [D3-Rep1]


title: epi_24_root_P1

value: root

value: 10 days old plant


title: male_cocaine_D1_H3K4me1_rep1

description:
MC1D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: epi_8_leaf_P1

value: rosette leaves

value: bolting


title: male_cocaine_D1_H3K4me1_rep2

description:
MC2D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine


title: undifferentiated mESCs  [D0-Rep2]

source_name: undifferentiated mESCs

value: day 0

value: undifferentiated mESCs


title: NMPs [D3-Rep3]


title: epi_8_leaf_P2

value: biological rep 2


title: WT_leaf_P2


title: undifferentiated mESCs  [D0-Rep1]


title: siKDM5BC H3K4me3_4-cell embryo_rep1

city: Wuhan

first: Wei

last: Zhu

address: No.1,Shizishan Street , Hongshan District

country: China

institute: Huazhong Agricultural University

description: 4-cell embryo H3K4me3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to pig genome susScr11  using bowtie2 v2.4.1 with default parameters. Reads mapped to organelle and mapping quality below 30, as well as PCR duplicates were removed.
Peaks were called with MACS2 with following options: "--nolambda -f BAMPE --broad -f 2e9 --keep-dup all". Signal intersity of Histone modification were calculated as FPKM. To compared FPKM across stages, FPKM was further z-score transformed.
Assembly: susScr11
Supplementary files format and content: bigWig files contain z-score transformed FPKM values and broadPeak file are called peaks

organism: Sus scrofa

source_name: embryo

extract_protocol:
ChIP experiment were performed with ULI-NChIP protocol
Libraries were prepared with KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer's instructions

value: 4-cell embryo

tag: histone modification


title: male_cocaine_D1_histone_control_rep3

description:
MC3D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)


title: siKDM5BC H3K4me3_4-cell embryo_rep2

description: 4-cell embryo H3K4me3


title: epi_10_leaf_P3


title: HIF-1a/2a, batch2, rep3 [polyA RNA-seq]

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_2a_merged_batch2_RNAseq_hg38.bw

data_processing:
Quality check: FastQC
Read alignment: STAR version 2.7 (--outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif); hg38 and gencode.v32.annotation.gtf
sam to bam conversion, sorting and indexing: Samtools version 1.9
Read counting: HTSeq version 0.11.1 (htseq-count --stranded=no -f bam --additional-attr=gene_name -m union); gencode.v32.annotation.gtf
Read coverage: deepTools (version 2.4.1) bamCoverage (-of bigwig --binSize 50 --normalizeUsingRPKM)
Assembly: hg38
Supplementary files format and content: bigWig files: read coverage per 50-bp bins across the whole genome (RPKM normalization; merged triplicates)
Supplementary files format and content: HTSeq counts: counts of reads mapping to genes as annotated in gencode.v32.annotation.gtf; one file for each replicate; input for DESeq2 differential gene expression analysis

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human 786-O ccRCC cells were cultured at 37°C with 5% CO2 in 4.5 g/L glucose DMEM (ThermoFisher, Waltham, MA, #10566016) supplemented with 10% Fetal Bovine Serum (HyClone, Logan, UT, Cat. #SH30396.03, lot #AE28209315), 1 mM Sodium Pyruvate (ThermoFisher #11360070) and 100 U/mL Penicillin-Streptomycin (ThermoFisher #15140122). Cells were subcultured at a ratio of 1:4 to 1:12 every 2 to 4 days for no longer than 30 days.

extract_protocol:
polyA RNA-seq batch1: RNeasy mini plus kit (Qiagen), according to manufacturer instructions
polyA RNA-seq batch2: TRIzol RNA extraction (Invitrogen), according to manufacturer instructions, with an additional chloroform extraction step after the phenol:chrloroform extraction
polyA RNA-seq batch1: 1 µg of purified RNA was added of ERCC RNA Spike-In Mix 2 (ThermoFisher Scientific # 4456740, 0.5-1 µl of a 1:100 dilution per sample) and the total volume brought to 50 µl with UltraPure Water (ThermoFisher Scientific # 10977-023). mRNA purification, RNA fragmentation, first and second strand cDNA synthesis were performed according to the TruSeq RNA Sample Preparation v2 Kit but using Superscript III for reverse transcription instead of Superscript II (50'C for 50' incubation time). cDNA was purified with AMPure XP beads, and eluted in 27.5 μl of 10mM Tris-HCl pH 7.9, 25 μl of which were transferred to a new tube and subjected to a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina with a few modifications (see linked manuscript)
polyA RNA-seq batch2: 5 µg of purified RNA were digested with the Ambion DNA-free DNase treatment (AM1906). 1 µg of digested RNA was subject to poly-A purification and library preparation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S) plus the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770S)

value: Clear cell renal cell carcinoma


title: male_cocaine_D1_histone_control_rep2

description:
MC2D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: H3K27me3_blastocyst_rep2

description: blastocyst H3K27me3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to pig genome susScr11  using bowtie2 v2.4.1 with default parameters. Reads mapped to organelle and mapping quality below 30, as well as PCR duplicates were removed.
Peaks were called with MACS2 with following options: "--nolambda -f BAMPE --broad -f 2e9 --keep-dup all". Signal intersity of Histone modification were calculated as FPKM. To compared FPKM across stages, FPKM was further z-score transformed.
Genome_build: susScr11
Supplementary_files_format_and_content: bigWig files contain z-score transformed FPKM values and broadPeak file are called peaks

value: blastocyst


title: epi_10_leaf_P2


title: epi_10_leaf_P1

value: biological rep 1


title: male_cocaine_D1_histone_control_rep1

description:
MC1D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: H3K27me3_morula_rep2

description: morual H3K27me3

value: morula


title: HIF-1a/2a, batch2, rep2 [polyA RNA-seq]


title: undifferentiated mESCs  [D0-Rep3]

value: mESCs


title: HIF-1a/2a, batch2, rep1 [polyA RNA-seq]


title: H3K27me3_8-cell embryo_rep2

description: 8-cell embryo H3K27me3

value: 8-cell embryo


title: male_saline_D1_H3K27me3_rep3

description:
MS3D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: H3K27me3 (9733, Cell Signaling)

