title: extended_1-W282_Twist_dil5_R1


title: pilot_W034_LTRI-233_R1

status: Public on Jan 24 2021

type: SRA

city: Toronto

first: Jeff

last: Wrana

state: ON

address: 600 Unv Ave

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description:
SparSeq multiplexed PCR library
Pilot_ReadCount_Table.csv

library_source: transcriptomic

data_processing:
Single-end reads mapped to amplicon sequences using Bowtie and allowing 3 mismatch for mapped read count / amplicon quantification.
Genome_build: Custom genome consists of amplicons targeted in GRCh38 and Sars-CoV-2 (Wuhan-Hu-1).
Supplementary_files_format_and_content: Sample name/ read count mapped to each targeted amplicon.

molecule: total RNA

organism: Homo sapiens

source_name: Human Sample

extract_protocol:
Total RNA extraction by Norgen total RNA Kit or RNA-XP beads.
C19-SparSeq-Barcoded multiplexed PCR reactions were pooled and cleaned with SPRIselect beads.

value: NASOP-swab


title: pilot_W033_LTRI-232_R2


title: pilot_W033_LTRI-232_R1


title: extended_1-W378_Twist_dil5_R1

description:
SparSeq multiplexed PCR library
Extended_ReadCount_Table.csv

organism: synthetic RNA

source_name: SARS-CoV-2 Synthetic RNA

tag: sample type

value: SARS-CoV-2 synthetic RNA


title: extended_1-W378_Twist_dil5_R2


title: extended_1-W090_Twist_dil5_R1


title: extended_1-W090_Twist_dil5_R2


title: pilot_W032_LTRI-231_R2


title: extended_1-W594_Twist_dil5_R1


title: pilot_W032_LTRI-231_R1


title: pilot_W031_LTRI-230_R2


title: extended_1-W474_Twist_dil5_R2


title: pilot_W036_LTRI-235_R2


title: pilot_W031_LTRI-230_R1


title: extended_1-W594_Twist_dil5_R2


title: extended_1-W092_Twist_dil7_R2


title: extended_1-W474_Twist_dil5_R1


title: extended_1-W188_Twist_dil7_R1


title: extended_1-W188_Twist_dil7_R2


title: pilot_W030_LTRI-229_R1


title: pilot_W030_LTRI-229_R2


title: pilot_W034_LTRI-233_R2


title: pilot_W029_LTRI-228_R1


title: extended_1-W092_Twist_dil7_R1


title: extended_2-W088_Twist-dil3_R2


title: pilot_W028_LTRI-227_R1

value: BAL


title: pilot_W026_LTRI-225_R1


title: extended_1-W764_Twist_dil7_R1


title: extended_2-W760_Twist-dil3_R2


title: extended_1-W666_Twist_dil7_R2


title: pilot_W024_LTRI-223_R1


title: extended_1-W666_Twist_dil7_R1


title: pilot_W026_LTRI-225_R2


title: pilot_W027_LTRI-226_R1


title: pilot_W028_LTRI-227_R2


title: extended_2-W472_Twist-dil3_R1


title: extended_2-W472_Twist-dil3_R2


title: pilot_W025_LTRI-224_R1


title: extended_2-W088_Twist-dil3_R1


title: extended_2-W760_Twist-dil3_R1


title: pilot_W025_LTRI-224_R2


title: extended_1-W764_Twist_dil7_R2


title: pilot_W027_LTRI-226_R2


title: pilot_W023_LTRI-222_R1


title: pilot_W022_LTRI-221_R2


title: extended_2-W184_Twist-dil3_R1


title: pilot_W023_LTRI-222_R2


title: extended_2-W184_Twist-dil3_R2


title: extended_2-W086_Twist-dil1_R2


title: pilot_W022_LTRI-221_R1


title: pilot_W029_LTRI-228_R2


title: extended_2-W086_Twist-dil1_R1


title: pilot_W024_LTRI-223_R2


title: pilot_W021_LTRI-220_R2


title: extended_2-W758_Twist-dil1_R2


title: pilot_W020_LTRI-219_R1


title: pilot_W021_LTRI-220_R1


title: extended_2-W470_Twist-dil1_R1


title: pilot_W020_LTRI-219_R2


title: extended_2-W758_Twist-dil1_R1


title: extended_2-W761_Twist-dil4_R1


title: pilot_W018_LTRI-217_R1


title: extended_2-W182_Twist-dil1_R2


title: extended_2-W089_Twist-dil4_R2


title: extended_2-W761_Twist-dil4_R2


title: pilot_W018_LTRI-217_R2


title: extended_2-W182_Twist-dil1_R1


title: extended_2-W473_Twist-dil4_R1


title: pilot_W019_LTRI-218_R1


title: pilot_W015_LTRI-214_R2


title: extended_2-W089_Twist-dil4_R1


title: extended_2-W473_Twist-dil4_R2


title: pilot_W017_LTRI-216_R2


title: pilot_W016_LTRI-215_R2


title: extended_2-W470_Twist-dil1_R2


title: extended_2-W185_Twist-dil4_R2


title: pilot_W019_LTRI-218_R2


title: pilot_W015_LTRI-214_R1


title: pilot_W014_LTRI-213_R2


title: pilot_W016_LTRI-215_R1


title: extended_2-W185_Twist-dil4_R1


title: pilot_W014_LTRI-213_R1


title: pilot_W017_LTRI-216_R1


title: pilot_W013_LTRI-212_R2


title: extended_2-W087_Twist-dil2_R2


title: pilot_W013_LTRI-212_R1


title: extended_2-W087_Twist-dil2_R1


title: pilot_W012_LTRI-211_R2


title: pilot_W012_LTRI-211_R1


title: pilot_W011_LTRI-210_R2


title: pilot_W010_LTRI-209_R2


title: pilot_W010_LTRI-209_R1


title: extended_2-W759_Twist-dil2_R2


title: extended_2-W759_Twist-dil2_R1


title: pilot_W009_LTRI-208_R2


title: pilot_W009_LTRI-208_R1


title: pilot_W007_LTRI-206_R2


title: pilot_W008_LTRI-207_R2


title: extended_2-W183_Twist-dil2_R2


title: pilot_W008_LTRI-207_R1


title: extended_2-W664_Twist-dil2_R1


title: extended_2-W664_Twist-dil2_R2


title: pilot_W007_LTRI-206_R1


title: pilot_W006_LTRI-205_R1


title: PC3_siHOXB13 48h

type: RNA

city: Tokyo

first: Aya

last: Misawa

address: 1-1-5 Sendagi Bunkyo-ku

department: Medicine

country: Japan

institute: Nippon Medical School

hyb_protocol: Hybridization was performed with GeneChip™ Hybridization Oven 645 at 45℃ for 16 h (60 rpm). Washing was performed with GeneChip™ Fluidics Station 450.

scan_protocol: Scanning was performed using GeneChip™ Scanner 3000 7G according to GeneChip™ Command Console (AGCC) 4.0 User Manual.

data_processing:
Data processing was performed according to GeneChip™ Command Console (AGCC) 4.0 User Manual.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

label_protocol: Total RNA QC was checked with Agilent 2100 Bioanalyzer. 250 ng of total RNA was used to synthesize fragmented and labeled cDNA using GeneChip™ WT PLUS Reagent Kit according to GeneChip™ WT PLUS Reagent Kit User Manual.

growth_protocol: PC3 cells were seeded into 24-well plates in RPMI medium supplemented with 10% FBS.

extract_protocol: Cells were washed with PBS and lysed with NucleoSpin RNA Plus lysis buffer. RNA was extracted according to manufcturer's protocol.

treatment_protocol: 24 h after seeding, cells were transfected with 20 uM siRNAs for 24 h or 48 h.

tag: cell line

tag: genotype/variation

value: siRNA targeting HOXB13


title: PC3_shIBSP(1) 48h

value: shIBSP


title: PC3_shNC 48h

value: control siRNA


title: pilot_W011_LTRI-210_R1


title: pilot_W006_LTRI-205_R2


title: PC3_siHOXA11 48h

value: siRNA targeting HOXA11


title: PC3_shIBSP(2) 48h


title: extended_2-W571_Twist-dil6_R2


title: pilot_W004_LTRI-203_R1


title: pilot_W004_LTRI-203_R2


title: pilot_W005_LTRI-204_R2


title: extended_2-W571_Twist-dil6_R1


title: PC3_siHOXA11-AS 48h

value: siRNA targeting HOXA11-AS


title: pilot_W005_LTRI-204_R1


title: PC3_siNC 48h


title: m6A-RP.Mettl3-WT.IP.rep1

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
Raw reads were trimmed with TrimGalore (v0.6.4) (https://github.com/FelixKrueger/TrimGalore), then aligned to the mouse genome (mm10) and transcriptome (GENCODE version M21) using HISAT2 (version 2.2.0)55. Mapped reads were separated by strands with samtools (version 1.9)51 and m6A peaks on each strand were called using MACS (version 2.1.2)52 with parameter ‘--nomodel’ and ‘--keep-dup 5’ separately. Significant peaks with q < 0.01 and fold-change enrichment to INPUT > 2 were considered.
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Male mouse embryonic stem cells (mESCs) were derived from 3.5 d.p.c inner cell mass (ICM) from female 129 mice (Stock No.: 217, Beijing Vital River Laboratory Animal Technology Co., Ltd.). Animal care and experimental protocols were approved by the animal ethics committee of the Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences. ESCs with genetic engineering, including Ythdc1-conditional knockout (cKO), MERVL::tdTomato reporter, and Halo- Ythdc1 knockin (KI) , and TurboID overexpression (OE) were constructed and cultured in feeder- free condition, using serum/LIF medium containing high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, #SH30022.01), 15% fetal bovine serum (FBS, Front Biomedical, # OPT500), 1× GlutaMAX, 1× nonessential amino acids (NEAA, Gibco, #11140076), 1× Penicillin- Streptomycin (Hyclone, #SV30010), 1× Sodium Pyruvate (Gibco, #11360070), 1 mM 2- Mercaptoethanol (Gibco, # 21985023), and 1000 U/ml LIF. HEK293T (ATCC, # CRL-1126) and NIH3T3 (ATCC, #CRL-1658) cells were maintained in high-glucose DMEM supplemented with 10% FBS (Natocor, #SFBE), 1× GlutaMAX (Gibco, #35050079), and 1× NEAA. All the cell lines were cultivated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
total RNA
RIP assay was performed based on GoldCLIP33 with modifications. The cells expressing Halo-GFP or Halo-YTHDC1 were harvested, lysed, and pulled-down using Halo-tagged beads (Promega, #G7282) as previously described33, except that no nuclease digestion or RNA fragmentation conducted throughout the experiment. The binding efficiency of Halo-tagged protein to the beads was evaluated by western blot. After the denaturing wash, the RNAs were released from the proteins by PK enzyme (NEB, #P8107S) digestion. For RIP-RT-qPCR, the equivalent input and IP RNAs were reverse-transcribed by SuperScript III Reverse Transcriptase (Invitrogen, #18080044) using random hexamers, followed by qPCR to quantify the transcripts. The enrichment score of a transcript was the ratio of the quantified IP fraction to its total input, using GFP as a standard for normalization. For RIP-seq, 200-500 ng RNAs from the input and IP samples were used to generate the libraries using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) according to the manufacturer’s instructions.

