title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 24h replicate 1 [sample_24]

value: triple negative metastatic mammary adenocarcinoma

value: ATACTT


title: h1hESC_TB-EQ-75pcnt_34

status: Public on Nov 03 2021

type: SRA

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

country: USA

institute: University of Florida

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_34

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads trimmed to have length 51 bp using seqtk 1.0
Sequencing reads were mapped to GRCh38 Ensembl using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts csv

molecule: total RNA

organism: Homo sapiens

source_name: differentiated human embryonic stem cells

growth_protocol: Cells were grown as in GSE75748. EC: H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days. TB: H1 were seeded in E7 (E8 minus FGF2) with 50ng/ml BMP4 and SB431542.

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system. For EQ, EQ-Vary and EQ-75%, we retrieved the harvested cDNA, which are amplified full-length single-cell cDNAs identical to those in GSE75748.
For the EQ and EQ-75% experiments, 2.0 µL of the amplified/tagmented cDNA were used for pooling. In the EQ-Vary experiment, a single scaling factor was applied to generate variable amounts of the pooling volume. These pooled single-cell libraries were used in an AMpure XP Bead-based Dual Bead Cleanup and Size Selection reaction (Agencourt AMPure XP PCR Purification modified Instructions for Use, Beckman Coulter). In both bead cleanup reactions, 90% of AMPure XP beads were added to the amplified single-cell libraries to select for an approximate size range of 150-700 bp and incubated for 15 minutes at room temperature. Libraries bound to beads were then placed on a magnet for 5 minutes, washed twice with 70% Ethanol, eluted with Suspension Buffer (Nextera XT DNA Sample Preparation Index Kit, Illumina), and transferred to a new tube.  Final amplified and pooled single-cell libraries were quantified with the Qubit dsDNA HS Assay Kit (Q32854, Thermofisher) and Bioanalyzer High Sensitivity DNA Analysis Kit (5067-4626, Agilent).Libraries were multiplexed with 96 samples per lane and sequenced on an Illumina HiSeq3000 with paired-end 65 or 78 bp reads.
Single-cell RNA-Seq

tag: cell line

value: H1 hESC cell line

tag: sample type

value: TB

tag: equilization amt


title: h1hESC_TB-EQ-75pcnt_29

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_29


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 24h replicate 2 [sample_37]

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

data_processing:
The data was separated by well barcode and the reads were converted to counts using the bcbio-nextgen single cell RNA-seq analysis pipeline (https://bcbio- nextgen.readthedocs.io/en/latest/). The pipeline removes any barcodes that differ by more than one base from an expected barcode and uses unique molecular identifiers (UMIs) to identify unique reads and remove PCR duplicates.
RapMap was used to align reads to the transcriptome (GRCh38). The R package DESeq2 (version 1.30.0) was used for differential expression analysis, and the R package gseaMultilevel was used for gene set enrichment analysis of all genes sorted by the log2 fold change (adjusted p-value < 0.05) using Molecular Signatures Database (MSigDB) gene sets.
Genome_build: GRCh38.98

molecule: polyA RNA

source_name: breast ductal carcinoma cell line

growth_protocol: MDAMB231 (ATCC cat no.) was maintained in DMEM media (Corning 10-017-CV) with 10% FBS (Life Technologies 26140-079) and 1% penicillin/streptomycin (Corning 30-002-Cl). MCF7 (ATCC cat no) was maintained in EMEM media with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were lysed 96 hours post crRNA transfection or 24 hours post inhibitor treatment; the plates were washed one time with PBS on a plate washer (BioTek). The PBS was removed (leaving ~15 uL/well residual volume), and 30 uL/well 1 X lysis buffer (1x Qiagen TCL, 1% beta-mercaptoethanol) was added. The plates were incubated for 5 minutes at room temperature to aid cell lysis, and then frozen at -80˚C until RNA extraction. The DGE RNA-seq was performed as previously published (Semrau et al., 2017; Soumillon et al., 2014) with modifications described previously (Schauer et al., 2020) (full protocol at https://www.protocols.io/view/3-39-dge-high-throughput-rna-library-preparation-bumynu7w).
The Nextera DNA kit was used to prepare the sequencing library following the manufacturer’s instructions. 55 ng of cDNA was tagmented for 5 minutes at 55 ̊C and purified using a Zymo DNA Clean & Concetrator-5 column. The cDNA was amplified (7 cycles) then purified using a 0.9x ratio of AMPure XP magnetic beads. The Agilent BioAnalyzer HS DNA Kit was used to assess the library size distribution before qPCR quantification and sequencing at the Harvard Medical School Biopolymers Facility (paired end sequencing was performed on an Illumina NextSeq).
high-throughput, low-cost RNA-sequencing method (3’ Digital Gene Expression or 3’DGE-seq)

treatment_protocol: MDAMB231 Cas9-Flag and MCF7 Cas9-Flag expressing cells were seeded in 96 well plates (4000 cells/well) and allowed to adhere for 24 hours. crRNAs were resuspended in 10 mM Tris-HCl Buffer pH 7.4 (Dharmacon B-006000-100) and four crRNA guides per DUB were pooled to increase knockout efficiency. Guide transfection was performed according to the recommended manufacturer protocol with optimized conditions as follows. Cells were transfected with 25 nM crRNA and 25 nM tracr RNA using 0.2 uL/well Dharmafect 4, triplicate transfections were performed per condition. The media was replaced 16-18 hours post transfection.    In parallel, MDAMB231 (12,000 cells/well), MCF7 parental (10,000 cells/well), and MCF7 TP53 shRNA (10,000 cells/well) were seeded in 96 well plate format and allowed to adhere for 24 hours. DUB inhibitors and DMSO were dispensed into the 96 well plate using a d300 digital dispenser (Hewlett-Packard).

value: breast ductal carcinoma cell line

value: compound

tag: treatment

tag: concentration

tag: time

tag: replicate

tag: library

tag: well

tag: barcode

value: AATTTC


title: h1hESC_TB-EQ-75pcnt_28

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_28


title: h1hESC_TB-EQ-75pcnt_42

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_42


title: h1hESC_TB-EQ-75pcnt_27

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_27


title: h1hESC_TB-EQ-75pcnt_39

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_39


title: h1hESC_TB-EQ-75pcnt_40

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_40


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 24h replicate 1 [sample_21]

source_name: triple negative metastatic mammary adenocarcinoma

value: ATAAAC


title: MDAMB231 cells treated with DMSO control at 24h replicate 1 [sample_23]

value: DMSO

value: ATACAA


title: h1hESC_TB-EQ-75pcnt_26

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_26


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 24h replicate 1 [sample_22]

value: ATAACA


title: h1hESC_TB-EQ-75pcnt_37

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_37


title: MCF7 cells treated with 0.96 uM bortezomib at 24h replicate 1 [sample_19]

value: bortezomib

value: AGATTA


title: MCF7 cells treated with DMSO control at 24h replicate 1 [sample_18]

value: ACTTTA


title: MCF7 cells treated with 10 uM SB1-F-78 at 24h replicate 1 [sample_20]

value: AGTAAT


title: h1hESC_TB-EQ-75pcnt_25

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_25


title: h1hESC_TB-EQ-75pcnt_24

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_24


title: h1hESC_TB-EQ-75pcnt_23

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_23


title: MCF7 cells treated with 0.96 uM HBX19818 at 24h replicate 1 [sample_15]

value: ACAATA


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 24h replicate 1 [sample_14]

value: AATTGA


title: h1hESC_TB-EQ-75pcnt_22

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_22


title: h1hESC_TB-EQ-75pcnt_21

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_21


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 24h replicate 1 [sample_13]

value: AATTCT


title: MCF7 cells treated with 0.96 uM CGM097 at 24h replicate 1 [sample_12]

value: AATGAT


title: h1hESC_TB-EQ-75pcnt_18

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_18

value: H1 hESC cell line


title: h1hESC_TB-EQ-75pcnt_19

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_19

value: TB


title: h1hESC_TB-EQ-75pcnt_20

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_20


title: MCF7 cells treated with 10 uM SB1-F-70 at 24h replicate 1 [sample_11]

value: breast ductal carcinoma cell line

value: AATCTT


title: h1hESC_TB-EQ-75pcnt_17

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_17


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 24h replicate 1 [sample_10]

value: compound

value: AATAGT


title: h1hESC_TB-EQ-75pcnt_16

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_16


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 24h replicate 1 [sample_9]

value: AATACA


title: h1hESC_TB-EQ-75pcnt_15

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_15


title: MCF7 cells treated with 10 uM P5091 at 24h replicate 1 [sample_8]

value: AAGTAT


title: h1hESC_TB-EQ-75pcnt_14

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_14


title: h1hESC_TB-EQ-75pcnt_13

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_13


title: h1hESC_TB-EQ-75pcnt_12

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_12


title: MCF7 cells treated with 4.96 uM ML323 at 24h replicate 1 [sample_16]

value: ACATAA


title: MCF7 cells treated with 0.96 uM nutlin3a at 24h replicate 1 [sample_17]

value: ACTTAT


title: MCF7 cells treated with 10 uM XL-9678-203C at 24h replicate 2 [sample_5]

value: AAATTG


title: MCF7 cells treated with 0.96 uM CS5405 at 24h replicate 1 [sample_4]

value: AAATAC


title: h1hESC_TB-EQ-75pcnt_11

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_11


title: h1hESC_TB-EQ-75pcnt_9

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_9


title: MCF7 cells treated with 10 uM XL-9678-203C at 24h replicate 1 [sample_3]

value: AAAGTT


title: MCF7 cells treated with 10 uM AZ1 at 24h replicate 1 [sample_2]

value: AAAATC


title: h1hESC_TB-EQ-75pcnt_8

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_8


title: h1hESC_TB-EQ-75pcnt_7

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_7


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 24h replicate 1 [sample_1]

value: AAAACT


title: h1hESC_TB-EQ-75pcnt_6

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_6


title: WT CD8+ effector T cells-input DNA

first: To-Ha

last: Thai

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

library_source: genomic

data_processing:
The 50-nt sequence reads identified by the Sequencing Service (using Illumina’s Hi-Seq) are mapped to the genome using the BWA algorithm with default settings.
Reads were aligned to the mouse genome (mm10), and after removal of duplicate reads.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using the UCSC Genome Browser wigToBigWig program.

molecule: genomic DNA

organism: Mus musculus

source_name: CD8+ effector T cells

growth_protocol: Ex vivo WT CD8+ T cells were purified from pooled spleen and peripheral lymph nodes by FACS. Purified naïve CD8+ T cells were avtivated/differentiated in vitro using plate-bound CD3 (clone 145-2C11)/CD28 (clone 37.51) antibodies for 2 days then cultures were switched to IL-2 (10 IU/ml final concentration) for an additional 3 days. On day 5 after activion/differentiation, CD8+ effector T cells were collected and flash-frozen to be shipped to Active Motif for librariy construction. IP and sequencing.