value: IP-injection


title: WT_No_HTP_R2 [CRAC]

city: Illkirch

first: Jérémy

last: Scutenaire

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description:
75 nt read length
Table S3

data_processing:
Sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
CRAC datasets were analyzed as previously described (Candelli et al., 2018) except for the normalization step. Briefly, samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (Webb et al., 2014). Data preprocessing steps include the 5’ adapter trimming with Cutadapt (Martin 2011, EMBnet Journal, 17, 10-12), PCR duplicates and poly-A stretch removal using pyFastqDuplicateRemover from the pyCRAC utility suite, and the reverse complement of the reads using Fastx reverse complement (part of the fastx toolkit) . BAM files were generated using bowtie2 (2.4.1) and the Saccharomyces cerevisiae genome (SK1 MvO V1 assembly).
The peaks were detected using the extractPeaks pipeline of the PeakCcall suite after gaussian kernel smoothing of the CRAC signal (Challal et al., MolCell 2018) and scored according to the “h2w” score, where “h” = height, and “w” = width of the peak.
The normalization between samples was done according to the internal Luc7-HTP spike-in. For that, the reads that did not map to the S.cerevisiae SK1 genome were mapped to the Schizosaccharomyces pombe genome (version ASM294v2) after filtering for a minimal length of 40 nt to avoid cross-species mapping. PeakCcall was used to determine the binding score of Luc7-HTP to its U1 snRNA target at the locus (chr II:3020203-3020352) in each sample. The resulted score was used to normalize the score of all S. cerevisiae peaks of the respective sample and relative to “Pho92-HTP Rep 1” sample.
Assembly: SK1 MvO V1: SK1_SGD_2018_NCSL00000000
Supplementary files format and content: Table S3. Excel file for the CRAC dataset with position of each detectable peaks, contigs information, score and normalized scores for each sample
Supplementary files format and content: 16 Bigwig (bw) files providing genome coverage for all samples on plus and minus strand

organism: Saccharomyces cerevisiae

source_name: SK1 pCUP-IME1

growth_protocol: Meiosis was induced as previously described (Schwartz et al., 2013) in 500 mL of SPO to OD600 = 2.0 at 30°C. To induce IME1 in the pCUP-IME1 background, 50 μM of copper (II) Sulfate was added after 2 hr in SPO. The sample used as “spike-in” from S. pombe cells expressing Luc7-HTP was grown independently in 800 mL of 1X EMM media (EMM Broth, Formedium, Cat #PMD0210) supplemented with 2% glucose and 125 mg/L each of adenine (Sigma, Cat #A2786), L-histidine (Sigma, Cat #H8000), uracil (Sigma, Cat #U750), L-lysine (Sigma, Cat #L5501) and L-leucine (Sigma, Cat #L8000).

extract_protocol:
Cells were broken and extracts were prepared as described in the corresponding manuscript of the data.
Library construction is described in the corresponding manuscript of the data. More informations in Candelli et al., EMBO J, 2018 and in Villa et al. Cell Reports 32, 107942 (2020).

treatment_protocol: At 5 hr following resuspension in SPO (corresponding to 3 hr after IME1 induction), samples were diluted to a final volume of 2 L with SPO media and UV-irradiated at 254 nm for 80 s using the Megatron W5 UV crosslinking unit (UVO3 Ltd). S. pombe cells used for "spike-in" were grown to 0D600 = 0.5 at 30°C and then diluted to a final volume of 2 L before UV-irradiation (254 nm for 80 s).

value: SK1 pCUP-IME1

value: diploid meiotic yeast

value: WT

value: UV-irradiated at 254 nm for 80 s


title: HIF-2a, batch2, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 39

value: Exogenous V5-Halo-HIF-2{alpha}


title: WT_No_HTP_R1 [CRAC]

description:
75 nt read length
Table S3


title: male_saline_D1_H3K27me3_rep2

description:
MS2D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: H3K27me3_4-cell embryo_rep2

description: 4-cell embryo H3K27me3

value: 4-cell embryo


title: HIF-2a, batch2, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 38

value: Clear cell renal cell carcinoma


title: Pho92-HTP_No_UV_R2 [CRAC]

description:
75 nt read length
Table S3

value: No treatment


title: male_saline_D1_H3K27me3_rep1

description:
MS1D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Pho92-HTP_No_UV_R1 [CRAC]

description:
75 nt read length
Table S3


title: H3K27me3_MII oocyte_rep2

description: MII oocyte H3K27me3

source_name: gamete

value: MII oocyte


title: male_saline_D1_H3K27ac_rep3

description:
MS3D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

source_name: nucleus accumbens

value: wild-type

value: H3K27ac (ab4729, Abcam)


title: Pho92-HTP_ime4_mut_R2 [CRAC]

description:
75 nt read length
Table S3

value: Pho92-HTP ime4 mutant


title: H3K27me3_2-cell embryo_rep2

description: 2-cell embryo H3K27me3

value: 2-cell embryo


title: HIF-2a, batch2, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 37


title: H3K27me3_blastocyst_rep1

description: blastocyst H3K27me3

value: blastocyst


title: HIF-2a/1a, batch2, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 36


title: male_saline_D1_H3K27ac_rep2

description:
MS2D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: HIF-2a/1a, batch2, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 34


title: H3K27me3_8-cell embryo_rep1

description: 8-cell embryo H3K27me3

value: 8-cell embryo


title: H3K27me3_morula_rep1

description: morual H3K27me3

value: morula


title: male_saline_D1_H3K27ac_rep1

description:
MS1D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: Pho92-HTP_R2 [CRAC]

description:
75 nt read length
Table S3

value: SK1 pCUP-IME1

value: diploid meiotic yeast


title: male_saline_D1_H3K4me3_rep3

description:
MS3D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me3 (13-0041, EpiCypher)


title: Pho92-HTP_R1  [CRAC]

description:
75 nt read length
Table S3

value: UV-irradiated at 254 nm for 80 s


title: male_saline_D1_H3K4me3_rep2

description:
MS2D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: male_saline_D1_H3K4me3_rep1

description:
MS1D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HUT2_1

city: Kepala Batas

first: Kristine

middle: Sandra

last: Pey Adum

state: Pulau Pinang

address: Bertam

department: Advanced Medicine and Dental Institute

country: Malaysia

institute: Universiti Sains Malaysia

data_processing:
Genomic workbench
Sequence reads were trimmed for adaptor and low-quality sequence
Trimmed sequence reads were mapped to Hg38 genome using HISAT2.
Read count extraction and normalization were performed.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HeLa cells were seeded in T25 flasks by SRB assay.