tag: cell type

value: embryonic stem cells (WT)


title: PC3_siHOXA11 24h


title: pilot_W003_LTRI-202_R1


title: extended_2-W283_Twist-dil6_R2


title: extended_2-W283_Twist-dil6_R1


title: m6A-RP.Mettl3-WT.Input.rep1


title: pilot_W002_LTRI-201_R2


title: pilot_W002_LTRI-201_R1


title: m6A-RP.Mettl3-KO.IP


title: extended_2-W183_Twist-dil2_R1


title: extended_2-W379_Twist-dil6_R2


title: pilot_W651_HEK293T_R2

source_name: Cell line


title: extended_2-W379_Twist-dil6_R1


title: PC3_siHOXB13 24h


title: pilot_W001_LTRI-200_R1


title: pilot_W001_LTRI-200_R2


title: pilot_W651_HEK293T_R1


title: pilot_W555_HEK293T_R2


title: m6A-RP.Mettl3-KO.Input


title: PC3_siNC 24h


title: extended_2-W091_Twist-dil6_R2


title: m6A-RP.Mettl3-WT.IP.rep2


title: pilot_W554_HEK293T_R1


title: m6A-RP.Mettl3-KO1.IP


title: pilot_W553_HEK293T_R2


title: extended_2-W763_Twist-dil6_R2


title: m6A-RP.Mettl3-WT.INPUT.rep2


title: extended_2-W763_Twist-dil6_R1


title: pilot_W459_HEK293T_R2


title: pilot_W459_HEK293T_R1


title: extended_2-W665_Twist-dil6_R2


title: m6A-RP.Mettl3-KO1.INPUT


title: ChIRP.Ythdc1-cKO.4OHTMalat1_Odd

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were aligned to mouse genome (mm10) using bowtie2 with the parameters “--very-sensitive --end-to-end --no-unal --phred33 --no-mixed -X 2000 --gbar 200”. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. BigWig files were generated using deeptools with the RPKM normalization method. Positive peaks were identified with DFilter17 program with parameters “-ks=100 -lpval=5”.  In order to eliminate false-positive hits, only the overlapped signal from both “even” and “odd” probes were considered. And then the Bam files of “even” and “odd” probes were merged using samtools (version 1.9).
Genome_build: mm10

molecule: genomic DNA

source_name: embryonic stem cells

extract_protocol:
DNA
ChIRP was performed as previously described with some modifications2,3. In brief, a set of biotinylated antisense oligos with 59-nt long probes tiled along the L1 consensus sequence (6.5 kb) or Malat1 RNA, and 20-nt probes tiled along the IAP consensus sequence or LacZ. Label probes based on their positions along the RNA, and separate them into ‘even’ and ‘odd’ pools, to create two independent probe sets for ChIRP experiments. Ythdc1 cKO ESCs were treated with DMSO or 4OHT (1 μg/ml) for 4 days, then cells were harvested by 0.25% trypsin digestion and cross-linked with 2 mM DSP (Thermo Scientific, # 22586) in PBS at room temperature for 30 min with gentle end to end rotation. The cells were further fixed in suspension for 10 min in 3.7% formaldehyde, and quenched with 250 mM Glycine for 5 minutes at room temperature. Cells were then washed with ice-cold PBS for three times and snap frozen in liquid nitrogen. 1 × 107 cells were resuspended with 500 μl DNase I digestion solution (20mM Tris-HCl, pH7.5, 5mM MgCl2, 0.5mM CaCl2, 0.5% Triton X-100) with 1/20 volume of Ribonucleoside Vanadyl Complex (RVC, NEB, #S1402S), 5 μl protease inhibitor cocktail (Roche, #4693132001), 5 μl 100mM PMSF and 12 U/ml Dnase I (Invitrogen, #AM2222); the reaction was rotated for 10 min at 37°C and stopped with 20 mM EDTA. After centrifugation, chromatin was resuspended in nuclear lysis buffer (50mM Tris-HCl, pH7.5, 10mM EDTA, 1% SDS, inhibitors) and sonicated with Bioruptor Pico (5 cycles, 30s on, 30s off, Diagenode). The supernatant was collected for ChIRP experiments after centrifuged at 14,000 ×g for 10 min at 4°C and save some lysate as ‘input’ samples. For the Rnase treatment control, samples were treated with 10 μg/ml Rnase A/T1 at 37°C for 20 min. For hybridization, samples were incubated with ChIRP probes (1 μl of 100 μM probes per 1 ml of lysate), supplemented with one-fourth volume of 5 x hybridization buffer (50 mM Tris-HCl, pH7.5, 10 mM EDTA, 1.5 M NaCl, 50% formamide). After rotated at 39°C for 3h, 50 μl prebalanced streptavidin M280 beads were then added into the hybridization and incubated for an additional 3h. The beads were washed 5 times with 0.2 × SSC wash buffer with 1% SDS at 42°C. To elute, the beads were washed once with SDS elution buffer (50 mM Tris-HCl, 5 mM MgCl2, 75 mM NaCl, 1% SDS) at 39°C for 20 min, and once with elution buffer (50 mM Tris-HCl, 5 mM MgCl2, 75mM NaCl, 0.1% Triton X-100) at 39°C for 5 min. DNA was eluted from the beads by RNase H treatment in two sequential incubations with Rnase H (NEB, #M0297L) at 37°C for 20 min, and with SDS elution buffer at room temperature for 2 min, combining all eluents. Crosslinking was reversed by treatment with 0.1 μg /μl protease K (NEB, #P8107S), 150 mM NaCl, and 10 mM EDTA at 65°C overnight and the DNA was purified using the MinElute PCR Purification Kit (Qiagen, #28006). ChIRP enrichments were analyzed by qPCR of the purified DNA. The libraries were constructed by a KAPA HTP/LTP Library Preparation Kit (#KK8234) according to the manufacturer’s instructions.

value: embryonic stem cells

tag: library strategy

value: ChIRP-seq

tag: genotype

value: Ythdc1-KO mESC


title: pilot_W458_HEK293T_R1


title: pilot_W457_HEK293T_R2


title: extended_2-W665_Twist-dil6_R1


title: ChIRP.Ythdc1-cKO.4OHTMalat1_Even


title: pilot_W457_HEK293T_R1


title: pilot_W555_HEK293T_R1


title: pilot_W554_HEK293T_R2


title: pilot_W363_HEK293T_R1


title: pilot_W553_HEK293T_R1


title: extended_2-W091_Twist-dil6_R1


title: pilot_W363_HEK293T_R2


title: ChIRP.Ythdc1-cKO.4OHTLacZ_Even


title: ChIRP.Ythdc1-cKO.4OHTLacZ_Odd


title: extended_2-W187_Twist-dil6_R1


title: pilot_W458_HEK293T_R2


title: pilot_W362_HEK293T_R2


title: test_W656_Twist_dil7_R2

description:
SparSeq multiplexed PCR library
Test_ReadCount_Table.csv


title: pilot_W362_HEK293T_R1


title: extended_2-W090_Twist-dil5_R2


title: extended_2-W090_Twist-dil5_R1


title: ChIRP.Ythdc1-cKO.4OHTLINE1_Odd


title: test_W655_Twist_dil6_R2


title: ChIRP.Ythdc1-cKO.4OHTLINE1_Even


title: ChIRP.Ythdc1-cKO.4OHTIAP_Odd


title: pilot_W361_HEK293T_R1


title: PC3_siHOXA11-AS 24h


title: test_W655_Twist_dil6_R1


title: ChIRP.Ythdc1-cKO.4OHTIAP_Even


title: extended_2-W187_Twist-dil6_R2


title: test_W654_Twist_dil5_R2


title: extended_2-W594_Twist-dil5_R1


title: ChIRP.Ythdc1-cKO.4OHTCHIRP_Input


title: pilot_W267_HEK293T_R1


title: test_W656_Twist_dil7_R1


title: extended_2-W474_Twist-dil5_R1


title: test_W654_Twist_dil5_R1


title: pilot_W267_HEK293T_R2


title: pilot_W361_HEK293T_R2


title: test_W653_Twist_dil4_R2


title: ChIRP.Mettl3-WT.LINE1.2

value: Mettl3-WT mESC


title: pilot_W266_HEK293T_R1


title: pilot_W265_HEK293T_R2


title: ChIRP.Mettl3-KO.LINE1.2

value: Mettl3-KO mESC


title: extended_2-W474_Twist-dil5_R2


title: ChIRP.Mettl3-WT.LINE1.1


title: test_W652_Twist_dil3_R2


title: extended_2-W594_Twist-dil5_R2


title: pilot_W266_HEK293T_R2


title: extended_2-W186_Twist-dil5_R2


title: pilot_W265_HEK293T_R1


title: ChIRP.Mettl3-KO.LINE1.1


title: extended_2-W186_Twist-dil5_R1


title: test_W652_Twist_dil3_R1


title: extended_2-W572_Twist-dil7_R1


title: test_W651_Twist_dil2_R2


title: test_W653_Twist_dil4_R1


title: extended_2-W284_Twist-dil7_R2


title: pilot_W171_HEK293T_R1


title: test_W651_Twist_dil2_R1


title: ChIRP.Mettl3-WT.LacZ.Odd


title: extended_2-W284_Twist-dil7_R1


title: pilot_W170_HEK293T_R2


title: test_W650_Twist_dil1_R2


title: extended_2-W380_Twist-dil7_R1


title: pilot_W170_HEK293T_R1


title: test_W650_Twist_dil1_R1


title: extended_2-W572_Twist-dil7_R2


title: extended_2-W092_Twist-dil7_R2


title: extended_2-W380_Twist-dil7_R2


title: pilot_W169_HEK293T_R2


title: ChIRP.Mettl3-WT.LacZ.Even


title: test_W560_Twist_dil7_R1


title: ChIRP.Mettl3-WT.Input


title: ChIRP.Mettl3-WT.IAP.Odd


title: ChIRP.Mettl3-WT.IAP.Even


title: ChIRP.Mettl3-WT.Malat1.Odd


title: test_W560_Twist_dil7_R2


title: pilot_W075_HEK293T_R2


title: pilot_W171_HEK293T_R2


title: test_W559_Twist_dil6_R2


title: ChIRP.Mettl3-WT.Malat1.Even


title: pilot_W075_HEK293T_R1


title: extended_2-W764_Twist-dil7_R2


title: test_W559_Twist_dil6_R1


title: ChIRP.Mettl3-KO.Malat1.Odd


title: extended_2-W764_Twist-dil7_R1


title: pilot_W169_HEK293T_R1


title: test_W558_Twist_dil5_R2


title: pilot_W074_HEK293T_R1


title: ChIRP.Mettl3-KO.Malat1.Even


title: test_W558_Twist_dil5_R1


title: ChIRP.Mettl3-KO.LacZ.Odd


title: ChIRP.Mettl3-KO.LacZ.Even


title: extended_2-W092_Twist-dil7_R1


title: pilot_W073_HEK293T_R2


title: test_W557_Twist_dil4_R2


title: pilot_W073_HEK293T_R1


title: extended_2-W188_Twist-dil7_R2


title: ChIRP.Mettl3-KO.Input


title: test_W557_Twist_dil4_R1


title: extended_2-W666_Twist-dil7_R1


title: test_W556_Twist_dil3_R2


title: pilot_W003_LTRI-202_R2


title: extended_2-W188_Twist-dil7_R1


title: pilot_W074_HEK293T_R2


title: pilot_W665_Twist_dil4_R2


title: test_W556_Twist_dil3_R1


title: ChIRP.Mettl3-KO.IAP.Odd


title: ChIRP.Mettl3-KO.IAP.Even


title: extended_2-W666_Twist-dil7_R2


title: 3T3-L1 media_D12_1~3

city: Tsukuba

first: Koichi

last: Ojima

address: 2 Ikenodai

institute: Institute of Livestock and Grassland Science, NARO

hyb_protocol: Each labeled Samples were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint HD miRNA Mouse 8X15K Microarrays, V21 (Agilent®), and then rotated at 20 rpm for 20 h at 55°C. Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System.