extract_protocol:
Extraction was performed by Active Motif.
Libraries were constructed by Active Motif.

tag: cell type

value: CD8+ effector T cells

tag: strain

tag: genotype

value: WT

tag: chip antibody


title: WT CD8+ effector T cells-HP1g

value: HP1g Millipore, cat#05-690, Lot# 2262769


title: h1hESC_TB-EQ-75pcnt_5

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_5

value: H1 hESC cell line

value: TB


title: h1hESC_TB-EQ-75pcnt_4

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_4


title: 2-cell embryos collected from 10-12 month mouse rep1

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

description:
10-12month rep1
10-12m_1
10-12month rep1

data_processing:
Raw sequencing data were trimmed and filtered to remove the bad quality sequence
Sequencing data were mapped mm10 reference genome using STAR seperately
The gene counts were calculated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Table-delimited file. The file contains six column as same as bed format, attached with three column describing the count, FPM, and FPKM.

source_name: oocyte collected from 10-12 month mouse

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
The collected 2-cell embryos were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences.
After the first reaction of reverse transcription, we used template-switching oligos to obtain the yield of full-length cDNA. Then, we performed RT-PCR to  maximize cDNA (After 90 min at 42 °C (the optimal conditions for Superscript II, according to the manufacturer), we raised the temperature to 50 °C for 2 min to promote the unfolding of any RNA secondary structures. We then lowered it to 42 °C again for 2 min and repeated this cycle a total of ten).After the first-strand reaction,We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The  quantity of the libraries was assessed and defined by qPCR, respectively. All samples showed a concentration of higher than 3nM and were sequenced using HiSeq XTen (Illumina) with paired-end 150-bp sequencing.

treatment_protocol: Female mice of three age groups were superovulated by injecting 5 IU pregnant mare serum gonadotropin (PMSG) (Ningbo Sansheng Pharmaceutical Corporation, Zhejiang, China) followed by 5 IU human chorionic gonadotropin (hCG) (Ningbo Sansheng Pharmaceutical Corporation) 46-48 h after PMSG priming. Oocytes were collected 14-15 h after hCG injection. Cumulus-oocyte complexes (COCs) were isolated from oviduct ampullae. Sperms were isolated from dissected epididymides of adult C57BL/6 mice and capacitated for 1.5 h at 37 °C in human tubal fluid fertilization medium (Fujifilm Irvine Scientific, Santa Ana, CA, USA) supplemented with 10 mg/ml bovine serum albumin. Dispersed spermatozoa were then added to drops of human tubal fluid medium containing COCs. After coincubation for 4-5 h in a 37 °C incubator, inseminated oocytes were washed to remove cumulus cells and excess sperms. Zygotes were transferred to KSOM medium (Millipore Sigma) and cultured to the 2-cell stage.

tag: age

value: 10-12month rep1


title: 2-cell embryos collected from 10-12 month mouse rep2

description:
10-12month rep2
10-12m_2
10-12month rep2

value: 10-12month rep2


title: h1hESC_TB-EQ-75pcnt_3

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_3


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 24h replicate 1 [sample_7]

value: breast ductal carcinoma cell line

value: compound

value: AAGATT


title: 2-cell embryos collected from 6-8 month mouse rep2

description:
6-8month rep2
6-8m_2
6-8month rep2

source_name: oocyte collected from 6-8 month mouse

value: 6-8month rep2


title: MCF7 cells treated with 10 uM nutlin3a at 24h replicate 1 [sample_6]

value: AACAAT


title: h1hESC_TB-EQ-75pcnt_2

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_2


title: h1hESC_EC-EQ-75pcnt_45

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_45

value: EC


title: h1hESC_TB-EQ-75pcnt_10

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_10


title: 2-cell embryos collected from 8-10 week mouse rep2

description:
8-10week rep2
8-10w_2
8-10week rep2

source_name: oocyte collected from 8-10 week mouse

value: 8-10week rep2


title: h1hESC_EC-EQ-75pcnt_44

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_44


title: h1hESC_EC-EQ-75pcnt_43

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_43


title: h1hESC_EC-EQ-75pcnt_42

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_42


title: h1hESC_EC-EQ-75pcnt_41

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_41


title: h1hESC_TB-EQ-75pcnt_1

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_1


title: SA2017_58

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

data_processing:
FASTQ files were  aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts

source_name: PDGFRa+ (CD140+) FBs

extract_protocol:
RNA was isolated using trizol according to manufacturer’s instructions
RNAseq: Libraries were prepared with Illumina RNA PolyA selection
NextEra XT DNA Library Preparation Kit with 15-20 million reads

treatment_protocol: MACS-sorted PDGFRa+ (CD140+) FBs from either RA or O2 PN4, PN7, and PN10 mouse lungs were prepared for bulk RNA-seq and used to determine changes to lung fibroblast populaton.

tag: cell population

value: PDGFRa+ (CD140+) alveolar fibroblasts

value: Hyperoxia


title: 2-cell embryos collected from 6-8 month mouse rep1

description:
6-8month rep1
6-8m_1
6-8month rep1

value: 6-8month rep1


title: SA2017_57

description: P10-Room Air3

value: Room Air


title: SA2017_40


title: SA2017_39

description: P10-Room Air2


title: SA2017_42


title: h1hESC_EC-EQ-75pcnt_38

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_38


title: SA2017_19


title: SA2017_17

description: P10-Room Air1


title: h1hESC_EC-EQ-75pcnt_37

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_37


title: SA2017_138

description: P4-Room Air2


title: h1hESC_EC-EQ-75pcnt_39

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_39


title: h1hESC_EC-EQ-75pcnt_35

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_35


title: SA2017_137


title: 2-cell embryos collected from 8-10 week mouse rep1

description:
8-10week rep1
8-10w_1
8-10week rep1

value: 8-10week rep1


title: h1hESC_EC-EQ-75pcnt_33

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_33


title: SA2017_134


title: h1hESC_EC-EQ-75pcnt_32

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_32


title: SA2017_133


title: SA2017_132

description: P4-Room Air1


title: SA2017_41

description: P7-Room Air1


title: SA2017_112

description: P7-Room Air3


title: h1hESC_EC-EQ-75pcnt_34

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_34


title: h1hESC_EC-EQ-75pcnt_40

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_40


title: h1hESC_EC-EQ-75pcnt_30

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_30


title: h1hESC_EC-EQ-75pcnt_31

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_31


title: SA2017_111

description: P7-Room Air2


title: SA2017_110


title: h1hESC_EC-EQ-75pcnt_27

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_27


title: h1hESC_EC-EQ-75pcnt_29

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_29


title: h1hESC_EC-EQ-75pcnt_28

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_28


title: SA2017_109


title: 10-12month rep3

data_processing:
Raw sequencing data were trimmed and filtered to remove the bad quality sequence
Sequencing data were mapped mm10 reference genome using STAR seperately
The gene counts were calculated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: The first column contains the gene name, the second column contains the raw counts.

value: 10-12 months


title: h1hESC_EC-EQ-75pcnt_26

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_26

value: H1 hESC cell line


title: SA2017_139

description: P4-Room Air3


title: h1hESC_EC-EQ-75pcnt_25

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_25


title: h1hESC_EC-EQ-75pcnt_24

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_24


title: h1hESC_EC-EQ-75pcnt_36

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_36


title: 10-12month rep1


title: 10-12month rep2


title: h1hESC_EC-EQ-75pcnt_23

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_23


title: h1hESC_EC-EQ-75pcnt_22

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_22


title: h1hESC_EC-EQ-75pcnt_21

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_21


title: 6-8month rep3

value: 6-8 months


title: 8-10week rep3

value: 8-10 weeks


title: 6-8month rep2


title: 6-8month rep1


title: h1hESC_EC-EQ-75pcnt_19

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_19


title: 8-10week rep2


title: h1hESC_EC-EQ-75pcnt_20

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_20


title: h1hESC_EC-EQ-75pcnt_17

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_17


title: h1hESC_EC-EQ-75pcnt_16

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_16


title: h1hESC_EC-EQ-75pcnt_15

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_15


title: h1hESC_EC-EQ-75pcnt_18

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_18


title: h1hESC_EC-EQ-75pcnt_14

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_14


title: TET2KO_RNAseq_Rep3

city: Miami

first: Stephen

last: Nimer

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description: RSEM.count.matrix.txt

data_processing:
Base calling using Illumina RTA 2.4.11
Reads were aligned to the mm10 transcriptome and ERCC spike-in indicies using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Excel file contains aggregated RSEM gene.results output with expected counts for all samples.

source_name: LSK Cells

growth_protocol: Lin- bone marrow cells were enriched using the Direct Lineage Cell Depletion kit with LS columns (Miltenyi Biotec). Enriched Lin- cells were stained with the mouse bone marrow biotin lineage panel, Streptavidin APC- cy7, APC-c-Kit and PEcy7-Sca-1, and after staining all HSPCs were sorted.

extract_protocol:
Total RNA was extracted from 1- 2x105 sorted HSPCs using AllPrep DNA/RNA Plus micro kit (Qiagen).  Ribosomal RNA was removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310) following manufacturer’s instructions.
RNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGEN Technologies).
Paired-End, 100bp sequenced on an Illumina HiSeq 2500 platform.

value: Tet2 Knockout

value: LSK Cells


title: p300KO_TET2KO_RNAseq_Rep2

description: RSEM.count.matrix.txt

value: p300 Tet2 Knockout


title: p300KO_TET2KO_RNAseq_Rep3

description: RSEM.count.matrix.txt


title: p300KO_TET2KO_RNAseq_Rep1

description: RSEM.count.matrix.txt


title: h1hESC_EC-EQ-75pcnt_13

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_13


title: h1hESC_EC-EQ-75pcnt_11

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_11


title: P300KO_RNAseq_Rep3

description: RSEM.count.matrix.txt

value: p300 Knockout


title: h1hESC_EC-EQ-75pcnt_10

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_10


title: P300KO_RNAseq_Rep2

description: RSEM.count.matrix.txt


title: P300KO_RNAseq_Rep1

description: RSEM.count.matrix.txt


title: h1hESC_EC-EQ-75pcnt_8

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_8


title: h1hESC_EC-EQ-75pcnt_7

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_7


title: WT_RNAseq_Rep2

description: RSEM.count.matrix.txt

value: WT


title: 8-10week rep1


title: h1hESC_EC-EQ-75pcnt_6

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_6


title: h1hESC_EC-EQ-75pcnt_5

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_5


title: WT_RNAseq_Rep1

description: RSEM.count.matrix.txt


title: h1hESC_EC-EQ-75pcnt_4

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_4


title: k2 2

city: Cleveland

first: Mukesh

last: Jain

address: 2103 Cornell Rd

institute: Case Western Reserve University

data_processing:
Software for the Illumina HiSeq 2500 was used for basecalling. 100bp paired-end sequencing performed
Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013).
Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010). A total of 1,465 differentially expressed genes (DEGs) were identified and were defined as genes having FPKM>2, absolute log2 fold change >0.35, and an adjusted p-value cutoff q <0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes table of FPKM values for each sample

source_name: peritoneal macrophage

growth_protocol: Mice were injected intraperitoneally with thioglycolate. 72 hours later, cells were isolated from the peritoneum. Cells were then plated in DMEM media containing 10% fetal bovine serum and 1% PenStrep + Glutamine. Cells were incubated for 24 hours at 5% CO2 and 37 degrees until harvesting cells for RNA.