extract_protocol:
Total RNA from HeLa treated and untreated with CN extract were isolated using Rneasy Mini Kit Qiagen.
Library construction and sequencing were performed by Beijing Genomics Institute (BGI, Hong Kong).

treatment_protocol: HeLa cells were treated with C. nutans extract. The untreated samples were exposed without C. nutans extract.

value: HeLa cells

value: untreated


title: HIF-1a, batch2, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 33

value: Clear cell renal cell carcinoma

value: Exogenous V5-Halo-HIF-1{alpha}


title: H3K27me3_2-cell embryo_rep1

description: 2-cell embryo H3K27me3


title: HUT1_1


title: HIF-1a, batch2, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 32


title: H3K27me3_MII oocyte_rep1

description: MII oocyte H3K27me3

value: MII oocyte


title: HIF-1a, batch2, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 31


title: WT, batch2, rep3 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 30

value: Wild type


title: Pho92-HTP_ime4_mut_R1 [CRAC]

description:
75 nt read length
Table S3

value: Pho92-HTP ime4 mutant


title: HIF-2a/1a, batch2, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_1a_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 35


title: WT, batch2, rep2 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 29


title: male_saline_D1_H3K4me1_rep3

description:
MS3D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: H3K4me1 (ab8895, Abcam)


title: HDCN1_1

value: C. nutans


title: HDCN2_1


title: H3K4me3_blastocyst_rep2

description: blastocyst H3K4me3

value: blastocyst


title: male_saline_D1_H3K4me1_rep2

description:
MS2D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: IP-injection


title: ChIP-seq Hmga2 sample

city: Napoli

first: Pietro

last: Zoppoli

state: Napoli

address: via S.Pansini,5

department: DMMBM

country: Italy

institute: Università degli Studi di Napoli Federico II

data_processing:
The nf-core/chipseq pipeline (version 1.2.2; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3966161) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Docker ( Dirk Merkel. 2014.).
All data was processed relative to the mouse mm9 genome (Karolchik et al., 2004).
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Assembly: mm9
Supplementary files format and content: bigwig

growth_protocol: E14Tg2a cells were expanded on gelatin-coated plates in GMEM supplemented with 2 mM glutamine, 100 U/mL penicillin/streptomycin, 1 mM sodium pyruvate, 1X non-essential amino acids, 0.1 mM β-mercaptoethanol, 10% FBS and 103 U/ml LIF.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and next quenched by addition of glycine (125 mM). The samples were sonicated to obtain fragments with a length of 500-1000bp. Chromatin extracts were incubated with anti-Hmga2 antibody.
ChIP-seq library was prepared using ChIP-Seq Sample Prep Kit and sequenced on the Illumina HiScanSQ Platform

treatment_protocol: To induce ESCs into EpiLCs, 2x10^4 cells/cm^2 were plated on plates coated with Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix in EpiLSC medium (DMEMF12/Neurobasal medium 1:1, 0,5% N2 supplement, 1% B27 supplement, BSA, 2 mM glutamine, 20 ng/mL Activin A, and 12 ng/mL bFGF).

value: embryonic stem cells

value: induced into EpiLC (stabilized)

tag: chip antibody

value: anti-Hmga2 antibody (Cell Signaling, #5269, 1:100)


title: ChIP-seq Hmga2 input

value: none (input)


title: H3K4me3_4-cell embryo_rep2

description: 4-cell embryo H3K4me3

value: 4-cell embryo


title: H3K4me3_morula_rep2

description: morual H3K4me3

value: morula


title: H3K4me3_1-cell embryo_rep2

description: 1-cell embryo H3K4me3

value: 1-cell embryo


title: male_saline_D1_H3K4me1_rep1

description:
MS1D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

tag: genotype

value: male


title: reference_0

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

description: Stratagene universal reference RNA for internal control. This sample was not used in the analysis.

data_processing:
FastQC
FastqScreen
fastx: clip front 14 bp: fastx_trimmer -Q33 -f 14
tophat:  -M -z0  --b2-very-sensitive
Cufflinks/merge/norm
Genome_build: GRCm37.2
Supplementary_files_format_and_content: gene expression abundance estimation generated by cuffnorm. GSE141680 samples are included.

organism: synthetic construct

source_name: reference RNA

extract_protocol:
RNeasy Mini
TruSeq mRNA Sample Prep v2


title: HIF-2aDM, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α dimerization domain mutant (R171A-V192D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 26

tag: cell type

value: Clear cell renal cell carcinoma

value: Exogenous V5-Halo-HIF-1{alpha} (R171A-V192D) mutant


title: H3K27me3_4-cell embryo_rep1

description: 4-cell embryo H3K27me3


title: male_saline_D1_histone_control_rep3

description:
MS3D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

tag: Sex

value: IgG (2729, Cell Signaling)


title: male_saline_D1_histone_control_rep2

description:
MS2D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

tag: treatment


title: HIF-2aDM, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α dimerization domain mutant (R171A-V192D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 27


title: Microwell-seq datasets of Drosophila_D16_10

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp).
scRNA-seq reads were aligned to the Drosophila melanogaster BDGP6.28 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Drosophila melanogaster BDGP6.28
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

organism: Drosophila melanogaster

extract_protocol:
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

tag: age

value: 16 day after laying eggs

value: whole organism

value: Female


title: male_saline_D1_histone_control_rep1

description:
MS1D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

tag: antibody

tag: administration


title: reference_1

tag: tissue


title: Homo_iPSCs

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

data_processing:
Clean reads were obtained by removing adapter dimers,, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats in the NCBI GenBank, Repbase, and Rfam databases.
Clean reads then were gathered and mapped to miRbase database (Release 22) by BLAST.
The potentially cleaved targets of clean reads were detected by the CleaveLand 3.0 pipeline.
Genome_build: GRCH38
Supplementary_files_format_and_content: Excel files include normalized degradome read number for each Sample.