scan_protocol: Slides were scanned on an Agilent Technologies G4900DA SureScan scanner using 3 µm resolution.

data_processing:
Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Array data were filtered by gIsGeneDetected =1 in all sampless ( 1 : detected). Selected miRNA gtotalGeneSignal value was transformed by logarithm and normalized by quantile method.
The comparative analysis between test sample and control sample was carried out using fold change.

source_name: Exosomal miRNA in day 12 cultured media

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to the manufacturer′s recommended protocol. The Agilent microRNA Spike-In Kit was used for in-process control to measure labeling and hybridization efficiency. Briefly, total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7 min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 h. The labeled RNA samples were purified in a Vacuum Concentrator for one hour. Once samples are completely dried.

growth_protocol: The 3T3-L1 mouse adipocyte cell line was cultured in growth medium (GM; 10% exosome depleted FBS in low‐glucose DMEM) for 3 days. To induce differentiation, the cells were cultured in adipocyte differentiation medium-1 (10% exosome depleted FBS, 0.5 mM of 1‐methyl‐3‐isobutylxanthine, 6.4 nM dexamethasone and 10 μg/ml insulin in high‐glucose DMEM). After 2 days of culture, cells were switched to adipocyte differentiation medium-2 (10% exosome depleted FBS in high‐glucose DMEM containing 10 μg/ml insulin) for further culturing. All media were supplemented with 100 U/ml penicillin and 0.1 mg/ml streptomycin. Media were changed every other day. We defined Day x (Dx) as day(s) after shifting cells to adipocyte differentiation medium-1 from growth medium.

extract_protocol: Total RNA containing miRNA was extracted from the 3T3-L1 cell-derived exosome fractions using a mirVana microRNA isolation kit (Thermo Fisher Scientific). RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cultured media (D0, D4, D12 and D16) were collected from 10-12 dishes 90 mm in diameter, which amounts to 60-72 mL. A total of three independent experiments were carried out. Exosome fraction was isolated from cultured media following the ultracentrifugation method. In brief, collected cultured media were centrifuged at 1,000 g for 10 min at 4°C to remove cellular debris. The supernatant fraction was centrifuged at 12,000 g for 30 min at 4°C and further centrifuged at 110,000 g for 70 min at 4°C. The pellet fraction was washed with phosphate-buffered saline (PBS) and then centrifuged at 110,000 g for 70 min at 4°C again. The final precipitation was resuspended in PBS and stored at -80°C until total RNA preparation.

tag: culture period

value: Day 12

value: 3T3-L1 adipocytes


title: test_W555_Twist_dil2_R1


title: Ythdc1_cKO_ESC#2_DMSO.8min.rep2

data_processing:
Library strategy: 4sUDRB-seq
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
Raw reads were aligned to mouse genome (mm10) using bowtie2 with the default parameters (only set -N 1). For each experiment we generated a genome-wide profile of the counts per disjoint 100bp adjacent bins. For gene/TE quantification using the sum of all bins within genes (exon and intron) or TEs. The counts of each experiment was normalized to rRNA counts
Genome_build: mm10
Supplementary_files_format_and_content: normalized count

extract_protocol:
total RNA was extracted using miRNeasy mini kit (Qiagen #217004) with RNase-free DNase set (Qiagen, #79254)
Metabolic labeling nascent RNA with 4sU and nascent RNA purification was performed as described4. In brief, Ythdc1 cKO ESCs were pre-treated with DMSO or 4OHT (1 μg/ml) for 4 days, then incubated with 100 μM DRB (Sigma, #D1916) for 3 h to block Pol II transcription. Cells were washed 3 times with PBS to remove DRB and recover transcription, and newly transcribed RNA was labeled with 1 mM 4sU (Sigma, #T4509) for 0, 4, 8 min. Transcription was stopped by adding TRizol (Invitrogen) into the cells and total RNA was extracted using miRNeasy mini kit (Qiagen, #217004) with RNase-free DNase set (Qiagen, #79254). 100 μg total RNA was used for biotinylation and purification of 4sU-labeled nascent RNA. 4sU labeled RNA was incubated with Biotin HPDP-DMF stock (Dissolve 50 mg of EZ-Link HPDP-biotin (Thermo Scientific, #21341) in 50 ml of DMF (Sigma, # D4551)) in biotinylation buffer (10 mM Tris pH 7.4, 1 mM EDTA) for 2 h on a tube rotator at room temperature. Unbound HPDP-biotin was removed by equal volume chloroform extraction twice, and RNA was precipitated at 14,000 rpm for 30 min at 4°C with 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The RNA pellet was washed twice with 75% ethanol and resuspended in 100 μl of nuclease-free water. Biotinylated RNA was enriched by 100 μl Streptavidin T1 (Invitrogen, #65601) at room temperature for 20 min. Beads were washed five times with 1 ml washing buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween 20). Nascent RNA was eluted with 100 μl 100 mM dithiotheitol (DTT, Thermo Scientific, #A39255) twice and was purified with the RNeasy MinElute clean-up kit (Qiagen, #74204) according to the manufacturer’s instructions.

tag: treatment

value: DMSO

tag: esc number

tag: 4su treatment duration

value: 8 min


title: 3T3-L1 media_D16_1~3

source_name: Exosomal miRNA in day 16 cultured media

value: Day 16


title: test_W555_Twist_dil2_R2

value: SARS-CoV-2 synthetic RNA


title: 3T3-L1 media_D4_1~3

source_name: Exosomal miRNA in day 4 cultured media

value: Day 4


title: Ythdc1_cKO_ESC#2_DMSO.8min.rep1


title: CS23(2)_calvarialbone_10x

city: Beijing

first: Jian

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
10X Genomics CellRanger version 3.0.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 3.0.1) with default mapping arguments.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human embryonic cells

extract_protocol: Chromium Single cell 3’ Library and Gel Bead Kit V2 (10X Genomics, PN120237) was used for scRNA-seq libraries construction

tag: tissue

value: Calvarial bone

tag: development stage

value: Week 8(CS23)


title: pilot_W662_Twist_dil1_R1


title: test_W554_Twist_dil1_R2


title: pilot_W570_Twist_dil5_R2


title: pilot_W570_Twist_dil5_R1


title: pilot_W665_Twist_dil4_R1


title: PoC_W624_Twist2-dil5_R2

description:
SparSeq multiplexed PCR library
PoC_ReadCount_Table.csv


title: 3T3-L1 media_D0_1~3

source_name: Exosomal miRNA in day 0 cultured media

value: Day 0


title: pilot_W662_Twist_dil1_R2


title: Ythdc1_cKO_ESC#2_+4OHT.8min.rep1


title: Ythdc1_cKO_ESC#2_+4OHT.8min.rep2


title: Ythdc1_cKO_ESC#1_DMSO.0min.rep2

value: 0 min


title: pilot_W569_Twist_dil4_R2


title: PoC_W624_Twist2-dil5_R1


title: pilot_W569_Twist_dil4_R1


title: PoC_W612_Twist2-dil4_R2


title: pilot_W568_Twist_dil3_R2


title: Ythdc1_cKO_ESC#1_+4OHT.0min.rep2


title: Ythdc1_cKO_ESC#1_+4OHT.0min.rep1


title: PoC_W612_Twist2-dil4_R1


title: pilot_W568_Twist_dil3_R1


title: ChIRP_Malat1_Even

data_processing:
Library strategy: ChIRP-seq
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were aligned to mouse genome (mm10) using bowtie2 with the parameters “--very-sensitive --end-to-end --no-unal --phred33 --no-mixed -X 2000 --gbar 200”. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. BigWig files were generated using deeptools with the RPKM normalization method. Positive peaks were identified with DFilter17 program with parameters “-ks=100 -lpval=5”.  In order to eliminate false-positive hits, only the overlapped signal from both “even” and “odd” probes were considered. And then the Bam files of “even” and “odd” probes were merged using samtools (version 1.9).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol: ChIRP was performed as previously described with some modifications2,3. In brief, a set of biotinylated antisense oligos with 59-nt long probes tiled along the L1 consensus sequence (6.5 kb) or Malat1 RNA, and 20-nt probes tiled along the IAP consensus sequence or LacZ. Label probes based on their positions along the RNA, and separate them into ‘even’ and ‘odd’ pools, to create two independent probe sets for ChIRP experiments. Ythdc1 cKO ESCs were treated with DMSO or 4OHT (1 μg/ml) for 4 days, then cells were harvested by 0.25% trypsin digestion and cross-linked with 2 mM DSP (Thermo Scientific, # 22586) in PBS at room temperature for 30 min with gentle end to end rotation. The cells were further fixed in suspension for 10 min in 3.7% formaldehyde, and quenched with 250 mM Glycine for 5 minutes at room temperature. Cells were then washed with ice-cold PBS for three times and snap frozen in liquid nitrogen. 1 × 107 cells were resuspended with 500 μl DNase I digestion solution (20mM Tris-HCl, pH7.5, 5mM MgCl2, 0.5mM CaCl2, 0.5% Triton X-100) with 1/20 volume of Ribonucleoside Vanadyl Complex (RVC, NEB, #S1402S), 5 μl protease inhibitor cocktail (Roche, #4693132001), 5 μl 100mM PMSF and 12 U/ml Dnase I (Invitrogen, #AM2222); the reaction was rotated for 10 min at 37°C and stopped with 20 mM EDTA. After centrifugation, chromatin was resuspended in nuclear lysis buffer (50mM Tris-HCl, pH7.5, 10mM EDTA, 1% SDS, inhibitors) and sonicated with Bioruptor Pico (5 cycles, 30s on, 30s off, Diagenode). The supernatant was collected for ChIRP experiments after centrifuged at 14,000 ×g for 10 min at 4°C and save some lysate as ‘input’ samples. For the Rnase treatment control, samples were treated with 10 μg/ml Rnase A/T1 at 37°C for 20 min. For hybridization, samples were incubated with ChIRP probes (1 μl of 100 μM probes per 1 ml of lysate), supplemented with one-fourth volume of 5 x hybridization buffer (50 mM Tris-HCl, pH7.5, 10 mM EDTA, 1.5 M NaCl, 50% formamide). After rotated at 39°C for 3h, 50 μl prebalanced streptavidin M280 beads were then added into the hybridization and incubated for an additional 3h. The beads were washed 5 times with 0.2 × SSC wash buffer with 1% SDS at 42°C. To elute, the beads were washed once with SDS elution buffer (50 mM Tris-HCl, 5 mM MgCl2, 75 mM NaCl, 1% SDS) at 39°C for 20 min, and once with elution buffer (50 mM Tris-HCl, 5 mM MgCl2, 75mM NaCl, 0.1% Triton X-100) at 39°C for 5 min. DNA was eluted from the beads by RNase H treatment in two sequential incubations with Rnase H (NEB, #M0297L) at 37°C for 20 min, and with SDS elution buffer at room temperature for 2 min, combining all eluents. Crosslinking was reversed by treatment with 0.1 μg /μl protease K (NEB, #P8107S), 150 mM NaCl, and 10 mM EDTA at 65°C overnight and the DNA was purified using the MinElute PCR Purification Kit (Qiagen, #28006). ChIRP enrichments were analyzed by qPCR of the purified DNA. The libraries were constructed by a KAPA HTP/LTP Library Preparation Kit (#KK8234) according to the manufacturer’s instructions.