extract_protocol:
RNA isolation was performed using the RNeasy kit (Qiagen, Hilden, Germany). cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit (poly A selection)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: peritoneal macrophage

value: KLF2 KO


title: k2 1


title: h1hESC_EC-EQ-75pcnt_3

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_3

tag: cell line

value: EC


title: k2 0


title: h1hESC_EC-EQ-75pcnt_2

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_2

tag: sample type


title: TET2KO_RNAseq_Rep2

description: RSEM.count.matrix.txt


title: h1hESC_EC-EQ-75pcnt_12

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_12

tag: equilization amt


title: wt 2


title: h1hESC_EC-EQ-75pcnt_1

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_1


title: TET2KO_RNAseq_Rep1

description: RSEM.count.matrix.txt


title: h1hESC_TB-EQ-Vary_51

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_51

value: TB

value: Vary


title: wt 1


title: wt 0


title: h1hESC_TB-EQ-Vary_49

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_49


title: h1hESC_TB-EQ-Vary_50

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_50


title: WT_RNAseq_Rep3

description: RSEM.count.matrix.txt


title: RNA-seq_FLC33_NYTS

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Fibrolamellar tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_RNA_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using STAR/Salmon.
Both sequencing types were processed with DESeq2.
Genome_build: hg19 (small RNAseq) or hg38 (RNAseq)
Supplementary_files_format_and_content: DESeq normalized counts

source_name: RNAseq Fibrolamellar carcinoma tissue sample #6

extract_protocol: Libraries were prepared according to the NEBNext Ultra II Directional RNA kit protocol

value: liver

tag: molecule subtype

value: RNA


title: RNA-seq_FLC34_YROP

source_name: RNAseq Fibrolamellar carcinoma tissue sample #7


title: h1hESC_TB-EQ-Vary_48

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_48


title: RNA-seq_FLC32_UOTX

source_name: RNAseq Fibrolamellar carcinoma tissue sample #5


title: RNA-seq_FLC31_OTOK

source_name: RNAseq Fibrolamellar carcinoma tissue sample #4


title: h1hESC_EC-EQ-75pcnt_9

description:
EQ-75pcnt_ExpectedCounts.csv
EC-EQ-75pcnt_9


title: RNA-seq_FLC30_KPKS

source_name: RNAseq Fibrolamellar carcinoma tissue sample #3


title: h1hESC_TB-EQ-Vary_45

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_45


title: h1hESC_TB-EQ-Vary_46

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_46


title: h1hESC_TB-EQ-Vary_44

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_44


title: RNA-seq_FLC29_QLXW

source_name: RNAseq Fibrolamellar carcinoma tissue sample #2


title: h1hESC_TB-EQ-Vary_43

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_43


title: RNA-seq_FLC06_SLVP

description:
Non-malignant liver tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_RNA_counts.csv

source_name: RNAseq Non-malignant liver tissue #1


title: RNA-seq_FLC06_DZIS

source_name: RNAseq Fibrolamellar carcinoma tissue sample #1


title: h1hESC_TB-EQ-Vary_39

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_39

source_name: differentiated human embryonic stem cells


title: h1hESC_TB-EQ-Vary_40

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_40


title: h1hESC_TB-EQ-Vary_41

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_41


title: h1hESC_TB-EQ-Vary_38

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_38


title: LOCE_2_HamF10

city: Leuven

first: Jasper

last: Wouters

address: ON IV Herestraat 49 - bus 602

country: Belgium

institute: KU Leuven - VIB

description:
raw_counts_media.tsv
norm_counts_media.tsv

data_processing:
RNA-seq reads were cleaned using fastq-mcf (ea-utils) and mapped to the genome (hg19) using STAR. Read counts per gene were obtained from the aligned reads using htseq-count. DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: count matrix: raw count matrix as generated by htseq-count
Supplementary_files_format_and_content: normalized count matrix: count matrix normalized wth DeSeq2 using a multi-factor design (including the sample variable).

source_name: primary cell cultures

growth_protocol: Melanoma biopsies were obtained from surgical procedures. Tumor tissues were cut to very small pieces, which were incubated overnight in a medium containing dispase, collagenase, and supplemented with penicillin G, kanamycin sulphate, streptomycin sulphate, and gentamycin at standard concentrations (100μg/ml). Then the detached cells were washed and seeded in culture flasks. Melanoma primary cultures were propagated in the following culture media: Ham’s-F10, Ham’s F10 supplemented with 100μM of tyrosine and RPMI1640 (Lonza). All of these culture media were supplemented with 10% heat-inactivated fetal calf serum, L-glutamine, penicillin, and streptomycin at standard concentrations (Thermo Fisher Scientific).  Cell cultures were kept in a humidified incubator with 5% CO2 at 37°C. Cell culture medium was renewed every 2–3 days. Once the cells were at or near confluence they were subcultured. Melanoma primary cultures were regularly checked for mycoplasma contamination using MycoAlert® Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA was extracted using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions.
RNA-seq libraries were prepared according to the Illumina Truseq stranded mRNA sample preparation guide. Final libraries were pooled and sequenced on a HiSeq4000 (LOCE#1 and #2 in Ham’s F10 and Ham’s F10 with tyrosine; Illumina) and NextSeq500 (LOCE#1 and #2 in Ham’s F10 and RPMI1640; Illumina).

treatment_protocol: Melanoma primary cultures were propagated in Ham’s-F10 culture medium, Ham’s F10 supplemented with 100μM of tyrosine or RPMI1640.

tag: culture

tag: culture medium

tag: treatment

value: no treatment


title: LOCE_1_RPMI1640


title: h1hESC_TB-EQ-Vary_37

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_37


title: LOCE_1_HamF10


title: NFKB1_KO - LPS_rep2

city: Glasgow

first: Domenico

last: Somma

address: 120 University Place

department: Institute of Infection, Immunity & Inflammation

country: United Kingdom

institute: University of Glasgow

data_processing:
University of Glasgow Galaxy platform (v18.09) was used
Sequenced reads were trimmed low-quality with Trimmomatic (v0.36.5), then mapped on human genome (Ensembl GRCh38.p13 sm primary assembly) using HISAT2 (v2.1.0)
Features were assigned using Infer Experiment (v2.6.4) and featureCounts (v1.6.0.3) against human genome annotation (Ensembl GRCh38.98 filtered to contain only protein coding genes).
DESeq2 (v2.11.40.2) was used to determine DE genes.
Genome_build: hg38

source_name: THP1 macrophage

growth_protocol: macrophage were differentiated using 25 nM PMA for 48h + 48h resting

extract_protocol:
total RNA extracted using RNeasy kits (QIAGEN), according to the manufacturer’s instructions and 1 ug of isolated RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ng/ml LPS for 3h

value: macrophage PMA-induced

value: 3h LPS


title: h1hESC_TB-EQ-Vary_36

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_36

value: H1 hESC cell line


title: RNA-seq_FLC34_PMVV

source_name: RNAseq Non-malignant liver tissue #2


title: NFKB1_KO - LPS_rep1


title: h1hESC_TB-EQ-Vary_35

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_35


title: NFKB1_KO - UNT_rep2

value: untreated


title: h1hESC_TB-EQ-Vary_47

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_47


title: WT - LPS_rep3

value: wild type


title: h1hESC_TB-EQ-Vary_34

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_34


title: h1hESC_TB-EQ-Vary_33

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_33


title: h1hESC_TB-EQ-Vary_32

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_32


title: h1hESC_TB-EQ-Vary_31

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_31


title: h1hESC_TB-EQ-Vary_42

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_42


title: h1hESC_TB-EQ-Vary_30

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_30


title: WT - LPS_rep2


title: WT - UNT_rep3


title: WT - UNT_rep2


title: WT - LPS_rep1


title: LOCE_2_RPMI1640


title: h1hESC_TB-EQ-Vary_27

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_27


title: h1hESC_TB-EQ-Vary_26

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_26


title: h1hESC_TB-EQ-Vary_25

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_25


title: h1hESC_TB-EQ-Vary_24

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_24


title: h1hESC_TB-EQ-Vary_23

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_23


title: SNC_EXP_M

city: Los Angeles

first: Desmond

middle: J

last: Smith

state: CA

address: 650 Charles E Young Drive South

institute: UCLA

description: Gene expression in Parkinson modeled mouse substantia nigra pars compacta at single cell resolution

data_processing:
Basecalls performed
Cell Ranger
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: Substantia nigra pers compacta

extract_protocol:
Three males, each from control (vehicle) and treated (MNPQ) treated mouse selected in random for single cell isolation from SNpc. Each animal was euthanized using isoflurane and following cervical dislocation. Immediately after euthanasia, the mouse brains were extracted and placed on ice cold mouse mold facing dorsal side to the inner side of brain slicer (1 mm slice) to slice out the region (1.28 bregma to 2.28 bregma) that presumably contains substantia nigra pars compacta. Substantia nigra were then dissected out from both slices (control and MNPQ treated) by punch dissection and single cells were dissociated by digestion using 2 mg ml-1 papain for 30 min at 34 degree and followed by trituration for 35 minutes. Debris were removed by filtration using a 40 mm filter. Cells were then pelleted, removed supernatant and resuspended in 1x PBS with 0.04 % FBS. Brain samples (single cells) quantified and quality was checked using 10x genomics cell counter. Total of 1 ml of volume of cells at approximately 1200 cells/ul were submitted for sequencing.
Sequencing libraries constructed from isolated single cells from each sample using 10X genomics chromium technology. Samples were sequenced using an Illumina NextSeq 500 SBS sequencing machine to obtain paired end sequences 1 x 75 with one read of 26 bp and the second read of 57 bp.

treatment_protocol: Each mouse was housed for two weeks (3 per each cage) to allow acclimation to the new environment. Each batches of mice were treated with saline (vehicle) and MNPQ (3 males, 3 females in each group). At 10 weeks of age each mouse weight was measured and based on their weight one IP injection of 10 mg kg-1 PQ and 30 mg kg-1 maneb given to each mouse twice per week for three weeks. (every Monday and Friday of the week, first paraquat was administered and an hour later maneb was administered). For each control mouse, saline was injected twice every week for three weeks.

