title: Donor3, AMD patient

description:
Library name: D3RPE
Donor3, AMD patient

data_processing:
Cell Ranger software
Assembly: hg38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
The tenets of the Declaration for Helsinki for research involving human tissue were followed. Human eyes (n=3) were obtained from the Advancing Sight Network (Birmingham, AL). Preliminary experiments were conducted to determine the viability of RPE that was based on death to enucleation (D-E) time. Single cell RNA-seq on normal eyes from two different 86 yr old female donors with D-E of 3.3 and 6 hr with experimentation time of <24 hours and found that the 3.3 hr D-E interval globe exhibited superior viability (>70%), and nearly double the number of genes detected per cell (1301 vs 708 genes/cell). Therefore, globes with D-E times of < 6 hr and death to experimentation of <24 hr. Specifically, human globes from a 79 yr old female nonsmoker without AMD with a death to enucleation (D-E) time of 4.9 hr, a 67 yr old male smoker without AMD with a D-E of 3.8 hr, and a 67 yr old female smoker with early AMD (Minnesota Grade 2) with a D-E of 1.8 hr were immediately preserved on ice for overnight shipping to Hopkins, and dissected no later than 16 hr postmortem. After removing the anterior segment, the fundus was examined both with the retina and with the retina removed and classified using the Minnesota Grading Scale105. A 6 mm sample of the RPE/choroid in the macula was obtained using a 6 mm punch (Integra Lifesciences, Princeton, NJ) that was centered around the fovea. RPE/choroidal cells were dissociated using Papain Dissociation System (Worthington Biochemical, Lakewood, NJ) following the manufacturer’s instructions. Dissociated cells were resuspended in ice-cold PBS, 0.04% BSA and 0.5 U/μl of RNAse inhibitors. Cells were then filtered through a 50μm filter and processed for single-cell RNA-sequencing. Cell viability (>90%) was confirmed by negative staining with trypan blue.
ScRNA-seq libraries were generated using the Chromium Next GEM single Multiome ATAC+Gene Expression kit protocol (10X Genomics, Inc.). Nuclei resuspended (10-15k) in 0.1X Nuclei Buffer were incubated with a transposition mix containing transposase. Gel Beads in Emulsion (GEMs) were generated by mixing transposed nuclei, barcoded Gel Beads, and partitioning oil on a chromium NEXT GEM Chip controller. After GEM generation, oligonucleotides included Illumina® P5 sequence barcodes for ATAC library and cDNA included an Illumina® TruSeq Read 1 (read 1 sequencing primer), 16 nt 10x Barcode (for GEX), 12 nt unique molecular identifier (UMI) and a 30 nt poly(dT) sequence. Magnetic beads (SILANE) were used to clean up barcoded products from the obtained GEM-RT reaction mixture. ATAC libraries were amplified with 10 PCR cycles and were sequenced on Illumina NovaSeq with 25,000 read pairs per nucleus. RNA libraries were amplified from cDNA with 14 PCR cycles and were sequenced on Illumina NovaSeq with 50,000 reads per nucleus.

value: Eye

value: RPE

value: tissue

value: AMD patient


title: ZE4-2

status: Public on Jan 03 2026

type: SRA

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

country: China

institute: Xiamen University

description:
Library name: ZE4-2
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

library_source: transcriptomic single cell

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/linl-linl/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

molecule: polyA RNA

organism: Danio rerio

source_name: Cleavage stage

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.

treatment_protocol: The cellular contents of SW480 cells were extracted initially prior to the ARV771 treatment, designated as the sample at 0 h. Immediately thereafter 250 nM ARV771 was added to the culture medium, and the cells were extracted at 1 h and 4 h.

tag: tissue

value: Cleavage stage

tag: cell line

value: Zebrafish blastomeres

tag: cell type

value: Cleavage

tag: genotype

value: WT


title: Donor2, healthy control

city: Baltimore

first: Yang

last: Jin

state: MD

address: 620 Boulton St. Bel Air

country: USA

institute: Johns Hopkins University

description:
Library name: D2RPE
Donor2, healthy control

molecule: total RNA

organism: Homo sapiens

source_name: Eye

tag: treatment

value: healthy control

tag: batch


title: RB_MG_2

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

description: Library name: RB_MG_2

library_source: transcriptomic

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Assembly: ASM333518v2
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Laodelphax striatellus

source_name: midgut

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

value: midgut

value: RBSDV infection


title: ZE4-1

description:
Library name: ZE4-1
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: RB_MG_1

description: Library name: RB_MG_1


title: WPS1

description:
Library name: WPS1
expression matrix (txt) and original file (fastq)
Each human sample represents a pool of single cells.

source_name: colon

value: colon

value: colon cancer cell line


title: Donor1, smoker control

description:
Library name: D1RPE_2
Donor1, smoker control

value: smoker control


title: ZE2-1

description:
Library name: ZE2-1
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: ZE1-1

description:
Library name: ZE1-1
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

source_name: Zygote

value: Zygote


title: ZE2-2

description:
Library name: ZE2-2
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: WPS2

description:
Library name: WPS2
expression matrix (txt) and original file (fastq)
Each human sample represents a pool of single cells.


title: 86488: TREM2-192  - BIONi010-C7 R47H

status: Public on Jan 02 2026

type: RNA

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg

country: Belgium

institute: Janssen Research & Development

description: TREM2-192  - BIONi010-C7 R47H

hyb_protocol: Biotin-labeled target samples were hybridized to the Clariom™ GO Screen. Target hybridization was processed on the GeneTitan® Instrument according to manufacturer’s instructions provided for Expression Array Plates (P/N 952361).

scan_protocol: Images were analyzed using the GeneChip® Command Console Software (GCC) (ThermoFisher)

data_processing: Microarray data were processed using the statistical computing R-program (R version 3.6.1) and Bioconductor tools. The gene expression values were normalized using Robust Multi-array Average (RMA). Individual probes were grouped into gene-specific probe sets based on Entrez Gene using the metadata package goscreenhuhsentrezg (version 25.0.0)

label: biotin

source_name: BIONi010-C7 R47H

label_protocol: Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902790).

growth_protocol: Human iPSC-derived microglia were differentiated using a method described by Cowley

extract_protocol: Total cellular RNA was isolated using the RNeasy96 kit (Qiagen, 74182) according to manufacturer’s protocol.

value: cultured human microglia

tag: aso


title: 86507: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86508: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86490: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO

source_name: BIONi010-C17 KO


title: 86461: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 86485: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 86440: TREM2-192  - BIONi010-C7 R47H

description: TREM2-192  - BIONi010-C7 R47H


title: 86464: TREM2-192  - BIONi010-C7 R47H

description: TREM2-192  - BIONi010-C7 R47H


title: 86465: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT

source_name: BIONi010-C WT


title: 86437: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 86442: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO


title: 86487: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 86489: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT


title: 86436: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 86439: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 86509: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86484: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 86460: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 86463: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 86438: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 86483: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 86441: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT


title: 86486: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 86466: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO


title: 86435: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 86462: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 86459: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 86517: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86516: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86515: Malat1  - BIONi010-C7 R47H

description: Malat1  - BIONi010-C7 R47H


title: 86448: TREM2-192  - BIONi010-C7 R47H

description: TREM2-192  - BIONi010-C7 R47H


title: 78977: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A

value: SCR ASO


title: 86496: TREM2-192  - BIONi010-C7 R47H

description: TREM2-192  - BIONi010-C7 R47H


title: 86472: TREM2-192  - BIONi010-C7 R47H

description: TREM2-192  - BIONi010-C7 R47H


title: 79024: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 86474: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO


title: 79025: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A


title: 86493: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 86469: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 79001: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A


title: 78975: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: 86495: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 79023: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: 86447: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 86450: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO


title: 78974: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A

value: Malat1 ASO


title: 78998: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A


title: 86445: TREM2-171  - BIONi010-C7 R47H

description: TREM2-171  - BIONi010-C7 R47H


title: 79000: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 79021: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: 86444: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 78976: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 79020: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: 78999: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: 79022: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A


title: 86492: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 86498: Malat1  - BIONi010-C17 KO

description: Malat1  - BIONi010-C17 KO


title: 78996: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: 86471: TREM2-192  - BIONi010-C17 KO

description: TREM2-192  - BIONi010-C17 KO


title: 86470: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 86468: TREM2-171  - BIONi010-C17 KO

description: TREM2-171  - BIONi010-C17 KO


title: 78964: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A

value: APOE-13 OPS


title: 86446: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 86491: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 78997: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: 86473: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT


title: 78965: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A


title: 86497: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT


title: 78972: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: 78898: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: 86494: TREM2-192  - BIONi010-C WT

description: TREM2-192  - BIONi010-C WT


title: 78897: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: 86443: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 86525: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H

value: no treatment


title: 78945: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: 78963: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A


title: 78921: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: 86524: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 86467: TREM2-171  - BIONi010-C WT

description: TREM2-171  - BIONi010-C WT


title: 78946: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: 86504: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 78973: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: 86523: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 78922: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: 78940: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3