value: Ythdc1 cKO mESC


title: pilot_W567_Twist_dil2_R2


title: PoC_W600_Twist2-dil3_R1


title: PoC_W588_Twist2-dil2_R2


title: pilot_W567_Twist_dil2_R1


title: test_W554_Twist_dil1_R1


title: PoC_W600_Twist2-dil3_R2


title: PoC_W588_Twist2-dil2_R1


title: ChIRP_LacZ_Odd

description: LacZ.ChIRP.bw

value: embryonic stem cells


title: ChIRP_LacZ_Even

description: LacZ.ChIRP.bw


title: pilot_W474_Twist_dil5_R2


title: Ythdc1_cKO_ESC#1_DMSO.0min.rep1


title: pilot_W566_Twist_dil1_R2


title: ChIRP_LINE1.Even


title: pilot_W566_Twist_dil1_R1


title: ChIRP_LINE1_Odd


title: ChIRP_IAP_Even

description: IAP.ChIRP.bw


title: PoC_W671_Twist2-dil1_R2


title: single cell RNAseq in 14 to 14.5h embryos using 10x Rep1

city: Kansas City

first: Julia

last: Zeitlinger

country: USA

institute: Stowers Institute

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
Gene expression values were calculated following the cellranger pipeline from 10x genomics with a FlyBase release 6.21 GFF annotation file. Default parameters were used for the pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: The calculated expression values are reported as tables.

organism: Drosophila melanogaster

source_name: 14 to 14.5h embryos

extract_protocol:
The polyA selected mRNA from cells was extraced using in droplets using the 10x genomics instrument. 10x genomics manufacturer's insturtions were followed for mRNA extration and amplification
fter RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions (see ChIP-seq)

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water. Embryos were then immediately processed for singlecell extraction. Single cell extraction was done by douncing the embryos in SFX medium+0.1% PF68. The cells werealso passed through a 22.5 gauge needle to maximize the single cell isolation efficiency. The debris were filterd by a 100micron filter followed by a 30micron filter. The cells were centrifuged and washed with SFX medium followed by wash in Schneider's medium.

value: embryo

tag: developmental stage


title: polyA selected mRNAseq in 2 to 4h embryos Rep2

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
Gene expression values were calculated following the pseudoalignment strategy using the Kallisto aligner with a FlyBase release 6.21 GFF annotation file
Genome_build: dm6
Supplementary_files_format_and_content: The calculated expression values are reported as tables.

source_name: 2 to 4h embryo

extract_protocol:
The total RNA from embryos was extraced using Maxwell simply RNA protocol according to the manufacturers protocol. mRNA-seq: polyA mRNA was purified from total RNA in two consecutive rounds of oligo(dT) selection. A
fter RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions (see ChIP-seq)

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water. Embryos were then imeidately processed for mRNA extraction.


title: pilot_W474_Twist_dil5_R1


title: Ythdc1-cKO.DMSO

description: Processed data file: GSE146466_raw_counts.tsv.gz

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v74
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol: The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).


title: ChIRP_Malat1.Odd


title: pilot_W473_Twist_dil4_R1


title: ChIRP_IAP_Odd

description: IAP.ChIRP.bw


title: pilot_W473_Twist_dil4_R2


title: pilot_W472_Twist_dil3_R1


title: polyA selected mRNAseq in 2 to 4h embryos Rep1


title: polyA selected mRNAseq in 14 to 17h embryos Rep4

source_name: 14 to 17h embryo


title: pilot_W471_Twist_dil2_R2


title: pilot_W471_Twist_dil2_R1


title: PoC_W671_Twist2-dil1_R1


title: polyA selected mRNAseq in 14 to 17h embryos Rep1


title: polyA selected mRNAseq in 14 to 17h embryos Rep2


title: pilot_W380_Twist_dil7_R1


title: pilot_W470_Twist_dil1_R1


title: WCE in 14-17hrs INTACT embryos in Trachea Rep1

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For ChIP-seq samples, reads were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, and saved in BigWig format
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

source_name: Trachea

extract_protocol:
Nuclei were isolated from INTACT embryos 14-17h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). The nuclei were further dissociated using syringe (22.5 gauge needle) 10 times. After washins with HBS buffer, nuclei were incubated with Dynabeads® M-280 Streptavidin beads( Invitrogen, # 11205D) for 30 minutes with end to end rotation at 4°C. A magnet was used to separate the bead bound nuclei, and the beads were washed thoroughly with HBS buffer. Purity of nuclei isolation was determined by staining nuclei with DAPI, and presence of free nuclei, unbound to beads, were used as indicators of contamination. Isolated nuclei were used for ChIP-seq. ChIP-Seq was was performed according to He et al. (2011) and He et al. (2015) with whole cell extract (WCE) derived from 100 mg embryos per ChIP
ChIP-seq libraries were constructed following He et al. (2011)

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

value: Trachea

tag: chip antibody

value: WCE


title: Ythdc1-cKO.DMSO.Dux-KO.rep1


title: pilot_W379_Twist_dil6_R1


title: WCE in 14-17hrs INTACT embryos in Muscle Rep2

source_name: Muscle

value: Muscle


title: Ythdc1-cKO.4OHT.Dux-KO.rep1


title: Mettl3.WT.rep2


title: pilot_W378_Twist_dil5_R2


title: pilot_W472_Twist_dil3_R2


title: Ythdc1-cKO.DMSO.Dux-Het.rep2


title: WCE in 14-17hrs INTACT embryos in Muscle Rep1


title: Ythdc1-cKO.4OHT.Dux-KO.rep2


title: WCE in 14-17hrs INTACT embryos in Gut Rep2

source_name: Gut

value: Gut


title: Ythdc1-cKO.4OHT.Dux-Het.rep2


title: pilot_W377_Twist_dil4_R2


title: Mettl3.KO.rep2


title: polyA selected mRNAseq in 14 to 17h embryos Rep3


title: ChIRP_Input

description: INPUT.bw


title: Ythdc1-cKO.4OHT(SETDB1)

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ChIP-seq reads were aligned to the mouse mm10 genome using bowtie247 with the options ‘-p 20– very-sensitive–end-to-end–no-unal–no-mixed -X 2000’. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. Whereas the reads mapping to mitochondrial DNA or unassigned sequences were discarded
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol: Native ChIP-seq was performed as described44. In brief, 1 × 107 cells were harvested and resuspended in 500 μl Buffer 1 (0.32 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 EDTA-free protease inhibitor cocktail [Roche, #4693132001]) supplemented with 0.1% IGEPAL CA-630 (Sigma, # I8896) on ice for 10 min. The lysates was carefully layered on the top of 1 ml Buffer 3 (1.2 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 PIC). After centrifugation (10,000 ×g for 20 min at 4°C), the nuclei were resuspended in 500 μl Buffer A (0.34 M sucrose, 60 mM KCl, 15 mM HEPES pH7.4, 15 mM NaCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF, 1:1000 PIC) supplemented with 3 mM CaCl2 and 2 U/μl MNase (NEB, # M0247S) and digested for 15 min at 37°C. Then 5 mM EGTA was added to stop the reaction. After centrifuged at 13,500 ×g for 10 min at 4°C, chromatin was resuspended in 10 mM EDTA (pH 8.0) supplemented with 1 mM PMSF and 1:1000 PIC, followed by rotation at 4 °C for 2-4 h. The mixture was adjusted to 500 mM NaCl and rotated for additional 45 min. After centrifugation, the supernatant containing chromatin was diluted to 100 ng/μl with buffer B (20 mM Tris-HCl pH8.0, 5 mM EDTA, 500 mM NaCl, 0.2% Tween 20) and the fragmentation of chromatin was detected by agarose electrophoresis. A total of 2.5 μg fragmented chromatin was kept as the input. For immunoprecipitation, the reaction mixture, including 20 μg fragmented chromatin, 2 μg anti-H3K9me3 antibody (Abcam, #ab8898), and 50 μl protein A/G dynabeads (GE Healthcare) was incubated overnight with gentle rotation at 4°C. The beads were washed three times with Buffer B, and once with Buffer B without Tween 20 at 4°C for 5 min. The DNA was eluted with 300 μl elution buffer (20 mM Tris-HCl pH8.0, 20 mM EDTA, 0.5% SDS), digested with PK enzyme (NEB, #P8107S), and purified using a MinElute kit (Qiagen, #28006). The ChIP DNA library was constructed by a KAPA HTP/LTP Library Preparation Kit according to the manufacturer’s instructions.