tag: disease model

value: Parkinson's disease

tag: Sex

value: pooled male and female

value: Substantia nigra pers compacta

value: treated with MNPQ


title: SNC_CTL_M


title: h1hESC_TB-EQ-Vary_21

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_21


title: h1hESC_TB-EQ-Vary_22

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_22


title: WTM2_tRFseq

city: New York

first: Jennifer

last: Blaze

state: New York

address: 1470 Madison Ave 9-202

institute: Icahn School of Medicine at Mount Sinai

description:
tRF seq processed data.xlsx
WTM2_tRFseq

data_processing:
Library strategy: tRF-seq
Reads were trimmed and aligned to mature tRNA reference sequences from GtRNAdb and mitotRNAdb allowing for 1 mismatch, and reads that did not map were then mapped to precursor tRNA sequences (pre-tRNAs) allowing for 1 mismatch with bowtie software. Expression of mapped tRNA fragments was reflected with CPM.

source_name: Mouse cortex

extract_protocol:
5ug total DNase-treated RNA was used for pre-treatment and library prep. Pre-treatment of RNA, library preparation, next-generation sequencing, and some aspects of data analysis were performed by Arraystar, Inc.
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

tag: tissue type

value: Cortex

value: Nsun2 floxed, Camk2a-Cre neg.

tag: developmental stage

value: Adult

tag: molecule

value: small RNA


title: h1hESC_TB-EQ-Vary_28

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_28

value: TB

value: Vary


title: WTM1_tRFseq

description:
tRF seq processed data.xlsx
WTM1_tRFseq

tag: strain


title: KOM2_tRFseq

description:
tRF seq processed data.xlsx
KOM2_tRFseq

value: Nsun2 floxed, Camk2a-Cre pos.


title: h1hESC_TB-EQ-Vary_19

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_19


title: KOM1_tRFseq

description:
tRF seq processed data.xlsx
KOM1_tRFseq


title: h1hESC_TB-EQ-Vary_20

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_20


title: KOM3_tRFseq

description:
tRF seq processed data.xlsx
KOM3_tRFseq


title: WT - UNT_rep1

tag: cell type

tag: genotype


title: h1hESC_TB-EQ-Vary_29

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_29


title: h1hESC_TB-EQ-Vary_18

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_18


title: h1hESC_TB-EQ-Vary_17

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_17


title: h1hESC_TB-EQ-Vary_15

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_15


title: WTF2_tRFseq

description:
tRF seq processed data.xlsx
WTF2_tRFseq


title: NFKB1_KO - UNT_rep1


title: h1hESC_TB-EQ-Vary_16

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_16


title: WTF1_tRFseq

description:
tRF seq processed data.xlsx
WTF1_tRFseq


title: KOF3_tRFseq

description:
tRF seq processed data.xlsx
KOF3_tRFseq


title: h1hESC_TB-EQ-Vary_12

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_12


title: h1hESC_TB-EQ-Vary_14

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_14


title: h1hESC_TB-EQ-Vary_13

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_13


title: C4

type: RNA

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

country: Brazil

institute: INCA

description: The normal breast tissues were obtained from healthy women that performed mamoplasty at Hospital Universitário de Londrina (Londrina, Paraná, Brazil)

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a GeneChip Human Exon 1.0 ST Array (Affymetrix, CA, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: Affymetrix Expression Console Software version 1.0 was used to create summarized expression values (CHP-files). The Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed with Partek® software (http://www.partek.com).

label: biotin

source_name: healthy woman with mamoplasty

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA from all normal breast tissues used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

value: normal breast tissue


title: C1


title: h1hESC_TB-EQ-Vary_11

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_11


title: h1hESC_TB-EQ-Vary_10

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_10


title: KOF1_tRFseq

description:
tRF seq processed data.xlsx
KOF1_tRFseq


title: h1hESC_TB-EQ-Vary_9

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_9


title: C3


title: C2


title: h1hESC_TB-EQ-Vary_8

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_8


title: h1hESC_TB-EQ-Vary_7

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_7


title: h1hESC_TB-EQ-Vary_6

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_6


title: WT3_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4242_HydrotRNAseq

data_processing:
Library strategy: HydrotRNA-seq
Raw sequencing read data that passed the Illumina chastity filter was used for further data analysis, including alignment of trimmed reads (cutadapt) to mature tRNA reference sequences from GtRNAdb and mitotRNAdb using BWA.  For tRNA alignment, the maximum number of mismatches were 2.  tRNA expression levels were measured with tag count and the multi-map-corrected number of reads overlapping the tRNA (mrcount) was then calculated.  Normalized tRNA counts are shown as CPM for each sample.


title: KO3_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4241_HydrotRNAseq


title: RCC4-SiJMJD2B-rep1

city: chengdu

first: Lei

last: Qiu

state: sichuan

address: No. 17, Section 3, Renmin South Road

department: Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, and Cancer Center, West China Hospital

institute: sichuan university

hyb_protocol: Samples were hybridized using Affymetrix kit materials in the following conditions: 45C , 17hr plus or minus 1hr , 60rpm using GeneChip Hybridization Oven 640. Arrays were washed using protocol FS450_0001

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000 7G with Autoloader

data_processing:
The exon-arrays were RMA-background corrected, quantile-normalized and gene-level summarized using the Median Polish algorithm (Irizarry et al. 2003). The resulting log (base 2) transformed signal intensities
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: RCC4-SiRNA to JMJD2B

label_protocol: mRNA was reverse transcribed using the Ambion WT Expression Sense Target Protocol, followed by TdT End labeling with the GeneChip WT Terminal Labeling Kit to incorporate biotin label

growth_protocol: RCC4 cells were maintained in DMEM media, supplemented with 10% FBS

extract_protocol: Total RNA was collected and purified using TriReagent (Sigma) according to manufacturer's protocol, and further purified using QIAGen RNeasy columns. Contaminating salts were removed by desalting column (Princeton separations)

value: clear cell renal cell carcinoma

tag: transduced with


title: RCC4-SiJMJD1A-rep3

source_name: RCC4-SiRNA to JMJD1A


title: h1hESC_TB-EQ-Vary_4

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_4


title: h1hESC_TB-EQ-Vary_5

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_5


title: RCC4-SiJMJD2B-rep3


title: h1hESC_TB-EQ-Vary_2

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_2


title: h1hESC_TB-EQ-Vary_3

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_3


title: RCC4-SiJMJD2B-rep2


title: RCC4-SiJMJD1A-rep2


title: KOF2_tRFseq

description:
tRF seq processed data.xlsx
KOF2_tRFseq


title: WT2_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4238_HydrotRNAseq


title: h1hESC_EC-EQ-Vary_44

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_44

value: EC


title: h1hESC_TB-EQ-Vary_1

description:
EQ-Vary_ExpectedCounts.csv
TB-EQ-Vary_1

value: H1 hESC cell line


title: h1hESC_EC-EQ-Vary_45

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_45


title: KO2_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4236_HydrotRNAseq


title: RCC4-SiControl-rep3

description: SiControl

value: SiControl


title: KO1_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4222_HydrotRNAseq


title: RCC4-SiJMJD1A-rep1


title: h1hESC_EC-EQ-Vary_43

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_43


title: h1hESC_EC-EQ-Vary_41

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_41


title: RCC4-SiControl-rep2

description: SiControl


title: h1hESC_EC-EQ-Vary_39

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_39


title: 35-P2ry1KO-IVM-RNA-4

city: Chicago

first: Benjamin

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Base-calling was performed on Basepace with default parameters (bcl2fastq2)
Fastq files were aligned using STAR (v2.7.2b) with options --runThreadN 12 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
Gene counts were obtained using rsem (v1.3.3) with options rsem-calculate-expression --bam -p 12 --paired-end --forward-prob 0
DESeq2 (v1.32.0) analysis was performed in Rstudio (v4.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every sample
Supplementary_files_format_and_content: DESeq2 normalized counts for every gene in every sample

source_name: BetaTC6 cells from ATCC (CRL- 11506)

growth_protocol: Approximately one million cells were plated and grown for 3 days in 15% FBS supplemented DMEM in 35 mm tissue-culture treated plates

extract_protocol:
Cells were lysed and collected from 35 mm plates using TRI reagent. RNA was purified by Directzol Microprep kit with Dnase digestion.
RNA was extracted from wild-type and P2ry1 receptor knockout BetaTC6 β-cell lines by Tri-reagent followed by Directzol purification. 125 ng of RNA was processed, barcoded, and amplified 11 cycles using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with polyA bead selection and then sequenced by paired-end 42x42 on an Illumina NextSeq 500

treatment_protocol: Cells were preincubated with 3% BSA supplemented Krebs Ringer Buffer (KRB) without glucose, followed by stimulation with 3% BSA KRB with 20 mM glucose with or without ivermectin for 30 minutes

value: BetaTC6 cells from ATCC (CRL- 11506)

tag: cell source

value: derived from insulinoma

value: ivermectin

value: P2ry1 knockout


title: RCC4-SiControl-rep1

description: SiControl

tag: cell line


title: h1hESC_EC-EQ-Vary_36

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_36

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads trimmed to have length 51 bp using seqtk 1.0
Sequencing reads were mapped to GRCh38 Ensembl using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts csv

tag: sample type


title: h1hESC_EC-EQ-Vary_38

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_38

tag: equilization amt


title: h1hESC_EC-EQ-Vary_37

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_37


title: HCT116-SiJMJD2B-Hypoxia-rep3

source_name: HCT116_SiRNA to JMJD2B_hypoxia

growth_protocol: HCT116 cells were maintained in DMEM media, supplemented with 10% FBS

value: colon carcinoma cells

tag: culture condition

value: Hypoxia, 0.5% O2


title: h1hESC_EC-EQ-Vary_34

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_34


title: HCT116-SiJMJD2B-Hypoxia-rep2


title: 34-P2ry1KO-IVM-RNA-3


title: HCT116-SiJMJD2B-Hypoxia-rep1


title: 32-P2ry1KO-IVM-RNA-1


title: WT1_HydrotRNAseq

description:
HydrotRNAseq processed data.xlsx
4219_HydrotRNAseq

value: Cortex

value: Nsun2 floxed, Camk2a-Cre neg.