value: APOE-1 OPS


title: 78917: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 79033: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A


title: 86449: Malat1  - BIONi010-C WT

description: Malat1  - BIONi010-C WT


title: 86501: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 86482: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 79032: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 86458: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 79009: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A


title: 86477: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 79008: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 86506: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 86456: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 78941: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 78893: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 78985: SCR ASO_UKBi011-A

description: SCR ASO_UKBi011-A


title: 78916: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3


title: 86480: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 78892: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3


title: 78939: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 79007: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 4 Gene Expression Library

city: SALT LAKE CITY

first: Clayton

last: Carey

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

description:
Library name: MIC-Drop-seq_pool4_rep4_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 16. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x16_filtered_barcodes.tsv.gz
50gene_x16_filtered_features.tsv.gz
50gene_x16_filtered_matrix.mtx.gz
50gene_x16_raw_barcodes.tsv.gz
50gene_x16_raw_features.tsv.gz
50gene_x16_raw_matrix.mtx.gz

data_processing:
For scRNAseq, Cell Ranger v7 was used to align and count features (using 'mic_drop_pilot_feature_reference.csv' for pilot samples and 'micdrop_50_gene_feature_reference.csv' for the 50-gene screen).. The output matrices contain both Gene Expression and CRISPR Guide Capture features. Consequently, the same processed matrix file is linked to both the GEX and CRISPR Sample entries for each biological replicate.
for amplicon sequencing (amplicon_injected, amplicon_wildtype), no data processing is performed
Assembly: GRCZ v4.3.2
Supplementary files format and content: Feature-barcode matricies, filtered and unfiltered, generated by cellranger v7
Supplementary files format and content: Amplicon sequencing: quantification of indel frequency at each locus in edited embryos and wt embryos.

source_name: whole embryo

growth_protocol: Zebrafish embryos raised in E3 medium at 28C for 24 hrs

extract_protocol:
enzymatic dissociation
10X genomics next-gem 3' V3 with feature barcoding

treatment_protocol: CRISPR RNP injection

value: whole embryo


title: 86453: no treatment - BIONi010-C7 R47H

description: no treatment - BIONi010-C7 R47H


title: 86499: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 78983: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: 79030: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A


title: 78982: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A


title: 78915: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 86503: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 86502: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 79029: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: 86478: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 86479: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 78891: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 78984: SCR ASO_UKBi011-A-3

description: SCR ASO_UKBi011-A-3


title: 86476: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 4 CRISPR Library

description:
Library name: MIC-Drop-seq_pool4_rep4_crispr
10x CRISPR Feature Barcoding library for Sample 16. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x16_filtered_barcodes.tsv.gz
50gene_x16_filtered_features.tsv.gz
50gene_x16_filtered_matrix.mtx.gz
50gene_x16_raw_barcodes.tsv.gz
50gene_x16_raw_features.tsv.gz
50gene_x16_raw_matrix.mtx.gz

library_source: other

molecule: other


title: 86452: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 79028: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 2 CRISPR Library

description:
Library name: MIC-Drop-seq_pool4_rep2_crispr
10x CRISPR Feature Barcoding library for Sample 14. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x14_filtered_barcodes.tsv.gz
50gene_x14_filtered_features.tsv.gz
50gene_x14_filtered_matrix.mtx.gz
50gene_x14_raw_barcodes.tsv.gz
50gene_x14_raw_features.tsv.gz
50gene_x14_raw_matrix.mtx.gz


title: 78981: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 3 CRISPR Library

description:
Library name: MIC-Drop-seq_pool4_rep3_crispr
10x CRISPR Feature Barcoding library for Sample 15. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x15_filtered_barcodes.tsv.gz
50gene_x15_filtered_features.tsv.gz
50gene_x15_filtered_matrix.mtx.gz
50gene_x15_raw_barcodes.tsv.gz
50gene_x15_raw_features.tsv.gz
50gene_x15_raw_matrix.mtx.gz


title: 79004: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: 86457: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 1 CRISPR Library

description:
Library name: MIC-Drop-seq_pool4_rep1_crispr
10x CRISPR Feature Barcoding library for Sample 13. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x13_filtered_barcodes.tsv.gz
50gene_x13_filtered_features.tsv.gz
50gene_x13_filtered_matrix.mtx.gz
50gene_x13_raw_barcodes.tsv.gz
50gene_x13_raw_features.tsv.gz
50gene_x13_raw_matrix.mtx.gz


title: 79031: SCR ASO_UKBi011-A-1

description: SCR ASO_UKBi011-A-1


title: 86505: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 86500: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 86455: no treatment - BIONi010-C17 KO

description: no treatment - BIONi010-C17 KO


title: 78968: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 1 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool4_rep1_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 13. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x13_filtered_barcodes.tsv.gz
50gene_x13_filtered_features.tsv.gz
50gene_x13_filtered_matrix.mtx.gz
50gene_x13_raw_barcodes.tsv.gz
50gene_x13_raw_features.tsv.gz
50gene_x13_raw_matrix.mtx.gz


title: 86481: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 78966: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A


title: 79005: Malat1 ASO_UKBi011-A-3

description: Malat1 ASO_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 2 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool4_rep2_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 14. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x14_filtered_barcodes.tsv.gz
50gene_x14_filtered_features.tsv.gz
50gene_x14_filtered_matrix.mtx.gz
50gene_x14_raw_barcodes.tsv.gz
50gene_x14_raw_features.tsv.gz
50gene_x14_raw_matrix.mtx.gz


title: 79006: Malat1 ASO_UKBi011-A

description: Malat1 ASO_UKBi011-A


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 4 CRISPR Library

description:
Library name: MIC-Drop-seq_pool3_rep4_crispr
10x CRISPR Feature Barcoding library for Sample 12. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x12_filtered_barcodes.tsv.gz
50gene_x12_filtered_features.tsv.gz
50gene_x12_filtered_matrix.mtx.gz
50gene_x12_raw_barcodes.tsv.gz
50gene_x12_raw_features.tsv.gz
50gene_x12_raw_matrix.mtx.gz


title: 86451: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 78954: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: 86475: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: 78930: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 4 Replicate 3 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool4_rep3_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 15. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x15_filtered_barcodes.tsv.gz
50gene_x15_filtered_features.tsv.gz
50gene_x15_filtered_matrix.mtx.gz
50gene_x15_raw_barcodes.tsv.gz
50gene_x15_raw_features.tsv.gz
50gene_x15_raw_matrix.mtx.gz


title: Control

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

description: Library name: Sample 1

data_processing:
Reads were aligned to the human genome (hg38) using Bowtie2. Gene-level counts were generated with HTSeq.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing  gene counts, and FC adn log2(FC)

source_name: Thyroid tissue

extract_protocol:
Total RNA was extracted from tissue and cell samples stored in TRIzol using the Direct-zol RNA kit (Zymo Research, USA), according to the manufacturer’s instructions. RNA concentration was measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and the 260/280 ratio was recorded. RNA integrity was assessed using a Fragment Analyzer system (Agilent, USA).
The RNA sequencing library from one patient was prepared using the MGIEasy RNA Library Prep Kit V3.1 (MGI, China) following rRNA depletion with the Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China). Library circularization was performed using MGIEasy Circularization Module V2.0 (MGI).

value: Thyroid tissue


title: Tumor

description: Library name: Sample 2


title: 78929: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: LM548

city: Barcelona

first: Pau

last: Sancho

address: C/ Rosselló, 149-153

country: Spain

institute: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)

description:
Library name: LM548
scRNA-seq 3'

data_processing:
High quality reads were mapped according to the Cellranger pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: h5 files containing gene expression values as UMI counts

source_name: liver organoid

extract_protocol:
Liver samples: Liver biopsies from ALD patien ts (n=2) were processed and dissociated into single cell suspensions following the protocol reported by MacParland SA et al. Organoids: Hep b-orgs (n = 4; n=1 early stage, n= 3 advanced stage) were dissociated into single cell by incubating for 30 minutes in a water bath with gently shaking at 37ºC with TrypLE Express (Gibco, 12604021) supplemented with 2mM EDTA (Life Technologies, 15575-020). Next, mild pipetting was performed to ensure organoids disaggregation. Cell suspension was filtered using a 40-um nylon mesh, pelleted, resuspended in 0.04% BSA in DPBS-/- and transported on ice until further processing.
Single-cell RNA sequencing libraries were prepared using the Chromium 3' protocol

value: epithelial cells

value: liver organoid


title: 86454: no treatment - BIONi010-C WT

description: no treatment - BIONi010-C WT


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 2 CRISPR Library

description:
Library name: MIC-Drop-seq_pool3_rep2_crispr
10x CRISPR Feature Barcoding library for Sample 10. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x10_filtered_barcodes.tsv.gz
50gene_x10_filtered_features.tsv.gz
50gene_x10_filtered_matrix.mtx.gz
50gene_x10_raw_barcodes.tsv.gz
50gene_x10_raw_features.tsv.gz
50gene_x10_raw_matrix.mtx.gz


title: LM545

description:
Library name: LM545
scRNA-seq 3'