value: SETDB1 (Proteintech,11231-1-AP )


title: Ythdc1-cKO.DMSO.Dux-Het.rep1


title: single cell RNAseq in 14 to 14.5h embryos using 10x Rep2


title: Ythdc1-cKO.4OHT.Dux-Het.rep1

value: DMSO


title: pilot_W470_Twist_dil1_R2


title: Ythdc1-cKO.DMSO.Dux-KO.rep2


title: pilot_W376_Twist_dil3_R1


title: WCE in 14-17hrs INTACT embryos in Epidermis Rep2

source_name: Epidermis

value: Epidermis


title: WCE in 14-17hrs INTACT embryos in Trachea Rep2


title: WCE in 14-17hrs INTACT embryos in Epidermis Rep1


title: pilot_W380_Twist_dil7_R2


title: pilot_W375_Twist_dil2_R2


title: WCE in 14-17hrs INTACT embryos in Neuron Rep2

source_name: Neuron

value: Neuron


title: WCE in 14-17hrs INTACT embryos in Neuron Rep1


title: Ythdc1-cKO.4OHT


title: pilot_W379_Twist_dil6_R2

value: SARS-CoV-2 synthetic RNA


title: Mettl3.WT.rep1


title: pilot_W378_Twist_dil5_R1


title: Pol II ChIP in 14-17hrs INTACT embryos in Trachea Rep1

value: anti-RPB3 rabbit polyclonal, custom (GenScript)


title: pilot_W374_Twist_dil1_R2


title: pilot_W374_Twist_dil1_R1


title: Mettl3.KO.rep1


title: WCE in 14-17hrs INTACT embryos in Gut Rep1


title: Ythdc1-cKO.DMSO.Dux-KO-H3K9me3.rep1

value: H3K9me3 (Abcam, ab8898)


title: pilot_W377_Twist_dil4_R1


title: pilot_W284_Twist_dil7_R2


title: pilot_W376_Twist_dil3_R2


title: pilot_W375_Twist_dil2_R1


title: pilot_W284_Twist_dil7_R1


title: YTHDC1(Ythdc1-WT).rep2


title: YTHDC1(Ythdc1-WT).rep1


title: Pol II ChIP in 14-17hrs INTACT embryos in Muscle Rep2


title: WCE in 14-17hrs INTACT embryos in Glia Rep1

source_name: Glia

value: Glia


title: pilot_W283_Twist_dil6_R1

source_name: SARS-CoV-2 Synthetic RNA


title: Ythdc1-cKO.DMSO(SETDB1)


title: Ythdc1-cKO.4OHT.Dux-KO-H3K9me3.rep2


title: Ythdc1-cKO.4OHT.Dux-KO-H3K9me3.rep1


title: Pol II ChIP in 14-17hrs INTACT embryos in Trachea Rep2


title: Ythdc1-cKO.DMSO.Dux-KO-H3K9me3.rep2


title: Pol II ChIP in 14-17hrs INTACT embryos in Gut Rep1


title: Pol II ChIP in 14-17hrs INTACT embryos in Neuron Rep2


title: Pol II ChIP in 14-17hrs INTACT embryos in Glia Rep2


title: INPUT(WT)

value: WT

value: none (input)


title: Pol II ChIP in 14-17hrs INTACT embryos in Neuron Rep1


title: pilot_W280_Twist_dil3_R2


title: Pol II ChIP in 14-17hrs INTACT embryos in Muscle Rep1


title: pilot_W281_Twist_dil4_R1


title: pilot_W283_Twist_dil6_R2


title: Mettl3.WT.H3K9me3.rep2


title: Ythdc1_cKO_ESC#2_DMSO.rep2

description: Processed data file: GSE146466_RNA-seq-expr.tsv.gz

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v74
Genome_build: mm10
Supplementary_files_format_and_content: expression matrx

extract_protocol:
total RNA
Total RNAs were extracted as described above. The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

tag: esc id


title: CS23_calvarialbone_10x

description: PolyA RNA

data_processing:
10X Genomics Cell Ranger version 3.0.1 was used for the basecalling.
Sequencing data from 10X Genomics was processed with Cell Ranger software package (version 3.0.1) with default mapping arguments.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_rawdata.txt: Tab-delimited text files include UMI values for each cell.

extract_protocol: Chromium Single cell 3’ Library and Gel Bead Kit V2 (10X Genomics, PN120237) was used for scRNA-seq libraries construction.

value: Calvarial bone

value: Week 8 (CS23)


title: Pol II ChIP in 14-17hrs INTACT embryos in Epidermis Rep1


title: Pol II ChIP in 14-17hrs INTACT embryos in Gut Rep2


title: WCE in 2-4hrs OregonR embryos Rep1

source_name: 2-4hrs OregonR embryo

extract_protocol:
ChIP-seq was performed according to He et al. (2011) and He et al. (2015) with whole cell extract (WCE) derived from 100 mg embryos per ChIP
ChIP-seq libraries were constructed following He et al. (2011)

value: embryos


title: CS22(2)_longbone_10x

description: PolyA RNA

value: Long bone

value: Week 8 (CS22)


title: Mettl3.WT.H3K9me3.rep1

source_name: embryonic stem cells

value: embryonic stem cells


title: pilot_W282_Twist_dil5_R2


title: WCE in 14-17hrs OregonR embryos Rep2

source_name: 14-17hrs OregonR embryo

value: WCE


title: pilot_W279_Twist_dil2_R2


title: pilot_W282_Twist_dil5_R1


title: Mettl3.KO.H3K9me3.rep2


title: Mettl3.KO.H3K9me3.rep1


title: Pol II ChIP in 14-17hrs INTACT embryos in Glia Rep1


title: WCE in 14-17hrs INTACT embryos in Glia Rep2


title: YTHDC1(Ythdc1-KO).rep2


title: TFIIF ChIP in 14-17hrs OregonR embryos Rep1

value: anti-TFIIF rabbit polyclonal, custom


title: Pol II ChIP in 14-17hrs INTACT embryos in Epidermis Rep2


title: CS15_limbbud_10x

description: PolyA RNA

value: Limb bud

value: Week 5 (CS15)


title: pilot_W278_Twist_dil1_R1


title: Ythdc1_cKO_ESC#2_DMSO.rep1

value: DMSO


title: pilot_W280_Twist_dil3_R1

value: SARS-CoV-2 synthetic RNA


title: pilot_W188_Twist_dil7_R2


title: CS22_longbone_10x

description: PolyA RNA


title: TFIIB ChIP in 14-17hrs OregonR embryos Rep1

value: anti-TFIIB rabbit polyclonal, custom


title: Ythdc1_cKO_ESC#1_+4OHT.rep2


title: Ythdc1_cKO_ESC#2_+4OHT.rep2


title: Ythdc1_cKO_ESC#1_DMSO.rep1


title: Ythdc1_cKO_ESC#1_+4OHT.rep1


title: CS20_longbone_10x

description: PolyA RNA

value: Week 8 (CS20)


title: MMTV-PRMT6 sample2

city: San Diego

first: Tae Gyu

last: Oh

address: North Torrey Pines Road

institute: Salk Institute

description: mammary tissue after lactation (PRMT6 Gain-of-function)

data_processing:
quality of fastq files were checked using fastqc
reads were aligned with STARaligner ver 2.5.1
htSeq was used to combine aligned reads
Deseq2 was utilized to calculate fold changes and statistics.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: htseq_counts

source_name: Mammary cells

growth_protocol: DMEM-F12 media

extract_protocol:
Qiagen Rneasy kit
Total RNA sample libraries were generated using the Illumina TruSeq Stranded mRNA LT sample preparation kit. The mRNA denaturation and elution were performed with 0.1 microgram to 0.2 microgram of total RNA depending on amount of sample available prior to a heat fragmentation step aimed at producing libraries with an insert size between 120 and 200 bp.

treatment_protocol: Invitrogen siRNA protocol

tag: strain

value: Mammary cells


title: pilot_W281_Twist_dil4_R2

extract_protocol:
Total RNA extraction by Norgen total RNA Kit or RNA-XP beads.
C19-SparSeq-Barcoded multiplexed PCR reactions were pooled and cleaned with SPRIselect beads.


title: pilot_W279_Twist_dil2_R1


title: WCE in 14-17hrs OregonR embryos Rep1


title: Ythdc1_cKO_ESC#1_DMSO.rep2


title: YTHDC1-RIP-INPUT

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
Raw reads were trimmed with TrimGalore (v0.6.4) (https://github.com/FelixKrueger/TrimGalore), then aligned to the mouse genome (mm10) and transcriptome (GENCODE version M21) using HISAT2 (version 2.2.0)55. Mapped reads were separated by strands with samtools (version 1.9)51 and m6A peaks on each strand were called using MACS (version 2.1.2)52 with parameter ‘--nomodel’ and ‘--keep-dup 5’ separately. Significant peaks with q < 0.01 and fold-change enrichment to INPUT > 2 were considered.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
total RNA
RIP assay was performed based on GoldCLIP33 with modifications. The cells expressing Halo-GFP or Halo-YTHDC1 were harvested, lysed, and pulled-down using Halo-tagged beads (Promega, #G7282) as previously described, except that no nuclease digestion or RNA fragmentation conducted throughout the experiment. The binding efficiency of Halo-tagged protein to the beads was evaluated by western blot. After the denaturing wash, the RNAs were released from the proteins by PK enzyme (NEB, #P8107S) digestion. For RIP-RT-qPCR, the equivalent input and IP RNAs were reverse-transcribed by SuperScript III Reverse Transcriptase (Invitrogen, #18080044) using random hexamers, followed by qPCR to quantify the transcripts. The enrichment score of a transcript was the ratio of the quantified IP fraction to its total input, using GFP as a standard for normalization. For RIP-seq, 200-500 ng RNAs from the input and IP samples were used to generate the libraries using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) according to the manufacturer’s instructions.

value: Halo-Ythdc1 knockin


title: CS15(2)_limbbud_10x

description: PolyA RNA


title: pilot_W278_Twist_dil1_R2

data_processing:
Single-end reads mapped to amplicon sequences using Bowtie and allowing 3 mismatch for mapped read count / amplicon quantification.
Genome_build: Custom genome consists of amplicons targeted in GRCh38 and Sars-CoV-2 (Wuhan-Hu-1).
Supplementary_files_format_and_content: Sample name/ read count mapped to each targeted amplicon.


title: YTHDC1-RIP


title: pilot_W186_Twist_dil5_R1


title: ATAC-seq in Neuron 14-17hrs embryo Rep2

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 50 bp each and aligned to the UCSC Drosophila melanogaster dm6 genome with Bowtie 2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
BigWig files contain per-base coverage of aligned read pairs of size 0-100bp.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files contain counts of the aligned reads for each coordinate

source_name: Neuron 14-17hrs embryo

growth_protocol: Drosophila melanogaster embryos INTACT lines were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).

extract_protocol:
Nuclei were isolated from INTACT embryos 14-17h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). The nuclei were further dissociated using syringe (22.5 gauge needle) 10 times. After washins with HBS buffer, nuclei were incubated with Dynabeads® M-280 Streptavidin beads( Invitrogen, # 11205D) for 30 minutes with end to end rotation at 4°C. A magnet was used to separate the bead bound nuclei, and the beads were washed thoroughly with HBS buffer. Purity of nuclei isolation was determined by staining nuclei with DAPI, and presence of free nuclei, unbound to beads, were used as indicators of contamination. Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.

treatment_protocol: Embryos were then dechorionated with 50% bleach solution for 2-3 minutes.