title: h1hESC_EC-EQ-Vary_35

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_35


title: 33-P2ry1KO-IVM-RNA-2


title: 29-P2ry1KO-Con-RNA-3

value: DMSO


title: HCT116-SiJMJD1A-Hypoxia-rep3

source_name: HCT116_SiRNA to JMJD1A_hypoxia


title: h1hESC_EC-EQ-Vary_32

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_32


title: h1hESC_EC-EQ-Vary_33

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_33


title: h1hESC_EC-EQ-Vary_27

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_27


title: 31-P2ry1KO-Con-RNA-4


title: h1hESC_EC-EQ-Vary_31

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_31


title: 28-P2ry1KO-Con-RNA-2


title: h1hESC_EC-EQ-Vary_42

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_42


title: h1hESC_EC-EQ-Vary_30

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_30


title: HCT116-SiJMJD1A-Hypoxia-rep1


title: HCT116-SiJMJD1A-Hypoxia-rep2


title: h1hESC_EC-EQ-Vary_26

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_26


title: HCT116-SiControl-Hypoxia-rep2

source_name: HCT116_control SiRNA_hypoxia


title: h1hESC_EC-EQ-Vary_29

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_29


title: h1hESC_EC-EQ-Vary_28

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_28


title: h1hESC_EC-EQ-Vary_22

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_22


title: h1hESC_EC-EQ-Vary_25

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_25


title: 26-P2ry1KO-Con-RNA-1


title: h1hESC_EC-EQ-Vary_24

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_24


title: h1hESC_EC-EQ-Vary_23

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_23


title: h1hESC_EC-EQ-Vary_21

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_21


title: h1hESC_EC-EQ-Vary_18

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_18


title: h1hESC_EC-EQ-Vary_19

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_19


title: 17-WT-IVM-RNA-3

value: wild type


title: HCT116-SiControl-Hypoxia-rep1


title: h1hESC_EC-EQ-Vary_16

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_16

value: Vary


title: HCT116-SiControl-Hypoxia-rep3


title: h1hESC_EC-EQ-Vary_20

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_20


title: HCT116-SiJMJD2B-Normoxia-rep2

source_name: HCT116_SiRNA to JMJD2B_normoxia

value: Normoxia, 21% O2


title: HCT116-SiJMJD2B-Normoxia-rep3


title: h1hESC_EC-EQ-Vary_40

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_40


title: h1hESC_EC-EQ-Vary_13

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_13


title: 27-WT-IVM-RNA-2


title: 25-WT-IVM-RNA-1


title: 23-WT-Con-RNA-4


title: h1hESC_EC-EQ-Vary_15

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_15


title: h1hESC_EC-EQ-Vary_12

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_12


title: 24-WT-IVM-RNA-4


title: HCT116-SiJMJD2B-Normoxia-rep1


title: 22-WT-Con-RNA-3


title: h1hESC_EC-EQ-Vary_17

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_17


title: HCT116-SiJMJD1A-Normoxia-rep2

source_name: HCT116_SiRNA to JMJD1A_normoxia


title: HCT116-SiControl-Normoxia-rep3

source_name: HCT116_control SiRNA_normoxia


title: h1hESC_EC-EQ-Vary_11

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_11


title: 21-WT-Con-RNA-2


title: h1hESC_EC-EQ-Vary_9

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_9


title: HCT116-SiJMJD1A-Normoxia-rep3


title: h1hESC_EC-EQ-Vary_10

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_10


title: 20-WT-Con-RNA-1


title: h1hESC_EC-EQ-Vary_7

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_7


title: aAm_late2cell_NT3

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description:
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis
2cell_gene-FPKM_name.txt

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Mouse 2-cell stage embryos

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 4-cell stage. At 40 hours post insemination (hpi), embryos were moved to KSOM medium containing 0.1 µg/ml demecolcine to arrest their cell cycle at G2/M phase. The demecolcine-treated embryos were subjected to nuclear transfer during 46-49 hpi, and the reconstructed NT embryos were further cultured in KSOM medium containing 0.1 µg/ml demecolcine with or without α-amanitin till 70 hpi. To examine the effect of DNA replication on transcriptional reprogramming, nuclear transfer to 4-cell embryos was performed during 40-43 hpi, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 64 hpi. To examine the reprogramming ability of 2-cell embryos, nuclear transfer to 2-cell embryos was performed during 21-24 hpi for early 2-cell NT and 30-33 hpi for late 2-cell NT, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 45 hpi and 54 hpi, respectively.

extract_protocol:
After the removal of zona pellucida, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
The produced cDNA was amplified by PCR with 13 -14 cycles. The amplified cDNA was purified using AMPure XP beads (BECKMAN COULTER, A63882). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit (Thermo Scientific).

treatment_protocol: As described in the growth protocol, embryos were treated with 0.1 µg/ml demecolcine to arrest their cell cycle. To identify newly transcribed genes, NT embryos were cultured with or without α-amanitin, and transcriptomes were compared.

tag: strains

value: C57BL/6, DBA/2, and C3H strains

tag: alpha-amanitin

value: Plus

value: 2-cell stage embryos


title: h1hESC_EC-EQ-Vary_14

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_14

source_name: differentiated human embryonic stem cells

value: H1 hESC cell line

value: EC


title: h1hESC_EC-EQ-Vary_8

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_8


title: h1hESC_EC-EQ-Vary_4

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_4


title: h1hESC_EC-EQ-Vary_5

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_5


title: h1hESC_EC-EQ-Vary_3

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_3


title: HCT116-SiJMJD1A-Normoxia-rep1


title: HCT116-SiControl-Normoxia-rep2

value: SiControl


title: aAm_late2cell_NT1


title: late2cell_NT3

value: Minus


title: HCT116-SiControl-Normoxia-rep1


title: h1hESC_TB-EQ_51

description:
EQ_ExpectedCounts.csv
TB-EQ_51

value: TB

value: equalized


title: h1hESC_EC-EQ-Vary_1

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_1


title: h1hESC_TB-EQ_50

description:
EQ_ExpectedCounts.csv
TB-EQ_50


title: h1hESC_EC-EQ-Vary_6

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_6


title: h1hESC_TB-EQ_48

description:
EQ_ExpectedCounts.csv
TB-EQ_48


title: h1hESC_TB-EQ_47

description:
EQ_ExpectedCounts.csv
TB-EQ_47


title: h1hESC_TB-EQ_49

description:
EQ_ExpectedCounts.csv
TB-EQ_49


title: late2cell_NT1


title: h1hESC_TB-EQ_46

description:
EQ_ExpectedCounts.csv
TB-EQ_46


title: late2cell_NT2


title: aAm_early2cell_NT3


title: aAm_late2cell_NT2


title: aAm_early2cell_NT2


title: h1hESC_TB-EQ_45

description:
EQ_ExpectedCounts.csv
TB-EQ_45


title: BEAS_10mg_24h_Pollen_rep1

city: Munich

first: Joana

last: Candeias

address: Biedersteinerstr. 29

department: Center Allergy and Environment (ZAUM)

country: Germany

institute: Technical University Munich & Helmholtz Center Munich

description: Gene expression after 24h in 10 mg whole birch pollen exposure

hyb_protocol: The Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes with Agilent fragmentation mix, according to the manufacturers instructions. After that, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40uL of the samples was hybridized to One-Color SurePrint G3 8x60K Human gene expression arrays (Agilent Technologies, Inc, Waldbronn, Germany) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After incubation time, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, at 500rpm and 1 minute with 32°C GE Wash buffer 2 (Agilent), at 500rpm. Slide was placed in a array gasket chamber for scan procedure.

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: Scanned images were analyzed with Feature Extraction Software Version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20200924) to obtain background and Processed Signal intensities.

source_name: BEAS-2B, 10mg, 24h, pollen, replicate 1

label_protocol: RNA samples (input of 100ng) were spiked (One-Color RNA Spike-in Kit, Agilent Technologies, Waldbronn, Germany), Cy3-labelled (Low Input Quick Amp Labeling Kit, one-color, Agilent Technologies, Waldbronn, Germany) and purified on RNeasy mini spin columns (QIAGEN). Generated Cy3-labelled cRNA was quantified with NanoPhotometer® N60, IMPLEN, Munich, Germany.

extract_protocol: RNA was obtained with the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), with additional 1% ß-Mercaptoethanol (Roth, Karlsruhe, Germany), according to the manufacturer’s protocol.  The quantification and quality of the RNA was assessed with an UV-vis spectrophotometer (NanoPhotometer® N60, IMPLEN, Munich, Germany) and the Agilent 2100 Bioanalyzer RNA Nano chip (Agilent Technologies, Waldbronn, Germany), respectively.

treatment_protocol: BEAS-2B cells  were cultured in 6-well Transwells with BEGM Medium. After 24h, basal medium was changed, apical medium was removed and cells were kept in Air-Liquid-Interface for 24h, before pollen exposure. Cells were exposed to 10 mg of whole birch pollen dispersing it with 0.5 bar pressured air into the Pollen Sedimentation Chamber, for different incubation times. Cells were kept all the time at 37°C and 5% CO2.

tag: doses

value: 10 mg

tag: time

tag: condition

value: pollen


title: BEAS_10mg_24h_Pollen_rep3

source_name: BEAS-2B, 10mg, 24h, pollen, replicate 3


title: BEAS_10mg_24h_Air_rep3

description: Gene expression control sample of 24h in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 24h, air, replicate 3

value: air


title: h1hESC_TB-EQ_42

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

description:
EQ_ExpectedCounts.csv
TB-EQ_42

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system. For EQ, EQ-Vary and EQ-75%, we retrieved the harvested cDNA, which are amplified full-length single-cell cDNAs identical to those in GSE75748.
For the EQ and EQ-75% experiments, 2.0 µL of the amplified/tagmented cDNA were used for pooling. In the EQ-Vary experiment, a single scaling factor was applied to generate variable amounts of the pooling volume. These pooled single-cell libraries were used in an AMpure XP Bead-based Dual Bead Cleanup and Size Selection reaction (Agencourt AMPure XP PCR Purification modified Instructions for Use, Beckman Coulter). In both bead cleanup reactions, 90% of AMPure XP beads were added to the amplified single-cell libraries to select for an approximate size range of 150-700 bp and incubated for 15 minutes at room temperature. Libraries bound to beads were then placed on a magnet for 5 minutes, washed twice with 70% Ethanol, eluted with Suspension Buffer (Nextera XT DNA Sample Preparation Index Kit, Illumina), and transferred to a new tube.  Final amplified and pooled single-cell libraries were quantified with the Qubit dsDNA HS Assay Kit (Q32854, Thermofisher) and Bioanalyzer High Sensitivity DNA Analysis Kit (5067-4626, Agilent).Libraries were multiplexed with 96 samples per lane and sequenced on an Illumina HiSeq3000 with paired-end 65 or 78 bp reads.
Single-cell RNA-Seq


title: h1hESC_TB-EQ_44

description:
EQ_ExpectedCounts.csv
TB-EQ_44


title: h1hESC_EC-EQ-Vary_2

description:
EQ-Vary_ExpectedCounts.csv
EC-EQ-Vary_2


title: aAm_early2cell_NT1


title: h1hESC_TB-EQ_43

description:
EQ_ExpectedCounts.csv
TB-EQ_43


title: BEAS_10mg_24h_Air_rep2

source_name: BEAS-2B, 10mg, 24h, air, replicate 2


title: early2cell_NT3


title: BEAS_10mg_24h_Air_rep1

source_name: BEAS-2B, 10mg, 24h, air, replicate 1


title: h1hESC_TB-EQ_39

description:
EQ_ExpectedCounts.csv
TB-EQ_39


title: BEAS_10mg_6h50min_Pollen_rep2

description: Gene expression after 6h50min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 6h50min, pollen, replicate 2