title: 78949: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 78925: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 78901: APOE-1 OPS_UKBi011-A

description: APOE-1 OPS_UKBi011-A


title: 78906: APOE-13 OPS_UKBi011-A-3

description: APOE-13 OPS_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 3 CRISPR Library

description:
Library name: MIC-Drop-seq_pool3_rep3_crispr
10x CRISPR Feature Barcoding library for Sample 11. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x11_filtered_barcodes.tsv.gz
50gene_x11_filtered_features.tsv.gz
50gene_x11_filtered_matrix.mtx.gz
50gene_x11_raw_barcodes.tsv.gz
50gene_x11_raw_features.tsv.gz
50gene_x11_raw_matrix.mtx.gz


title: 78967: APOE-13 OPS_UKBi011-A

description: APOE-13 OPS_UKBi011-A


title: 78905: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 4 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool3_rep4_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 12. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x12_filtered_barcodes.tsv.gz
50gene_x12_filtered_features.tsv.gz
50gene_x12_filtered_matrix.mtx.gz
50gene_x12_raw_barcodes.tsv.gz
50gene_x12_raw_features.tsv.gz
50gene_x12_raw_matrix.mtx.gz


title: 78899: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 78953: APOE-13 OPS_UKBi011-A-1

description: APOE-13 OPS_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 3 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool3_rep3_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 11. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x11_filtered_barcodes.tsv.gz
50gene_x11_filtered_features.tsv.gz
50gene_x11_filtered_matrix.mtx.gz
50gene_x11_raw_barcodes.tsv.gz
50gene_x11_raw_features.tsv.gz
50gene_x11_raw_matrix.mtx.gz


title: LM547

description:
Library name: LM547
scRNA-seq 3'


title: 78980: Malat1 ASO_UKBi011-A-1

description: Malat1 ASO_UKBi011-A-1


title: 79017: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 4 CRISPR Library

description:
Library name: MIC-Drop-seq_pool2_rep4_crispr
10x CRISPR Feature Barcoding library for Sample 8. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x8_filtered_barcodes.tsv.gz
50gene_x8_filtered_features.tsv.gz
50gene_x8_filtered_matrix.mtx.gz
50gene_x8_raw_barcodes.tsv.gz
50gene_x8_raw_features.tsv.gz
50gene_x8_raw_matrix.mtx.gz


title: LM526

description:
Library name: LM526
scRNA-seq 3'


title: 78948: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 2 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool3_rep2_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 10. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x10_filtered_barcodes.tsv.gz
50gene_x10_filtered_features.tsv.gz
50gene_x10_filtered_matrix.mtx.gz
50gene_x10_raw_barcodes.tsv.gz
50gene_x10_raw_features.tsv.gz
50gene_x10_raw_matrix.mtx.gz


title: 78924: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3


title: 78993: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: 78923: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 78900: APOE-1 OPS_UKBi011-A-3

description: APOE-1 OPS_UKBi011-A-3


title: 78990: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: L216

description: scRNA-seq 3'

tag: strain

value: organoid


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 1 CRISPR Library

description:
Library name: MIC-Drop-seq_pool3_rep1_crispr
10x CRISPR Feature Barcoding library for Sample 9. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x9_filtered_barcodes.tsv.gz
50gene_x9_filtered_features.tsv.gz
50gene_x9_filtered_matrix.mtx.gz
50gene_x9_raw_barcodes.tsv.gz
50gene_x9_raw_features.tsv.gz
50gene_x9_raw_matrix.mtx.gz


title: MIC-Drop-seq 50 gene screen. Pool 3 Replicate 1 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool3_rep1_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 9. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x9_filtered_barcodes.tsv.gz
50gene_x9_filtered_features.tsv.gz
50gene_x9_filtered_matrix.mtx.gz
50gene_x9_raw_barcodes.tsv.gz
50gene_x9_raw_features.tsv.gz
50gene_x9_raw_matrix.mtx.gz


title: L322

description: scRNA-seq 3'


title: B2BX

description: scRNA-seq 3'

source_name: liver

value: liver cells

value: liver

value: tissue


title: L285

description: scRNA-seq 3'


title: 78970: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: 79041: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: L286

description: scRNA-seq 3'


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 3 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool2_rep3_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 7. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x7_filtered_barcodes.tsv.gz
50gene_x7_filtered_features.tsv.gz
50gene_x7_filtered_matrix.mtx.gz
50gene_x7_raw_barcodes.tsv.gz
50gene_x7_raw_features.tsv.gz
50gene_x7_raw_matrix.mtx.gz


title: 79038: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: 79014: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: 78947: APOE-1 OPS_UKBi011-A-1

description: APOE-1 OPS_UKBi011-A-1


title: 78957: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 4 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool2_rep4_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 8. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x8_filtered_barcodes.tsv.gz
50gene_x8_filtered_features.tsv.gz
50gene_x8_filtered_matrix.mtx.gz
50gene_x8_raw_barcodes.tsv.gz
50gene_x8_raw_features.tsv.gz
50gene_x8_raw_matrix.mtx.gz


title: 78933: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 3 CRISPR Library

description:
Library name: MIC-Drop-seq_pool2_rep3_crispr
10x CRISPR Feature Barcoding library for Sample 7. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x7_filtered_barcodes.tsv.gz
50gene_x7_filtered_features.tsv.gz
50gene_x7_filtered_matrix.mtx.gz
50gene_x7_raw_barcodes.tsv.gz
50gene_x7_raw_features.tsv.gz
50gene_x7_raw_matrix.mtx.gz


title: 78971: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: A10B

description: scRNA-seq 3'


title: hi_naive_m_wt_replicate 3

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count

organism: Mus musculus

source_name: hippocampus

growth_protocol: Adult

extract_protocol:
RNA was isolated using TRIzol reagent followed by RNeasy mini kit for purification
Total RNA samples about 1-2 ug were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end sequencing protocol.

treatment_protocol: Alcohol injection, 2g EtOH/body weight

value: Naïve

tag: Sex

value: male

tag: genotype/variation

value: WT

value: Hippocampus


title: 78909: no treatment_UKBi011-A

description: no treatment_UKBi011-A

value: cultured human microglia


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 2 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool2_rep2_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 6. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x6_filtered_barcodes.tsv.gz
50gene_x6_filtered_features.tsv.gz
50gene_x6_filtered_matrix.mtx.gz
50gene_x6_raw_barcodes.tsv.gz
50gene_x6_raw_features.tsv.gz
50gene_x6_raw_matrix.mtx.gz


title: 78969: no treatment_UKBi011-A

description: no treatment_UKBi011-A


title: hi_naive_m_wt_replicate 4


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 2 CRISPR Library

description:
Library name: MIC-Drop-seq_pool2_rep2_crispr
10x CRISPR Feature Barcoding library for Sample 6. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x6_filtered_barcodes.tsv.gz
50gene_x6_filtered_features.tsv.gz
50gene_x6_filtered_matrix.mtx.gz
50gene_x6_raw_barcodes.tsv.gz
50gene_x6_raw_features.tsv.gz
50gene_x6_raw_matrix.mtx.gz


title: hi_naive_m_wt_replicate 1


title: 78989: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: 78992: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: hi_naive_m_KO_replicate 3

value: KO


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 1 CRISPR Library

description:
Library name: MIC-Drop-seq_pool2_rep1_crispr
10x CRISPR Feature Barcoding library for Sample 5. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x5_filtered_barcodes.tsv.gz
50gene_x5_filtered_features.tsv.gz
50gene_x5_filtered_matrix.mtx.gz
50gene_x5_raw_barcodes.tsv.gz
50gene_x5_raw_features.tsv.gz
50gene_x5_raw_matrix.mtx.gz


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 4 CRISPR Library

description:
Library name: MIC-Drop-seq_pool1_rep4_crispr
10x CRISPR Feature Barcoding library for Sample 4. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x4_filtered_barcodes.tsv.gz
50gene_x4_filtered_features.tsv.gz
50gene_x4_filtered_matrix.mtx.gz
50gene_x4_raw_barcodes.tsv.gz
50gene_x4_raw_features.tsv.gz
50gene_x4_raw_matrix.mtx.gz


title: 79037: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: hi_naive_m_wt_replicate 2


title: 78938: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: 79013: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 2 Replicate 1 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool2_rep1_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 5. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x5_filtered_barcodes.tsv.gz
50gene_x5_filtered_features.tsv.gz
50gene_x5_filtered_matrix.mtx.gz
50gene_x5_raw_barcodes.tsv.gz
50gene_x5_raw_features.tsv.gz
50gene_x5_raw_matrix.mtx.gz


title: hi_naive_m_KO_replicate 4


title: 78962: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: 79016: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: hi_naive_m_KO_replicate 2


title: 78932: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: 79040: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 4 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool1_rep4_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 4. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x4_filtered_barcodes.tsv.gz
50gene_x4_filtered_features.tsv.gz
50gene_x4_filtered_matrix.mtx.gz
50gene_x4_raw_barcodes.tsv.gz
50gene_x4_raw_features.tsv.gz
50gene_x4_raw_matrix.mtx.gz