value: Neuron


title: CS13_limbbud_10x

description: PolyA RNA

source_name: human embryonic cells

value: Week 5 (CS13)


title: MMTV-PRMT6 sample3


title: Pol II ChIP in 2-4hrs OregonR embryos Rep1

value: anti-RPB3 rabbit polyclonal, custom (GenScript)


title: pilot_W188_Twist_dil7_R1


title: WT sample2

value: wildtype


title: WT sample1


title: TFIIB ChIP in 14-17hrs OregonR embryos Rep2

value: embryos


title: Pol II ChIP in 14-17hrs OregonR embryos Rep2


title: Ythdc1-KO.rep1-H3K9me3

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the genome(mm10) with bowtie2
ChIP-seq reads were aligned to the mouse mm10 genome using bowtie247 with the options ‘-p 20– very-sensitive–end-to-end–no-unal–no-mixed -X 2000’. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. Whereas the reads mapping to mitochondrial DNA or unassigned sequences were discarded
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
genomic DNA
Native ChIP-seq was performed as described. In brief, 1 × 107 cells were harvested and resuspended in 500 μl Buffer 1 (0.32 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 EDTA-free protease inhibitor cocktail [Roche, #4693132001]) supplemented with 0.1% IGEPAL CA-630 (Sigma, # I8896) on ice for 10 min. The lysates was carefully layered on the top of 1 ml Buffer 3 (1.2 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 PIC). After centrifugation (10,000 ×g for 20 min at 4°C), the nuclei were resuspended in 500 μl Buffer A (0.34 M sucrose, 60 mM KCl, 15 mM HEPES pH7.4, 15 mM NaCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF, 1:1000 PIC) supplemented with 3 mM CaCl2 and 2 U/μl MNase (NEB, # M0247S) and digested for 15 min at 37°C. Then 5 mM EGTA was added to stop the reaction. After centrifuged at 13,500 ×g for 10 min at 4°C, chromatin was resuspended in 10 mM EDTA (pH 8.0) supplemented with 1 mM PMSF and 1:1000 PIC, followed by rotation at 4 °C for 2-4 h. The mixture was adjusted to 500 mM NaCl and rotated for additional 45 min. After centrifugation, the supernatant containing chromatin was diluted to 100 ng/μl with buffer B (20 mM Tris-HCl pH8.0, 5 mM EDTA, 500 mM NaCl, 0.2% Tween 20) and the fragmentation of chromatin was detected by agarose electrophoresis. A total of 2.5 μg fragmented chromatin was kept as the input. For immunoprecipitation, the reaction mixture, including 20 μg fragmented chromatin, 2 μg anti-H3K9me3 antibody (Abcam, #ab8898), and 50 μl protein A/G dynabeads (GE Healthcare) was incubated overnight with gentle rotation at 4°C. The beads were washed three times with Buffer B, and once with Buffer B without Tween 20 at 4°C for 5 min. The DNA was eluted with 300 μl elution buffer (20 mM Tris-HCl pH8.0, 20 mM EDTA, 0.5% SDS), digested with PK enzyme (NEB, #P8107S), and purified using a MinElute kit (Qiagen, #28006). The ChIP DNA library was constructed by a KAPA HTP/LTP Library Preparation Kit according to the manufacturer’s instructions.

value: H3K9me3 (Abcam, ab8898)


title: Ythdc1_cKO_ESC#2_+4OHT.rep1

value: embryonic stem cells


title: pilot_W185_Twist_dil4_R1


title: pilot_W187_Twist_dil6_R2


title: MMTV-PRMT6 sample1


title: pilot_W187_Twist_dil6_R1


title: Pol II ChIP in 14-17hrs OregonR embryos Rep1


title: Blastoid -hTSCs; hTSM

city: Dallas

first: Gary

last: Hon

address: 5323 Harry Hines Blvd.

department: Department of Obstetrics and Gynecology

institute: UT Southwestern

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 4.0.0).
Reads were processed to generate expression (UMI count) matrix using Cell Ranger pipeline (version 4.0.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

source_name: Blastoid -hTSCs; hTSM

growth_protocol: Briefly, individual human blasotid was transferred onto MEFs and cultured in 5iLA medium (blastoid-nESCs), NACL medium (blastoid-nEND) and hTSC medium (blastoid-hTSCs). Within 4-5 days outgrowth could be observed. Then outgrowth was dissociated with Tryple Express (GIBCO) and passaged onto newly prepared MEF plate. Individual colonies were manually picked, dissociated, and cultured in their corresponding media. NACL medium was generated using the following: 1:1 (v/v) mixture of DMEM/F12 (Invitrogen), and Neurobasal medium (Invitrogen), 1x N2 supplement (Invitrogen), 1x B27 supplement (Invitrogen) 1x Glutamax (GIBCO), 1x Nonessential amino acids (GIBCO), 0.1 mM β-mercaptoethanol (GIBCO), 0.5% penicillin-streptomycin (GIBCO), 100 ng/mL Activin A (Peprotech), 3 μM CHIR99021 (Selleckchem) and 10 ng/mL recombinant human LIF (Peprotech).

extract_protocol:
Single cell suspension was washed with 1X PBS (0.04% BSA) before 10x Genomics procedure. The concentration of single cell suspension was adjusted to about 500 to 1000 cells/µL and was loaded on the 10x Genomics’ Chromium™ system (10x Genomics, Pleasanton, CA) with the aim of 6000 to 10000 cells per channel (Chromium Next GEM Single Cell 3ʹ v3.1, catalog number 1000121).
Single cell RNA sequencing libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).

tag: internal sample


title: pilot_W186_Twist_dil5_R2

tag: sample type


title: WT sample3


title: WT.rep1-H3K9me3

value: WT


title: Ythdc1-KO.rep2-H3K9me3


title: pilot_W185_Twist_dil4_R2


title: ATAC-seq in Muscle 14-17hrs embryo Rep2

source_name: Muscle 14-17hrs embryo

value: Muscle


title: ATAC-seq in Muscle 14-17hrs embryo Rep1


title: Blastoid-nEND; NACL

source_name: Blastoid-nEND; NACL


title: pilot_W184_Twist_dil3_R2


title: Blastoid-nESCs; 5iLA

source_name: Blastoid-nESCs; 5iLA


title: shScramble.H3K9me3

value: shScramble


title: ATAC-seq in Epidermis 14-17hrs embryo Rep2

source_name: Epidermis 14-17hrs embryo

value: Epidermis


title: pilot_W183_Twist_dil2_R2


title: ATAC-seq in Neuron 14-17hrs embryo Rep1


title: ATAC-seq in Epidermis 14-17hrs embryo Rep1


title: pilot_W184_Twist_dil3_R1


title: ChIP.Input

value: none (input)


title: Naïve WIRB3; 5iLA

source_name: Naïve WIRB3; 5iLA


title: shMettl3.H3K9me3


title: WT.rep2-H3K9me3


title: LW61

source_name: human blastoids

growth_protocol: Naïve hPSCs were cultFor the generation of human blasatoids, 60~70% confluent naïve hPSCs were dissociated into single cells by incubation with Tryple Express (GIBCO) at 37°C for 3 min. Then, the cell resuspension was pre-incubated at 37 °C in 5% CO2 on gelatinized tissue culture plates for 30 min to remove MEF cells. The supernatant containing the naïve hPSCs cells were collected, passed through a 40 μm cell strainer, and counted. Meanwhile, the AggreWell™400 (STEMCELL Technologies) was prepared according to manufacturer’s instructions. Briefly, wells were rinsed with anti-adhesion rinsing solution (STEMCELL Technologies) then centrifuged at 2,000g for 5 min and incubated at room temperature for 10 min. After incubation, wells were washed with naïve hPSC medium once and 0.5 mL fresh naïve hPSC medium containing 5 μM Y-27632 was added (Selleckchem).  Approximately 30,000 cells (~25 cells / microwell for 5iLA-cultured WIRB3 hESCs. For other cell lines, starting cell number need to be optimized) were resuspended in 1mL 5iLA medium supplemented with 5μ M Y-27632 and seeded into one well of prepared AggreWell™400 24-well plate. The plate was centrifuged at 200 g for 1 min and placed in a 37 °C and 5% CO2 incubator. Aggregates formed following ~12 hours culture, and the medium was replaced with HDM or TDM. The first day of changing to differentiation medium (HDM or TDM was designated as day 1.   Naïve hPSC medium is first changed to HDM (day 1). On day 3, carefully remove as much as possible of the medium and add 1ml TDM, repeat this step once to fully remove the HDM. Fresh TDM is replaced every 2 days. After 6-8 days (usually 7 days for 5iLA-WIRB3-hESCs, and the time varies among different cell lines, different starting culture conditions, different starting cell numbers and sometimes different batches) of culture in TDM human blastoids can be observed in some microwells.

tag: naive hescs cultrue medium

value: naive hESCs grown in PXGL

tag: collection day


title: A_qCSC_2

city: Hangzhou

last: Lu

address: Yuhangtang street 866

institute: Zhejiang university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/52?genome_assembly_id=334509
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cells

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: breast

tag: cell state

value: activated CSCs


title: A_qCSC_3


title: pilot_W182_Twist_dil1_R1

value: SARS-CoV-2 synthetic RNA


title: polyA selected mRNAseq in 2 to 4h embryos Rep3

source_name: 2 to 4h embryo

value: embryo


title: pilot_W183_Twist_dil2_R1


title: A_qCSC_1


title: pilot_W092_Twist_dil7_R2


title: LW60

value: naive hESCs grown in 5iLA


title: polyA selected mRNAseq in 17 to 17.5h embryos Rep2

source_name: 17 to 17.5h embryo


title: LW58


title: LW59


title: qCSC_3

value: quiescent CSCs


title: qCSC_2


title: qCSC_1


title: polyA selected mRNAseq in 14 to 14.5h embryos Rep2

source_name: 14 to 14.5h embryo


title: pilot_W092_Twist_dil7_R1

source_name: SARS-CoV-2 Synthetic RNA


title: pilot_W091_Twist_dil6_R2


title: human blastoids, scRNA-Seq

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 4.0.0).
Reads were processed to generate expression (UMI count) matrix using Cell Ranger pipeline (version 4.0.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.

Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count matrix representing gene expression values (comma-separated) were generated as described above. Each column represents a single cell, each row represents a single gene.

growth_protocol: For the generation of human blasatoids, 60~70% confluent naïve hPSCs were dissociated into single cells by incubation with Tryple Express (GIBCO) at 37°C for 3 min. Then, the cell resuspension was pre-incubated at 37 °C in 5% CO2 on gelatinized tissue culture plates for 30 min to remove MEF cells. The supernatant containing the naïve hPSCs cells were collected, passed through a 40 ?m cell strainer, and counted. Meanwhile, the AggreWell?400 (STEMCELL Technologies) was prepared according to manufacturer?s instructions. Briefly, wells were rinsed with anti-adhesion rinsing solution (STEMCELL Technologies) then centrifuged at 2,000g for 5 min and incubated at room temperature for 10 min. After incubation, wells were washed with naïve hPSC medium once and 0.5 mL fresh naïve hPSC medium containing 5 ?M Y-27632 was added (Selleckchem). Approximately 30,000 cells (~25 cells / microwell for 5iLA-cultured WIRB3 hESCs. For other cell lines, starting cell number need to be optimized) were resuspended in 1mL 5iLA medium supplemented with 5? M Y-27632 and seeded into one well of prepared AggreWell?400 24-well plate. The plate was centrifuged at 200 g for 1 min and placed in a 37 °C and 5% CO2 incubator. Aggregates formed following ~12 hours culture, and the medium was replaced with HDM or TDM. The first day of changing to differentiation medium (HDM or TDM was designated as day 1. Naïve hPSC medium is first changed to TDM (day 1). Fresh TDM is replaced every 2 days until the cavity structures appear (usually it takes 6-7 days for 5iLA-WIRB3-hESCs, and the time varies among different cell lines, different starting culture conditions, different starting cell numbers and sometimes different batches), then the medium is replaced with HDM and cultured for 1-2 days.