title: h1hESC_TB-EQ_41

description:
EQ_ExpectedCounts.csv
TB-EQ_41


title: early2cell_NT2


title: early2cell_NT1


title: h1hESC_TB-EQ_37

description:
EQ_ExpectedCounts.csv
TB-EQ_37


title: h1hESC_TB-EQ_38

description:
EQ_ExpectedCounts.csv
TB-EQ_38


title: h1hESC_TB-EQ_35

description:
EQ_ExpectedCounts.csv
TB-EQ_35


title: h1hESC_TB-EQ_36

description:
EQ_ExpectedCounts.csv
TB-EQ_36


title: h1hESC_TB-EQ_34

description:
EQ_ExpectedCounts.csv
TB-EQ_34


title: BEAS_10mg_24h_Pollen_rep2

source_name: BEAS-2B, 10mg, 24h, pollen, replicate 2


title: BEAS_10mg_6h50min_Pollen_rep3

source_name: BEAS-2B, 10mg, 6h50min, pollen, replicate 3


title: BEAS_10mg_6h50min_Pollen_rep1

source_name: BEAS-2B, 10mg, 6h50min, pollen, replicate 1


title: h1hESC_TB-EQ_40

description:
EQ_ExpectedCounts.csv
TB-EQ_40


title: h1hESC_TB-EQ_29

description:
EQ_ExpectedCounts.csv
TB-EQ_29


title: BEAS_10mg_6h50min_Air_rep3

description: Gene expression control sample of 6h50min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 6h50min, air, replicate 3


title: h1hESC_TB-EQ_31

description:
EQ_ExpectedCounts.csv
TB-EQ_31


title: h1hESC_TB-EQ_27

description:
EQ_ExpectedCounts.csv
TB-EQ_27


title: h1hESC_TB-EQ_33

description:
EQ_ExpectedCounts.csv
TB-EQ_33


title: h1hESC_TB-EQ_26

description:
EQ_ExpectedCounts.csv
TB-EQ_26


title: h1hESC_TB-EQ_30

description:
EQ_ExpectedCounts.csv
TB-EQ_30


title: h1hESC_TB-EQ_28

description:
EQ_ExpectedCounts.csv
TB-EQ_28


title: Naive3: BM Tregs isolated from naïve mice_rep3

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: BM Tregs isolated from naïve mice_rep3

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.15 and analyzed using ArrayStar software v.15 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: BM Tregs

extract_protocol:
Total RNA was extracted from FACS-purified BM Tregs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic Foxp3-DTR-GFP recipients. BM Tregs from CML or naive mice were then isolated for RNA extraction.

tag: tissue

value: Bone marrow derived Tregs

tag: age

value: post natal week 8


title: h1hESC_TB-EQ_32

city: Gainesville

description:
EQ_ExpectedCounts.csv
TB-EQ_32


title: h1hESC_TB-EQ_24

description:
EQ_ExpectedCounts.csv
TB-EQ_24


title: Injured heart tissue, scRNAseq-CKO

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

description:
scRNAseq_CKO.csv.gz
Single cell RNA-seq of the non-myocyte population in ENPP1CKO animals at 7 days following cardiac injury.

data_processing:
Sequencing was done using  Illumina with 50bp paired end reads.
For bulk RNA-seq, the reads were mapped with STAR 2.5.3a to the mouse genome (mm10 or rn6). The counts for each gene were obtained by using –quantMode GeneCounts commands in STAR, and the other parameters during alignment were set to default.
For scRNA-seq, raw reads were aligned to the mouse genome (mm10) and the digital expression matrix was generated using cellranger count.
Genome_build: mm10 and rn6
Supplementary_files_format_and_content: csv file with raw expression values

source_name: injured heart tissue

growth_protocol: (1) Immortalized CFs were seeded at low density at approximately 20-30% confluency in 24 well plates in high glucose DMEM  supplemented with 10%FBS  and 1% penicillin and streptomycin and cultured for 24 hours (500 μL/well). Cells were then washed with PBS and maintained for another 24 hours in serum-free DMEM/ITS medium which was made with high glucose DMEM supplemented with 0.1% Insulin-Transferrin-Selenium (ITS) and 1% penicillin and streptomycin. After 24 hours, DMEM/ITS medium was replaced by conditioned medium and then cells incubated for 24 or 48 hours. (2). NRVMs were seeded at low density at approximately 20-30% confluency in 24 well plates in high glucose DMEM  supplemented with 10%FBS  and 1% penicillin and streptomycin and cultured for 24 hours (500 μL/well). Cells were then washed with PBS and maintained for another 24 hours in serum-free DMEM/ITS medium which was made with high glucose DMEM supplemented with 0.1% Insulin-Transferrin-Selenium (ITS) and 1% penicillin and streptomycin. After 24 hours, DMEM/ITS medium was replaced by conditioned medium and then cells incubated for 24 hours.

extract_protocol:
Total RNA from cells was extracted using RNA mini Kit (BioRad, 7326830). For heart tissue RNA extraction, the uninjured and injured regions of the heart were harvested and homogenized in lysis buffer and then extracted using RNA mini kit. cDNA was synthesized by using iScript cDNA Synthesis Kit (BioRad, 1708890)
RNA libraries were prepared for sequencing using standard Illumina protocols
bulk RNA-seq and scRNA-seq

treatment_protocol: (1). Immortalized cardiac fibroblasts were treated with conditioned medium and extract RNA after 24 hours and 48 hours. (2). NRVMs were treated with conditioned medium and extract RNA after 24 hours. (3). Harvest cardiac non-myocyte population in Control or ENPP1 CKO at 7 days following myocardial infarction.

value: injured heart tissue

value: non-myocyte population

value: ENPP1 CKO

tag: treatment

value: 7 days myocardial infacrtion

value: 7 days


title: Injured heart tissue, scRNAseq-CTR

description:
scRNAseq_CTR.csv.gz
Single cell RNA-seq of the non-myocyte population in control animals at 7 days following cardiac injury.

tag: strain

value: wild type


title: CML3: BM Tregs isolated from CML mice_rep3

description: BM Tregs isolated from CML mice_rep3


title: BEAS_10mg_6h50min_Air_rep2

source_name: BEAS-2B, 10mg, 6h50min, air, replicate 2


title: h1hESC_TB-EQ_23

description:
EQ_ExpectedCounts.csv
TB-EQ_23

value: H1 hESC cell line


title: h1hESC_TB-EQ_22

description:
EQ_ExpectedCounts.csv
TB-EQ_22


title: h1hESC_TB-EQ_21

description:
EQ_ExpectedCounts.csv
TB-EQ_21


title: BEAS_10mg_2h25min_Pollen_rep3

description: Gene expression after 2h25min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 2h25min, pollen, replicate 3


title: BEAS_10mg_6h50min_Air_rep1

source_name: BEAS-2B, 10mg, 6h50min, air, replicate 1


title: BEAS_10mg_2h25min_Pollen_rep2

source_name: BEAS-2B, 10mg, 2h25min, pollen, replicate 2


title: Naive2: BM Tregs isolated from naïve mice_rep2

description: BM Tregs isolated from naïve mice_rep2


title: CML2: BM Tregs isolated from CML mice_rep2

description: BM Tregs isolated from CML mice_rep2


title: h1hESC_TB-EQ_25

description:
EQ_ExpectedCounts.csv
TB-EQ_25

source_name: differentiated human embryonic stem cells


title: BEAS_10mg_2h25min_Air_rep3

description: Gene expression control sample of 2h25min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 2h25min, air, replicate 3


title: h1hESC_TB-EQ_20

description:
EQ_ExpectedCounts.csv
TB-EQ_20


title: Naive1: BM Tregs isolated from naïve mice_rep1

description: BM Tregs isolated from naïve mice_rep1


title: h1hESC_TB-EQ_19

description:
EQ_ExpectedCounts.csv
TB-EQ_19


title: CML1: BM Tregs isolated from CML mice_rep1

description: BM Tregs isolated from CML mice_rep1


title: h1hESC_TB-EQ_18

description:
EQ_ExpectedCounts.csv
TB-EQ_18


title: ESC derived motor neuron progenitor

first: Michael

last: Closser

institute: Columbia University

data_processing:
MACS/GEM for ChIP peak calling
CID for ChIA-PET interaction calls
STAR/Cufflinks for RNA quatification
bedtools for cell specific genomic features
n/a
Genome_build: mm10
Supplementary_files_format_and_content: all files are tab delimited text. tpm for expression, peak calls with ChIP/ATAC, interaction calls for ChIA-PET

source_name: ESC derived motor neuron progenitor

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on a monolayer of Mitomycin-C–treated mouse embryonic fibroblasts (GlobalStem) in EmbryoMax D-MEM (Life Technologies) supplemented with 15% Knockout serum replacement (Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM β-mercaptoethanol and 100 U ml−1 leukemia inhibitory factor (Millipore), 1.25uM GSK3i (Selleckchem), and 100nM FRI (Gift from Austin Smith).

extract_protocol: ChIA-PET experiments were performed similar to previously described (Fullwood et al., 2009; Li et al., 2012). Briefly, on the appropriate day of differentiation, embryoid bodies were dissociated in trypsin into single cell suspension. Cells were cross-linked using 2mM DSG for 15 mins followed by 1% formaldehyde for 15 mins. Fixation was quenched with 2M Glycine (125mM final concentration) for 10 mins at room temp. Cross-linked chromatin was fragmented by sonication to a size of approximately 300bp. Chromatin complexes were immunoprecipitated with monoclonal anti-RNAPII (Covance, 8WG16) coated protein G Dynabeads (Life Technologies). To prepare ChIA-PET libraries DNA was end polished with T4 DNA polymerase and then ligated with biotinylated half linker fragments with T4 DNA Ligase (Life Technologies). Next ligation was performed under dilute conditions to promote intramolecular ligation events and avoid inter-ligation products from distinct chromatin complexes. Following ligation, DNA was purified by reverse crosslinking followed by phenol-chloroform extraction and ethanol precipitation. Ligation products were released via Mme1 restriction digest followed by purification on streptavidin beads. Finally adapters were ligated and PET constructs were amplified and subjected to Illumina 40bp PE sequencing.

treatment_protocol: Motor neuron differentiation was performed as previously described6,12. Briefly, mESCs were dissociated with .05% trypsin (Invitrogen) and seeded in single cell suspension at 5-7 × 105 cells per ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout Serum Replacemtn (vol/vol), Pen/Strep, 2 mML-glutamine, and 0.1 mM 2- mercaptoethanol) to initiate formation of embryoid bodies (EBs) (day 0). Medium was exchanged on day 2 of differentiation and motor neuron identity was induced by supplementing media with 1 μM all-trans retinoic acid (RA) to caudalize and 500nM Sonic Hedgehog agonist (SAG) to ventralize EBs for directed differentiation or 1 μM RA and 1ug/ml doxycycline to induce programming factor expression for direct programming.