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 2 CRISPR Library

description:
Library name: MIC-Drop-seq_pool1_rep2_crispr
10x CRISPR Feature Barcoding library for Sample 2. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x2_filtered_barcodes.tsv.gz
50gene_x2_filtered_features.tsv.gz
50gene_x2_filtered_matrix.mtx.gz
50gene_x2_raw_barcodes.tsv.gz
50gene_x2_raw_features.tsv.gz
50gene_x2_raw_matrix.mtx.gz


title: 78956: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: 78914: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: hi_naive_m_KO_replicate 1


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 3 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool1_rep3_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 3. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x3_filtered_barcodes.tsv.gz
50gene_x3_filtered_features.tsv.gz
50gene_x3_filtered_matrix.mtx.gz
50gene_x3_raw_barcodes.tsv.gz
50gene_x3_raw_features.tsv.gz
50gene_x3_raw_matrix.mtx.gz


title: 79012: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: 79036: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: 79039: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 3 CRISPR Library

description:
Library name: MIC-Drop-seq_pool1_rep3_crispr
10x CRISPR Feature Barcoding library for Sample 3. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x3_filtered_barcodes.tsv.gz
50gene_x3_filtered_features.tsv.gz
50gene_x3_filtered_matrix.mtx.gz
50gene_x3_raw_barcodes.tsv.gz
50gene_x3_raw_features.tsv.gz
50gene_x3_raw_matrix.mtx.gz


title: 78908: no treatment_UKBi011-A-3

description: no treatment_UKBi011-A-3


title: hi_naive_f_wt_replicate 3

value: female


title: hi_naive_f_wt_replicate 1


title: 78955: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1

value: no treatment


title: 78991: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: hi_naive_f_wt_replicate 4


title: hi_naive_f_wt_replicate 2


title: 78937: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: 79015: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 1 CRISPR Library

description:
Library name: MIC-Drop-seq_pool1_rep1_crispr
10x CRISPR Feature Barcoding library for Sample 1. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
50gene_x1_filtered_barcodes.tsv.gz
50gene_x1_filtered_features.tsv.gz
50gene_x1_filtered_matrix.mtx.gz
50gene_x1_raw_barcodes.tsv.gz
50gene_x1_raw_features.tsv.gz
50gene_x1_raw_matrix.mtx.gz


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 2 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool1_rep2_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 2. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x2_filtered_barcodes.tsv.gz
50gene_x2_filtered_features.tsv.gz
50gene_x2_filtered_matrix.mtx.gz
50gene_x2_raw_barcodes.tsv.gz
50gene_x2_raw_features.tsv.gz
50gene_x2_raw_matrix.mtx.gz


title: MIC-Drop-seq 50 gene screen. Pool 1 Replicate 1 Gene Expression Library

description:
Library name: MIC-Drop-seq_pool1_rep1_gex
10x Gene Expression library for 50 gene mic-drop-seq screen Sample 1. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
50gene_x1_filtered_barcodes.tsv.gz
50gene_x1_filtered_features.tsv.gz
50gene_x1_filtered_matrix.mtx.gz
50gene_x1_raw_barcodes.tsv.gz
50gene_x1_raw_features.tsv.gz
50gene_x1_raw_matrix.mtx.gz


title: 78931: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: MIC-Drop-seq proof-of-concept screen CRISPR Library - 8 genes in pooled embryos

description:
Library name: MIC-Drop-seq_pilot_crispr
10x CRISPR Feature Barcoding library for mic-drop-seq pilot study. Note: The processed counts for this library are contained within the combined processed data files for the associated gene expression library
pilot_scRNA_filtered_barcodes.tsv.gz
pilot_scRNA_filtered_features.tsv.gz
pilot_scRNA_filtered_matrix.mtx.gz
pilot_scRNA_raw_barcodes.tsv.gz
pilot_scRNA_raw_features.tsv.gz
pilot_scRNA_raw_matrix.mtx.gz


title: Control male N2

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample8

library_source: genomic

data_processing:
Reads were mapped to Mus musculus genome build mm10 with Bowtie2
bam files from two sequencing runs were merged for each biological replicate and all reads merged using SAMTools for downstream analysis
NGSplot was used to generate metaplots
deepTools was used to generate bigwig files
MACS3 was used for peak-calling
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: cortex

extract_protocol:
Cortices were microdissected and flash-frozen 2h after seizure. Nuclei were isolated using an iodixanol gradient and collected in Wash-Buffer (Kaya-Okur et al. 2019)
Diagenode pA-Tn5 Transposase (loaded) was used for CUT&Tag, Nextera primer sets with NEBNext Master Mix was used to generate libraries with AMPure beads used for cleanup

treatment_protocol: Seizures were induced by intraperitoneal injection of 50mg/kg pentylenetetrazol (PTZ)

value: cortex

value: Control


title: 78988: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: MIC-Drop-seq proof-of-concept screen Gene Expression Library - 8 genes in pooled embryos

description:
Library name: MIC-Drop-seq_pilot_gex
10x Gene Expression library for  mic-drop-seq pilot study. Note: The processed data files are cellranger outputs containing combined data for for both this GEX library and the corresponding CRISPR library.
pilot_scRNA_filtered_barcodes.tsv.gz
pilot_scRNA_filtered_features.tsv.gz
pilot_scRNA_filtered_matrix.mtx.gz
pilot_scRNA_raw_barcodes.tsv.gz
pilot_scRNA_raw_features.tsv.gz
pilot_scRNA_raw_matrix.mtx.gz

value: whole embryo


title: PTZ male N2

description: Library name: Sample10

value: PTZ


title: 78961: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: hi_naive_f_KO_replicate 2


title: PTZ male N1

description: Library name: Sample9


title: 78913: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: 78907: no treatment_UKBi011-A-1

description: no treatment_UKBi011-A-1


title: Control IgG

description: Library name: Sample5


title: Control male N1

description: Library name: Sample7


title: hi_naive_f_KO_replicate 4


title: CD34.BMT.tdt, tdTomato+ cells of transplanted hearts from cd34+ lineage tracing recipients with BMT, scRNAseq

city: Hangzhou

first: 小桐

last: 孙

address: 88 Jiefang Road

institute: The Second Affiliated Hospital, School of Medicine, Zhejiang University

description:
Library name: CD34.BMT.tdt
10x Genomics

data_processing:
scRNA-seq raw data were processed using Cell Ranger (version 6.0.0) to align reads to the mouse reference, to count the number of barcode and UMI, and to generate feature-barcode matrices.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
To generate single-cell suspensions, fresh heart tissues were cut into 1 mm3 pieces, and were digested by 0.5 mg/mL liberase solution  at 37 °C for 20 minutes. To ensure full digestion of tissues, heart tissue pieces were gently shaken in a 37 °C shaker during the process. After digestion, the supernatant medium was harvested and add the same volume of Dulbecco's Modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) to terminate the digestive reaction, new liberase solution was added in residual tissue pieces for further digestion. The mixture of supernatant and DMEM was then filtered through a 40 μm cell strainer to obtain single cell suspension. The collected cells were centrifuged at 300 g/min at 4°C for 5 minutes. Subsequently, cell pellets were suspended in PBS or DEME for further experiments.
Single cell library was generated using Chromium Single Cell 3' Reagent Kit v2 and v3 chemistry (10X Genomics) following standard protocol. Library was generated and sequenced on a NovaSeq platform (Illumina) with paired-end 150 bp (PE 150) sequencing strategy.

value: Heart

value: Non-cardiomyocytes

value: Female

tag: age

value: 8-10 weeks

value: heart transplantation; bone marrow transplantation


title: hi_alc_m_wt_replicate 4

value: Alcohol


title: RFP, RFP+ cells of transplanted hearts from mRFP recipients, scRNAseq

description:
Library name: RFP
10x Genomics

value: heart transplantation


title: Allograft2, transplanted hearts, scRNAseq

description:
Library name: Allograft2
10x Genomics


title: hi_alc_m_wt_replicate 3

value: male

value: WT


title: PTZ IgG

description: Library name: Sample6


title: CD34.tdt, tdTomato+ cells of transplanted hearts from cd34+ lineage tracing recipients, scRNAseq

description:
Library name: CD34.tdt
10x Genomics


title: hi_naive_f_KO_replicate 3

value: Naïve

value: Hippocampus


title: hi_alc_m_wt_replicate 2


title: H2BE-BDNF_N3

description: Library name: Sample10

data_processing:
Reads were mapped to Mus musculus genome build mm10 with Star
files from two sequencing runs were merged for each biological replicate using SAMTools for downstream analysis
DESeq2 was used for gene expression analysis
deepTools was used to generate bigwig files
batch correction for different embryos (biological replicates) were applied
Assembly: mm10
Supplementary files format and content: raw count output from DESeq2
Supplementary files format and content: normalized count output from DESeq2

source_name: primary cortical neurons

growth_protocol: Cortices were dissected from E16.5 C57BL/6J embryos and cultured in supplemented neurobasal medium in TC-treated plates coated with 0.05 mg/mL Poly-D-lysine. At 3-4 DIV, neurons were treated with 0.5 µM AraC.