source_name: Pooled sample of the disease-specific ADO2-iPSCs with the mutation of CLCN7 (R286W) and normal control human iPSCs (NC-iPSCs).

extract_protocol:
Total RNA was extracted from the ADO2-iPSCs and NC-iPSCs using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s methods.
The urine-derived iPSCs were used for degradome sequencing library preparation according to the manufacturer's instruction.

value: Urine cells

value: human iPSCs


title: H3K4me3_8-cell embryo_rep2

description: 8-cell embryo H3K4me3

tag: developmental stage

value: 8-cell embryo


title: HIF-2a R27E, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α DNA binding domain mutant (R27E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_R27E_merged_batch1_RNAseq_hg38
polyA RNA-seq library 24

value: Exogenous V5-Halo-HIF-2{alpha} (R27E) mutant


title: H3K4me3_2-cell embryo_rep2

description: 2-cell embryo H3K4me3

value: 2-cell embryo


title: female_cocaine_D2_Brg1_control_rep3

description:
FC3D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: IP-injection


title: H3K4me3_morula_rep1

description: morual H3K4me3

value: morula


title: H3K4me3_MII oocyte_rep2

description: MII oocyte H3K4me3

value: MII oocyte


title: female_cocaine_D2_Brg1_control_rep2

description:
FC2D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: HIF-2a R27E, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α DNA binding domain mutant (R27E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_R27E_merged_batch1_RNAseq_hg38
polyA RNA-seq library 23

value: Clear cell renal cell carcinoma


title: female_cocaine_D2_Brg1_control_rep1

description:
FC1D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)


title: H3K4me3_GV oocyte _rep2

description: GV oocyte  H3K4me3

value: GV oocyte


title: WT, batch2, rep1 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch2_RNAseq_hg38.bw
polyA RNA-seq library 28

value: Wild type


title: H3K4me3_8-cell embryo_rep1

description: 8-cell embryo H3K4me3


title: Microwell-seq datasets of Drosophila_D16_9

value: 16 day after laying eggs

value: whole organism


title: female_cocaine_D1_Brg1_control_rep1

description:
FC1D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: HIF-2a R27E, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α DNA binding domain mutant (R27E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_R27E_merged_batch1_RNAseq_hg38
polyA RNA-seq library 22


title: female_cocaine_D1_Brg1_control_rep3

description:
FC3D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-2a, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 21

value: Exogenous V5-Halo-HIF-2{alpha}


title: H3K4me3_blastocyst_rep1

description: blastocyst H3K4me3

value: blastocyst


title: female_saline_D2_Brg1_control_rep2

description:
FS2D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: HIF-1aDM, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α dimerization domain mutant (R170A-V191D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 18

value: Exogenous V5-Halo-HIF-1{alpha} (R170A-V191D) mutant


title: Microwell-seq datasets of Drosophila_D16_7

value: Female


title: HIF-1aDM, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α dimerization domain mutant (R170A-V191D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 17


title: HIF-2aDM, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α dimerization domain mutant (R171A-V192D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 25

value: Exogenous V5-Halo-HIF-1{alpha} (R171A-V192D) mutant


title: female_cocaine_D1_Brg1_control_rep2

description:
FC2D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: IP-injection


title: Microwell-seq datasets of Drosophila_D16_6


title: HIF-2a, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 20


title: Microwell-seq datasets of Drosophila_D16_5


title: HIF-1aDM, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α dimerization domain mutant (R170A-V191D) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1aDM_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 16


title: HIF-2a, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_2a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 19


title: female_saline_D2_Brg1_control_rep3

description:
FS3D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Drosophila_D16_1


title: Microwell-seq datasets of Drosophila_D16_2


title: H3K4me3_4-cell embryo_rep1

description: 4-cell embryo H3K4me3

value: 4-cell embryo


title: female_saline_D1_Brg1_control_rep2

description:
FS2D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: H3K4me3_2-cell embryo_rep1

description: 2-cell embryo H3K4me3

value: 2-cell embryo


title: Microwell-seq datasets of Drosophila_D16_4


title: HIF-1a R30E, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α DNA binding domain mutant (R30E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_R30E_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 14

value: Clear cell renal cell carcinoma

value: Exogenous V5-Halo-HIF-1{alpha} (R30E) mutant


title: female_saline_D1_Brg1_control_rep1

description:
FS1D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)


title: Micorwell-seq datasets of Zebrafish_24h_COL2

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For raw file in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp).
scRNA-seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Danio rerio GRCz11
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

organism: Danio rerio

extract_protocol:
Whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

value: AB

value: 24 hours


title: H3K4me3_MII oocyte_rep1

description: MII oocyte H3K4me3

value: MII oocyte


title: female_saline_D2_Brg1_control_rep1

description:
FS1D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: female_saline_D1_Brg1_control_rep3

description:
FS3D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-1a R30E, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α DNA binding domain mutant (R30E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_R30E_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 15


title: H3K4me3_GV oocyte _rep1

description: GV oocyte  H3K4me3

value: GV oocyte


title: Microwell-seq datasets of Drosophila_D11_7

value: 11 day after laying eggs

value: whole organism

value: Male


title: Microwell-seq datasets of Drosophila_D16_3

value: 16 day after laying eggs

value: Female


title: Microwell-seq datasets of Drosophila_D11_8


title: HIF-1a R30E, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α DNA binding domain mutant (R30E) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_R30E_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 13


title: C3-Cont-Tau

city: Piscataway

first: Mengmeng

last: Jin

state: NJ

address: 604 Allison Rd

institute: Rutgers University

description: scRNA-seq library

data_processing:
The sequencing data was aligned with the pooled mouse (mm10, Ensembl 93) and human (hg19, Ensembl 87) reference genomes via Cell Ranger software.
Cells were summarized for all genes by species and those with >75% of reads aligning with hg19 were selected as human.
Raw hg19 counts from these cells were loaded into a new Seurat object, normalized and clustered.
Genome_build: hg19 + mm10
Supplementary_files_format_and_content: Processed Seurat object

organism:
Homo sapiens
Mus musculus

source_name: chimeric mouse brain cells with human microglia

growth_protocol: PMPs were generated from the three pairs of Cont and DS hiPSC cell lines using a previously established protocol (Haenseler et al., 2017). The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months. Human pNPCs were generated from Cont2 hiPSCs (Chen et al., 2016; Xu et al., 2019).