value: blastoids


title: pilot_W182_Twist_dil1_R2


title: pilot_W091_Twist_dil6_R1


title: polyA selected mRNAseq in 14 to 14.5h embryos Rep1


title: MNase in 14-17hrs OregonR embryos Rep2

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For MNAse samples, reads were aligned to the reference genome using bowtie v2, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Fragemnts of size 100-200bp are used to calculate the nucleosome occupupancy. Genome-wide coverage counts were calculated, and saved in BigWig format
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

extract_protocol:
Cell lysates were digested with micrococcal nuclease and mononucleosomal DNA was purified.
Sequencing libraries were prepared following Illumina's instructions:


title: MNase in 2-4hrs OregonR embryos Rep1

source_name: 2-4hrs OregonR embryo


title: MDA-231 PRMT6 SiRNA-1

description: Breast cancer cell line (PRMT6 knockdown, Loss-of-Function)

source_name: Breast cancer cells

tag: cell type

value: Basal breast cancer cells

tag: cell line

tag: passage

tag: sirna

value: PRMT6 SiRNA


title: pilot_W090_Twist_dil5_R2


title: MDA-231 PRMT6 SiRNA-2


title: polyA selected mRNAseq in 17 to 17.5h embryos Rep1


title: btaCL-4RPM

city: Campobasso

first: Valentino

last: Palombo

address: via Francesco De Sanctis

department: Dipartimento Agricoltura Ambiente e Alimenti

country: Italy

institute: Università degli Studi del Molise

data_processing:
Quality control metrics were performed on raw sequencing reads using the FASTQC (v0.11.15) application.
An index of the reference genome was built and single-end clean reads for each individual were aligned to the reference genome by STAR (v2.5.3a).
Reads aligned were quantified with Subread package (v1.5.2) based on the Refseq gene annotation (Sus scrofa genome v10.2.86).
Genome_build: Bos taurus genome (UMD v.3.1.1).
Supplementary_files_format_and_content: Tab-delimited text files include data matrix containing read counts for each feature in each library obtained by featureCounts (Subread package). The data frame includes six columns:  GeneID, Chr, Start, End and Length.

organism: Bos taurus

source_name: Calf liver_ethyl-cellulose rumen-protected methionine

growth_protocol: Heifer calves were born to cows fed a control diet (CON) or the control plus ethyl-cellulose rumen-protected methionine (MET) for the last 28 d prepartum and were fed and managed similarly after birth.

extract_protocol:
Tissue was harvested and immediately frozen in liquid N2 and preserved at - 80°C until RNA extraction. Total RNA from 0.4 to 1.4 g of tissue was extracted with ice-cold Trizol reagent (Invitrogen, Carlsbad, CA). Tissue was weighed, placed in 10–15 ml of ice-cold TRIzol reagent, homogenized, and RNA extracted according to the manufacturer's protocol. RNA was resuspended in RNA storage buffer (Ambion, Austin, TX) and stored at −80°C until use. Quantity and purity of isolated RNA samples were analyzed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a Illumina HiSeq 2500 using a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina). Adaptors have been trimmed from the reads with Trimmomatic (v0.33).

treatment_protocol: Calves in the present study were a subset from a larger cohort of animals born to Holstein cows randomly assigned to receive a basal control (CON) close-up diet (from −28 ±2 d to parturition) [1.47 Mcal/kg dry matter and 15.3% crude protein] with no added Met or CON plus ethyl cellulose MET (MET, Mepron®, Evonik Nutrition & Care GmbH, Germany) .

tag: breed

value: Heifer

tag: treatment

value: Post-ruminal maternal supplied

value: liver


title: MNase in 14-17hrs OregonR embryos Rep1

source_name: 14-17hrs OregonR embryo

tag: tissue

value: embryos


title: MDA-231 control SiRNA-3

value: control SiRNA


title: pilot_W090_Twist_dil5_R1


title: btaCL-3RPM


title: WCE in 2-4hrs OregonR embryos Rep2

value: WCE


title: MDA-231 control SiRNA-2


title: Pol II ChIP in 2-4hrs OregonR embryos Rep2

value: anti-RPB3 rabbit polyclonal, custom (GenScript)


title: MDA-231 PRMT6 SiRNA-3


title: MDA-231 control SiRNA-1


title: pilot_W089_Twist_dil4_R1


title: btaCL-2RPM


title: btaCL-6RPM


title: ATAC-seq in Trachea 14-17hrs embryo Rep2

source_name: Trachea 14-17hrs embryo

value: Trachea


title: btaCL-1RPM


title: btaCL-5RPM


title: pilot_W088_Twist_dil3_R2


title: ATAC-seq in Trachea 14-17hrs embryo Rep1


title: MCF-7 PRMT6 SiRNA-2

value: Luminal breast cancer cells


title: YTHDC1(Ythdc1-KO).rep1

source_name: embryonic stem cells

value: embryonic stem cells

tag: genotype


title: ATAC-seq in Gut 14-17hrs embryo Rep2

source_name: Gut 14-17hrs embryo

value: Gut

tag: developmental stage


title: btaCL-5CTR

source_name: Calf liver_control

value: Control


title: MCF-7 PRMT6 SiRNA-1


title: pilot_W087_Twist_dil2_R2

value: SARS-CoV-2 synthetic RNA


title: ATAC-seq in Gut 14-17hrs embryo Rep1


title: MCF-7 control SiRNA-3


title: pilot_W089_Twist_dil4_R2


title: pilot_W087_Twist_dil2_R1


title: ATAC-seq in 14-17hrs embryo Rep2

source_name: 14-17hrs embryo

growth_protocol: Drosophila melanogaster embryos OregonR were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).

extract_protocol:
Nuclei were isolated from Oregon-R embryos 2-4h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.

treatment_protocol: Embryos were then dechorionated with 50% bleach solution for 2-3 minutes


title: MCF-7 control SiRNA-2


title: btaCL-3CTR


title: pilot_W086_Twist_dil1_R2


title: btaCL-2CTR


title: MCF-7 control SiRNA-1


title: pilot_W086_Twist_dil1_R1


title: ATAC-seq in 14-17hrs embryo Rep1

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 50 bp each and aligned to the UCSC Drosophila melanogaster dm6 genome with Bowtie 1.1.2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
BigWig files contain per-base coverage of aligned read pairs of size 0-100bp.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files contain counts of the aligned reads for each coordinate


title: MCF-7 PRMT6 SiRNA-3


title: btaCL-1CTR


title: btaCL-6CTR


title: pilot_W088_Twist_dil3_R1


title: btaCL-4CTR


title: Zscan4+mervL+ cells – H3K27me3_rep2

status: Public on Jan 23 2021

city: Shanghai

first: Yanping

last: zhang

address: Siping Road 1239

institute: Tongji University

description: Normalized tag counts

data_processing:
ChIP-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.4.2) using the default parameters.
Chip-seq reads were aligned to the mouse genome (mm9) using Bowtie2 v.2.3.5 with the parameters -N 1 -L 25 -X 1000 --no-mixed --no-discordant.
ChIP-seq peaks were called with MACS2 with the parameters  –nomodel --nolambda --shiftsize =73 over input files
Genome_build: mm9
Supplementary_files_format_and_content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)

source_name: ESCs

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: Wild type

value: 2-Cell-like Embryonic Stem Cells (ESCs)

tag: chip antibody

value: H3K27me3 (Diagenode no.C15410195)


title: Zscan4+ cells – H3K27me3_rep4

description: Normalized tag counts


title: zscan4+mervL+ cells - H3K27me3 input

description: Normalized tag counts

value: Wild type input


title: Zscan4+mervL+ cells – H3K27me3_rep1

description: Normalized tag counts


title: zscan4+ cells - H3K4me3 input

description: Normalized tag counts


title: Embryonic stem cells - input

description: Normalized tag counts


title: zscan4+mervL+ cells - H3K4me3 input

description: Normalized tag counts


title: zscan4+ cells - H3K27me3 input

description: Normalized tag counts


title: Zscan4+ mervL+ cells – H3K27me3_rep3

description: Normalized tag counts


title: Zscan4+ cells – H3K27me3_rep3

description: Normalized tag counts


title: zscan4+ cells – H3K27me3_rep2

description: Normalized tag counts


title: Zscan4+mervL+ cells – H3K27me3_rep4

description: Normalized tag counts


title: Embryonic stem cells – H3K27me3_rep3

description: Normalized tag counts


title: Zscan4+mervL+ cells - H3K4me3_rep1

description: Normalized tag counts

value: H3K4me3 (Cell Signaling Technology no.9727S)


title: Zscan4+ cells - H3K27me3_rep1

description: Normalized tag counts


title: Embryonic stem cells – H3K27me3_rep2

description: Normalized tag counts


title: Zscan4+ cells - H3K4me3_rep3

description: Normalized tag counts


title: Zscan4+mervL+ cells - H3K4me3_rep2

description: Normalized tag counts


title: Embryonic stem cells – H3K27me3_rep1

description: Normalized tag counts


title: Embryonic stem cells - H3K4me3_rep3

description: Normalized tag counts


title: 03/04/20 Sequencing Run

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

description: Please see our code at https://github.com/skannan4/wls for demultiplexing of the Multiseq barcodes. Mapping was done in Kallisto|Bustools using 10xv3 custom setting (-x 10xv3). Note that for this sample, we didn’t demultiplex the individual 10x i7 barcodes, so there should only be 1 R1 and 1 R2 file for this data.

data_processing:
Mapping of the data was done with kallisto|bustools (0.46.1), using an index generated from the CellRanger mouse reference.
Genome_build: GRCm38_r92
Supplementary_files_format_and_content: Please see our code at https://github.com/skannan4/wls for the full approach used to demultiplex the Multiseq barcode tags. Likewise, the code there contains our entire strategy for clustering and labeling cells; additional files may be found there. The processed files provided here are the UMI tables for all the runs combined (combined_data.txt) as well as the metadata for these cells (combined_pheno.txt). UMI counts are also provided in sparse format.

source_name: Mesp1+ cells (Wls fl/+ and Wls fl/fl)

growth_protocol: The following mice were used to generate the appropriate samples for this experiment: Mesp1-Cre (Saga et al., 1999), Ai9 (stock no. 007909, Jackson Laboratory, (Madisen et al., 2010)), and Wntless flox (stock no. 027484, Jackson Laboratory, (Fu et al., 2011)).

extract_protocol:
Embryos were dissected, staged, and stored on ice in cold PBS -/-. Embryos were dissociated and barcoded using MULTI-seq anchor and primers , before FACS on Mesp1+/tdTomato cells using Sony SH800. Cells were then captured for 10x library prep and single cell RNA sequencing.
We performed cell capture and library construction using 10x Chromium v3. For the experiments sequenced on 10/21/19, sequencing of the endogenous transcripts was done on a NextSeq500 high output lane using a 28/8/91 bp design for R1/i7/R2. Sequencing of the barcodes was done a NextSeq500 mid output lane using a 28/8/8 design for R1/i7/R2. For the experiments sequenced on 03/04/20, sequencing for both endogenous and barcode transcripts was done on a NovaSeq6000 S1 flow cell, using a 28/8/91 bp design; the barcode transcripts were subsequently trimmed using the BBMap/BBTools suite.