extract_protocol:
RNA was isolated from primary cortical neurons using Zymo Quick-RNA Miniprep Plus Kit (R1057)
NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: Cells were treated with lentivirus to express H2BE under a constitutively active promoter and stimulated with BDNF.

value: primary cortical neurons

value: H2BE overexpression

value: BDNF


title: Control Female N1

description: Library name: Sample1

value: cortex

value: Control


title: Control Female N2

description: Library name: Sample2


title: H2BE_N3

description: Library name: Sample8


title: PTZ Female N2

description: Library name: Sample4

value: PTZ


title: PTZ Female N1

description: Library name: Sample3


title: H2BE-BDNF_N2

description: Library name: Sample9


title: hi_alc_m_wt_replicate 1


title: NC2, non-transplanted hearts of negative control, scRNAseq

description:
Library name: NC2
10x Genomics

value: Heart


title: Control_N3

description: Library name: Sample6


title: Allograft1, transplanted hearts, scRNAseq

description:
Library name: Allograft1
10x Genomics

value: Non-cardiomyocytes


title: Control_N2

description: Library name: Sample5


title: hi_naive_f_KO_replicate 1

value: female

value: KO


title: hi_alc_m_ko_replicate 2


title: BDNF_N2

description: Library name: Sample2


title: NC1, non-transplanted hearts of negative control, scRNAseq

description:
Library name: NC1
10x Genomics

value: BALB/cJ

value: Female

value: 8-10 weeks


title: BDNF_N1

description: Library name: Sample1


title: hi_alc_m_ko_replicate 4

value: Alcohol

value: male


title: hi_alc_m_ko_replicate 1


title: BDNF_N3

description: Library name: Sample3

value: WT


title: 36_Zfy_DKO_rs

city: Honolulu

first: Monika

middle: A

last: Ward

state: Hawaii

address: 1960 East-West Rd

department: Institute for Biogenesis Research

institute: University of Hawaii

data_processing:
FASTQ files were trimmed and filtering using BBduk (v38.23) and were aligned with STAR (v2.7.2d) on the mouse genome (GRCm38.p6).
STAR and samtools package (v1.3.1) were used to estimate raw read counts.
Assembly: mm10
Supplementary files format and content: tab delimited file containing raw gene counts for each sample

source_name: Testis

extract_protocol:
RNA was harvested using RNAeasy Micro Kit (Quiagen). Total RNA was quality-checked using Bioanalyzer (Agilent) and used for the construction of libraries.
The cDNA libraries were prepared using the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs) before quality assessment with the Agilent Bioanalyzer.

value: Testis

value: RS

value: Zfy DKO


title: Lung_Tie2_KO

city: Helsinki

first: Madeleine

middle: Helena

last: Lackman

state: Uusimaa

address: Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

description: Library name: S10_Lung_Tie2_KO

data_processing:
Cell ranger (version 6.1.2, 7.0.0, or 7.0.1) was used to align the reads, quantify gene expression, generate custom references, and call the cells.
CellBender V0.3.0 was used to remove ambient RNA with default parameters due to the presence of a contaminating cell type. For this, raw matrix files (*raw_gene_bc_matrices.h5) were used. The final processed data files (*CellBender.h5) represent the filtered matrix output (including genes and barcodes) after CellBender processing.
Assembly: mm10
Supplementary files format and content: Matrix files containing raw (*raw_gene_bc_matrices.h5) and filtered+CellBender processed (*CellBender.h5) genes and barcodes

source_name: Lung

extract_protocol:
Hearts were minced using scissors and enzymatically dissociated in 1 mg/ml each of lyophilized collagenase type I, II and IV (Gibco) at 37°C for 25 min. The suspensions containing cell clumps were repeatedly pipetted to achieve single-cell suspension. RBC lysis buffer (Sigma-Aldrich) was used to lyze the leftover erythrocytes. Cell suspension was further filtered through the series of nylon mesh of 70, 40, 35 and 20 µm pore sizes. Single-cell suspensions were washed using DPBS with 2% heat inactivated FCS and resuspended in DPBS containing 0.04% BSA. This sample represented stromal-vascular fraction. To obtain cardiac cell suspension enriched for ECs, the cells were incubated with mouse Fc blocker (rat-anti-mouse CD16/CD32 (BD Biosciences) for 5 min followed by the antigen-specific antibody fluorescent conjugates for 30 min (list of the antibodies is in Supplemental Table 12). The live cardiac ECs (CD31+ CD45- Ter119- CD140a- DAPI-) were sorted in FACS Aria II (BD Biosciences). After the FACS step, cardiac ECs were washed using DPBS with 2% heat inactivated FCS and were resuspended in DPBS containing 0.04% of BSA. The cell viability and cell cluster levels of FACS sorted ECs were determined using automated cell counter (Luna, Logos Biosystems). The single cells were captured using 10X chromium Single-Cell 3’RNA sequencing system (10x genomics, Pleasanton, CA) with the reagent kit v2 according to the manufacturer’s instructions. In essentially the same way the cell suspensions from kidney and lung were obtained by enzymatic digestion, enriched for ECs by FACS-sorting and prepared for scRNAseq analysis (PMID: 35050301).
Library was performed according to the manufacturer`s instructions (single cell 3' protocol, 10x Genomics)

value: Lung

value: endothelial cell


title: Lung_Tie2_WT

description: Library name: S9_Lung_Tie2_WT


title: 33_Zfy_DKO_sc1

value: SCI


title: Control_N1

description: Library name: Sample4

value: primary cortical neurons

value: Control


title: Heart_Tie1Tie2_DKO

description: Library name: S6_Heart_Tie1Tie2_DKO

value: Heart

value: Stromal-vascular fraction


title: 32_Zfy_DKO_sc1


title: 35_Zfy_DKO_rs


title: Kidney_Tie2_KO

description: Library name: S8_Kidney_Tie2_KO

source_name: Kidney

value: Kidney


title: hi_alc_f_wt_replicate 3

value: female

value: Hippocampus


title: 31_Zfy_DKO_sc1


title: hi_alc_f_wt_replicate 2


title: 30_Zfy1_KO_rs

value: Zfy1 KO


title: 29_Zfy1_KO_rs


title: hi_alc_m_ko_replicate 3

value: Alcohol

value: KO


title: H2BE_N2

description: Library name: Sample7

value: H2BE overexpression


title: 28_Zfy1_KO_rs

value: Testis


title: Heart_Tie1Tie2_WT

description: Library name: S5_Heart_Tie1Tie2_WT

value: WT


title: hi_alc_f_wt_replicate 1


title: hi_alc_f_wt_replicate 4


title: 34_Zfy_DKO_rs

value: RS

value: Zfy DKO


title: 27_Zfy1_KO_sc2

value: SCII


title: Kidney_Tie2_WT

description: Library name: S7_Kidney_Tie2_WT

value: endothelial cell


title: 26_Zfy1_KO_sc2


title: 25_Zfy1_KO_sc2


title: hi_alc_f_ko_replicate 4


title: Heart_Tie2_WT

description: Library name: S3_Heart_Tie2_WT


title: 24_Zfy1_KO_sc1

value: SCI


title: Heart_Tie1_KO

description: Library name: S2_Heart_Tie1_KO

value: Endothelial cell


title: 21_Zfy2_KO_rs

value: Zfy2 KO


title: hi_alc_f_ko_replicate 3


title: 22_Zfy1_KO_sc1


title: hi_alc_f_ko_replicate 2


title: hi_alc_f_ko_replicate 1


title: 15_Zfy2_KO_sc1


title: Heart_Tie1_WT

description: Library name: S1_Heart_Tie1_WT

value: Heart


title: mitochondrial fraction from rat pancreatic islets, 5% low-protein diet, 22 days of age_3

city: Lausanne

first: Cecile

last: Jacovetti

address: Rue du Bugnon 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

description: Library name: Low-protein diet_Mitochondrial RNA_LM3

data_processing:
Small non-coding RNA-sequencing (sncRNA-seq) was performed using Illumina HiSeq 2500. For small RNA sequencing, the sequencing type was 50-bp single-read at 145 M reads.Unique sequences (considering UMI codes) were counted.
3' adapter (AACTGTAGGCACCATCAAT) trimmed and identical reads collapsed based on Unique Molecular Indentifier (UMI)
Sequencing quality was examined by FastQC software and trimmed reads were aligned to mouse and rat mature-tRNA and pre-tRNA sequences from GtRNAdb, with a perfect mapping to tRNAs using bowtie (version 1)
To investigate the expression profiles of tRNA fragments, the frequency of tRF counts were normalized to TPM using the following formula: normalized expression = actual tRF read count / total clean read count × 1000000.
We set the minimum cpm value as at least 5 reads in the smallest library. Only sequences above the minimum cpm value in at least 3 samples were retained.
The remaining reads were aligned to the transcriptome sequences (miRNA, piRNA, rRNA, snRNA, snoRNA) with a Total read counts ≥ 13 per sample cutoff.
Assembly: GRCm38.p6 and UCSC (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv6/Rnorv6-seq.html)
Supplementary files format and content: raw counts (reads) for each sample.
Supplementary files format and content: unique molecular identifier (UMI) counts for each sample.