extract_protocol:
Single cells were collected after running dissociated cell through mouse cell removal column, RNA molecules were reverse transcriped and labeled with barcodes by folloing 10x Genomics' established protocol.
Libraries were constructed by folloing 10x Genomics' established protocol.

treatment_protocol: PMPs were injected into P0 mouse brain using a digital sterotaxic device, human tau proteins were injected into each human microglial chimeric mouse at 2 months old.

value: Injected soluble tau from healthy human brain


title: Micorwell-seq datasets of Zebrafish_24h_COL1


title: Microwell-seq datasets of Drosophila_D11_4


title: B2-DSAD-Tau

description: scRNA-seq library

value: Injected soluble pathological tau from DSAD human brain


title: female_cocaine_D1_Brg1_rep3

description:
FC3D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

data_processing:
The NGS-Data-Charmer pipeline (Github commit date: June 18, 2020) was used for preprocessing, QC, and alignment of the dataset. Read alignment was performed with Bowtie2 (v2.4.1) (--dovetail --phred33) to the mm10 genome. Duplicated read pairs were subsequently removed using the samtools (v1.10) ‘rmdup’ module.
For generating combined bigwig files, bam files were merge using samtools  ‘merge’ module and corresponding index files were created using samtools ‘index’ module; bigwig files were then generated using Deeptools ‘bamCoverage’ module (bamCoverage --extendReads --ignoreDuplicates --centerReads --normalizeUsing CPM --binSize 10)
For each biological replicate and corresponding IgG control, peaks were called with MACS2 (v2.2.6) (macs2 callpeak -f BAMPE --pvalue 0.05 --keep-dup) and filtered through Irreproducible Discovery Rate (IDR) (v2.0.4.2) using 1% IDR threshold for bulk NAc datasets and 5% IDR threshold for NAc D1- and D2-MSN datasets. IDR output for each group were combined with Bedtools41 (v2.29.2) ‘merge’ module and the output containing high confidence peaks were utilized for further analysis.
Supplementary_files_format_and_content: combined bigwig files
Supplementary_files_format_and_content: peak text files

value: male

value: cocaine

value: Brg1 (13-2002, EpiCypher)

value: IP-injection


title: female_cocaine_D2_Brg1_rep3

description:
FC3D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-2a KIN, batch1, rep3 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
HIF_2a_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 9

value: Clear cell renal cell carcinoma

value: V5-Halo-HIF-2a endogenous knock-in, clone A31


title: Microwell-seq datasets of Drosophila_D11_6


title: C3-DSAD-Tau

description: scRNA-seq library


title: female_cocaine_D2_Brg1_rep2

description:
FC2D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: H3K4me3_1-cell embryo_rep1

description: 1-cell embryo H3K4me3

value: 1-cell embryo


title: HIF-1a, batch1, rep3 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 12

value: Exogenous V5-Halo-HIF-1{alpha}


title: Microwell-seq datasets of Drosophila_D11_5


title: HIF-1a, batch1, rep2 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 11


title: HIF-1a, batch1, rep1 [polyA RNA-seq]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
HIF_1a_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 10


title: female_cocaine_D2_Brg1_rep1

description:
FC1D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: female_saline_D2_Brg1_rep3

description:
FS3D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: Microwell-seq datasets of Drosophila_D11_3

value: 11 day after laying eggs


title: B2-Cont-Tau

description: scRNA-seq library


title: female_cocaine_D1_Brg1_rep2

description:
FC2D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_cocaine_D1_Brg1_rep1

description:
FC1D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Drosophila_D11_2

value: whole organism


title: Micorwell-seq datasets of Earthworm_8m_COL73

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For 6m earthworm dataset in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp). For 8m earthworm dataset in each COL, cellbarcode: in read1, the bases 1-6, 7-12, 13-18 are merged (18bp); UMI: in read1, the bases 19-24 (6bp).
scRNA-seq reads were aligned to the Eisenia andrei GWHACBE00000000 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Eisenia andrei GWHACBE00000000
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

organism: Eisenia andrei

value: 8 month


title: female_saline_D2_Brg1_rep1

description:
FS1D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Drosophila_D11_1


title: Micorwell-seq datasets of Earthworm_8m_COL72


title: HIF-2a KIN, batch1, rep1 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
HIF_2a_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 7


title: Lynch-DL-3532-12

city: San Francisco

first: Din

last: Lin

state: California

address: 513 Parnassus Ave.

institute: University of California, San Francisco

data_processing:
Quality control was performed using FASTQC v0.11.3 and quality trimming and adapter filtering with Trimmomatic v0.33 (Bolger et al., 2014)
The data in fastq format were mapped to mouse GRCm38
Gene list annotations were based on ensembl_mg_104 for mouse
RNA-seq datasets, raw read counts were converted to cpm using the edgeR package in R (www.R-project.org)
Assembly: GRCm38

source_name: Lung

extract_protocol:
RNA was harvested using RNAqueousTM-Micro Kit (Thermo Fisher Scientific). 4 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Preparation Kit (Illumina) following manufacturer's protocols.

value: Lung

value: WT

tag: treatment 1

value: Glycerol

tag: treatment 2

value: PBS


title: Lynch-DL-3532-09


title: female_saline_D1_Brg1_rep3

description:
FS3D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

extract_protocol:
Nuclei were prepared through discontinuous sucrose gradient centrifugation, isolated through INTACT approach, and subject to CUT&RUN procedures.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacture instructions.