tag: strain/background

value: Mesp1-Cre; Ai9; Wlsfl/+ and Wlsfl/f

value: Mesp1+ cells


title: zscan4+ cells - H3K4me3_rep2

description: Normalized tag counts

tag: strain


title: Refractory_Hour18_Bird1

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

data_processing:
adapter trimmimg: trimmomatic
Assembly: Trinity
Pseudo Alignment: Kallisto (Bray et al., 2016)
Supplementary_files_format_and_content: abundance file TPM values

organism: Emberiza melanocephala

source_name: Hypothalamus

extract_protocol:
The tissues were homogenized to powder form in the liquid Nitrogen with the help of mortar and pestle and total RNA extraction was done using Tri reagent (AM7020; Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard illumina HiSeq2500 protocols and sequenced as 150 bp reads.

treatment_protocol: Hour 10, 14, 18, 22 are with respect to the time of light onset which we call as hour 0 of the day. So, here in this experiment, the samples were collected after 10, 14, 18 and 22 hours of lights on.

value: Hypothalamus

tag: source

value: Caught from wild

tag: photoperiod sensitivity

value: Refractory

tag: time


title: Refractory_Hour22_Bird1


title: Refractory_Hour18_Bird2


title: aml12 PA-OA-1-7-3

city: Guangzhou

first: Yijie

last: Zhang

state: Guangdong

address: Nanfang Hospital

institute: Nanfang Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.2.5 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM/counts for each Sample

source_name: aml12 PA-OA-1-7

growth_protocol: AML12  (Cell Bank of the Chinese Academy of Sciences in Shanghai) were cultured in DMEM (Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (10% FBS, Excell) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was extracted using Qiazol followed by purification using the miRNeasy kit (Qiagen)

treatment_protocol: To create in vitro models of hepatic steatosis, cells were exposed to a 0.2mM concentration of the PA and 0.4mM OA for 24 h to induce lipid accumulation. Cells were pretreated with 100nM Ang(1-7) 30 minutes before PA stimulation to generate Ang(1-7) treatment group

tag: source tissue

value: Liver

value: Murine hepatocyte cell line


title: Refractory_Hour14_Bird2


title: Refractory_Hour14_Bird1


title: aml12 PA-OA-1-7-1


title: AML12 PA-OA-1

source_name: AML12 PA-OA

value: PA+OA


title: AML12 Ctr-3

source_name: AML12 Ctr


title: AML12 Ctr-2


title: Zscan4+ cells - H3K4me3_rep1

description: Normalized tag counts


title: aml12 PA-OA-1-7-2


title: AML12 PA-OA-2


title: AML12 PA-OA-3


title: AML12 Ctr-1


title: Embryonic stem cells - H3K4me3_rep2

description: Normalized tag counts


title: Refractory_Hour10_Bird1


title: Sensitive_Hour14_Bird1

value: Sensitive


title: Sensitive_Hour22_Bird1


title: Sensitive_Hour14_Bird2


title: Sensitive_Hour18_Bird2


title: Embryonic stem cells - H3K4me3_rep1

description: Normalized tag counts


title: Sensitive_Hour10_Bird1


title: ES-10-OSM-1

city: Tianjin

first: Xiaoying

last: Ye

address: 94 Weijin Road

department: Cell Biology and Genetics

institute: Nankai University

data_processing:
RNA-seq raw reads with low-quality bases, adapters were trimmed by Trimmomatic to obtain clean reads
clean reads were aligned to the UCSC mouse mm10 reference genome using the Hisat2 with default settings
Read counts of each gene annotated in RefGene were calculated by featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every sample

growth_protocol: The mESCs used in this study was derived from the C57BL/6X129S6 blastocytes and were cultured on mitomycin C-inactivated MEF feeder cells in ESC culture medium for 5 passages, then were transferred to different culture mediums (-LIF, LIF, OSM medium). The mESC culture medium was changed daily and cells routinely passaged every 2 days.

extract_protocol:
The RNA of rOvaries were extracted by Rneasy Plus Mini Kit(Cat. No. 74134)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: mESCs were transferred to different conditions including ESC basic medium (-LIF medium), ESC basic medium with 1,000 U/mL LIF (LIF medium), and ESC basic medium with OSM (OSM medium), for another 5 passages (P5) and 10 passages (P10). The ESC basic medium consisted of knockout DMEM (Invitrogen), 20% ESC-quality FBS (Hyclone) , 0.1 mM non-essential amino acids (Sigma), 0.1 Mm β-mercaptoethanol (Invitrogen), 1 mM L-glutamine (Invitrogen), penicillin (100 U/ml) and streptomycin (100 mg/mL) (Invitrogen).

value: embryonic stem cells

value: cultured in OSM medium


title: ES-10-OSM-2


title: Sensitive_Hour10_Bird2


title: ES-LIF-2

value: cultured in -LIF medium


title: Refractory_Hour10_Bird2


title: Sensitive_Hour22_Bird2


title: ES-LIF-1


title: ES+LIF-2

value: cultured in LIF medium


title: HN30E - replicate 4

city: Stellenbosch

first: Caylin

last: Bosch

state: Western Cape

address: JC Smuts Building, Van der Byl road

department: Microbiology

country: South Africa

institute: Stellenbosch University

data_processing:
Torrent Suite Version 5.12.0 Software used for basecalling
Data were quality filtered (Q>20) using FastX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and length-filtered (<10 bp) using the awk command (Yalamanchili, Wan and Lui 2017)
Read quality assessed with FastQC, whereafter reads were aligned to the reference genome of C. neoformans H99 (Janbon et al. 2014) using HISAT2 v2.1.0 (Kim, Langmead and Salzberg 2015)
Alignment quality assessed using Qualimap2 v2.2.1 (Okonechnikov, Conesa and García-Alcalde 2016) and transcript assembly performed using StringTie v1.3.3b (Pertea et al. 2015)
Differential gene expression analysis was performed using DeSeq2 v1.20.0 (Love, Huber and Anders 2014)
Genome_build: C. neoformans H99
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cryptococcus neoformans

source_name: Yeast cells

growth_protocol: Ammonium chloride (NH4Cl) was used as a nitrogen source in all experimentation and was supplemented as follows: 0.53 g/L NH4Cl for a higher nitrogen concentration (HN) and 0.21 g/L NH4Cl for a lower nitrogen concentration (LN). These nitrogen concentrations were selected based on the lowest ammonium-nitrogen (NH4-N) concentration (ca. 0.16 g NH4-N/kg) of the woody debris from which pathogenic cryptococci were previously isolated. C. neoformans cells were inoculated into 100 mL yeast carbon base (contained in 1L conical flasks) supplemented with HN or LN at a final concentration of 1×106 cells/mL. Following agitated incubation for either 38 h or 28 h at 30°C or 37°C, respectively, total RNA was extracted.

extract_protocol:
Total RNA was extracted using an Ambion RiboPureTM-Yeast kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Four biological repeats were performed for each culture condition.
RNA libraries were prepared for sequencing using standard protocols for Ion Torrent sequencing

value: Yeast cells

tag: protocol

value: High nitrogen, 30°C


title: ES+LIF-1

tag: cell type


title: HN30D - replicate 3


title: HN30C - replicate 2


title: Sensitive_Hour18_Bird1


title: LN30D - replicate 3

value: Low nitrogen, 30°C


title: CMML patient classical monocytes [CMML_2056]

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
Read were trimmed using CUTADAPT
Trimmed reads were mapped to hg19 using bismark
methylation is called after file sorted
differentail methylated regions were called using methylKit and methylSig
Genome_build: hg19
Supplementary_files_format_and_content: called methylation txt file

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were sorted using density centrifugation Pancoll (Pan-Biotech, Dutscher, Brumath, France) and CD14+ monocytes through negative selection with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris, France).
Total DNA AND RNA were extracted using RNA/DNA/Protein Purification Plus Kit (Cat. 47700) (Norgen Biotek Corp.)
libraries were prepared for sequencing using standard Illumina protocols

tag: apoptosis

value: defective


title: CMML patient classical monocytes [CMML_2108]


title: LN30E - replicate 4


title: CMML patient classical monocytes [CMML_2059]


title: CMML patient classical monocytes [CMML_2086]


title: CMML patient classical monocytes [CMML_2050]


title: HN37D - replicate 3

value: High nitrogen, 37°C


title: LN30B - replicate 2


title: CMML patient classical monocytes [CMML_1989]


title: HN37E - replicate 4


title: LN30A - replicate 1


title: CMML patient classical monocytes [CMML_2025]


title: CMML patient classical monocytes [CMML_1964]


title: HN37B - replicate 2


title: LN37B - replicate 2

value: Low nitrogen, 37°C


title: CMML patient classical monocytes [CMML_1944]


title: LN37A - replicate 1


title: CMML patient classical monocytes [CMML_1740]


title: HN37A - replicate 1


title: CMML patient classical monocytes [CMML_1637]


title: CMML patient classical monocytes [CMML_1603]


title: LN37D - replicate 4


title: CMML patient classical monocytes [CMML_1541]


title: 40LB+IL-21+IL-13_IgG#3

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL
featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for genes

growth_protocol: B cells were cultured on the CD154+  fibroblast cell line expressing CD40L and BAFF, NB21.2D9 feeder cells in the presence of recombinant murine IL-4, or IL-21 and/or IL-13

extract_protocol:
IgG+ B cells and IgE reporter (Venus) positive B  cells were sorted by flow cytometer, and RNA was harvested using Trizol reagent. Lexogen 3'mRNA-seq library prep kit (Cat#015) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Lexogen 3'QuantSeq protocols

value: spleen

tag: age

value: 8 weeks

tag: agent

value: Verigem KI/+


title: 40LB+IL-21+IL-13_IgE#3


title: CMML patient classical monocytes [CMML_1750]


title: 40LB+IL-21+IL-13_IgG#2


title: 40LB+IL-13_IgG#3


title: LN37C - replicate 3


title: HN30B - replicate 1


title: 40LB+IL-13_IgE#2


title: CMML patient classical monocytes [CMML_1714]


title: CMML patient classical monocytes [CMML_1900]


title: 40LB+IL-21_IgG#3


title: 40LB+IL-13_IgE#1


title: CMML patient classical monocytes [CMML_1660]


title: CMML patient classical monocytes [CMML_1550]


title: CMML patient classical monocytes [CMML_1529]


title: 40LB+IL-21+IL-13_IgG#1


title: 40LB+IL-21+IL-13_IgE#2


title: 40LB+IL-21_IgG#2


title: 40LB+IL-21+IL-13_IgE#1


title: 40LB+IL-13_IgG#2


title: NF-7_E15 embryo cortex total RNA

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

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

source_name: cerebral cortex

extract_protocol: Total mRNA profiles of E15 wild type (WT) and Serpina3/+;Nestin-Cre mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

value: serpina3 conditional knock-in mice


title: NF-2_E15 embryo cortex total RNA


title: 40LB+IL-13_IgE#3


title: L12KO-rep03

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: DMEM with 10% FBS

extract_protocol:
RNA were isolated and purified with standard Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: breast cancer cell line

tag: passage

tag: origin tissue

value: breast

tag: genotype/variation

value: LATS1/2 knockout


title: 40LB+IL-21_IgE#3

tag: tissue

tag: genotype


title: 40LB+IL-13_IgG#1


title: L12KO-rep02


title: 40LB+IL-21_IgE#2


title: 40LB+IL-21_IgG#1


title: 40LB+IL-4_IgG#1


title: WT-rep01

value: wild type


title: 40LB+IL-21_IgE#1


title: 40LB+IL-4_IgE#1