tag: cell type

value: ESC derived motor neuron progenitor

tag: background

value: 129/Ola embryonic motor neurons

tag: conditions

value: Cultured in ADFNK for 2 days followed by RA/Hh for 2 days to induce motor neuron differentiation

tag: purification

value: pure population


title: h1hESC_TB-EQ_16

description:
EQ_ExpectedCounts.csv
TB-EQ_16

tag: cell line

value: TB

value: equalized


title: h1hESC_TB-EQ_17

description:
EQ_ExpectedCounts.csv
TB-EQ_17

tag: sample type


title: h1hESC_TB-EQ_15

description:
EQ_ExpectedCounts.csv
TB-EQ_15

tag: equilization amt


title: DR-2

description:
A pool of 4 embryos at the 4-cell stage were subjected to cDNA synthesis
Replication_gene-FPKM_name.txt

source_name: Mouse 4-cell stage embryos

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 4-cell stage. At 40 hours post insemination (hpi), embryos were moved to KSOM medium containing 0.1 µg/ml demecolcine to arrest their cell cycle at G2/M phase. The demecolcine-treated embryos were subjected to nuclear transfer during 46-49 hpi, and the reconstructed NT embryos were further cultured in KSOM medium containing 0.1 µg/ml demecolcine with or without ?-amanitin till 70 hpi. To examine the effect of DNA replication on transcriptional reprogramming, nuclear transfer to 4-cell embryos was performed during 40-43 hpi, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 64 hpi. To examine the reprogramming ability of 2-cell embryos, nuclear transfer to 2-cell embryos was performed during 21-24 hpi for early 2-cell NT and 30-33 hpi for late 2-cell NT, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 45 hpi and 54 hpi, respectively.

value: C57BL/6, DBA/2, and C3H strains

value: Minus

tag: developmental stage

value: 4-cell stage embryos


title: DR-3

tag: strains


title: BEAS_10mg_2h25min_Air_rep2

source_name: BEAS-2B, 10mg, 2h25min, air, replicate 2

value: 10 mg

value: air


title: h1hESC_TB-EQ_14

description:
EQ_ExpectedCounts.csv
TB-EQ_14


title: DR-1

tag: alpha-amanitin


title: h1hESC_TB-EQ_11

description:
EQ_ExpectedCounts.csv
TB-EQ_11


title: BEAS_10mg_2h25min_Pollen_rep1

source_name: BEAS-2B, 10mg, 2h25min, pollen, replicate 1

tag: doses

value: pollen


title: h1hESC_TB-EQ_10

description:
EQ_ExpectedCounts.csv
TB-EQ_10


title: h1hESC_TB-EQ_9

description:
EQ_ExpectedCounts.csv
TB-EQ_9


title: D-3


title: h1hESC_TB-EQ_8

description:
EQ_ExpectedCounts.csv
TB-EQ_8


title: BEAS_10mg_2h25min_Air_rep1

source_name: BEAS-2B, 10mg, 2h25min, air, replicate 1

tag: time


title: h1hESC_TB-EQ_7

description:
EQ_ExpectedCounts.csv
TB-EQ_7


title: D-1


title: BEAS_10mg_55min_Pollen_rep2

description: Gene expression after 55min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 55min, pollen, replicate 2

tag: condition


title: BEAS_10mg_55min_Air_rep3

description: Gene expression control sample of 55min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 55min, air, replicate 3


title: BEAS_10mg_55min_Pollen_rep3

source_name: BEAS-2B, 10mg, 55min, pollen, replicate 3


title: h1hESC_TB-EQ_12

description:
EQ_ExpectedCounts.csv
TB-EQ_12


title: h1hESC_TB-EQ_4

description:
EQ_ExpectedCounts.csv
TB-EQ_4


title: BEAS_10mg_55min_Pollen_rep1

source_name: BEAS-2B, 10mg, 55min, pollen, replicate 1


title: h1hESC_TB-EQ_3

description:
EQ_ExpectedCounts.csv
TB-EQ_3


title: BEAS_10mg_55min_Air_rep1

source_name: BEAS-2B, 10mg, 55min, air, replicate 1


title: BEAS_10mg_55min_Air_rep2

source_name: BEAS-2B, 10mg, 55min, air, replicate 2


title: h1hESC_TB-EQ_2

description:
EQ_ExpectedCounts.csv
TB-EQ_2


title: NT-3

description:
A pool of 3 embryos at the 4-cell stage were subjected to cDNA synthesis
C2C12_gene-FPKM_name.txt


title: BEAS_10mg_10min_Pollen_rep3

description: Gene expression after 10min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 10min, pollen, replicate 3


title: h1hESC_TB-EQ_1

description:
EQ_ExpectedCounts.csv
TB-EQ_1


title: h1hESC_TB-EQ_6

description:
EQ_ExpectedCounts.csv
TB-EQ_6


title: h1hESC_EC-EQ_45

description:
EQ_ExpectedCounts.csv
EC-EQ_45

value: EC


title: BEAS_10mg_10min_Pollen_rep1

source_name: BEAS-2B, 10mg, 10min, pollen, replicate 1


title: D-2


title: NT-1


title: BEAS_10mg_10min_Air_rep3

description: Gene expression control sample of 10min in 10 mg whole birch pollen exposure

source_name: BEAS-2B, 10mg, 10min, air, replicate 3


title: h1hESC_EC-EQ_44

description:
EQ_ExpectedCounts.csv
EC-EQ_44


title: NT-2


title: h1hESC_EC-EQ_43

description:
EQ_ExpectedCounts.csv
EC-EQ_43


title: h1hESC_TB-EQ_5

description:
EQ_ExpectedCounts.csv
TB-EQ_5


title: h1hESC_EC-EQ_42

description:
EQ_ExpectedCounts.csv
EC-EQ_42


title: TxIB injection after alcohol withdrawal 3

city: Haikou

first: Kailin

last: Mao

state: Hai Nan

address: Hai Dian Campus of Hainan University, No.58 of Ren Min Road, Mei Lan District, Haikou, Hainan Province,China

department: School of Life Sciences

institute: Hainan University

data_processing:
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 ( 2.0.4) were used to map with reference genome (GRCz11) with the following setting: --dta -p 6 --max-intronlen 5000000.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and FPKM values for every gene and every sample. N refers to Normal group, S refers to alcohol-withdrawal group, and T refers to TxIB group.

organism: Danio rerio

source_name: brain

growth_protocol: Zebrafish were treated with the escalating alcohol concentration to minimize their mortality. Briefly, zebrafish were first introduced to  0.1% (volume/volume) alcohol-water on the first day, then alcohol concentration was increased by 0.1% every other day, which was 0.2% on the third day. The alcohol concentration reached the top (0.2%) and was held for the next 14 days. From the third week, zebrafish were taken back to the non-alcohol water for 3 hours per day to produce an alcohol withdrawal process. On the 21st day, zebrafish were withdrawn from 0.2% alcohol for the last time before the drug injection and the behavior test. The final concentration of 0.2% was determined through a preliminary experiment to insure the alcohol does not cause a substantial number of deaths during the long-term exposure. Normal group zebrafish were housed in a seperate tank with non-alcohol water.

extract_protocol:
Following five hours after drug injection, zebrafish were anesthetized by immersion into the ice-water bath. After cutting the head instantly from the fish body, the brain was dissected from the head and rinsed in the cold PBS solution. The brain tissue was then put into a freezing tube and transferred into the liquid nitrogen immediately. Ten brains were pooled together for one biological replicate and the total RNA was extracted using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme Biotech co., Ltd) following the manufacturer’s instructions. The purity, concentration, and integrity of RNA samples were identified to guarantee the quality of samples for transcriptome sequencing.
Library construction was conducted with the following processes: The mRNA was enriched with magnetic beads with Oligo (dT), and randomly interrupted by adding Fragmentation Buffer, then the first cDNA strand was synthesized with six-base random primers (random hexamers) using mRNA as the template, then dNTPs, RNase H and DNA polymerase I were added to synthesize the second cDNA strand and the cDNA was purified using AMPure XP beads. The purified double-stranded cDNA was then terminally repaired, A-tailed, and ligated to sequencing junctions, followed by fragment size selection using AMPure XP beads. Finally, the cDNA library was enriched by PCR.After the library construction, the effective concentration of the library ( > 2nM) was accurately quantified using Q-PCR method to ensure the quality of the library. Then the high-throughput RNA sequencing was performed on an Illumina NovaSeq 6000 sequencer. The sequencing read length was 150 bp paired-end. The clean data of each sample reached 5.79Gb, and the Q30 base percentage was 93.22% and above.

treatment_protocol: Lyophilized TxIB was dissolved in normal saline solution (0.9%) and then injected at 10 μL per fish for a final dose of 1 mg/kg using the retro-orbital injection method. Briefly, zebrafish were anesthetized in an ice/water bath within 10 seconds and then removed to a sponge pad for injection. Normal and withdrawal group injected 10 μL normal saline solution per fish to serve as controls. After injection, fish were transferred into freshwater for recovery. Brain tissue dissection were conducted five hours after injection to ensure fish were recovered from anesthesia.