value: male


title: Micorwell-seq datasets of Earthworm_8m_COL74


title: HIF-1b KIN, batch1, rep3 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-1b loci N-terminally tagged with V5 and Halo moieties
HIF_1b_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 6

value: V5-Halo-HIF-1b endogenous knock-in, clone A21


title: Lynch-DL-3532-11


title: Lynch-DL-3532-10


title: WT, batch1, rep3 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 3

value: Wild type


title: HIF-1b KIN, batch1, rep1 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-1b loci N-terminally tagged with V5 and Halo moieties
HIF_1b_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 4


title: HIF-2a KIN, batch1, rep2 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
HIF_2a_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 8


title: female_saline_D1_Brg1_rep2

description:
FS2D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Brg1 (13-2002, EpiCypher)

value: IP-injection


title: HIF-1b KIN, batch1, rep2 [polyA RNA-seq]

description:
Homozygous clonal cell line with endogenous HIF-1b loci N-terminally tagged with V5 and Halo moieties
HIF_1b_KIN_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 5

value: Clear cell renal cell carcinoma


title: Micorwell-seq datasets of Earthworm_8m_COL71


title: Micorwell-seq datasets of Earthworm_8m_COL70


title: Lynch-DL-3532-08


title: female_saline_D2_Brg1_rep2

description:
FS2D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Lynch-DL-3532-06

value: CRA


title: WT, batch1, rep2 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 2


title: Lynch-DL-3532-07


title: female_saline_D1_Brg1_rep1

description:
FS1D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_Brg1_control_rep3

description:
MC3D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: IgG (2729, Cell Signaling)


title: WT, batch1, rep1 [polyA RNA-seq]

description:
Wild type 786-O ccRCC line
WT_merged_batch1_RNAseq_hg38.bw
polyA RNA-seq library 1


title: Lynch-DL-3532-05


title: HIF-1a/2a, IgG, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC076_on_YC069_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 36

data_processing:
library strategy: CUT&RUN
Quality check: FastQC
Read alignment: bowtie2 version 2.3.4.1 (--local --no-unal --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 ); hg38
sam to bam conversion, sorting and indexing: Samtools version 1.8
Read coverage: deepTools (version 3.5.1) bamCoverage (--binSize 20 --normalizeUsing BPM --smoothLength 60)
Peak calling: MACS2 (--keep-dup all --max-gap 400 -g hs --bdg -q 0.01 -f BAMPE), using correspongind IgG controls
Remove blacklist: bedtools version 2.28.0 (intersect -v)
Assembly: hg38
Supplementary files format and content: bigWig files: read coverage per 20-bp bins across the genome; one file for each replicate
Supplementary files format and content: narrowPeak: narrowPeak output from MACS2, generated with anti-V5 data file and corresponding IgG control data file

extract_protocol:
Chromatin was digested with final 0.1% SDS and 0.25 mg/ml Proteinase K for 1h at 50 °C, and extracted once with equal volume of Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) and then with equal volume of chloroform (Fisher)
Up to 40 ng of purified DNA was used for preparing library, using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®  (NEB E7645)


title: Micorwell-seq datasets of Earthworm_8m_COL67


title: male_cocaine_D2_Brg1_control_rep1

description:
MC1D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: Lynch-DL-3532-04


title: male_cocaine_D2_Brg1_control_rep2

description:
MC2D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-1a/2a, IgG, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC038_on_YC032_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 34


title: male_cocaine_D1_Brg1_control_rep3

description:
MC3D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-1a/2a, IgG, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC062_on_YC056_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 35


title: HIF-1a/2a, anti-V5, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC076_on_YC069_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 33


title: Micorwell-seq datasets of Earthworm_8m_COL66


title: Lynch-DL-3532-02


title: male_cocaine_D1_Brg1_control_rep2

description:
MC2D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Lynch-DL-3532-01


title: Micorwell-seq datasets of Earthworm_8m_COL64


title: Micorwell-seq datasets of Earthworm_8m_COL63


title: HIF-1a, IgG, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC075_on_YC068_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 30

value: Exogenous V5-Halo-HIF-1{alpha}


title: Micorwell-seq datasets of Earthworm_8m_COL65

value: whole organism


title: male_saline_D2_Brg1_control_rep3

description:
MS3D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: Lynch-DL-3532-03

value: Lung


title: male_saline_D2_Brg1_control_rep1

description:
MS1D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Micorwell-seq datasets of Earthworm_8m_COL69

value: 8 month


title: Micorwell-seq datasets of Earthworm_8m_COL68


title: male_saline_D2_Brg1_control_rep2

description:
MS2D2CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D1_Brg1_control_rep1

description:
MC1D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-1a/2a, anti-V5, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC062_on_YC056_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 32


title: Micorwell-seq datasets of Earthworm_8m_COL62


title: HIF-1a, IgG, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC037_on_YC031_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 28


title: HIF-1a/2a, anti-V5, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-1α/2α chimeric protein (aa 1-363 of HIF-1α and aa 366-870 of HIF-2α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC038_on_YC032_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 31


title: Micorwell-seq datasets of Earthworm_8m_COL61


title: Micorwell-seq datasets of Earthworm_8m_COL58


title: HIF-1a, IgG, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC061_on_YC055_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 29


title: Micorwell-seq datasets of Earthworm_8m_COL59


title: Micorwell-seq datasets of Earthworm_8m_COL60


title: male_saline_D1_Brg1_control_rep3

description:
MS3D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-1a, anti-V5, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC075_on_YC068_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 27


title: male_saline_D1_Brg1_control_rep2

description:
MS2D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Micorwell-seq datasets of Earthworm_8m_COL56


title: HIF-1a, anti-V5, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC061_on_YC055_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 26


title: male_saline_D1_Brg1_control_rep1

description:
MS1D1CC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_Brg1_rep3

description:
MC3D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_Brg1_rep2

description:
MC2D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: R367N_siSOX9_S9

city: Gothenburg

first: Martin

last: Johansson

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

data_processing:
Quality of the data was assessed using FastQC (version 0.11.3)
Data was mapped to the human reference genome from Ensembl database (hg19/GRCh37) using STAR (version 2.5.2b)
Mapped reads for each gene were counted using FeatureCount (version 1.6.4)
Differentially expressed genes analysis was performed using DESeq2 (version 1.28.1) in R (version 3.6.1)
Assembly: hg19/GRCh37
Supplementary files format and content: matrix_fixed.txt is a text file containing counts for each sample (columns) and gene (rows)

source_name: Kidney

growth_protocol: Cells were maintained in DMEM low glucose supplemented with 10% FBS and 1% PEST in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Trizol and Qiagen RNeasy kit. 500 ng of total RNA was used for library construction.
Illumina TruSeq Stranded mRNA Library Prep was used for library construction following the manufacturer's protocol with a modification of 15 to 13 PCR cycles in the "Enrich DNA Fragment" step.