organism: Rattus norvegicus

source_name: pancreatic islets

growth_protocol: Rat pancreatic islets were isolated by collagenase digestion followed by Histopaque density gradient and handpicking.

extract_protocol:
Total RNA from mouse islets was extracted using miRNeasy micro kit (Qiagen # 217084) and miRNeasy mini kit (Qiagen # 217004).
Libraries were prepared with QIAseq miRNA Library Kit (Qiagen) following manufacter's protocol.

value: pancreatic islets

value: mitochondria

value: Sprague Dawley rat

value: 5% low-protein diet


title: 17_Zfy2_KO_sc2


title: mitochondrial fraction from rat pancreatic islets, 5% low-protein diet, 22 days of age_4

description: Library name: Low-protein diet_Mitochondrial RNA_LM4


title: 20_Zfy2_KO_rs


title: 23_Zfy1_KO_sc1

value: Zfy1 KO


title: 19_Zfy2_KO_rs


title: CREB_antibody_E185 testis

city: Cincinnati

first: Shuyun

last: Li

state: NC

address: 3333 Burnet Ave

institute: CCHMC

description: Library name: CREB_E185

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore!  Version 0.6.10 with default settings except for specifying Illumina adapter sequences and paired-end validation.
Trimmed sequences were aligned to mm10 genomes using bowtie2 (Version 2.5.2) with maximum fragment length 2,000, forward-reverse mate orientation, local read alignment, and no mixed or discordant read alignments
MACS2  was used to call peaks for each sample with default parameters except mode of operation set to factor and single-end reads. Peak calls for all samples were collapsed to a set of union peaks which were subsequently assigned as positive or negative for CREB signal per sample at a threshold of 5x the median IgG signal.
Assembly: mm10 genome [GCA_000001635.2 GCF_000001635.20]
Supplementary files format and content: consensus.bed files contain consensus peaks in bed format.
Supplementary files format and content: bigwig files for each sample.
Library strategy: CUT&Run

source_name: fetal testis

extract_protocol:
Male gonads were dissected and dissociated into individual cells by pipetting. The resulting cell suspension was filtered using a 70 µm filter, and 100,000 gonadal cells were used for CUT&RUN assays following an alternative protocol from Protocol.io (dx.doi.org/10.17504/protocols.io.zcpf2vn).
DNA was quantified and prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: fetal testis

tag: antibody

value: CREB

tag: developmental stage


title: IgG_antibody_E135 testis

description: Library name: IgG_E185

value: IgG


title: H3K4_antibody_E185 testis

description: Library name: H3K4_E185


title: 18_Zfy2_KO_sc2

value: Testis


title: CREB_antibody_E165 testis

description: Library name: CREB_E165


title: 13_Zfy2_KO_sc1


title: mitochondrial fraction from rat pancreatic islets, 5% low-protein diet, 22 days of age_1

description: Library name: Low-protein diet_Mitochondrial RNA_LM1


title: 14_Zfy2_KO_sc1


title: 12_XY_sc1

value: WT


title: 16_Zfy2_KO_sc2


title: mitochondrial fraction from rat pancreatic islets, 5% low-protein diet, 22 days of age_2

description: Library name: Low-protein diet_Mitochondrial RNA_LM2


title: whole cell lysate from rat pancreatic islets, 5% low-protein diet, 22 days of age_4

description: Library name: Low-protein diet_Total RNA_LT4

value: whole cells


title: 9_XY_rs

value: RS


title: Heart_Tie2_KO

description: Library name: S4_Heart_Tie2_KO

value: Stromal-vascular fraction


title: 10_XY_sc1

value: SCI


title: 11_XY_sc1


title: 5_Zfy_DKO_sc2

value: SCII

value: Zfy DKO


title: whole cell lysate from rat pancreatic islets, 5% low-protein diet, 22 days of age_1

description: Library name: Low-protein diet_Total RNA_LT1


title: 7_XY_rs


title: HEK_ms_IgG_rep1

data_processing:
Reads were mapped to Homo sapiens genome build hg38 with Bowtie2 (v2.4.5).
7.5 million reads from each replicate were subset and each condition was then merged across replicates (SAMtools v1.15).
Metaplots were generated using ngs.plot (v2.63).
Peaks were called using MACS3 (v3.0.0b1) and annotated using Homer (v4.10).
Assembly: hg38
Supplementary files format and content: narrowPeak files from MACS3
Library strategy: CUT&RUN

extract_protocol:
~500K HEK293T cells per sample were detached from plates using trypsin and immediately washed 2X in CUT&RUN wash buffer according to EpiCypher CUTANA CUT&RUN protocol v2.0. CUT&RUN was performed with mouse anti-FLAG (Sigma F3165), rabbit anti-myc (CST 13987), rabbit IgG (Sino Bio CR1) and mouse IgG (sc-2025) antibodies.
CUT&RUN libraries were generated using the EpiCypher CUTANA CUT&RUN Library Prep Kit v1.5.

value: Human embryonic kidney


title: CREB_antibody_E135 testis

description: Library name: CREB_E135


title: 6_Zfy_DKO_sc2


title: HEK_rbt_IgG_rep1


title: mitochondrial fraction from rat pancreatic islets, control diet, 22 days of age_4

description: Library name: Control_Mitochondrial RNA_CM4

value: pancreatic islets

value: chow diet


title: mitochondrial fraction from rat pancreatic islets, control diet, 22 days of age_3

description: Library name: Control_Mitochondrial RNA_CM3

value: mitochondria

value: Sprague Dawley rat


title: HEK_endog_myc_rep1


title: HEK_endog_myc_rep2


title: 3_XY_sc2


title: sample12_S12


title: whole cell lysate from rat pancreatic islets, 5% low-protein diet, 22 days of age_3

description: Library name: Low-protein diet_Total RNA_LT3

value: 5% low-protein diet


title: whole cell lysate from rat pancreatic islets, 5% low-protein diet, 22 days of age_2

description: Library name: Low-protein diet_Total RNA_LT2


title: HEK_endog_myc_rep3


title: 8_XY_rs


title: 2_XY_sc2


title: HEK_myc_FLAG_rep3


title: sample10_S10


title: 4_Zfy_DKO_sc2


title: mitochondrial fraction from rat pancreatic islets, control diet, 22 days of age_1

description: Library name: Control_Mitochondrial RNA_CM1


title: HEK_myc_FLAG_rep1


title: sample6_S6


title: sample9_S9


title: whole cell lysate from rat pancreatic islets, control diet, 22 days of age_4

description: Library name: Control_Total RNA_CT4


title: HEK_edit_myc_FLAG_rep2


title: HEK_myc_FLAG_rep2


title: whole cell lysate from rat pancreatic islets, control diet, 22 days of age_3

description: Library name: Control_Total RNA_CT3


title: sample11_S11


title: sample2_S2


title: sample4_S4


title: sample8_S8


title: HEK_edit_myc_FLAG_rep1


title: Editing_Oct-Cold-3_1.fastq.gz

status: Public on Jan 01 2026

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

description: Library name: Editing_Oct-Cold-3_1.fastq.gz

data_processing:
FastQC
TrimGalore
Trinity
TransDecoder
Kallisto
RNA editing analysis using JACUSA
Assembly: de-novo transcriptome assembly using Trinity
Supplementary files format and content: csv
Supplementary files format and content: Kallisto count files, JACUSA output file

organism: Octopus bimaculoides

source_name: Arm

growth_protocol: California two-spot octopuses (O. bimaculoides) were wild-caught male and female adults (aged 1-2 years, Aquatic Research Consultants) and fed a daily diet of fiddler crabs (Leptuca pugilator, Northeast Brine Shrimp, Oak Hill, FL). Adult (aged 6-8 months) hummingbird bobtail squid (E. berryi) were laboratory cultured (Marine Biological Laboratory, Woods Hole, MA) and fed daily with grass shrimp (Palaemonetes pugio, Aquatic Indicators). All cephalopods were euthanized using established methods with sedation in 15% ethanol followed by pithing for tissue harvesting. All housed animals were kept under a 12 h–12 h light/dark cycle in filtered natural seawater.