value: TxIB injection after alcohol withdrawal

value: AB

value: adult

tag: drug injected

value: TxIB

tag: injection method

value: retro-orbital injection

tag: injected dose

value: 1 mg/kg, 10 uL per fish

tag: tissue

value: brain


title: BEAS_10mg_10min_Air_rep2

source_name: BEAS-2B, 10mg, 10min, air, replicate 2


title: NT_Amanitin-3

value: Plus


title: NT_Amanitin-2


title: h1hESC_EC-EQ_41

description:
EQ_ExpectedCounts.csv
EC-EQ_41

source_name: differentiated human embryonic stem cells

value: H1 hESC cell line


title: h1hESC_EC-EQ_39

description:
EQ_ExpectedCounts.csv
EC-EQ_39

value: equalized


title: h1hESC_EC-EQ_40

description:
EQ_ExpectedCounts.csv
EC-EQ_40


title: h1hESC_EC-EQ_37

description:
EQ_ExpectedCounts.csv
EC-EQ_37


title: h1hESC_EC-EQ_36

description:
EQ_ExpectedCounts.csv
EC-EQ_36


title: h1hESC_EC-EQ_38

description:
EQ_ExpectedCounts.csv
EC-EQ_38


title: TxIB injection after alcohol withdrawal 2

tag: treatment

tag: strain


title: TxIB injection after alcohol withdrawal 1


title: BEAS_10mg_10min_Air_rep1

source_name: BEAS-2B, 10mg, 10min, air, replicate 1


title: h1hESC_EC-EQ_35

description:
EQ_ExpectedCounts.csv
EC-EQ_35


title: alcohol-withdrawal 3

value: alcohol-withdrawal

value: saline

value: 10 uL per fish


title: h1hESC_EC-EQ_34

description:
EQ_ExpectedCounts.csv
EC-EQ_34


title: h1hESC_EC-EQ_33

description:
EQ_ExpectedCounts.csv
EC-EQ_33


title: alcohol-withdrawal 2


title: D10_M1_BCR

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

description: processed data file: RSEM_Gene_VST_D0-D10TLR.BCR.txt.gz

data_processing:
The fastq files were assessed for initial quality using FastQC v0.11.8, trimmed for adapter sequences using TrimGalore v0.6.0  and aligned to GRCh38.p12 (Gencode release 28) with STAR aligner (v2.6.0c) using twopassMode.
Transcript abundance was estimated using RSEM v1.3.0 and imported into R v3.5.1 using txImport v1.10.1 and then processed using DESeq2 v1.22.2, generating VST transformed data.
Genome_build: GRCm38.p6/mm10 (Gencode release M20)
Supplementary_files_format_and_content: Tab separated sheets containing DESeq2 rLog transformed data

source_name: Spleen

extract_protocol:
Spleen tissue was harvested from sex- and age-matched C57BL/6, Blimp-1-Venus19 or Prdm1Δex1A mice16 (provided by E. Bikoff, University of Oxford) between 6-12 weeks old that had been maintained in specific-pathogen-free (SPF) conditions. All procedures were performed under the approved UK Home Office project license in line with the Animal (Scientific Procedures) Act 1986 and in accordance with the UK National Cancer Research Institute Guidelines for the welfare of animals. Single cell suspensions were obtained after density centrifugation using lympholyte-M (Cedarlane). The EasySep™ mouse B-cell isolation kit (STEMCELL Technologies) containing anti-CD43 was used to isolate B2 cells. Following isolation, B cells were phenotyped to ensure >95% purity before culture
RNA was extracted with TRIzol (Invitrogen) then subjected to DNAseI treatment (DNAfree, Ambion).
RNA samples were quantified with a Qubit HS RNA assay kit (Thermo Fisher Scientific) and the quality was assessed by RNA HS assay using the TapeStation system (Agilent). Sequencing libraries were generated by using a TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina) according to the manufacturer’s protocol. Library performance was checked on the TapeStation followed by picogreen quantification. Equimolar pooling was performed across all the libraries and the final pool was sequenced on a NextSeq 500 platform (Illumina) using 76-bp single-end sequencing.

treatment_protocol:
isolation-conditions: Spleen tissue was harvested from sex- and age-matched C57BL/6, Blimp-1-Venus19 or Prdm1Δex1A mice (provided by E. Bikoff, University of Oxford) between 6-12 weeks old that had been maintained in specific-pathogen-free (SPF) conditions. All procedures were performed under the approved UK Home Office project license in line with the Animal (Scientific Procedures) Act 1986 and in accordance with the UK National Cancer Research Institute Guidelines for the welfare of animals. Single cell suspensions were obtained after density centrifugation using lympholyte-M (Cedarlane). The EasySep™ mouse B-cell isolation kit (STEMCELL Technologies) containing anti-CD43 was used to isolate B2 cells. Following isolation, B cells were phenotyped to ensure >95% purity before culture
culture-conditions: Day 0:  for BCR signalling, isolated B-cells were seeded in 24 well plates at 2.5x10^5 cells/mL (0.5mL/well; 1.25x10^5 cells/well) with irradiated CD40L expressing murine L cells (0.5mL/well; 6.25x10^4/well), 12µg/mL F(ab’)2 anti-IgM/IgG (Jackson Immunoresearch), 50ng/mL IL-4 and 50ng/mL IL-5 (Miltenyi) for 2 days. For TLR signalling, B-cells were seeded at the same density as above with CD40L expressing murine L cells, 5µg/mL LPS (0111:B4, Sigma-Aldrich), IL-4 and IL-5. Day 2: On subsequent days, both mechanisms followed the same steps. At day 2, cells were removed from the CD40L cells and transferred across to new 24 well plates. Day 4: On day 4, plasmablasts were re-seeded in 10ng/mL IL-6 (Miltenyi), 100ng/mL APRIL (Caltag), MEM amino acids and Lipid Mixture 1 (Sigma-Aldrich) at 5x105 cells/mL in 96 well plates (0.2mL/well; 1x105 cells/well). Cells were fed with fresh media every 3-4 days containing APRIL, IL-6, amino acids and lipids. Feeding was carried out until elective termination.

tag: strain background

tag: genotype/variation

value: wild type

tag: Sex

value: male

tag: age

value: 7 weeks old

value: spleen

tag: time point

value: Plasmacell


title: D10_M2_BCR


title: alcohol-withdrawal 1

value: AB

tag: developmental stage


title: D10_M3_TLR


title: h1hESC_EC-EQ_30

description:
EQ_ExpectedCounts.csv
EC-EQ_30

tag: cell line

tag: sample type

value: EC

tag: equilization amt


title: h1hESC_EC-EQ_32

description:
EQ_ExpectedCounts.csv
EC-EQ_32


title: Normal 3

value: untreated

value: adult


title: h1hESC_EC-EQ_29

description:
EQ_ExpectedCounts.csv
EC-EQ_29


title: D10_M2_TLR


title: h1hESC_EC-EQ_31

description:
EQ_ExpectedCounts.csv
EC-EQ_31


title: h1hESC_EC-EQ_28

description:
EQ_ExpectedCounts.csv
EC-EQ_28


title: NT_Amanitin-1

source_name: Mouse 4-cell stage embryos

tag: strains

value: C57BL/6, DBA/2, and C3H strains

tag: alpha-amanitin

value: 4-cell stage embryos


title: D10_M1_TLR


title: D7_EX1A2_BCR

description: processed data file: RSEM_Gene_VST_D0-D7LPS.TLR.BCR.txt.gz

value: female

value: 9 weeks old

value: Plasmablast


title: h1hESC_EC-EQ_25

description:
EQ_ExpectedCounts.csv
EC-EQ_25

value: H1 hESC cell line

value: equalized


title: h1hESC_EC-EQ_23

description:
EQ_ExpectedCounts.csv
EC-EQ_23


title: h1hESC_EC-EQ_22

description:
EQ_ExpectedCounts.csv
EC-EQ_22


title: BEAS_10mg_10min_Pollen_rep2

source_name: BEAS-2B, 10mg, 10min, pollen, replicate 2

tag: doses

value: 10 mg

tag: time

tag: condition

value: pollen


title: h1hESC_EC-EQ_21

description:
EQ_ExpectedCounts.csv
EC-EQ_21


title: D10_M3_BCR

value: wild type

value: male

tag: tissue


title: h1hESC_EC-EQ_20

description:
EQ_ExpectedCounts.csv
EC-EQ_20


title: Normal 2

tag: treatment

tag: drug injected

value: saline

tag: injection method

value: retro-orbital injection

tag: injected dose

value: 10 uL per fish

value: brain


title: h1hESC_EC-EQ_26

description:
EQ_ExpectedCounts.csv
EC-EQ_26

value: EC


title: Normal 1

value: untreated

tag: strain

value: AB

value: adult


title: h1hESC_EC-EQ_19

description:
EQ_ExpectedCounts.csv
EC-EQ_19


title: KO1_Riboseq

description:
Riboseq processed data.xlsx
4609_Riboseq

data_processing:
Library strategy: Ribo-seq
The adapters in the sequencing reads were removed using cutadapt (v3.1) with options ‘--trimmed-only -m 15 -a AGATCGGAAGAGCAC ’. The PCR duplicates in the reads were collapsed using CLIPflexR v0.1.19. The Unique Molecule Identifiers (UMIs) for each read were extracted using umi_tools v1.1.1 with the options 'extract --bc-pattern=NN' for the 5' end and options 'extract --3prime --bc-pattern=NNNNN ' for the 3' end.  Reads corresponding to rRNA and other non-nuclear mRNA were removed by aligning out the reads using Bowtie2 v2.4.2 on a depletion reference (rRNA, tRNA and mitochondrial RNA sequences). This depletion reference was built from the non-coding transcriptome for Mus musculus (Ensembl release v96). The reads that did not align to the depletion reference were aligned to the Mus Musculus mRNA transcriptome using Bowtie2 with options '--sensitive --end-to-end --norc'. The mRNA transcriptome was built using the cDNA longest CDS reads of Mus Musculus downloaded from Ensembl release v96. The resulting reads were converted to bam files and then sorted using samtools v1.11. The duplicate reads in the sorted files were removed using umi_tools v1.1.1 with options 'dedup'.  The quality check and downstream processing of the processed reads was performed using Ribolog v0.0.0.9. After quality check, the psite information was converted to codon counts in Ribolog. The codon reads resulting from stalling were corrected using the CELP (Consistent Excess of Loess Preds) method in Ribolog. After median normalization and removal of transcripts with 0 counts, the translational efficiency testing was performed in Ribolog as well.

source_name: Mouse cortex

extract_protocol:
Cortical tissue was homogenized in lysis buffer (containing cycloheximide) and cleared for 10 minutes at 20,000 x g at 4oC.  Monosomes obtained by RNase I digestion were purified using spin-column chromatography. Briefly, MicroSpin S-400 HR columns (Cytiva) were equilibrated with 3 mL of Polysome buffer by gravity flow, then spun down 4 mins at 600 g. 100 µl of RNase I digested lysate was loaded onto the column and spun 2 mins at 600 g. The flow through was collected and the RNA was extracted using RNA Clean & Concentrator-25 kit (Zymo). The rRNA depletion was performed onto linker ligated RPFs using riboPOOLs (siTOOLs).  RNAseq libraries were constructed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara), as recommended by the manufacturer. RiboSeq and RNAseq libraries were sequenced on HiSeq4000 (Illumina) at the Center for Advanced Technology (UCSF).
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

tag: tissue type

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.

value: Adult

tag: molecule

value: Ribosome-protected mRNA


title: h1hESC_EC-EQ_24

description:
EQ_ExpectedCounts.csv
EC-EQ_24

value: H1 hESC cell line

value: equalized


title: D7_EX1A3_BCR

tag: strain background

tag: genotype/variation

tag: Sex

value: female

tag: age

value: 9 weeks old

value: spleen

tag: time point

value: Plasmablast


title: h1hESC_EC-EQ_15

description:
EQ_ExpectedCounts.csv
EC-EQ_15

tag: cell line

tag: sample type

tag: equilization amt


title: h1hESC_EC-EQ_16

description:
EQ_ExpectedCounts.csv
EC-EQ_16


title: WT2_Riboseq

description:
Riboseq processed data.xlsx
4619_Riboseq

value: Nsun2 floxed, Camk2a-Cre neg.

tag: developmental stage


title: D7_EX1A1_BCR

tag: tissue