treatment_protocol: Cells were transfected with 50 nM siRNA for SOX9 (siSOX9), negative control (siSCR) or control medium (ctrl) for 24 h before harvest.

value: Kidney

value: Primary tubular epithelial cells

value: WT

value: siSOX9 transfection


title: Micorwell-seq datasets of Earthworm_8m_COL55


title: HIF-2a/1a, IgG, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC060_on_YC054_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 23


title: HIF-1a, anti-V5, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-1α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC037_on_YC031_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 25


title: male_cocaine_D1_Brg1_rep3

description:
MC3D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: Micorwell-seq datasets of Earthworm_8m_COL57


title: R367N_siSCR_S8

value: siSCR transfection


title: male_cocaine_D2_Brg1_rep1

description:
MC1D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Brg1 (13-2002, EpiCypher)

value: IP-injection


title: HIF-2a/1a, IgG, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC074_on_YC067_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 24

value: Clear cell renal cell carcinoma


title: R367N_ctrl_S7

value: Control


title: HIF-2a/1a, IgG, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC036_on_YC030_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 22


title: R362N_siSCR_S5


title: Micorwell-seq datasets of Earthworm_8m_COL52


title: male_cocaine_D1_Brg1_rep2

description:
MC2D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine


title: Micorwell-seq datasets of Earthworm_8m_COL51


title: HIF-2a/1a, anti-V5, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC036_on_YC030_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 19


title: HIF-2a/1a, anti-V5, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC074_on_YC067_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 21


title: Micorwell-seq datasets of Earthworm_8m_COL50


title: HIF-2a/1a, anti-V5, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of a HIF-2α/1α chimeric protein (aa 1-365 of HIF-2α and aa 364-826 of HIF-1α) N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC060_on_YC054_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 20


title: R362N_ctrl_S4


title: male_saline_D2_Brg1_rep3

description:
MS3D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: HIF-2a, IgG, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC073_on_YC066_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 18

value: Exogenous V5-Halo-HIF-2{alpha}


title: R358N_siSOX9_S3


title: Micorwell-seq datasets of Earthworm_8m_COL53

value: whole organism


title: HIF-2a, IgG, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC059_on_YC053_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 17


title: R362N_siSOX9_S6


title: R358N_siSCR_S2


title: Microwell-seq datasets of Zebrafish_24hpf_COL56

value: AB

value: 24 hours


title: HIF-2a, IgG, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC035_on_YC029_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 16


title: R358N_ctrl_S1


title: Microwell-seq datasets of Zebrafish_24hpf_COL55


title: male_cocaine_D1_Brg1_rep1

description:
MC1D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_saline_D2_Brg1_rep1

description:
MS1D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: HIF-2a, anti-V5, rep3 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC073_on_YC066_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 15


title: HIF-2a, anti-V5, rep2 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC059_on_YC053_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 14


title: male_saline_D1_Brg1_rep3

description:
MS3D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_saline_D1_Brg1_rep2

description:
MS2D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Zebrafish_24hpf_COL53


title: male_saline_D1_Brg1_rep1

description:
MS1D1B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Zebrafish_24hpf_COL52


title: HIF-2a, anti-V5, rep1 [CUT&Run]

description:
Stable cell line with an L30 promoter driving exogenous expression of wild type HIF-2α N-terminally fused with V5-HaloTag through a short peptide linker sequence (GDGAGLIN)
YC035_on_YC029_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 13


title: Media, 4Hr, Donor B

data_processing:
Quality control was performed using FASTQC v0.11.3 and quality trimming and adapter filtering with Trimmomatic v0.33 (Bolger et al., 2014)
The data in fastq format were mapped to human GRCh38
Gene list annotations were based on ensembl_hg_100 for human
RNA-seq datasets, raw read counts were converted to cpm using the edgeR package in R (www.R-project.org)
Assembly: GRCh38

source_name: Primary macrophage

value: Primary macrophage

value: Media

tag: time

tag: individual

value: donor B


title: Media, 8Hr, Donor B

value: WT


title: Media, 8Hr, Donor A

value: donor A


title: female_cocaine_D2_FosB_control_rep3

description:
FC3D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: IgG (2729, Cell Signaling)


title: Media, 4Hr, Donor A


title: HIF-2a KIN, IgG, rep3 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC072_on_YC065_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 12

tag: cell line

value: V5-Halo-HIF-2a endogenous knock-in, clone A31


title: Microwell-seq datasets of Zebrafish_24hpf_COL58


title: Microwell-seq datasets of Zebrafish_24hpf_COL57


title: female_cocaine_D2_FosB_control_rep2

description:
FC2D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: male_saline_D2_Brg1_rep2

description:
MS2D2B1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Brg1 (13-2002, EpiCypher)


title: Microwell-seq datasets of Zebrafish_24hpf_COL50


title: HIF-2a KIN, IgG, rep2 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC058_on_YC052_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 11

value: Clear cell renal cell carcinoma


title: female_cocaine_D2_FosB_control_rep1

description:
FC1D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: cocaine


title: Microwell-seq datasets of Zebrafish_72hpf_COL104

value: 72 hours

value: whole organism


title: Media, 24Hr, Donor B


title: HIF-2a KIN, IgG, rep1 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC034_on_YC028_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 10


title: Media, 24Hr, Donor A


title: female_cocaine_D1_FosB_control_rep3

description:
FC3D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: DMSO, 8Hr, Donor B

value: DMSO


title: Microwell-seq datasets of Zebrafish_72hpf_COL103

value: AB


title: female_cocaine_D1_FosB_control_rep2

description:
FC2D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: HIF-2a KIN, anti-V5, rep3 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC072_on_YC065_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 9