extract_protocol:
Tissues were dissected, stored in RNALater, and immediately flash frozen in loquid nitrogen. Samples were stored at -80C until they were shipped on dry ice. All subsequent steps were performed by Azenta (Genewiz)
Poly(A) selected mRNA was used for library prep by Azenta (Genewiz)

value: Arm

value: Cold acclimation


title: Editing_Oct-Warm-1_1.fastq.gz

description: Library name: Editing_Oct-Warm-1_1.fastq.gz

value: Control


title: sample5_S5

value: Testis


title: whole cell lysate from rat pancreatic islets, control diet, 22 days of age_2

description: Library name: Control_Total RNA_CT2


title: 1_XY_sc2

value: WT


title: sample7_S7


title: mitochondrial fraction from rat pancreatic islets, control diet, 22 days of age_2

description: Library name: Control_Mitochondrial RNA_CM2


title: MIC-Drop-seq CRISPR editing validation -  genomic amplicon sequencing data - wild type embryos

description:
Library name: amplicon_wildtype
Amplicon sequencing library of genomic DNA extracted from control uninjected embryos, for quantifying CRISPR editing frequency at the target loci
rhamp_results.csv

value: whole embryo


title: sample3_S3


title: MIC-Drop-seq CRISPR editing validation -  genomic amplicon sequencing data -  MIC-Drop injected embryos

description:
Library name: amplicon_injected
Amplicon sequencing library of genomic DNA extracted from embryos in the MIC-Drop-seq pilot experiment, for quantifying CRISPR editing frequency at the target loci
rhamp_results.csv


title: Editing_Oct-Warm-3_1.fastq.gz

description: Library name: Editing_Oct-Warm-3_1.fastq.gz


title: Editing_Oct-Cold-2_1.fastq.gz

description: Library name: Editing_Oct-Cold-2_1.fastq.gz


title: sample1_S1


title: Editing_Oct-Warm-2_1.fastq.gz

description: Library name: Editing_Oct-Warm-2_1.fastq.gz


title: SSc_1_Fib_3D_Hama04_back_1

type: genomic

city: Lebanon

first: Rezvan

last: Parvizi

state: NH

address: 1 Medical Center Drive

department: Biomedical Data Science

institute: Dartmouth College

hyb_protocol: MethylationEPIC microarray slides are prepared and conditioned according to manufacturer specifications.

scan_protocol: High-resolution images were generated for each slide, with the scanner recording intensity values for both the methylated (red) and unmethylated (green) fluorescent signals at each probe. The scanning generated raw intensity data files (IDAT files) that contain the fluorescence intensities for all probes on each sample.

data_processing:
Methylated and unmethylated signal intensities were obtained for each sample. Data were normalized using the minfi::preprocessQuantile function, which generated normalized beta values and detection p-values for each sample. The results are provided in tab-delimited text file format.
The minfi package from bioconductor was used to process the data.

label: Cy3 and Cy5

label_protocol: Between 500 ng and 1 µg of DNA from these 2D and 3D samples were bisulfite converted and processed according to the Illumina Infinium MethylationEPIC array protocols.

growth_protocol: Isolated fibroblasts were cultured in either 2D monolayer or 3D tissue culture systems.

extract_protocol: Genomic DNA was extracted using the Qiagen QIAcube by QIAamp DNA Mini Kit.

tag: disease state

value: SSc

tag: culture

tag: biopsy

value: flunk


title: HEK_edit_myc_FLAG_rep3


title: SSc_2_Fib_3D_BIIB4_1

value: forarm


title: SSc_1_Fib_3D_Hama04_back_2


title: SSc_1_Fib_3D_Hama04_arm_2


title: whole cell lysate from rat pancreatic islets, control diet, 22 days of age_1

description: Library name: Control_Total RNA_CT1

value: whole cells


title: Oct-Brain-3_1.fastq.gz

description: Library name: Oct-Brain-3_1.fastq.gz

source_name: Brain

value: Brain


title: SSc_2_Fib_3D_BIIB4_2


title: Normal_Fib_3D_Norm02_2

value: Normal


title: Oct-Arm-3_1.fastq.gz

description: Library name: Oct-Arm-3_1.fastq.gz


title: Oct-Brain-2_1.fastq.gz

description: Library name: Oct-Brain-2_1.fastq.gz


title: Oct-Arm-2_1.fastq.gz

description: Library name: Oct-Arm-2_1.fastq.gz


title: PMMa1

city: St. Paul

first: Nicole

last: Marquez Reyes

state: Minnesota

address: 1445 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota - Twin Cities

description: Library name: Sample 9

data_processing:
Using Kbase (https://www.kbase.us/), paired - end reads raw data was trimmed (Trimmomatic (v.0.36))
Using Kbase (https://www.kbase.us/), we then mapped the genome of R. palustris CGA009 (HISAT2 (v.2.1.0)).
Using Kbase (https://www.kbase.us/), transcripts were assembled from the aligned reads by using StringTie (v.2.1.5).
Using Kbase (https://www.kbase.us/), assembled transcripts were used to do differential expression analysis matrix with DESeq2 (v.1.20.0)
Transcript regulation was further analyzed through heat and volcano plots in R.
Assembly: NZ_CP116810.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rhodopseudomonas palustris CGA009

source_name: Prokaryote

growth_protocol: WT cells were maintained in anaerobic hungate tubes with 10mL of either PM or Low Sulfate PM or Low Sulfate PM with No Molybdenum supplemented with 10mM Malate as carbon source. These anaerobic media was prepared using an anaerobic chamber with an atmosphere of 98%N2, 2%H2, <10ppm O2.

extract_protocol:
QIAgen miRNeasy Mini Kit (QIAgen, Hilden, Germany). ~1ug of total RNA was used to send to Azenta
Library preparation done by Azenta with Illumina 2x150bp, RNA with rRNA depletion, ~350M PE reads (~105GB), single index

treatment_protocol: Only the samples stating they have MT-EtOH were added 1mM MT-EtOH as sulfur source

value: Prokaryote


title: NoMoMT-EtOH2

description: Library name: Sample 8


title: SSc_1_Fib_3D_Hama04_arm_1


title: Oct-Brain-1_1.fastq.gz

description: Library name: Oct-Brain-1_1.fastq.gz


title: PMMa3

description: Library name: Sample 10


title: SSc_1_Fib_2D_Hama04_back_1


title: Editing_Oct-Cold-1_1.fastq.gz

description: Library name: Editing_Oct-Cold-1_1.fastq.gz


title: SSc_1_Fib_2D_Hama04_arm_2


title: Normal_Fib_2D_Norm02_2


title: NoMoMa2

description: Library name: Sample 5


title: SSc_1_Fib_2D_Hama04_back_2


title: SSc_2_Fib_2D_BIIB4_2


title: NoMoMT-EtOH1

description: Library name: Sample 7


title: Oct-Arm-1_1.fastq.gz

description: Library name: Oct-Arm-1_1.fastq.gz


title: SSc_1_Fib_2D_Hama04_arm_1


title: SSc_2_Fib_2D_BIIB4_1


title: LowSMT-EtOH3

description: Library name: Sample 4


title: LowSMT-EtOH2

description: Library name: Sample 3


title: ATAC-Seq - h1W3

city: Guangzhou

first: Xiaolin

last: Luo

address: Dongfeng Road No.651

institute: Sun Yat-sen University Cancer Center

description: Library name: sample 2

data_processing:
150 bp paired-end reads were mapped to the reference genome build (human, hg38). Differentially sites were detected from ATAC-seq experiments using DiffBind R package.
Assembly: human, hg38
Supplementary files format and content: bigwig

source_name: ovary

extract_protocol:
50,000 cells were processed using the ATAC protocol. Libraries were quantified with Bioptic Qsep100 Analyzer（Bioptic lnc.）and paired-end sequenced with read lengths of 150.
The ENCODE ATAC-seq pipeline was used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of en-richment.

value: ovary

value: cancer cells


title: Combo_03

city: Chicago

first: DUY BINH

last: TRAN

state: IL

address: 840 S. Wood St

department: Surgery

institute: University of Illinois Chicago

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_12

hyb_protocol: A cartridge containing a hybridization reaction for each sample was set up using the following components: 3 μl Reporter CodeSet, 5 μl Hybridization Buffer, 5 μl (50 ng) sample RNA, and 2 μl Capture ProbeSet at room temperature. Samples were hybridized to target-specific reporter and capture probes overnight at 65 °C in a thermocycler.

data_processing:
Following hybridization, 35 μL of each hybridized product was pipetted to the nCounter cartridge, sealed, and loaded into the drawer of the SPRINT Profiler.
Reporter code counts (RCC) and reporter library file (RLF) obtained from the nCounter SPRINT Profiler were utilized for gene expression analysis though the nSolver Advanced Analysis Software v4.0. Background correction, quality assessment, and inter-sample normalization was performed in accordance with the Gene Expression Data Analysis Guidelines (MAN-C0011–04). Imaging quality control measurements were set to flag any lane failing to have a registered FOV above 75%. Binding density was flagged if any lane recorded an optical feature per square micron outside the range of 0.1 to 1.8. Positive control linearity, used to assess the efficiency of hybridization, was flagged if any resulting count was below a correlation of 0.95. Positive control limit of detection flagged any sample if the 0.5 fM positive control counts were ≤ 2 SD above the mean of the negative controls. Background thresholds were set to the mean of the manufactured negative controls plus two standard deviations. Positive control normalization was performed using the geometric mean to compute normalization factors for each sample; lanes with a normalization factor outside of the 0.3–3.0 range were flagged. Codeset content normalization was performed with the geometric mean of the twenty housekeeping genes, flagging lanes if the normalization factor was outside of the 0.1–10.0 range. Normalized mRNA counts were analyzed for differential expression in four comparative analyses: aurB vs. PBS, Combination vs. IR, IR vs. PBS, and Combination vs. IR. Differential expression analysis was performed via the nSolver Advanced Analysis module.