title: HIF-2a KIN, anti-V5, rep2 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC058_on_YC052_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 8


title: Microwell-seq datasets of Zebrafish_72hpf_COL102


title: DMSO, 8Hr, Donor A

value: Primary macrophage


title: female_cocaine_D1_FosB_control_rep1

description:
FC1D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: DMSO, 4Hr, Donor B


title: Microwell-seq datasets of Zebrafish_24hpf_COL51

value: 24 hours


title: female_saline_D2_FosB_control_rep3

description:
FS3D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: Microwell-seq datasets of Zebrafish_72hpf_COL101


title: WT, IgG, rep3 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC071_on_YC064_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 6

value: Wild type


title: Microwell-seq datasets of Zebrafish_72hpf_COL100


title: DMSO, 4Hr, Donor A

value: WT

value: donor A


title: DMSO, 24Hr, Donor B

value: donor B


title: Microwell-seq datasets of Zebrafish_72hpf_COL99


title: WT, IgG, rep2 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC057_on_YC051_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 5


title: Microwell-seq datasets of Zebrafish_72hpf_COL98


title: WT, IgG, rep1 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC033_on_YC027_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 4


title: female_saline_D1_FosB_control_rep3

description:
FS3D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: IgG (2729, Cell Signaling)


title: 12,13-diHOME & Peanut, 8Hr, Donor B

value: 12,13-diHOME & Peanut


title: DMSO, 24Hr, Donor A


title: WT, anti-V5, rep3 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC071_on_YC064_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 3

value: Clear cell renal cell carcinoma


title: Microwell-seq datasets of Zebrafish_72hpf_COL97


title: female_saline_D1_FosB_control_rep2

description:
FS2D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: IP-injection


title: 12,13-diHOME & Peanut, 8Hr, Donor A


title: Micorwell-seq datasets of Zebrafish_72hpf_COL95

value: 72 hours


title: 12,13-diHOME & Peanut, 4Hr, Donor B


title: HIF-2a KIN, anti-V5, rep1 [CUT&Run]

description:
Homozygous clonal cell line with endogenous HIF-2a loci N-terminally tagged with V5 and Halo moieties
YC034_on_YC028_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 7

value: V5-Halo-HIF-2a endogenous knock-in, clone A31


title: female_cocaine_D2_FosB_rep3

description:
FC3D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: FosB (2251, Cell Signaling)


title: WT, anti-V5, rep2 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC057_on_YC051_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 2


title: female_cocaine_D2_FosB_rep2

description:
FC2D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Micorwell-seq datasets of Zebrafish_72hpf_COL93

value: AB

value: whole organism


title: female_saline_D2_FosB_control_rep2

description:
FS2D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: female_saline_D2_FosB_control_rep1

description:
FS1D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 12,13-diHOME & Peanut, 24Hr, Donor B

value: Primary macrophage


title: WT, anti-V5, rep1 [CUT&Run]

description:
Wild type 786-O ccRCC line
YC033_on_YC027_peaks_peaks.removedblacklist.narrowPeak
CUT&Run library 1

value: Wild type


title: 12,13-diHOME & Peanut, 4Hr, Donor A

value: WT

value: donor A


title: female_saline_D1_FosB_control_rep1

description:
FS1D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: 12,13-diHOME & Peanut, 24Hr, Donor A


title: Micorwell-seq datasets of Zebrafish_72hpf_COL94


title: Micorwell-seq datasets of Zebrafish_72hpf_COL92


title: female_cocaine_D1_FosB_rep3

description:
FC3D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: TL_MOLM14_UT_2

city: Orange

first: Matthew

middle: D

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
library strategy: TimeLapse-seq (TL-seq)
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For TL-seq, reads were aligned to the GRCh38 genome using HISAT-3N aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Assembly: GRCh38
Supplementary files format and content: tdf

source_name: MOLM-14 cells

growth_protocol: MOLM-14 cells were cultured in RPMI (ATCC 30-2001) supplemented with 10% fetal bovine serum (Biological Industries; cat. No. S1480) and 1% Pen/Strep (ThermoFisher; cat. no. 15140122).

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq (TL-seq) genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TimeLapse-seq RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry using mCPBA as the oxidant as described in Schofield et al. Nature Methods 2018.
TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: MOLM-14 cells were treated with 1 µM JCS-1, JCS-2, RG3039, or DMSO for 6 hours,  and/or 100 µM s4U for 120 minutes. In all cases the s4U labeling was the last 120 minutes of small molecule treatment.

value: none; untreated

tag: s4u feed

value: Yes


title: Micorwell-seq datasets of Zebrafish_72hpf_COL91


title: female_cocaine_D2_FosB_rep1

city: New York

first: Eric

last: Nestler

address: 1425 Madison Ave L10-26

institute: Icahn School of Medicine at Mount Sinai

description:
FC1D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 12,13-diHOME, 8Hr, Donor B

value: donor B


title: female_cocaine_D1_FosB_rep2

description:
FC2D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: Micorwell-seq datasets of Zebrafish_72hpf_COL96


title: 12,13-diHOME, 8Hr, Donor A


title: TL_MOLM14_RG3039_1


title: Micorwell-seq datasets of Zebrafish_72hpf_COL90


title: TL_MOLM14_JCS2_2


title: Micorwell-seq datasets of Zebrafish_72hpf_COL89


title: TL_MOLM14_UT_1


title: female_cocaine_D1_FosB_rep1

description:
FC1D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: 12,13-diHOME, 4Hr, Donor B


title: female_saline_D2_FosB_rep3

description:
FS3D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: TL_MOLM14_JCS2_1


title: 12,13-diHOME, 4Hr, Donor A


title: Micorwell-seq datasets of Zebrafish_72hpf_COL87

value: 72 hours


title: Micorwell-seq datasets of Zebrafish_72hpf_COL88


title: TL_MOLM14_RG3039_2


title: TL_MOLM14_JCS1_2


title: female_saline_D2_FosB_rep2

description:
FS2D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_saline_D2_FosB_rep1

description:
FS1D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.