source_name: tibial tumor

growth_protocol: DU145 cells were cultured in MEM-E supplemented with 10% FBS, 100 units/ml penicillin, and 100 μg/ml streptomycin. DU145 cells stably expressing the luciferase gene (pGL4.51[luc2/CMV/Neo], Promega) were generated through chemical transfection using FuGENE HD (Promega) in the presence of G418 antibiotics (GoldBio). The DU145-luc cell line was maintained at 70% confluency and regularly monitored for luminescence activity. DU145-luc cells were resuspended in Matrigel Growth Factor Reduced (Sigma) at a concentration of 5 × 105 cells/20 µl. Intratibial bone injections were performed on 4- to 5-week-old athymic female mice. Briefly, the proximal end of the left tibia was surgically exposed, the knee was flexed, and 20 µl of Matrigel containing DU145-luc cells were injected into the bone marrow space using a 26-gauge needle.

extract_protocol: RNA from tumor tissues was extracted by RNeasy Mini Kit (Qiagen).

treatment_protocol: After 2 weeks, the mice injected with DU145-luc cells were randomly divided into groups receiving PBS, irradiation (focal radiation at 2.0 Gy, X-Rad320, Precision X-Ray Inc, Madison, CT), aAurB (10 mg/kg, i.p., three times per week), or a combination of irradiation (2.0 Gy) and aAurB (10 mg/kg, i.p., three times per week) (N=5). Irradiation was targeted to the proximal end of the left tibia and administered in a single fraction of 2.0 Gy. The day of irradiation was designated as day 0 of treatment.

value: tibial tumor


title: ATAC-Seq - h2W6

description: Library name: sample 3


title: LowSMa2

description: Library name: Sample 2


title: Normal_Fib_2D_Norm02_1

value: Noraml


title: H2W6

description: Library name: Sample 3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads 325 that contained adaptor contamination, low quality bases and undetermined bases with 326 default parameter. Then sequence quality was also verified using fastp. We used HISAT2 327 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapi- 328 ens GRCh38. The mapped reads of each sample were assembled using StringTie 329 (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes 330 from all samples were merged to reconstruct a comprehensive transcriptome using gff- 331 compare (https://github.com/gpertea/gffcompare/). After the final transcriptome was gen- 332 erated, StringTie and was used to estimate the expression levels of all transcripts. String- 333 Tie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [to- 334 tal_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially ex- 335 pressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with para- 336 metric F-test comparing nested linear models (p value < 0.05) by R package edgeR 337 (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: h38
Supplementary files format and content: text file including rawcount

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is pu- rified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, Int. J. Mol. Sci. 2025, 26, x FOR PEER REVIEW 11 of 1 cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second- stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we per- formed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC- Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended pro- tocol

value: cancer cell

value: KO

value: no treatment


title: LowSMa1

description: Library name: Sample 1


title: ATAC-Seq - hO8910

description: Library name: sample 1


title: HO8910

description: Library name: Sample 1


title: Combo_01

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_10


title: Combo_02

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_11


title: IR 2.0 Gy_03

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_9


title: aurB_03

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_6


title: IR 2.0 Gy_01

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_7


title: KYSE150-hypoxia-so-nala

city: Beijing

first: Ji

last: Cong

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Sample 4

data_processing:
Raw reads were quality checked with FastQC v0.11.9 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg38) genome with Bowtie2 v2.5.0 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.6.
Peaks were called using macs2 2.2.7.1 with the default setting. Visualization of detected peaks was performed using deeptools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: KYSE150 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
For ATAC-seq experiment, 50,000 KYSE30 cells were collected for ATAC-seq followed commercial manual ATAC kit (cat. #N248, Novoprotein Inc.).
DNA libraries were prepared through PCR using a commercial ATAC kit (cat. #N248, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina NovaSeq 6000 platform for each library.

treatment_protocol: KYSE150 cells were cultured under normoxia or hypoxia condition and treated with sodium oxamate or sodium lactate.

value: esophageal squamous cell carcinoma

value: hypoxia+oxamate+NALA


title: IR 2.0 Gy_02

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_8


title: KYSE150-normoxia

description: Library name: Sample 1

value: normoxia


title: KYSE150-hypoxia-so-HIF1α

description: Library name: Sample 3

data_processing:
Raw reads were quality checked with FastQC v0.11.9 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg38) genome with Bowtie2 v2.5.0 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.6.
Peaks were called using SEACR 1.3 with the default setting. Visualization of detected peaks was performed using deeptools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
For CUT&Tag experiment, 100,000 cells were collected for CUT&Tag followed manuals (cat. #N259-YH01, Novoprotein Inc.) to get HIF1α-enriched DNA.
DNA libraries were prepared through PCR using a commercial  CUT&Tag kit (cat. #N259-YH01, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina NovaSeq 6000 platform for each library.

value: hypoxia+oxamate


title: aurB_01

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_4


title: aurB_02

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_5


title: H1W3

description: Library name: Sample 2


title: KYSE150-normoxia-HIF1α

description: Library name: Sample 1


title: KYSE150-hypoxia-oxamate-NALA-rep2

description:
Library name: Sample 8
Column name in gene_count_mat.txt:hypoxia-so-nala-rep2

data_processing:
Read quality was calculated for all samples by using FastQC (v0.11.9) (Andrews.2010) software with the default parameters.
Fastp(v0.20.1) (Chen S, el at. 2018) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed.
RNA-seq reads were aligned to the human genome hg38 using STAR (v2.7.8a), and the number of reads mapped to each gene was calculated by RSEM (v1.3.3).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes counts for each sample

extract_protocol:
RNA purification, reverse transcription, library construction and sequencing were performed in Mingma Technologies at Shanghai according to the manufacturer's instructions. The agarose gel electrophoresis was used to detect the integrity of the extracted RNA. And NanoDrop was used to measure the concentration of RNA.
The mRNAs containing oligoDT were enriched from the total RNA by magnetic beads, and the captured mRNAs were fragmented, then the reverse transcriptase was used to synthesize the strands of cDNA and repair the end of the transcripts product. An “A” base was added to the 3’ end of the product and the sequencing adapters were connected to the ends. The incomplete ligation products and empty linker self-ligation products were removed by the ligation products purification, and the primers complementary to the linker sequence were used for PCR amplification. Finally, the sequencing library was purified by magnetic beads.


title: PBS_02

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_2


title: KYSE150-hypoxia-HIF1α

description: Library name: Sample 2

value: hypoxia


title: KYSE150-hypoxia-so-nala-HIF1α

description: Library name: Sample 4


title: KYSE150-hypoxia

description: Library name: Sample 2


title: PBS_03

description:
Tumor was generated by injecting DU145 cell, human prostate cancer cells, into the tibial of mouse
Sample_3


title: KYSE150-hypoxia-oxamate-rep1

description:
Library name: Sample 5
Column name in gene_count_mat.txt:hypoxia-so-rep1


title: KYSE150-hypoxia-rep1

description:
Library name: Sample 3
Column name in gene_count_mat.txt:hypoxia-rep1


title: KYSE150-hypoxia-oxamate-NALA-rep1

description:
Library name: Sample 7
Column name in gene_count_mat.txt:hypoxia-so-nala-rep1


title: MUT7_Condition D

city: Avaino

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: DRDAT

country: Italy

institute: Centro di Riferimento Oncologico Aviano IRCCS

hyb_protocol: The hybridization was performed at 55°C for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides. Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green.

data_processing: Threshold: 1.0   Logbase: 2. Technology: Agilent.miRNA.70156_v21_0. Normalization: Quantile. Baseline Transformation: median of all samples

source_name: Peripheral Blood, anti-IgM beads, Ibrutinib, agonist mix

label_protocol: The microarray was performed according to miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent). A total of 100ng of total RNA for each condition was used and labelled with Cyanine 3-pCp molecule.

extract_protocol: RNA was extracted with miRNeasy tissue/cell Advance kit (Quiagen), according to manufacturer's instruction, and RNA was quantified using a NanoDrop1000 spectrophotometer .

treatment_protocol: CLL cells were stimulated with agonist mix in presence of anti-IgM and Ibrutinib 1 uM (Condition D) or with DMSO and control beads (Condition C) vs CLL cells treated only with anti-IgM and Ibrutinib 1 uM (Condition B) or with DMSO and control beads (Condition A). Condition A: DMSO+control beads; Condition B: Anti-IgM beads+Ibrutinib 1uM; Condition C: DMSO+control beads+agonist mix (IL-10; CpG; CD40L); Condition D: Anti-IgM beads+Ibrutinib 1uM+agonist mix (IL-10; CpG; CD40L)

tag: peripheral blood cd19 purity (%)

tag: FISH analysis (% of deletion)

tag: tp53 mutation (%)


title: KYSE150-normoxia-rep1

description:
Library name: Sample 1
Column name in gene_count_mat.txt:normoxia-rep1

tag: cell line

tag: cell type